A2 BIOLOGY

SEM TER THREE 2021

Student N es
12s8

PHOTOSYNTH IS
Learning objectives:
I. 5.1 understand the overall reaction of photosynthesis as requiring energy
from light to split apart the strong bonds in water molecules, storing the
hydrogen in a fuel (glucose) by combining it with carbon dioxide and
releasing oxygen into the atmosphere
II. 5.2 understand how photophosphorylation of ADP requires energy and that
hydrolysis of ATP provides an immediate supply of energy for biological
processes
III. 5.3 understand the light-dependent reactions of photosynthesis, including
how light energy is trapped by exciting electrons in chlorophyll and the role
of these electrons in generating ATP, reducing NADP in cyclic and non-cyclic
photophosphorylation and producing oxygen through photolysis of water
IV. 5.4 (i) understand the light-independent reactions as reduction of carbon
dioxide using the products of the light-dependent reactions (carbon fixation
in the Calvin cycle, the role of GP, GALP, RuBP and RUBISCO)

(ii) know that the products are simple sugars that are used by plants,
animals and other organisms in respiration and the synthesis of new
biological molecules (polysaccharides, amino acids, proteins, lipids and
nucleic acids)

1
 V. 5.5 understand the structure of chloroplasts in relation to their role in
photosynthesis
VI. 5.6 understand what is meant by the terms absorption spectrum and action
spectrum
VII. 5.7 understand that chloroplast pigments can be separated using
chromatography and the pigments identified using Rf values

ATP molecule

★ Made up of adenine (nitrogenous base), a

ribose sugar and three phosphate groups.
★ Second and third covalent bonds are unstable and can be broken down
easily.
★ Break down of ATP release energy - Hydrolysis (exergonic)
★ Synthesis of ATP from ADP and phosphate – Phosphorylation (endergonic)

2
Structure of a chloroplast

3
Structure of a thylakoid

4
Photosystems

★ On the thylakoid membrane photosensitive pigments

are organized into complex systems.
★ Primary pigments, accessory pigments and electron
carriers are assembled together in this chlorophyll
complex.
★ These chlorophyll complexes are called photosystems.
★ There are two photosystems:- PSI and PSII

Photosystem I

★ Accessory pigments or antennae pigments (chlorophyll a, carotenoid,

chlorophyll b) are arranged around the primary pigment chlorophyll a.
★ PSI is found on the single thylakoids.
★ The absorption peak of this chlorophyll a is 700 nm and it is the reaction
centre.
★ Antennae pigments absorb light energy (different wavelengths), transfer to
the reaction centre.
★ Reaction centre molecule (Chlorophyll) gets oxidized and releases high
energy electrons.

Photosystem II

★ It is larger than PSI.

★ PSII is found on the thylakoids
which are stacked into grana.
★ The reaction centre is chlorophyll a, with an absorption peak of 680 nm.

5
Chlorophyll

★ Chlorophyll is present in the thylakoid membrane.

★ Have a polar porphyrin head and a nonpolar hydrocarbon tail.
★ Tail is lipid soluble.
★ The hydrocarbon tail anchors the
pigment molecules into the lipid bilayer.
★ The head absorb light energy

Adaptations of leaf for photosynthesis

Thin lamina

★ Fast / maximum gas exchange /uptake of carbon dioxide

★ Help in the penetration of light ;
★ Carbon dioxide is used in the Calvin cycle
★ Light is used in light-dependent stage / photolysis / photophosphorylation.

Veins / vessels in the midrib

★ Xylem transport water to the leaves

★ Phloem transport sucrose / sugar /carbohydrates away from the leaves
★ Water is the source of hydrogen ions in light-dependent reactions.
★ Transporting sugar to make more room for more carbohydrate synthesis

6
Adaptations of Spongy mesophyll for gas exchange

★ The gas exchange surface is the cell wall and membrane

★ The spongy mesophyll cells are loosely packed and have air spaces between
them and large surface area to volume ratio.
★ So the diffusion distance is small between air space and cytoplasm
★ Air spaces and loosely packed cells make diffusion fast
★ Carbon dioxide can continuously enter the leaf and circulate around the cells
★ This maintains a concentration gradient between air space and cell

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Chloroplast

★ A double membrane bound organelle found in green plant cells.

★ Two membranes are separated by an intermembrane space.
★ Envelope is semi permeable.
★ The matrix of the chloroplast is called stroma.
★ Stroma contains enzymes (RUBISCO) that catalyzes light independent
reactions of photosynthesis.
★ Disc shaped structures in the stroma are called thylakoids ,surrounded by
the thylakoid membrane.
★ These are the sites of light dependent reactions of photosynthesis.
★ Thylakoids contain chlorophyll molecules, accessory pigments and
electron transport systems.
★ Light absorbing molecules are arranged in photosystems.
★ This is the site of ATP synthesis in chloroplast
★ Stalks of thylakoids are called grana (granum).
★ Grana are connected with each other by lamella.
★ Lamella acts as the skeleton of the chloroplast and maximizes the efficiency
of the chloroplast.
★ Chloroplast also contains a circular DNA, lipid globules, starch granules
and 70s ribosomes.

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Thylakoid:- t e t o g d e d s e f to n s

★ Thylakoid membrane-
○ provide a space for accumulation of H+
○ Chlorophyll / carotenoids / photosystems / electron carrier proteins /
ATP synthase / NADP reductase are present.
○ compartmentalization from stroma
○ site of light-dependent reaction
★ Photosystem- Contains pigments for trapping light energy
★ Proteins-
○ pump the hydrogen ions into the thylakoid space.
○ Electron carrier proteins- high energy electrons pass along and
undergo redox reaction and provide energy for ATP synthesis
★ ATP synthase-
○ Channels allow hydrogen ions to pass through into stroma.
○ Energy released from this movement of hydrogen ions results in the
production of ATP
★ Lumen- provide space for the accumulation of H+ which is needed for
photophosphorylation.

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Chloroplast- s uc re d o n on

★ Compartmentalisation (from cytoplasm);

★ Thylakoid membranes are site of
light-dependent reaction
★ Chlorophyll / carotenoids / photosystems / electron carrier proteins / ATP
synthase / NADP reductase are present within/ on thylakoid membranes
★ Thylakoid membranes provide a space for accumulation of H+ ;
★ Stroma is the site of Calvin cycle
★ Stroma contains RuBP / RUBISCO

Mechanism of photosynthesis
➔ A process of energy transduction.
➔ Light energy into electrical energy.
➔ Electrical energy into chemical energy.

Three main phases of photosynthesis

★ Light harvesting- light energy is captured by the pigments.

★ Light dependent stage (photolysis)- splitting of water into Hydrogen ion and
oxygen.

+ −
2𝐻 2𝑂 → 4𝐻 + 𝑂 2
+ 4𝑒

★ Light independent stage- the reduction of carbon dioxide and form sugars.

6𝐶𝑂 2
+ 12𝐻 2𝑂 → 𝐶 6𝐻 𝑂
12 6
+ 6 𝐻 2𝑂 + 6𝑂 2

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Light Dependent Stage of photosynthesis

★ Occurs in the thylakoid of chloroplast.

★ It involves the splitting of water by light (photolysis) and producing ATP.
★ Accessory pigments absorb light energy and transfer it into the reaction
centre.
★ The electron within the molecule gets excited and possesses high energy.
★ These electrons are emitted by the chlorophyll a molecule and are received
by the electron carriers.
★ Then passed on to other molecule.
★ The light dependent stage leads to the synthesis of ATP (phosphorylation)
and the production of reduced NADP.
★ This stage includes cyclic and non-cyclic photophosphorylation

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Non-cyclic photophosphorylation

★ Light energy is trapped in PSII and boosts electrons to higher energy levels.
★ The electrons are received by electron acceptor (TM).
★ The electrons are passed along a series of electron carriers to PSI.
+
★ 𝐻 ions pump from stroma to the lumen of the thylakoid.
+
★ Concentration of 𝐻 increases in the thylakoid which diffuse back to stroma
by chemiosmosis.
★ The energy from chemiosmosis is used for the synthesis of ATP from ADP
and Pi by the enzyme ATP synthase.
★ PSI also absorbs light and emits electrons even to a higher energy level which
are received by the electron acceptor.
★ The protons from the water molecule combine with the electron from the
electron acceptor and reduces NADP (temporary store of energized
electrons) to NADPH
★ This passes to the reactions of the light independent stage.
★ The PSI gains its lost electron from the PSII, and PSII gains its lost electron
from the splitting of water (photolysis).
★ Oxygen is produced as a waste gas during the photolysis of water.

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Differences between PS I andPS II

PS I PS II

Found mainly on the lamellae and the Found mainly on the inner surface of
outer surface of grana. granal thylakoid.

Reaction centre is P700. Reaction centre is P680

Both cyclic and non-cyclic Participate only in non-cyclic

photophosphorylation. photophosphorylation.

Can undergo cyclic photophosphorylation No independent function.

independently.

Lost electron is regained from PSII Lost electrons are regained from
photolysis of water.

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Cyclic photophosphorylation
★ Cyclic photophosphorylation involves only photosystem I (PSI).
★ Light hits a chlorophyll molecule in PSI and energizes electrons.
★ Light-excited electrons leave the chlorophyll molecule and are collected by
the electron acceptor.
★ These high energy electrons pass down directly along an electron transport
chain and the energy released is used to pump hydrogen ions from the
stroma into the lumen of the thylakoid.
★ Hydrogen ion concentration increases within the lumen of the thylakoid.
★ So, these hydrogen ions diffuse back into the stroma through a protein
channel on the thylakoid membrane.
★ Diffusion of Hydrogen ions from lumen to stroma (chemiosmosis) activates
ATP synthase to phosphorylate ADP to form ATP.This is called
photophosphorylation.
★ The electron will be returned to the
chlorophyll molecule in PSI.

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Light Independent Stage of photosynthesis

★ Takes place whether or not light is present.

★ The details of this stage were analyzed by Melvin Calvin.
★ It is the reduction of 𝐶𝑂 2
using the reduced NADP and ATP from the light

reaction.
★ The light-independent reactions of photosynthesis take place in the stroma
of the chloroplasts, using the reduced NADP and ATP from the
light-dependent reactions.
★ NADP acts as a hydrogen carrier.
★ Carbon dioxide is reduced to carbohydrate.
★ This stage consists of a series of reactions known as the Calvin cycle and
each stage of the cycle is controlled by enzymes.

LIS

★ 𝐶𝑂 2
diffuse into the leaf through stomata.

★ 𝐶𝑂 2
combine with a 5C compound- Ribulose bisphosphate (RuBP) and

form an unstable 6C compound. (Ribulose bisphosphate carboxylase-

RuBISCO)
★ The 6C compound breaks down into two molecules of 3C compound –
Glycerate-3-phosphate (GP).
★ GP is converted (reduced) to Glyceraldehyde-3-phosphate (GALP) by using
reduced NADP and ATP.
★ From every 12 GALP formed 10 are used to regenerate RuBP and the
remaining two into Glucose.
★ The high concentration of RuBP keeps running the Calvin Cycle at a high rate.

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 IN OUT

six 𝐶𝑂 2
One glucose

18 ATP 18 ADP

12 NADPH 12 NADP

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Interdependence between light dependent and Calvin
cycle

Summary of photosynthesis

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Fate of glucose

Glucose can be converted, using enzymes, into starch, cellulose, fats, amino
acids/proteins and nucleic acids. The extra elements needed to make some of these
compounds, such as nitrogen and phosphorus, are taken up by the roots of the
plant from the soil

The calvin cycle is the starting point for making all the organic substances a plant
needs. Glyceraldehyde-3-phosphate (GALP) and glycerate-3-phosphate (GP)
molecules are used to make essential biological molecules:

★ Carbohydrates:- simple sugars (eg. glucose) are made by joining two GALP
molecules together, and polysaccharides (eg. starch and cellulose) are made
by joining hexose sugars together in different ways.

The production of glucose is very important as it's used in respiration, which

provides energy needed for biological processes.

★ Lipids:- these are made using glycerol, which is synthesised from GALP, and
fatty acids which are synthesised from GP.
★ Amino acids:- some amino acids are made from GP.
★ Nucleic acids:- the sugar in RNA (ribose) is made using GALP.

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Using the products of photosynthesis

★ Two molecules of GALP join to form glucose (gluconeogenesis).

★ This glucose may be converted into disaccharides such as sucrose for
transport round the plant.
★ (Alpha glucose molecule joins with fructose by 1,2-glycosidic bond through
condensation reaction and forms sucrose).
★ (starch is a polymer of alpha glucose. Glucose monomers join together by
glycosidic bond through condensation reaction. Starch has two polymers-
unbranched amylose with only 1,4-glycosidic bond and branched
amylopectin with 1,4 and 1,6-glycosidic bond).
★ (cellulose is a polymer of beta glucose. Beta glucose molecules join by
I,4-glycosidic bond through condensation reaction. This forms a long
unbranched chain of beta glucose molecule-cellulose).
★ The GALP that enters cellular respiration is used to provide energy in the
form of ATP for the functions of the cells and for the active uptake of nitrates
and phosphates from the soil.
★ The compounds from the respiration pathways are used as the building
blocks of amino acid by combining with nitrates from the soil.
★ GALP may continue round the Calvin cycle and combine with phosphates
from the soil and form nucleic acids.
★ GALP is converted to glucose which again is converted to deoxyribose.
★ Glucose is used in respiration and provides energy in the form of ATP for
DNA synthesis or active transport of substances such as nitrates.
★ GALP is also used in the synthesis of bases such as adenine, thymine,
cytosine and guanine.
★ GALP also synthesises amino acids for enzymes involved in the synthesis of
DNA.

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 ★ Some of the GALP that enters the cellular respiration pathways is converted
into a chemical called acetyl coenzyme A.
★ This compound is then used to synthesise the fatty acids.
★ GALP is converted to glycerol. One molecule of glycerol joins with three
molecules of fatty acids by ester bond through condensation reaction and
form lipids.

GP to Strach

★ Using energy from ATP and hydrogen from NADPH, GP is converted to GALP.
★ Two molecules of GALP joined to form glucose, which is alpha glucose.
★ Starch is a polymer of alpha glucose and consists of two polymers amylose
and amylopectin.
★ Glycosidic bonds are formed between glucose molecules by condensation
reaction and form two polymers.
★ amylose is straight chained with only 1.4-glycosidic bonds and amylopectin is
branched with 1,4 and 1,6-glycosidic bonds.

GALP to Cellulose

★ Two molecules of GALP joined to form glucose, which is beta glucose.

★ Cellulose is a polymer of beta glucose.
★ Beta glucose molecules joined by 1,4-glycosidic bonds through condensation
reaction and form a long unbranched chain of glucose.

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GALP to Triglycerides/lipids

★ GALP is used to produce glucose which is a source of energy for lipid/

triglyceride synthesis.
★ GALP is used to make glycerol and GP is used to make fatty acids.
★ Three fatty acids and one glycerol joined by ester bonds through
condensation reaction and form triglyceride.
★ GALP is converted to amino acids which are used to synthesise enzymes.
★ These enzymes are involved in lipid synthesis

GALP to Protein

★ Two molecules of GALP joined to form glucose.

★ Amino acids are made from glucose and nitrates.
★ Proteins are formed by joining these amino acids by peptide bond through
condensation reaction.
★ Glucose is used in respiration to produce ATP for protein synthesis

GALP to DNA

★ GALP is converted to Glucose which is converted to deoxyribose.

★ Glucose is used in respiration to produce ATP which provides energy for the
active transport of substances such as nitrates and sulphates.
★ GALP is used in the synthesis of nitrogen bases using nitrates.
★ GALP also synthesises amino acids for enzymes involved in the synthesis of
DNA.
★ DNA is polynucleotide, where mononucleotide is made up of deoxyribose,
nitrogen base and phosphate group.
★ Mononucleotides joined together by phosphodiester bond through
condensation reaction and form polynucleotide.

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Factors Affecting The Rate Of photosynthesis
Mainly three factors which affect the rate of photosynthesis:

01.Light intensity
02. 𝐶𝑂 2
concentration

03.Temperature

Limiting factor: Among the factors that control the rate of photosynthesis, the
factor which is closest to its minimum.The rate is limited by that factor and only a
change in that factor changes the rate of photosynthesis.

Light intensity and rate of photosynthesis

★ At very low light intensity, the rate of photosynthesis is very low.
★ Further increase in light intensity increases the rate of photosynthesis until
light saturation is reached.
★ This is the maximum rate of photosynthesis.
★ Beyond this no change in rate of photosynthesis as high light intensity
destroys chloroplast.
★ Light is trapped by chlorophyll and excites high energy electrons.
★ Light splits water molecules to produce protons
★ Electrons and protons are involved in photophosphorylation

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The effect of reduced light levels on
the relative concentrations of GP,TP
and RuBP in the Calvin cycle

1. GP cannot be reduced to TP.

2. TP levels fall and GP accumulates.
3. If TP levels fall, RuBP cannot be
regenerated.

Temperature and rate of photosynthesis

★ Calvin cycle is temperature dependent as enzyme Rubisco is involved in it.

★ The minimum temperature for photosynthesis is 0°C.
★ The optimum temperature is 25°C.
★ The rate doubles for each rise of 10°C up to an optimum temperature.
★ KE of molecules increases so does effective collision between enzyme and
substrate
★ Above 25°C bonds in
enzymes are broken
down
★ Changes the shape of
the active site.

23
Concentration of 𝐶𝑂 2
and rate of photosynthesis

★ Major limiting factor to photosynthesis.

★ Increasing concentration increases the rate of photosynthesis till a certain
level.
★ Further increase in 𝐶𝑂 2
will add no effect.

1. As the amount of carbon dioxide goes

up, so does the rate. The limiting
factor is carbon dioxide.
2. Here, increasing the amount of carbon
dioxide has no effect on the rate. Light
or warmth is now the limiting factor

The effect of changing the carbon dioxide concentration on the

Calvin cycle

If the concentration carbon dioxide

falls below 0.01%:

1. RuBP cannot accept it, and

accumulates.
2. GP cannot be made.
3. Therefore, TP cannot be made.

24
Absorption and action spectra

Absorption spectrum:Graph showing the degree of absorbance of different

wavelengths of light by a pigment.

Action spectrum:Graph showing the effectiveness of different wavelengths of light

stimulating photosynthesis.

25
Chromatography: Sep in h me s

26
 ★ The pigments can be separated by chromatography using paper or silica gel.
★ Draw a pencil line about 25 ㎜ from the bottom edge.
★ Extract the pigments from a plant by grinding up the leaves with 10㎤
propanone and then filter it.
★ The extract should be as concentrated as possible.
★ Place one small drop of this extract in the centre of the pencil line and allow
to dry before adding another drop on top.
★ Build up a pigment spot that is as small as possible but dense enough that it
contains sufficient pigment.
★ Carefully pour the chromatography solvent into a boiling tube to a depth of
no more than 1 ㎝.
★ Suspend the chromatography paper inside the boiling tube by pinning it to
the underside of the bung.
★ The bottom of the paper should be dipped into the solvent but the pigment
spot must not be immersed in the solvent at any time.
★ The pigments travel up the solid medium at different speeds and are
separated.
★ The distance travelled by the solvent needs to be marked as soon as you
remove the paper or plate from the solvent bath (Several of the pigments
fade quickly in light so you may need to draw around the spot in pencil and
label it).
★ Once the pigments are separated, determine their Rf values and compare
them to the Rf values of known pigments in the same solvent (pigments can
have very different Rf values with different solvents).
★ The Rf value is the ratio of the distance travelled by the pigment to the
distance travelled by the solvent alone.
★ The Rf value is always between 0 and 1.

27
 QU TIONS
*With reference to the structures in a chloroplast, explain how the energy
from light is made available in ATP molecules for the synthesis of organic
materials. (6)

★ Stack of thylakoids present in grana.

★ Thylakoid membrane contains photosystems.
★ Chlorophyll molecule and accessory pigments in the photosystem absorb
light energy and electrons are excited from chlorophyll
★ These high energy electrons passed down through electron carrier and
undergo a series of redox reactions
★ While passing through the carriers energy level of electrons falls
+
★ The released energy is used by the proton pump to pump 𝐻 ions into the
thylakoid lumen from stroma.
+
★ Diffusion of 𝐻 ions from lumen to stroma activate ATP synthase to
phosphorylate ADP to form ATP
★ This is called photophosphorylation ;
★ Electrons from photolysis is used to replace those lost from PSII ;

Describe the structures in a chloroplast that are involved in the

light-dependent reactions of photosynthesis.

★ Chloroplast contain disc shaped structures called thylakoids ;

★ Thylakoids are made of membranes ;
★ These are arranged as stacks called grana
★ It contain pigment / chlorophyll
★ These pigments are arranged as photosystems

28
Explain the role of light in the photosynthesis

★ Light results in excitation of electrons from chlorophyll / photosystems

★ This results in energy to generate in the form of ATP ;
★ Light is needed for breakdown of water (photolysis)
★ Electrons from photolysis replace electrons lost by chlorophyll /
photosystems
+
★ Photolysis produce 𝐻 ions / protons
+
★ Both ATP and reduced NADP / 𝐻 ions are needed in the light-independent
reaction / Calvin cycle to convert GP to GALP
★ ATP / reduced NADP / hydrogen ions used in production of GALP from GP .
★ Study well

Structures in a chloroplast that are involved in photophosphorylation

★ Grana present in the chloroplast

★ A granum is a stack of thylakoids and grana are connected by lamellae ;
★ Thylakoids contain electron carriers /chlorophyll / photosystems ;
★ Thylakoid membranes contain ATPase

Explain how oxygen is produced during the light-dependent reactions of

photosynthesis

★ By the photolysis of water using energy from light

Describe and explain how the products of the light dependent reaction are
involved in the production of glyceraldehyde-3-phosphate (GALP). (4)

★ In the light independent stage of photosynthesis, GP is reduced to GALP

using hydrogen from reduced NADP and energy from ATP. These ATP and
reduced NADP are the products of light dependent stage.

29
One of the reactions of photosynthesis can be summarised as shown below.

Water → hydrogen ions + oxygen gas + electrons

(A) name the reaction shown.

★ Photolysis (of water) ;

(b) give one other factor, not shown above, that would be required for this
reaction to occur in a chloroplast.

★ Light / enzyme / chlorophyll /

Describe the role of the electrons in the light dependent reaction of

photosynthesis. (4)

★ Electrons passed to photosystems to replace electrons lost by chlorophyll.

★ Light energy promotes electrons to higher energy level and the electrons
emitted ;
★ High energy electrons carried through the electron transport chain.
★ Occurs as a series of redox reactions.
★ Energy released is used in ATP production ;
★ Electron is used in reduction of NADP / production of NADPH

Describe the role of the proteins in the thylakoid membrane in the formation
of ATP.

★ Electron carriers pump the hydrogen ions into the thylakoid space
★ ATPase channels allow hydrogen ions to pass through into stroma
★ Energy released from this movement of hydrogen ions results in
phosphorylation of ADP.

30
GALP does not accumulate in a chloroplast during photosynthesis. Explain
how GALP is used following its production. (2)

10
★ is used for the regeneration of RuBP
12

★ Rest is used to form glucose and which is for starch / other organic chemical

The graph below shows the results of the investigationDescribe and suggest
an explanation for
the changes in the
concentrations of
RuBP and GP
shown in the
graph.

★ Both RuBP and GP levels constant until carbon dioxide lowered

★ RuBP and GP are produced in Calvin cycle ;
★ RuBP: At lower carbon dioxide levels the RuBP increases and drops and then
stays constant ;
★ Rises because being regenerated
★ Falls as being used to fix carbon dioxide ;
★ RuBP level remains constant once new equilibrium reached ;
★ GP: At lower carbon dioxide levels the GP drops and then stays constant
★ Drops because less carbon dioxide is available to convert into GP) / less
carbon fixation
★ Levels out at a lower level as carbon dioxide still available but at lower level;

31
A2 BIOLOGY
SEM TER THREE 2021
Student N es
12s8

Energy Flow Through an Ecosystem

LEARNING OBJECTIV :
I. Carry out calculations of net primary productivity and explain the
relationship between gross primary productivity(GPP), net primary
productivity(NPP) and plant respiration(R).
II. Calculate the efficiency of energy transfers between trophic levels.

★ Study of energy flow through an ecosystem- ecological energetics

★ 1-5% of the radiant energy is captured by the green plants.
★ Energy is ultimately derived from the sun.
★ The captured energy is converted into chemical energy and flow through the
ecosystem

1
Trophic level: the level at which an organism feeds in a food chain

★ Energy is lost between trophic levels due to several reasons such as inedible
body parts and energy loss to decomposers.
★ There will not be enough
energy to sustain many
trophic levels.

Productivity

★ It is the rate of generation of biomass in an ecosystem.

−2 −1
★ Its unit is 𝐽𝑚 𝑦𝑒𝑎𝑟 (it is the energy per unit area per unit time)
★ Productivity of autotrophs- primary productivity.
★ Productivity of heterotrophs- secondary productivity

Gross primary production (GPP)

★ The total amount of energy captured in the organic material by green plants
in the process of photosynthesis.
−2 −1
★ Its unit is 𝑘𝐽𝑚 𝑦𝑒𝑎𝑟

Net primary production (NPP)

★ It is the net useful chemical energy.

★ It is the amount of energy trapped in
the plant biomass that is available for
consumption by heterotrophic
organisms.

𝑁𝑃𝑃 = 𝐺𝑃𝑃 − 𝑟𝑒𝑠𝑝𝑖𝑟𝑎𝑡𝑖𝑜𝑛 𝑏𝑦 𝑝𝑙𝑎𝑛𝑡𝑠

2
Mean annual rainfall and NPP

★ Increase in rainfall increases the availability of water.

★ Water is needed for light-dependent reaction and transport of mineral ions.
★ This increases the GPP and there by increases NPP

Why an increase in temperature may cause an increase in NPP

★ Increase in temperature increases the kinetic energy of molécules and leads

to more successful collisions between enzyme and substrate.
★ So the rate of Photosynthetic reactions increases.

3
Depth of water and NPP

★ As depth increases NPP decreases.

★ Light is reduced by the deeper water ;
★ Carbon dioxide levels might be lower deeper down ;
★ Temperature might be lower deeper down ;
★ Photosynthesis will be reduced ;
★ Less glucose / GALP / GP will be produced to convert into biomass / NPP
★ GPP goes down but respiration stays the same / increases

NPP values would be of use to a farmer who wanted to use a particular

land for cattle

★ Cattle is primary consumer

★ They gain energy available as NPP
★ Farmer is ensuring that there is enough NPP in the grassland
★ This affects the yield of milk and meat.
★ So if the NPP is not sufficient they can move to a more efficient NPP yielding
farm.

NPP decreases with the age of the forest

★ More growth occurs in young trees / less growth in older trees.

★ The rate of photosynthesis decreases with age
★ This decrease may be due to lower ratio of leaves or ‘trunk is thickening but
no more leaves’ produced or trees shade each other
★ The mineral ions in the soil will be depleted

4
 ★ As age of the forest increases, R also decreases because some of the trees
are not respiring / dead.
★ Due to these reasons GPP also decreases

Biomass

★ Biological material derived from living or recently living organisms.

★ It is the mass of living biological organisms in a given area or ecosystem at a
given time. (Kg/hectare)

Secondary production

★ Formation of heterotrophic biomass through time.

★ It is the energy used to make new animal biomass.

5
Measurement of biomass in a grassland in a year is more useful than on
a particular day

★ NPP varies over short periods of time.

★ Whole year gives an average value of NPP.
★ Because biomass includes all inedible organic materials.

6
Transfer of energy from producers to consumers

★ A part of the energy is lost as it passes from one trophic level to the next.
★ Only 10% is stored to make new biomass.
★ That 10% is transferred to the next trophic level.
★ Plants respire using the products of photosynthesis
★ 𝑁𝑃𝑃 = 𝐺𝑃𝑃 − 𝑟𝑒𝑠𝑝𝑖𝑟𝑎𝑡𝑖𝑜𝑛 𝑏𝑦 𝑝𝑙𝑎𝑛𝑡𝑠
★ All plant materials are not edible.
★ Remaining 90% of the energy is lost during the transfer.

The fate of light energy that reaches the green leaf

Why the energy transfer from sunlight to the producer is low

7
 ★ Light is reflected back into space
★ Light energy reflected from leaves
★ Light energy is used in evaporating water
★ Light energy is missing chloroplast/passing through the leaf
★ Incorrect wavelength of light

Percentage efficiency of photosynthesis

It can be calculated by dividing GPP by the total amount of energy striking the plant
multiplied by 100

Explain why the energy efficiency between secondary and tertiary

consumer is greater than that between producers and primary
consumers

★ In plants some parts are inedible;

★ Cannot digest cellulose or lignin;
★ More material goes to decomposers than consumers;
★ Plant material is less energy rich;

Ways in which energy is transferred from primary consumers to

decomposers

★ Death/ dead remains, Excretion, Egestion, Moulting of fur

8
9
10
 QU TIONS
The diagram below shows what happens to 200 J of energy eaten by a
caterpillar.Calculate the percentage of this energy available to any bird
that eats this caterpillar. Show your working.

(energy used ) = 100 + 67 / 167 (J)

(energy available) = 200 - 167 / 33 (J)

Ans =16.5 (%)

Biomass energy (trophic level 1)= 5300 kJ

Ingested food by the animal (trophic level 2) = 2800 kJ
Energy lost during respiration (trophic level 2)= 1750 kJ
Calculate the percentage energy transfer between these two trophic
levels
★ Ans (1050/5300)*100 =19.8

Of the 800 000 kJ of energy reaching the producers only 10 000 kJ of

energy is converted to growth in the producers.Calculate the
percentage of energy reaching the producers that is converted to
growth in the producers. Show your working.

★ Ans (10 000/ 800 000)*100

★ 1.25%/ 1.3%/ 1%

11
Only 10% of the energy in the robins passes to the owls. Describe what
happens to the other 90% of the robins’ energy.

★ Some amount of energy is lost to the surroundings as heat;

★ Some will be used for movement / keeping the body warm;
★ Not all parts of the robin are eaten by the owl.

Keeping cattle indoors, in barns, leads to higher efficiency of energy

transfer. Explain why

★ Less energy lost as heat/in maintaining body temperature/in movement

tion

12
Q. A farmer’s livelihood depends on the efficiency of energy transfers
between trophic levels. The farmer will be interested in how efficient
grass is at turning solar energy into NPP, and how efficient a bullock is
in converting the energy in grass into beef production. Examine Figure
3 showing energy flow through a typical grazing food chain. Calculate
the following values:

a) Efficiency of photosynthesis (percentage of incident solar energy that is

converted to GPP). Ans 2.24%
b) The energy lost to the environment through plant respiration. Ans 1968
−2 −1
𝑘𝐽𝑚 𝑦𝑒𝑎𝑟
c) The percentage of solar energy falling on the grass that becomes beef
(secondary production). Ans 0.012%
d) Assuming all the grass in 1m2 were eaten by just the bullocks, how
much energy would be incorporated as beef in a year? Ans 876.8 kJ

13
A2 BIOLOGY
SEM TER THREE 2021
Student N es
12s8

Distribution and abundance

Learning objectives:
5.11 understands what is meant by the terms population, community,

habitat and ecosystem.

5.12 understand that the numbers and distribution of organisms in a habitat

are controlled by biotic and abiotic factors

5.13 understand how the concept of niche accounts for the distribution and

abundance of organisms in a habitat

1
Ecology is the study of the interaction between organisms and their environment.

These interrelationships determine the distribution and abundance of organisms

within a particular environment.

Ecosystem – it is a life supporting environment which includes all of the living

organisms, the nutrients that cycle throughout the system and the physical and

chemical environment in which the organisms are living.

Habitat- the place where an organism lives (examples: rocky shore, rain forest)

Many organisms live in a small part of a habitat and such type of habitat is called

microhabitat.

Population- a small group of organisms of the same species, living and breeding

together in a habitat.

Community- all the populations of all the different species of organisms living in a

habitat at any one time.

Niche- the role of the organism in the community or its way of life.

Abiotic factors- the non- living elements of the habitat of an organism which has

an effect on the success of an organism

Biotic factors- the living elements of the habitat that affect the ability of a group of

organisms to survive.

2
Major biomes- a community of plants and animals that have common

characteristics for the environment they exist

Abi ic factors affecting the distribution of organisms

★ Climatic factors e.g. temperature, water availability, light, wind

★ Edaphic factors (associated with soil) e.g. pH, texture

★ Aquatic factors e.g. salinity, amount of dissolved oxygen

★ Topographic factors- aspect, inclination, altitude

3
 Climatic factors

Temperature
An organism will survive only within a range of temperature- limits of tolerance.

★ If temperature falls below zero- freezing of protoplasmic water and the cell

becomes physiologically damaged.

★ If the temperature is too high- proteins become denatured.

Temperature and rate of development

At higher temperatures metabolic rate increases.

KE of the molecules increases.

More effective collision and more enzyme substrate complexes formed.

Decrease in temperature leads to inactivation of enzymes.

Temperature above optimum results in denaturation of enzymes. This affects

differentiation.

Each species need a particular range of temperature

Temperature affects metabolism.

Enzymes affect metabolism.

Temperature affects enzymes.

Different species have different enzymes.

4
Why temperatures below 0 °C or above 40 °C would be unsuitable for

most organisms
Metabolism stops or become slow

Below 0°c

enzymes are inactive / cells disrupted

Inactivity / cell disruption is because of freezing of protoplasm or lower kinetic

energy

Above 40 °c

More vibrations in the enzyme break bonds

Enzyme denatures.

This changes the shape of active site

Fewer enzyme substrate complexes form

5
 Light
★ Light is the source of energy for photosynthesis.

★ This influences primary productivity.

★ All other organisms depend upon primary

productivity directly or indirectly.

★ Some plants reproduce early to avoid the

shade caused by larger plants.

★ Other plants are able to photosynthesize and reproduce successfully in low

light levels.

★ They may have extra chlorophyll or different ratios of photosynthetic

pigments that are sensitive to lower light levels.

★ Some will have very large leaves to collect light.

★ Animals are affected by light levels indirectly as a result of the distribution of

food plants

★ Seasonal light changes affect the reproductive pattern of many animals.

★ This also changes much of the animal

physiology and behaviour

6
 Wind and water current

★ Wind increases cooling and water loss from the body.

★ Strong winds (hurricanes) can cause extreme damage to populations.

★ This results in the loss of plant and animal communities.

★ In water when the strength of currents increases suddenly this may damage

the entire population.

★ Only strong swimmers or one which is able to attach to a surface can resist

the force of water and can survive.

★ Air movements accelerate dissemination of spores and seeds of plants which

help them to colonize in favourable habitats.

Water availability

★ The availability of water is affected by several factors such as the amount of

rain, snow or hail, the rate of evaporation and the rate of loss by drainage

through the soil.

★ Availability of water leads to germination of seeds, and growth of plants. This

changes the habitat and increases the population size.

★ The population size of organisms which are directly or indirectly dependent

on those plants also will increase.

7
 Oxygen availability

★ When water is cold or fast flowing, there will be enough oxygen dissolved in

it.

★ So, organisms which need oxygen for their survival can exist.

★ With rise in temperature of the water or if the water becomes still and no

longer flows, then the oxygen content will drop.

★ Mostly anaerobic organisms survive in those areas.

★ In terrestrial habitat, the spaces between the soil particles contain air, so

there is plenty of oxygen for the respiration of plant roots.

★ In waterlogged soil, as the air spaces are filled with water oxygen availability

is very less. So, plants with special adaptation (aerial roots) to obtain oxygen

only can survive there.

8
 Edaphic factors- factors related to the structure of the soil

Soil structure and mineral content affect the survival of various populations.

Soil pH

★ Measure of hydrogen ion concentration in aqueous solution.

★ This indicates the level of acidity or alkalinity.

Low altitudes have high pH (4.5-8) and support many microbes.

★ Microbes help to break down the litter into humus.

Higher altitude have low pH (3-6.5)

★ Fewer microbes survive and fungi help to form humus

9
 pH and growth of organisms
★ pH affects enzymes and enzymes affect metabolism

★ Due to change in pH the shape of active site is altered by the ionisation of the

R groups

★ This affects the metabolism as substrates cannot fit into the active site.

Topographic factors

★ Aspect (slope):- angle of the sun on a south facing slope is greater. So

receive more sunlight and are warmer.

★ Inclination (steepness):- water drains more readily from steep slopes.

★ Altitude (height):- at higher altitude the temperature is lower, the wind

speed is greater and there is more rainfall.

10
 Bi ic factors
Involve all those factors that are living.

★ Competitors

★ Predators

★ Decomposers

★ Population Density

★ Disease

Competition
Organisms compete with each other for various available resources.

Animals compete for food, water, shelter, mate and nesting sites.

Two types of competition- interspecific competition and intraspecific competition

11
 Intraspecific competition

Competition between members of the same species within the same niche for a

limited source.

★ If the territory is small or relatively little food available

★ Intraspecific competition occurs.

★ They may not survive and reproduce, and population growth slows down.

★ If large quantities of resources are available, there is little or no competition

for the resources

★ and the number of individuals increases

12
 Interspecific competition
★ Competition between members of two different species within a community

for the same resource.

★ The niches of the species overlap.

★ Competition will reduce the abundance of the competing species.

★ The greater density and faster reproduction rate in a species leads to the

extinction of the other competitor

13
Ecological niche

It is the status or the role of an organism in its environment.

Different niches avoid competition

The abiotic and biotic factors affecting the number of organisms occupying a

particular niche may be density-independent or density-dependent

★ The density-independent factors- regardless of population size.

Extremes of temperature will adversely affect all the individuals in the population.

This type of factor will limit the distribution of species.

14
The density-dependent factors- depend on the number of organisms in a

specific area.

Examples: Disease and parasitism, territory

★ If the number of individuals are more in a specific area, there will be more

chance of transmission of disease and parasites.

★ Breeding success is density dependent.

★ Individuals without territory or reduced territory are less able to breed.

★ Density-dependent factors also will limit the abundance of species.

Parasitism and disease- biotic factors

★ Diseased animals will be weakened.

★ They do not reproduce successfully.

★ They cannot hunt well, and they are more likely to

be caught by their predators.

★ Some diseases are infectious which will spread very fast without direct

contact.

★ Parasites affect their hosts.

★ They usually feed off the living body of the host and weaken it.

★ This may wipe out the entire population of the host.

15
 Mutualism – relationship between two organisms where both partners benefit by

their association.

Predation

★ Interactions of predators and prey are a factor in regulating the population size.

★ A predator is any organism that feeds on another living organism called the prey.

★ The population is an oscillating population.

★ Predator –prey population was regulated by a negative feedback mechanism.

★ Predation affects the abundance of species.

★ Here the population of prey and predator change between two extremes.

★ As prey population increases, more food is available for the predator and its

population increases.

★ The rate at which the prey are being eaten is greater than the rate of reproduction.

So the number of prey will fall.

★ This reduces the food supply of the predators.

★ This reduces their reproduction rate and the number will fall.

★ This allows the abundance of prey to

increase.

16
Antibiosis

★ Organisms sometimes produce deterrent chemicals to repel other

organisms.

★ Many mammals use these chemicals to mark their territories.

★ Example: pheromones produced by ants warn off other members of the

species.

★ Penicillium produces antibiotics to prevent the competition with bacteria for

the sources either by inhibiting the growth or killing them.

Dispersal of seeds enables plants to colonize new and favourable habitats.

This prevents competition with the parent and the offspring for available resources.

17
Pollination Angiosperms utilize insects to transfer their pollen grains from one
member of a species to another.

Mimicry The resemblance of an animal species to another species object to

escape from the predators

18
 Anthropogenic factors
As hunters, farmers, fishers, developers, polluters etc.

Introduction of grazers and removal of predators of grazing animals .

19
20
A2 BIOLOGY
SEM TER THREE 2021
Student N es
12s8

Ecological Succession
Learning objective:
I. Understand the stages of succession from colonization to the formation of a
climax community

1
 ★ Succession is the process by which an ecosystem changes over time.
★ The biotic conditions (e.g. plant and animal communities) change as the
abiotic conditions (e.g. water availability) change.
★ Succession is the gradual replacement of one plant community by another
through natural processes over time.
★ There are two types of succession- primary succession and secondary
succession.

Primary Succession

★ This type of succession starts with an empty

inorganic surface such as bare rock.
★ There is no soil or organic material to start with.
★ The first stage of this succession is colonization and
the first organism to appear are pioneer species
(e.g. lichen).

Why only pioneer species and what is its role?

★ The abiotic conditions are hostile (harsh), e.g. there is no soil to retain water.
★ Only pioneer species grow because they are specially adapted to cope with
the harsh conditions.
★ The pioneer species secrete acids which will dissolve the rocks.
★ They can penetrate the rock and help to break the rock into small grains.
★ When they die the microorganisms decompose the organic material to form
humus and mix up with small grains of rock and form a shallow layer of soil.

2
Primary succession

★ The pioneer community lichens and mosses started to grow. They are able to
grow in little / no soil.
★ This breaks up rock fragments and forms a thin shallow layer of soil.
★ Plants with small roots are able to grow in thin / shallow soil.
★ This changes the soil by holding more water and minerals. As plants die it
adds organic material to the soil and increases the soil fertility.
★ Competition occurs between organisms and better adapted ones survive.
★ Changes in soil structure enable trees to grow.
★ Biodiversity increases.
★ Finally reaches a stable stage of community called climax community.

Biomass change during primary succession

★ There are few very small plants at the beginning.

★ So, the initial biomass is very low.
★ The biomass increases during succession as the
plants in the later stages are larger than the
pioneer plants and grasses.

3
Climax Community

★ A stable group of plants and animals that is the end result of the succession
process.
★ It has high biodiversity and there will be more interaction between species.
★ There is a balanced equilibrium of species and contains dominant plant or
animal species.
★ It is stable if no change to environment / human influence

Different ecosystems have different climax communities

★ The species which make up the climax community depends upon the climatic
condition in that ecosystem.
★ Such a type of climax community is climatic climax.
★ In a temperate climate, the climatic climax will contain large trees because
they can grow in these conditions (plenty of water, mild temperatures and
not much change between the seasons.) once deep soils have developed.
★ In a polar climate the climatic climax contains only herbs or shrubs, but it is
still the climax community (not much available water, temperatures are low
and there are massive changes between the seasons).

4
Succession can be Prevented

★ Human activities can prevent succession, stopping a climax community from

developing. When succession is stopped artificially like this the climax
community is called a plagioclimax.
★ Such type of succession is deflected succession.
★ A plagioclimax is a sub- climax community where succession has been
deflected by human activity.
★ Example: A regularly mown grassy field will not develop shrubs and trees
(woody plants), even if the climate of the ecosystem could support them.
★ With more frequent mowing, succession cannot progress, and diversity will
be lower — only the grasses can survive being mowed.

5
Trends of succession

★ The kind of plants and animals change continuously.

★ Increasing biomass and decomposing plant and animal material.
★ Species diversity increases.
★ A progressive reduction in net community production.
★ Increase in community respiration.

Mixed woodland and biodiversity

★ Different food items are available.

★ Provide many niches.
★ Provide many nesting places and shelter.
★ Species diversity increases.

6
Secondary succession

★ This type of succession happens on land that has been cleared of all the
plants, but where the soil remains, e.g. after a forest fire or where a forest
has been cut down by humans.
★ The sequence of events is similar to that seen in primary succession.
★ The numbers of plants and animals present right from the beginning of this
succession is much higher because the soil is already formed and contains
seeds, roots, and small organisms.

Which type of succession would occur faster?

★ Secondary succession occurs faster.

★ Soil is already present.
★ Seeds or roots of earlier plants might be still existing in the soil.
★ They can grow quickly into new
plants when enough water and
sunlight is available.

7
Describe the effect of change in the plant community on the number of
species of small birds. GIVE REASONS

★ Increased number of species as succession progresses / number of species

increases from grassland to woodland (Any suitable manipulation of data)
★ Grassland is open habitat, but trees provide more cover
★ Birds easily spotted by predators in grass / converse for trees and shrubs
★ Trees provide roosting / nesting sites
★ Mixed woodland provides greater variety of food to support more species
★ Trees provide more niches for species

(b) the population density of birds drops when shrubs are replaced by
pine trees, but then increases with the change to mixed woodland.
Suggest reasons for these changes in population density.

★ Pine trees have less food available for birds

★ Reduction in the variety of niches

8
A2 BIOLOGY
SEM TER THREE 2021
Student N es
12s8

THE CARBON CYCLE

Learning objective

Understand how knowledge of the carbon cycle can be applied to

methods to reduce atmospheric levels of carbon dioxide

CARBON CYCLE

The movement of carbon between organisms and the atmosphere is called the

carbon cycle

1
CARBON CYCLE

★ Carbon (in the form of CO2 from the atmosphere) is absorbed by plants

when they carry out photosynthesis — it becomes carbon compounds in

plant tissues.

★ Carbon is passed on to animals when they eat the plants and to

decomposers when they eat dead organic matter.

★ Carbon is returned to the atmosphere as all living organisms carry out

respiration, which produces CO2

★ If dead organic matter ends up in places where there aren't any

decomposers, e.g. deep oceans or bogs, the carbon compounds can be

turned into fossil fuels over millions of years.

★ The carbon in fossil fuels is released as CO2 when they’re burnt — this is

called combustion.

To reduce atmospheric CO2 concentration

Either

★ The amount of CO2 going into the atmosphere (due to respiration and

combustion) needs to be decreased

Or

★ The amount of CO2 being taken out of the atmosphere (by

photosynthesis) needs to be increased.

2
Carbon in oceans

★ Additional carbon is stored in the ocean.

★ Many animals pull carbon from water to use in shells, etc.

★ Animals die and carbon substances are deposited at the bottom of the

ocean.

★ Oceans contain earth’s largest store of carbon.

Human Impact

★ Fossil fuels release carbon stores very slowly

★ Burning anything releases more carbon into atmosphere — especially

fossil fuels

★ Increased carbon dioxide in atmosphere increases global warming

★ Fewer plants mean less CO2 removed from atmosphere

What We Need to Do:

★ Burn less, especially fossil fuels

★ Promote plant life, especially trees

3
Carbon sinks

★ The ultimate place where carbon compounds are locked up for a long

period of time.

★ These are reservoirs.

★ In the biotic part of the system carbon is removed from the atmosphere

by photosynthesis and stored in the bodies of living organisms.

★ In the abiotic system rocks (limestone and chalk) and fossil fuels contain

large amounts of inorganic carbon.

★ Limestone- largest Carbon reservoir in Carbon cycle

★ Ocean is also a carbon reservoir.

★ Carbon once trapped in these sinks rarely escapes.

★ CO2 concentration is increased by the destruction of natural sinks (things

that keep CO2 out of the atmosphere by storing carbon).

★ E.g. trees are a big CO2 sink — they store the carbon as organic

compounds.

★ CO2 is released when trees are burnt, or when decomposers break down

the organic compounds and respire them.

4
The concentration of carbon dioxide

The accurate measurement of the amount of Carbon dioxide began in the year

1957

The results are:

★ Atmospheric carbon dioxide is low in summer and high in winter.

★ This is due to the difference in rate of photosynthesis.

★ In winter carbon dioxide concentration is higher than in summer.

★ This is due to reduced photosynthesis.

★ Trees are leafless or temperature is limiting.

★ There is a rising trend in atmospheric carbon dioxide concentration.

★ 1957- 315ppm

★ 1988-350ppm

Rise in atmospheric carbon dioxide concentration

★ Combustion of fossil fuels

★ Deforestation

Combustion of fossil fuels

Fossil fuels are carbon sinks.

Burning fossil fuels releases the additional

carbon as carbon dioxide in the atmosphere.

5
 Deforestation

Trees would act as carbon reservoirs.

Plants use carbon dioxide for growth.

Deforestation creates an increase in

atmospheric carbon dioxide .

Carbon dioxide released by the respiration

process is absorbed by various natural sinks

like rivers and lakes

Maintaining balance

Using biofuels Reforestation

6
 Biofuels and Reforestation Decrease the Atmospheric 𝐶𝑂
2

concentration

★ Biofuels are fuels produced from biomass — material that is or was recently

living. They’re often made from crops, which can be replanted after harvesting

— making biofuels a sustainable resource.

★ Biofuels are burnt to release energy, which produces CO2.

★ There is no net increase in atmospheric CO2 concentration when biofuels are

burnt — the amount of CO2 produced is the same as the amount of CO2 taken in

when the material was growing (carbon neutral).

★ So using biofuels as an alternative to fossil fuels stops the increase in

atmospheric CO2 concentration caused by burning fossil fuels.

Biofuel production is not carbon neutral

★ Biofuel production may overall results in more carbon dioxide in the

atmosphere

★ Forests are carbon sinks.

★ Deforestation results in net increase in carbon dioxide in atmosphere

★ Less plants means less carbon dioxide is removed by photosynthesis ;

★ Burning of trees would produce carbon dioxide ;

★ Increased decomposition produces carbon dioxide;

★ Using fossil) fuels by vehicles and machinery produces carbon dioxide ;

★ Burning of biofuels produces carbon dioxide ;

7
 ADVANTAGES DISADVANTAGES

Reduce the use of limited fossil fuels Destruction of carbon sinks release
stored carbon

Provide renewable energy source and Loss of habitat and reduces

reduce C emission biodiversity

Waste biomass can be recycled to Food shortage can occur where

produce biofuels biofuels are replacing food crops

Reforestation

★ Planting young and fast growing trees.

★ Because of rapid growth they absorb more carbon dioxide for

photosynthesis.

★ Rate of photosynthesis is greater than respiration.

★ So net carbon dioxide absorption occurs.

★ As the forest matures respiration= photosynthesis.

★ The wood of the tree becomes a carbon store.

★ Continuous reforestation slows down increase in CO2

★ More carbon dioxide removed from the atmosphere by photosynthesis ;

★ Carbon (dioxide) is used in forming permanent plant biomass

★ Carbon is incorporated in organic molecules

Limitations of reforestation

★ Mature forest is carbon neutral as respiration= photosynthesis.

★ So benefits only last while the forest grows.

★ Limited amount of land can be used for reforestation.

8
More carbon in soil (carbon sinks) due to less ploughing / farming

★ Less oxygen can enter the soil

★ Oxygen is needed for aerobic respiration in soil microorganisms like

bacteria and fungi.

★ Less breakdown of organic matter / humus / dead plants / dead animals

★ Less carbon dioxide released

9
10
Role of microbes in soil

★ It helps for decomposition of plants / animals

★ Helps to improve the quality / mineral content of the soil

★ Release carbon dioxide back into the atmosphere by respiration.

★ This carbon dioxide is used in photosynthesis

★ Also help to recycle the nitrogen

★ Microbes provide food for other soil organisms

★ Pls study

Role of microorganisms in recycling carbon

★ Microorganisms like bacteria and fungi release extracellular enzymes onto

organic material.

★ This breaks down complex organic materials like starch and cellulose into

simpler soluble monomers such as glucose.

★ It is done by breaking glycosidic bonds by these enzymes.

★ Then glucose is used as a respiratory substrate by the microorganism and

releases carbon dioxide into the atmosphere.

★ This carbon dioxide is used by green plants for photosynthesis

11
A2 BIOLOGY
SEM TER THREE 2021
Student N es
12s8

GreenHouse Gases And Climate Change

Learning objective:

understand the different types of evidence for climate change and its

causes, including records of carbon dioxide levels, temperature records,

pollen in peat bogs and dendrochronology, recognizing correlations and

causal relationships

Understand the causes of anthropogenic climate change, including the

role of greenhouse gases in the greenhouse effect.

Understand that data can be extrapolated to make predictions and that

these are used in models of future climate change

Understand that models for climate change have limitations.

Understand the effects of climate change (changing rainfall patterns and

changes in seasonal cycles) on plants and animals (distribution of species,

development and life cycles)

Understand the effect of temperature on the rate of enzyme activity and

its impact on plants, animals and microorganisms, to include Q10

1
Greenhouse effect

★ Solar energy reaches the earth in the form of short wave radiation.

★ When the radiation strikes a surface much of its energy is converted into

heat (long wavelength radiation).

★ Greenhouse gases like Carbon dioxide and water vapour in the

atmosphere absorb and retain these long wave radiation and prevent

them from escaping into space.

★ Some may reflect towards the earth surface.

★ This is a natural process of warming up the earth’s atmosphere. This is

greenhouse effect

★ without this greenhouse effect the Earth would be as cold as the moon

2
Global warming

★ Because of human activities like burning of fossil fuels greenhouse gases

like Carbon dioxide and methane accumulate in the atmosphere.

★ Solar radiation reaches the earth surface as short wave radiation.

★ Reflect back from the earth’s surface as long wave IR radiation

★ These are trapped by greenhouse gases and re-radiate back towards

earth’s surface.

★ This increases the earth’s mean surface temperature.

★ This is global warming.

3
Greenhouse gases

★ CO2 - by the combustion of fossil fuel and deforestation. / Naturally by

volcanic eruption and respiration

★ CH4 - Produced by the activity of anaerobic

bacteria in landfill sites, guts of certain insects

and ruminants. (anaerobic respiration by

microorganisms like bacteria release methane)

★ CFC- from refrigerator and aerosol spray

★ Water vapour - transpiration and evaporation

These gases accumulate in the atmosphere and trap infrared radiation resulting in

an increase in the temperature of the Earth's atmosphere / surface

Climate - the average weather in a relatively large area such as a country over a

long period of time.

Weather - the conditions in the atmosphere at a particular time.

Climate change - a large-scale change in the global or regional weather

patterns that happens over a period of many years.

Abundance - abundance is the number of a particular organism

Distribution - distribution is where the organism is found

4
 Evidence for global warming

1) Temperature records

2) Dendrochronology –tree ring analysis

3) Pollen in peat bogs

4) Ice core samples

Temperature record
★ A data set of the annual mean surface temperature that was made in

central England and Toronto, Canada over 3 centuries to the present time

shows a fluctuating trend.

★ The Central England Temperature dataset is the oldest in the world – with

351 years of temperature records drawn from "multiple weather stations

located both in urban and rural areas of England.

★ Starting in 1659, the Central England Temperature Record (CET) is the

world's longest continuous temperature record,

★ Line of best fit suggests temperature has gradually increased by about

1.8oC between mid C17 and present.

★ Closer analysis of the trend line shows fluctuations between 1700 and

1900 then a gradual rise until the present day.

5
 Dendrochronology
★ Tree ring analysis (dating of past events using tree ring growth)

★ Tree ring is growing yearly

★ Tree rings can be dated by counting inwards

★ Thicker / wider tree rings reflects amount of growth

★ In warmer conditions the rings are thicker and it shows better growth

★ Scientists can see what the climate is like each year

How it provide evidence for climate change

Each year a new tree ring is formed.

So the number of rings can be used to work out the timescale.

The size of the ring reflects the growth of the tree that year

Size of ring / growth is affected by climatic factors like temperature.

Because photosynthesis is affected by these climatic factors.

★ The diagram shows a core taken from a tree in 2000.

★ The most recent rings are the thickest and the rings get steadily thinner

the further in the past they were formed.

★ The trend of increasingly thicker rings from 1920 to 2000 suggests that

the climate where the tree lived had become warmer over the last century

6
In order to know more about climate over an even longer period of time, in

some cases thousands of years, it is possible to look at dead trees of an

unknown age that are still well preserved. One can correlate their rings to

the rings of a living tree (whose age you know), and see where the rings

match up and get a longer record of climate through time.

7
How global warming may affect tree ring growth

★ An increase in temperature increases ring thickness

/ tree ring growth.

★ So the rate of photosynthesis is faster as enzymes

work faster with higher temperature.

★ So more material is laid down in the tree trunks.

★ At higher temperatures (above optimum) enzymes

denature.

★ So the rate of enzyme activity and photosynthesis decreases and the tree

rings would be thinner.

1) Which two separate years were particularly cold or dry?

900 AD and 1450 AD

2) Which was probably the warmest or the wettest?

1150 AD

8
Problems

★ If conditions vary a lot within one year more than one ring may be

produced.

★ Tree growth depends on many factors- amount of sunshine, temperature,

carbon dioxide levels and the amount of rainfall.

★ So it is hard to say what led to the large cells being laid down.

★ Was it one of the above factors or was it a combination of several of

them?

The diagram above shows a core taken from a pine tree in 2009. Analyse

the data shown in the diagram to explain how the core provides evidence

for climate change.

★ The diagram shows that the thickness of the pine tree rings fluctuated,

but there was a trend of increasingly thicker rings from 1909 to 2009.

★ The thickness of each tree ring depends on the climate when the ring was

formed.

★ Warmer climates tend to give thicker rings than colder climates as the

rate of photosynthesis increases due to increased rate of enzyme action.

★ This suggests that the climate where the pine tree lived became warmer

over the last century, which is evidence of climate change

9
 Pollen in Peat Bogs

★ Pollen in peat bogs can be used to show how temperature has changed

over thousands of years.

★ Pollen is often preserved in peat bogs- partly decomposed plant material

(acidic wetland areas).

★ Peat bogs accumulate in layers so the age of the preserved pollen

increases with depth. The lowest layers are the oldest

★ Scientists can take cores from peat bogs and extract pollen grains from

the different aged layers. They then identify the plant species the pollen

came from.

★ The samples only show the species that were successful at that time.

★ Scientists know the climates that different plant species live in now. When

they find preserved pollen from similar plants, it indicates that the climate

was similar when that pollen was produced.

★ Because plant species vary with climate the preserved pollen will vary as

climate changes over time.

★ So a gradual increase in pollen from a plant species that’s more successful

in warmer climates would show a rise in temperature (a decrease in

pollen from a plant that needs cold conditions would show the same

thing).

10
Pollen in peat bogs is preserved for many years

★ The condition in peat is very acidic and anaerobic.

★ Lack of decomposition due to lack of microorganisms like bacteria.

★ Low pH reduces enzyme activity

★ Low oxygen affects respiration of microorganisms

★ Bacteria cannot produce enzymes to breakdown the outer covering of

pollen

This is a pollen diagram taken from peat cores from Hockham Mere in
Norfolk. Describe the changes that have occurred in the species abundance
from the distant past to the present

★ Initially almost exclusively birch

★ this was replaced by pine,

★ then elm then oak

★ pine disappeared,

★ lime and alder appeared

★ elm disappeared

★ leaving mainly oak and alder,

with some lime, until the present day.

Example: oak grows best in warmer conditions than pine, so in warm conditions
oak will out-compete pine. So if the amount of oak pollen increases and pine
pollen decreases we can infer that the climate was getting warmer

11
Explain how the pollen of present-day species can be used to show what

the climate was like in the past.

★ Peat bogs can preserve pollen and are formed in layers

★ Pollen in different layers can be used to identify plant species in different

time periods, with pollen in deeper layers being older.

★ Scientists know the climate that different plant species live in now.

★ When they find preserved pollen from similar plants, they know that the

climate must have been similar when that pollen was produced.

Continued draining and clearance of peat lands may contribute towards

global warming

★ Combustion of biofuels releases carbon dioxide recently removed from

atmosphere

★ There is no net increase in carbon dioxide in atmosphere

★ Carbon dioxide is a greenhouse gas

★ That absorbs infra-red radiation reflected from earth’s surface

★ And prevents infra-red from escaping into space ;

★ Therefore mean temperature of earth’s surface increases ;

★ Carbon in peat land was trapped a long time ago

★ Peat land clearance releases the trapped carbon dioxide ;

★ So there is a net gain of carbon dioxide in the atmosphere

★ Removal of plants during clearance reduces photosynthesis and reduces

the removal of carbon dioxide from the atmosphere

★ Carbon dioxide is also released from clearance machinery ;

12
 Ice core sampling

★ Bubbles in the ice core preserve actual samples of the world’s ancient

atmosphere.

★ Seasonal differences in the snow properties create layers – just like rings

in trees.

★ Examining the ice cores gives you a history of what happened in the

atmosphere for hundreds and thousands of years.

★ Bubbles in the ice trap prehistoric atmosphere, which can be analyzed.

★ Scientists analyse the air trapped in different layers.

★ Measure the carbon dioxide levels in the air trapped in the ice core

sample.

★ The oxygen isotopes in the melted ice reflect the air temperature at the

time the ice layer was formed.

13
 Climate Change Can be Caused by Human Activity

★ An increase in human activities (anthropogenic causes) like burning fossil fuels

(for industry and in cars), farming and deforestation has increased

atmospheric concentrations of CO2 and methane.

★ This has enhanced the greenhouse effect

and caused a rise in average global

temperature — global warming

★ greenhouse gases absorb outgoing energy,

so that less is lost to space.

★ The greenhouse effect is essential to keep

the planet warm, but too much greenhouse

gas in the atmosphere means the planet warms up.

★ CO2 concentration is increasing as more fossil fuels like coal, oil, natural gas

and petrol are burnt, e.g. in power stations or in cars.

★ Burning fossil fuels releases CO2.

★ It is also increased by destroying of natural sinks like forest(deforestation)

★ Methane concentration is increasing because more fossil fuels are being

extracted, there’s more decaying waste and there are more cattle which give

off methane as a waste gas.

★ Methane can also be released from natural stores, e.g. frozen ground

(permafrost).

★ As temperatures increase it is thought these stores will thaw and release large

amounts of methane into the atmosphere.

14
 Scientists do not agree that a reduction in the use of fossil

fuel will prevent further global warming

★ Carbon dioxide produced by burning fossil fuels.

★ No direct evidence that increased carbon dioxide leads to global warming.

★ Because carbon dioxide is released from other processes like

decomposition.

★ Removal of carbon sinks like forests also leads to an increase in carbon

dioxide.

★ Other greenhouse gases like CFC, water vapour and methane are

released from other source;

★ Methane is from ruminant animals, paddy fields and CFC from

refrigerator aerosol spray

★ Natural phenomena like volcanic eruptions may also be involved in global

warming.

★ Evidence from past is being used and is not in indicator of future events

15
Interpret Evidence for the Causes of Climate Change

Interpret data on things like atmospheric CO2 concentration and

temperature, and recognize correlations and causal relationships

★ The temperature fluctuated between 1950 and 2006, but the general

trend was a steady increase from around 13.8 °C to around 14.5 °C.

★ The atmospheric CO2 concentration also showed a trend of increasing

from around 310 ppm in 1950 to around 380 ppm in 2006.

★ There’s a positive correlation between the temperature and CO2

concentration.

★ The increasing CO2 concentration could be linked to the increasing

temperature.

★ However, there is no causal relationship — other factors may have been

involved, e.g. changing solar activity.

★ Other studies would need to be carried out to investigate the effects of

other factors

16
Climate Change can be Extrapolated to make Predictions

★ Data that has already been collected on atmospheric greenhouse gas

concentrations can be extrapolated — used to make predictions about

how it will change in the future.

★ These predictions can then be used to produce models of how the global

climate might change in the future

★ If they extrapolate the data by ignoring the annual fluctuation the

prediction will not be accurate.

★ Photosynthesis may vary during winter and summer and carbon dioxide

production by natural processes also will change.

★ Scientists use computer models to study the interaction of different

factors.

★ By extrapolating the data, prediction can be made about how it will

change in the future

★ Use investigation of correlations Providing evidence for global warming

★ By using graphs showing increase in temperature

★ Using this data along with data from other sources

17
Climate models and limitation

There are many limitations even with the best models. This is because:

★ It is impossible to tell the exact impact of carbon dioxide on global

warming

★ Impossible to predict the impact of global warming on particular aspects

of the world climate.

★ The change in atmospheric greenhouse gas concentrations due to natural

causes (without human influence) is not known

★ Extrapolations from the past data cannot take into account unknown

factors in the future (including how current trends in resource usage and

technologies may change)

★ Limited data

★ Limited knowledge about how the climate system works

★ Limited computer resources

★ Failure to consider all the factors affecting climate change

★ Change in trends in CO2emission and ice cover.

18
Global warming affects plants and animals

An increasing temperature affects the rate of enzyme activity which can

affect organisms’ life cycles, development and distribution.

★ The rate of an enzyme-controlled reaction increases when the temperature

is increased.

★ This is because more heat means more kinetic energy, so molecules move

faster.

★ This makes the enzymes more likely to collide with the substrate molecules.

★ But, if the temperature gets too high, the reaction stops.

★ This is due to the denaturation of the enzyme at higher temperatures.

★ An organism’s metabolic reactions are controlled by enzymes.

★ An increase in temperature will mean that the metabolic reactions in some

organisms will speed up, so their rate of growth will increase.

★ This also means they will develop and progress through their life cycle

faster.

★ But the temperature will become too high for some organisms.

★ Their metabolic reactions will slow down, so their rate of growth will

decrease and they will progress through their life cycle slower.

★ Global warming will also affect the distribution of some species — all

species exist where their ideal conditions for survival are, e.g. their ideal

temperature.

★ When these conditions change, they will have to move to a new area where

the conditions are better.

★ If they can’t move they may die out in that area.

★ Also, the range of some species may expand if the conditions in previously

uninhabitable areas

19
Describe and explain how global warming could affect plant species

★ Due to global warming earth’s mean surface temperature is increasing

★ Loss of existing species in places where the temperature is not ideal for

them to survive

★ Changes in distribution of plant species.

★ There will be changes in rainfall patterns and growing seasons

★ Temperature may become too hot for some species and this may affect

enzyme activity.

★ Increased carbon dioxide results in more photosynthesis / GPP/ NPP /

biomass

★ This changes the numbers / size / growth of plants

The Effects Of Global Warming On Plant Species Affect Animal Species.

★ If the temperature increases above the optimum temperature some of

the plant species may die

★ So, there is a reduction of herbivore because of reduction in food supply

★ Results in a reduction of predator or secondary consumers.

★ A change in distribution of plants could result in a change in distribution

of herbivores.

★ Loss of habitat decreasing the numbers of animal species

★ Loss of shelter provides more food for predators so the predator would

increase in number

20
Effect of increased temperature for animals from global warming

★ Global warming increases the earth’s mean surface temperature

★ When the temperature increases up to optimum temperature metabolic

reactions speed up

★ So, the rate of growth increases and the life cycle becomes faster.

★ Above optimum temperature, metabolic reactions fall

★ So their rate of growth falls and life cycle slows down

[***Anytime you see temperature having an effect, consider the activity of enzymes

as a reason for the effect]

Global warming causes other types of climate change-

Global rainfall patterns and the timing of seasonal cycles affect plants and

animals

Changing Rainfall Patterns

Due to Global warming some areas will get more rain, others will get less rain.

Changing rainfall patterns will affect the development and life cycles of some

organisms

Changing rainfall patterns will also affect the distribution of some species, e.g.

deserts could increase in area because of decreases in rainfall

So, species that are not adapted to live in deserts will have to move to new areas

or they will die out.

21
 Seasonal Cycles

Global warming is thought to be changing the timing of the seasons, e.g. when

winter changes to spring.

Organisms are adapted to the timing of the seasons and the changes that

happen, e.g. changes in temperature, rainfall and the availability of food.

Changing seasonal cycles will affect the development and life cycles of some

organisms

Changing seasonal cycles will also affect the distribution of some species

Example:-

★ Some swallows live in South Africa over the winter and fly to different

parts of Europe to breed at the start of spring (when more food is

available).

★ An early British spring will produce flowers and insects earlier than usual,

so the swallows that migrate to Britain at the normal time will arrive when

there isn’t as much food available (there will be fewer insects because the

flowers will have disappeared earlier).

★ This will reduce the number of swallows that are born in Britain, and

could eventually mean that the population of

swallows that migrate to Britain will die out.

★ The distribution of swallows in Europe will have

changed.

22
23
Effect of global warming on distribution

★ Because of global warming temperature may be too high

★ Organisms migrate to places with suitable temperature

★ This results in a change of biodiversity. Biodiversity increases at places

with suitable temperature.

★ Increased competition effects

★ Range of organisms increasing as the place is suitable for the organism

★ Plants can move less easily than animals (accept converse)

★ So the animals / plants survive more / less

★ If organisms involved in the spread of disease are affected, patterns of

world health could change as well.

★ Global warming could be responsible for a major increase in insect-borne

diseases.

★ Because the condition could be ideal for disease-carrying organisms such

as mosquitoes in many new areas of the world.

24
Seasonal cycle affect life cycles

★ Global warming affects the beginning of the seasons.

★ This affects both the life cycle and the distribution of species.

★ In warmer temperature plants grow and flower earlier.

★ Insects become active earlier in this warmth and the food they need for

their caterpillars is available.

★ Some birds can adapt to these changes and some cannot.

Example: Great tits in UK

★ According to the changes in global temperature, their life cycle has also

moved forward (The UK tits lay eggs two weeks earlier now).

★ So the winter moth larvae that form the main food for the baby birds are

also present on the leaves.

Great tit in Netherlands

★ Their breeding time is becoming earlier every year but the caterpillars are

emerging even earlier.

★ So the birds are missing the peak population of caterpillars and raising

fewer chicks.

Changes in temperature could change the male female sex ratio.

★ Example: embryos of some reptiles are sensitive to temperature during

development.

★ Male crocodiles develop only if the eggs are incubated at 32-330C.

★ If the eggs are cooler or warmer, females develop.

★ Due to global warming if all the females develop, then it could be the end

of that species

25
 Global warming and decomposition

★ As temperature of soil increases enzyme activity of decomposers increases

★ So more decomposition of dead organic matter in soil occurs.

★ Products of decomposition are used by the decomposers, like bacteria for

respiration which itself increases as a result of the warmer temperatures.

★ So more greenhouse gases like CO2 and methane are released.

★ Climate change already involves changes in temperature.

★ In many parts of the world, this change will be an increase in temperature, but

some places will get colder.

★ Temperature has an effect on enzyme activity, which in turn affects the whole

organism.

★ A 100℃ increase in temperature will double the rate of an enzyme - controlled

reaction.

★ This effect of temperature on the rate of any reaction can be expressed as

temperature coefficient (Q10)

★ Q10 for any reaction between 0℃ and 400℃ is 2.

★ This means that a 100℃ rise in temperature produces a doubling of the rate of

reaction within the temperature range where most living things live.

26
Potato tuber moths infest potato crops in warm climates, such

as southern Europe.

a) They complete their life cycle faster at 21 °C than at 16 °C. Explain why

this is the case. [4 marks]

An increase in temperature causes an increase in enzyme activity which speeds

up metabolic reactions. Increasing the rate of metabolic reactions in a potato

tuber moth will increase its rate of growth, so it will progress through its life

cycle faster

b) Describe what may happen to their range in Europe over the next 25

years if global warming continues. [2 marks]

The range of the potato tuber moth may expand northwards into the rest of

Europe because rising temperatures due to global warming may make the

climate in northern Europe more suitable for the moth than it was previously

27
 Climate Change And Evolution
Learning objectives:

Understand how evolution (a change in allele frequency) can come about

through gene mutation and natural selection

Understand how isolation reduces gene flow between populations,

leading to allopatric or sympatric speciation

Climate change and selection pressure

★ In many places the climate is becoming warmer.

★ In some places the climate is becoming colder or wetter or drier.

★ These climatic changes are acting as selection pressures.

★ This changes the allele frequency and results in evolution through natural

selection.

Evolution is when the frequency of an allele in a population changes over

time. It occurs by natural selection.

Rising temperatures do not cause mutations.

Rising temperatures cause environmental variation which results in selection

pressure on the organisms.

28
Individuals within a population vary because they have different alleles due to

gene mutations.

This means some individuals are better adapted to their environment than

others.

Individuals that have an allele that increases their chance of survival are more

likely to survive, reproduce and pass on their genes (including the beneficial

allele), than individuals with different alleles.

This means that a greater proportion of the next generation inherit the

beneficial allele.

They, in turn, are more likely to survive, reproduce and pass on their genes.

So the frequency of the beneficial allele increases from generation to

generation.

Isolation reduces gene flow leading to Speciation

★ Speciation happens when populations of the same species become

reproductively isolated, reducing gene flow (transfer of genes) between

two populations.

★ This means that natural selection acts on each population separately —

so new species can develop.

★ Reproductive isolation may occur because of geographical isolation

(allopatric speciation) or because random mutations produce changes in

phenotype that prevent populations from mating (sympatric speciation).

29
 Allopatric Speciation Requires Geographical isolation

★ Populations that are geographically separated will experience slightly

different conditions. E.g. there might be a different climate on each side of

the physical barrier.

★ The populations will experience different selection pressures and so

different changes in allele frequencies could occur

★ The changes in allele frequency will lead to differences accumulating in

the gene pools of the separated populations, causing changes in

phenotype frequencies.

★ Eventually, the different populations will have become genetically distinct

— their DNA will have become significantly different.

★ Individuals from the different populations will have changed so much that

they won’t be able to breed with one another to produce fertile offspring

★ They have become reproductively isolated.

★ The two groups will have become separate species

30
 Reproductive Isolation Occurs in Many ways

Reproductive isolation occurs because the changes in the alleles and

phenotypes of the two populations prevent them from successfully breeding

together.

Prezygotic mechanisms prevent interspecies mating and fertilization.

I. Seasonal changes/temporal - individuals from the same population

develop different flowering or mating seasons, or become sexually active

at different times of the year.

II. Mechanical changes - changes in genitalia prevent successful mating.

III. Behavioural changes - a group of individuals develop courtship rituals

that aren’t attractive to the main population

IV. Ecological changes – species occur in the same area but they occupy

different habitats and rarely encounter each other.

Seasonal isolation Behavioural isolation

31
Post-zygotic mechanisms prevent the hybrid zygote from developing into

healthy and fertile adults. There are two likely cases that will occur to ensure

that the hybrid does not reproduce:

I. Hybrid inviability is when the embryo does develop but the hybrid

experiences reduced fitness and often an early death.

II. Hybrid sterility occurs when a hybrid develops into a mature adult but is

unable to undergo successful meiotic division, and is unable to produce

offspring. (seen in donkey-horse hybrids: mules)

32
Sympatric Speciation Doesn’t Require Geographical Isolation

Speciation without geographic isolation is called sympatric speciation.

A population doesn’t have to become geographically isolated to become

reproductively isolated.

Random mutations could occur within a population, resulting in changes which

prevent members of that population breeding with other members of the

species.

33
A2 BIOLOGY
SEM TER THREE 2021
Student N es
12s8

CORE PRACTICAL 13
INV TIGATE THE RATE OF GROWTH OF MICROORGANISMS IN A LIQUID
CULTURE, TAKING INTO ACCOUNT THE SAFE AND ETHICAL USE OF
ORGANISMS

Learning objectives:
I. To understand how microorganism growth rate in liquid culture can be
measured
II. To be able to culture microorganisms with due regard for safe practice

Independent Variable: Time / hours (since initiation of experiment)

Dependent variable: Light absorbance (turbidity) / a.u. (OR)

number of yeast cells / cells cm-3

Confounding variables:

● Volume of culture tested - 3 cm3

● Temperature - Using a temperature controlled room (25oC)
● Concentration of nutrients in culture medium
● Concentration of cells in culture medium at start

1
 Risk assessment
RISK HAZARD PRECAUTION

Spillage that could cause ★Wipe up any liquid spillages as soon as they
Liquids surfaces to be slippery leading occur
to an accident ★Put lids on bottles and put them away once used

Glassware Cuts from sharp objects ★Take care when handling glass objects
★Keep away from edge of desk

★Wear gloves when handling to avoid skin

★May cause an allergic contact, if it gets on skin rinse thoroughly with
reaction. cold water
Yeast ★Contamination of yeast with ★Use aseptic techniques throughout
other microorganisms could ★Give the culture to the lab technician to destroy
occur. after the experiment
★Wear eye protection

★Avoid skin contact by wearing gloves and allow it

Disinfectant May cause an allergic reaction. to soak into the work bench (10 mins) before
carrying out the experiment

★ The culture of yeast is a possible biological hazard as there is potential for

contamination.

★ A single yeast culture flask should be set up for the class.

★ If samples are taken this should be over a period of no more than 12 hours.

★ Wear eye protection.

★ Avoid skin contact with disinfectant or any other stain used

2
 ★ Measuring the growth of yeast culture
★ A colorimeter can be used to measure turbidity or absorbance
○ The more yeast cells in the culture, the more turbid the culture is

Method 1:- Colorimetry

Method 2:- Light Sensor with Datalogger

Method

1. Before starting the experiment disinfect the workbench, this helps to

prevent contamination when preparing the yeast culture.
2. Fill a 500 cm³ conical flask with 250 cm³ of the glucose solution and then
weigh out 1.25g of yeast and add it to the flask.
3. Place the flask on the magnetic stirrer to stir it continuously and stopper
the flask with some cotton wool secured with a covering of aluminium foil.
4. The flask can be incubated at room temperature.

3
 Measuring growth: Method 1 - Colorimetry

1. Use a pipette to fill a cuvette with the 0.5% glucose solution and take a
colorimetry reading to set the reference absorbance of the colorimeter to zero.
2. Once the yeast sample has been prepared, use a sterile pipette to transfer
3 cm³ of the culture into a cuvette and take an absorbance reading, recording
the age of the culture in minutes and its absorbance in a table.
3. Repeat steps 1 and 2 at the following ages of the culture: 30 minutes,1 hour,
90 minutes, 2 hours, 5 hours, 8 hours, 11 hours.

Results: Changes in optical density against time in 3 cultures of yeast Saccharomyces sp.
incubated at 25 °C.

Optical Density / a.u

Time/ hours
culture 1 culture 2 culture 3 Mean Log mean OD

0.00 0.06 0.04 0.05 0.05 log (0.05)=-1.30

0.75 0.05 0.07 0.07 0.06 -1.22

2.25 0.19 0.28 0.25 0.24 -0.62

3.75 0.66 0.87 0.85 0.79 -0.10

5.25 1.27 1.10 1.30 1.22 0.09

6.75 1.47 1.16 1.32 1.32 0.12

8.25 1.53 1.18 1.40 1.37 0.14

9.75 1.65 1.23 1.55 1.48 0.17

11.25 1.78 1.30 1.72 1.60 0.20

15.00 1.97 1.29 1.90 1.72 0.24

4
Analysis of the results
1. Plot a graph of absorbance or light reading against time.
2. Identify the lag and exponential (log) phases of the growth curve on your
graph.
3. From the exponential (log) phase of the growth curve, estimate the time
taken in hours for the population size to double.

ANS: 3.9 – 2.85 = 1.05 hours. It takes 1.05 hrs for the population to double

4. Re-plot of absorbance-time graph using a semi logarithmic scale

5
 5. Examine & compare

Both graphs show microbial growth over a period of time. Exponential growth and
stationary phase is observed in both graphs of yeast. Bacterial growth curve
shows the number of bacterial cells at different time periods. The yeast ones
show an indirect measure of number, optical density. Thus, over time we observe
the OD increasing.

6. Calculate exponential growth rate constant

−0.1 − (−1.2)
𝑘= 𝑙𝑜𝑔2 × 3
1.1
= 0.903
= 1. 22

QUESTION: Using an optical microscope, the student determined there were 15

cells in 0.004 mm³ of the 1 in 1000 dilution of the culture. Calculate the
number of cells in 1cm³ of undiluted liquid culture.

ANS: 3.75 x 109 / 3 750 000 000;

6
Extension work - Counting yeast cells using a haemocytometer

1. Take 0.5 ml of yeast culture into a watch glass.

2. Add 0.5 ml of methylene blue into watch glass and mix
3. Transfer a drop of mix into counting chamber of haemocytometer, place coverslip
4. Place the haemocytometer under the x10 objective lens of the microscope and
count cells in any 3 triple lined square grids.
5. Calculate the number of cells per cm3

7
Sample calculation

3
★ Volume of 1 tripled lined grid = 0. 2 × 0. 2 × 0. 1 = 0. 004 𝑚𝑚
3 (19 + 18 + 20)
★ Number of cells per 0. 004 𝑚𝑚 = 3
= 19 cells
3 (19 × 1000)
★ Number of cells per 𝑐𝑚 = 0.004
= 4 750 000 cells

★ Since half of mix was dye, multiply this value by 2

3
★ thus 9 500 000 yeast cells were present in 1𝑐𝑚 of culture

8
 Questions

★ The optical method for examining growth gives no indication of actual

numbers of microorganisms, suggest how this method could be improved to
provide this information

Calibrate OD readings using either dilution plating or direct counting (using a

haemocytometer).

Produce a calibration curve for a range of OD readings and use the graph to
estimate the number of microorganisms present.

★ yolo
★ Describe how using turbidity measurements to follow the growth of
microorganism populations affect the validity of the investigation

The method is valid because most of the change in turbidity will be a result of
microorganism cells in suspension. However, the method does not distinguish
between live cells and other particles in suspension such as dead cells, spores or
cell fragments, which reduces the validity.

★ so
★ Suggest why a magnetic stirrer was used

The magnetic stirrer keeps cells in suspension and ensures that nutrients are
evenly distributed. It also oxygenates the culture to allow aerobic respiration.

★ study
★ Explain why it is more ethical to use yeast for this investigation, rather than
insects
○ Yeast does not have a nervous system so it cannot feel the pain or distress
○ Disposal of yeast does not require that it be killed
○ Yeast not endangered or in short supply
○ There is no danger of yeast escaping and damaging the local environme

9
A2 BIOLOGY
SEM TER THREE 2021
Student N es
12s9

MICROBIOLOGY
BACTERIA & VIRUS
Learning objectives:
I. (6.3) Understand the different phases of a bacterial growth curve (lag phase,
exponential phase , stationary phase and death phase) and be able to
calculate exponential growth rate constants .

1
LIFE CYCLE: Binary fission

[EXTRA INFO: S. pneumoniae cells have the shape of a rugby ball and elongate by
inserting new cell wall material at the so called equatorial rings (A), which
correspond to an outgrowth of the cell wall that encircles the cell. An initial ring is
duplicated, and the two resultant rings are progressively separated, marking the
future division sites of the daughter cells. The division septum is then synthesized
in the middle of the cell (B). Round cells such as S. aureus do not seem to have an
elongation mode of cell wall synthesis. Instead, new peptidoglycan is inserted only
at the division septum (B)]

2
Bacterial reproduction

★ The time between cell divisions is known as the generation time

★ Bacteria can reproduce at very high speed. (The small size and relative
simplicity of the prokaryotic cells mean that they can undergo binary fission
every 20 minutes when conditions are favourable but it often takes longer.)
★ Limited nutrients and an accumulation of waste products always slow down
the rate of growth.

3
Calculating growth of bacterial colonies: Logarithmic Scale

★ Growth of bacteria, the numbers involved are so enormous it rapidly

becomes impossible to show what is happening. If we use a logarithmic
scale, the data becomes much easier to manage.
★ Numbers from the initial organism to the billions of descendants is too great
to represent using standard numbers
★ This means that every number on the y-axis represents a power of 10. So
1
○ 1 is actually 10 (10),
2
○ 2 is 10 (100)
3
○ 3 is 10 (1000) and so on.

4
Formula for number of bacteria in a population:

𝑘𝑡
𝑁𝑡 = 𝑁0 × 2

● 𝑁𝑡 = the number of organisms at time t

● 𝑁0 = the number of organisms at time 0(the beginning of the experiment).

● k = the exponential growth rate constant

● t = the time the colony has been growing
● Study well

Formula for exponential growth rate constant (k):

𝐿𝑜𝑔10𝑁𝑡 − 𝐿𝑜𝑔10𝑁0
𝑘= 𝐿𝑜𝑔102 × 𝑡

● 𝑁𝑡 = number of bacteria at one particular time (e.g. at 5 hours)

● 𝑁0 = number of bacteria initially

● 𝐿𝑜𝑔102 = 0.301

● t = time of 𝑁𝑡 (e.g. 5)

Example: Using the data from the following graph, if the number of bacteria at the
beginning is 1 and the colony has 1024 bacteria after growing for 5 hours.

𝐿𝑜𝑔10𝑁𝑡 − 𝐿𝑜𝑔10𝑁0
𝑘= 𝐿𝑜𝑔102 × 𝑡

𝐿𝑜𝑔10(1024) − 𝐿𝑜𝑔10(1)
𝑘= 𝐿𝑜𝑔102 × 5
∴k=2

5
Example 2: Find the population size at 15 hours

𝑘𝑡
𝑁𝑡 = 𝑁0 × 2

2 × 15
𝑁𝑡 = 1 × 2

𝑁𝑡 = 1073741824

3
Example 3: A liquid medium was inoculated with 6 × 10 bacterial cells and the

culture was incubated for a period of time. At the end of this incubation period,
7
there were 1. 2 × 10 bacterial cells. Calculate the time (t) of this incubation period.
Use a value of 0.963 for the growth rate constant (k) and the equation.

𝐿𝑜𝑔10𝑁𝑡 − 𝐿𝑜𝑔10𝑁0
𝑘= 𝐿𝑜𝑔102 × 𝑡

7
(
𝐿𝑜𝑔10 1.2 × 10 ) − 𝐿𝑜𝑔10(6 × 103)
0. 963 = 𝐿𝑜𝑔102 × 𝑡
∴ t = 11.4

Example 4: The formula used to calculate the growth rate constant can only be
applied to one phase of bacterial growth.To which phase of bacterial growth can
the formula be applied?

(A) death
(B) exponential
(C) lag
(D) stationary

6
 MICROBIAL TECHNIQU & MEASURING
BACTERIAL CULTUR
Learning objectives:
I. Understand the principles and techniques involved in culturing
microorganisms, using aseptic technique
II. Understand the different methods of measuring the growth of
microorganisms, as illustrated by cell counts, dilution plating, mass and
optical methods (turbidity)

SAFETY AND ASEPTIC PRECAUTIONS

Even if culture is harmless once, there is risk of a mutant strain developing that’s
pathogenic. A risk of contamination of the culture by pathogenic microorganisms
from the environment.

Aseptic techniques

★ Careful handling, culturing or disposing of microorganisms.

★ Use only sterile equipment
★ Dispose all cultures safely( decontamination)
○ Sterilize them at 121 °C for 15 minutes under high pressure using an
Autoclave
○ Seal them in plastic bags

7
 CULTURING MICROORGANISMS

★ Microorganisms ( can’t see with your naked eyes)

★ To investigate microorganisms , culturing (growing) is required.
★ Culturing - growing large numbers of the microorganisms to be measured
★ Bacteria and fungi -most commonly cultured.

Growth for multicellular organisms is typically measured in terms of the increase in

size of a single organism, microbial growth is measured by the increase in
population, either by measuring the increase in cell number or the increase in
overall mass.

8
ASEPTIC CULTURING OF MICROORGANISMS

1. Decide & obtain a pure culture of the microbe.

2. Provide them with the right nutrient (carbon, nitrogen
& specified minerals)
3. Sterile nutrient medium
■ Nutrient broth (liquid)
■ Nutrient agar (Solid)

Most grow on or in a medium enriched with good protein sources

Selective medium: a medium with specific nutrients where only a select group of
microorganisms will grow.

Example :

★ MacConkey for gram negative bacteria

★ YM media with low pH for fungi

Uses of selective media

★ Identifying mutant microbial strains(Species).

★ Identify antibiotic resistance strains.
★ Identifying genetically modified microbes.
○ Scientists genetically modify a microbe by adding a marker
gene(antibiotic resistance) along with the gene of interest and growing
on an antibiotic containing medium - so only GMO will survive.

9
GROWING A PURE CULTURE
Single type of Bacterium
Microorganism is isolated and grown by providing specific conditions & free of
possible contamination nutritional requirements – different for different microbes.

★ Growing a culture under anaerobic conditions

○ only anaerobic bacteria survives
★ Growing organisms with oxygen
○ only aerobic organisms can survive.
★ Can add antibiotics or antifungal chemicals (selective growth inhibitors)
○ reduce or prevent the growth of all microorganisms except the one
that is culturing.
★ Can use indicator media that cause certain types of bacteria to change
colour
○ Colonies that do (or do not) change colour can be isolated and
cultured.

10
Example: Temperature affects the rate of growth of bacteria.The diagram
shows some information about the growth of bacteria in different ranges of
temperature.

(a) Explain why most types of bacteria are killed at

temperatures above 60 °C, but bacteria can grow slowly
in a temperature range of 50 °C to 60 °C. (4)

An explanation that includes the following points:

● above 60 °C the enzymes are denatured (1)

● so there will be no metabolic reactions (1)
● because between 50 °C to 60 °C the enzymes are
working slowly (1)
● because the enzymes are denaturing (1)

Between 50 °C to 60 °C the enzymes are working slowly as the enzymes start to get
denatured. However, above 60 °C the enzymes are denatured and the bacteria are
killed

(b) (i) Explain why some foods are kept in refrigerators at a temperature
between 0 °C and 5 °C. (3).

An explanation that includes the following points:

● decomposition will be slower (1)

● because the enzymes will be less active (1)
● as there is less {heat / kinetic} energy (1)

When the temperature is between 0 °C and 5 °C , there is less kinetic energy in

enzymes making enzymes less active, slowing down the process of decomposition
which is controlled by enzymes released by decomposers.

11
(ii) Explain why there is no growth of bacteria in a freezer at a temperature of
−18°C. (2).

An explanation that includes the following points:

● cytoplasm will be frozen (1)

● therefore enzymes and substrates will not be able to {move / collide} (1)

When the temperature is -18 °C , the cytoplasm of the bacterial cell will be frozen
and enzymes and substrate do not move to collide with each other

Techniques to measure bacterial cultures

12
 CELL COUNT: Haemocytometer

Hemo = blood

Cyto= cell

Meter = measurement

➢ An instrument used to count the blood cells

➢ Can also be used to count prokaryotic cells.

Preparing to count

1. Dilute the sample of nutrient broth by half with equal

volume of trypan blue (stains dead cells blue)
2. Use a microscope to view the slide

How to take measurements

★ Each corner of the grid contain a square divided into 16 small squares
★ Number of bacteria cell in each square counted and a mean is calculated
★ Number of bacteria in each set of 16 square = number of cells X 104 per cm3 of
broth
★ Measurement is repeated at a regular interval to see the
change in number

13
14
 OPTICAL METHOD: Turbidity

★ Turbidimetry - specialized form of colorimetry

★ More cells – cloudy
★ This indirectly indicates how many microorganisms are present.
★ You can produce a calibration curve by growing a control culture and taking
samples at regular time intervals.
★ You can measure the turbidity of each sample and also count the cells using
a haemocytometer for each sample. This gives you a relationship between
the turbidity of the culture and the number of bacterial cells present.
★ You can then use this calibration curve to measure the number of
microorganisms simply using turbidimetry .

15
DILUTION PLATING

★ Prepare a series of dilutions

★ Spread a sample of diluted culture on nutrient rich agar
★ A single bacteria (colony forming unit) divides several times to form a colony
★ Number of bacteria in original culture determined by using CFUs and dilution
factor

○ Used to find the total viable cell count

Assumption: Each of the colonies on the agar plate

has grown from single microorganism

16
Example: A student used a dilution series box to investigate the number of
cells present in a liquid culture of bacteria. Describe how he made a 1 in 10
dilution and then used this to make a 1 in 1000 dilution of the original liquid
culture of bacteria.

1. Add 1 part (bacteria) culture to 9 parts (sterile) liquid / water / nutrient /

broth (to make 10−1 dilution);
2. Mix (well);
3. Repeat using 9 parts fresh (sterile) liquid / water / nutrient / broth and 1 part
of 10−1 and 10−2 dilutions to make 10−3 dilution; OR Add 1 part 10−1
(suspension) to 99 parts (sterile) liquid / water / nutrient / broth (to make
10−3 dilution);

Area of Fungi

In Fungi growth is measured by measuring the diameter of the individual areas of

mycelium. To find the optimum temperature for growth follow these steps.

★ Inoculate identical Petri dishes containing identical growth mediums with the
same number of fungal spores.
★ Culture the Petri dishes at different temperatures, with several identical
dishes grown at each temperature.
★ After a specific period of time, measure the diameter of each fungal colony
and calculate the mean value for the diameter at each temperature.
★ The optimum temperature for growth is close to the temperature at which
you obtained the largest mean diameter.

17
Cell mass of fungi

Measuring dry mass using a liquid growth medium

★ Remove samples of broth at regular intervals

★ Separate the fungi from the liquid by centrifugation
★ Dry the material thoroughly until you record no more loss of mass
★ The conditions which produce the greatest dry mass of fungus are the
optimum conditions for growth.

18
 SUMMARY: Techniques to measure
TECHNIQUE DESCRIPTION ADVANTAGE DISADVANTAGE

★ Rapid, simple & easy

method requiring ★ Small cells are difficult to
Direct count of number minimum equipment locate, some bacteria may
CELL
COUNT of bacteria cells or ★ Morphology of bacteria is not be stained properly
single celled fungi using observed while counting less precision
a haemocytometer ★ Use of trypan blue ★ Motile cells are difficult to
identifies dead cells from count, must be immobilised
the live cells

★ Detection of bacteria size is

An indirect not possible
TURBIDITY
measurement of cell ★ A fast method to estimate ★ Gives a false reading when
density using a cell density light enters along the sample
spectrophotometer which is detected by
detector

★ Takes time for dilution,

plating, media preparation &
★ Easy to perform & more incubation
DILUTION sensitive than turbidity ★ Only living cells develop
PLATING Used to find the total ★ It is possible to correlate colonies that are counted
viable cell count turbidity readings to the ★ Clumps develop into single
actual number of cells by colony
performing a viable plate ★ Colonies develop from
count organisms which can grow in
the culture conditions
provided

19
 A2 BIOLOGY
SEM TER THREE 2021
Student N es
12s8

MICROBIOLOGY
Learning objectives:
I. 6.5(i)be able to compare the structure of bacteria and viruses (nucleic acid,
capsid structure and envelope) with reference to Ebola virus, tobacco mosaic
virus (TMV), human immunodeficiency virus (HIV) and lambda phage (λ
phage)

(ii) understand what is meant by the terms lytic and latency

II. 6.6 understand how Mycobacterium tuberculosis and human

immunodeficiency virus (HIV) infect human cells, causing symptoms that may
result in death

III. 6.7 (i) know the major routes pathogens may take when entering the body

(ii) understand the role of barriers in protecting the body from infection,
including skin, stomach acid, and gut and skin flora

1
Structure of Bacteria

2
All bacteria have:

★ A bacterial cell wall containing peptidoglycan

★ Cell surface membrane similar to those in eukaryotic cells
★ A nucleoid (a single, circular strand of DNA that is the genetic material of the
bacterium)
★ 70s ribosomes which are the site of protein synthesis

Some bacteria have:

★ Pili- thread like projections from the surface of the cell wall. This helps
bacteria to stick together and can be used in gene transfer.
★ Flagella- a long rapidly rotating whip-like structures which can move the
bacteria about
★ A capsule or a slime layer- a thick slippery substance around the outside of
the cell wall. It helps to protect the bacterium from attack by cells of the
immune system/ antibiotics.
★ Mesosomes- internal extensions of the membrane which fold into the
cytoplasm and may be the site of respiration
★ Plasmids- small circles of additional DNA that code for specific
characteristics such as antibiotic resistance

3
Structure of virus

They are not cells. They are just particles composed of genetic
material and protein.They are obligate intracellular parasites.

They can exist and reproduce only within a living organism.

★ Genetic material / nucleic acid is either DNA or RNA (viral

genome contain the genetic material for the viral
protein synthesis)
★ Nucleic acid is either single-stranded or
double-stranded
★ Nucleic acid is surrounded by a capsid / protein coat
★ Outer to the capsid a lipid envelope may be
present. This makes it easier for the virus to pass
from cell to cell.
★ Spikes or glycoproteins present. These let the virus bind onto a specific
receptor on the host cell. These are specific proteins (antigens) known as
virus attachment particles (VAPs)
★ Some viruses contain enzymes like reverse transcriptase (which makes DNA
molecules corresponding to the viral RNA) / integrase (integrate viral genome
with host cell genome)

4
Viruses are classified by their genome and their mode of replication.

★ DNA virus- they have DNA as the genetic material

This viral DNA acts both as template for the new viral DNA and for the
mRNAs needed to induce the synthesis of viral proteins. (example:
smallpox virus)

★ RNA virus- RNA is the genetic material

RNA virus do not produce DNA as part of their life cycle. Majority of the RNA viruses
contain a single strand of RNA. (example:TMV, Ebola)

★ Retrovirus- a type of RNA virus that controls the production of DNA

corresponding to the viral RNA and inserts it into the host cell DNA.

Special type of RNA virus. They have a protein capsid and a lipid envelope.
(example: HIV) The single strand of viral RNA controls the synthesis of a special
enzyme called reverse transcriptase.This is responsible for making DNA molecules
corresponding to the viral genome.

Bacteria vs Virus
Bacteria Virus

Bacteria are cells Viruses are {not / particles}

Bacteria surrounded by cell wall Viruses surrounded by protein /

/slime / capsule capsids / envelope

Bacteria have plasmids Viruses do not have plasmids

Bacteria (genome) is DNA Viruses can be DNA or RNA

Bacterial DNA is double-stranded Viral genetic material is single or

double stranded

Bacteria have circular genetic Viruses have linear / straight genetic

material material

5
Human immunodeficiency virus (HIV)

★ HIV is a retrovirus.
★ The nucleic acid is RNA.
★ Contains reverse transcriptase enzyme
★ Two viral strands of RNA found in the core surrounded by the protein outer coat.
★ Outer to capsid a lipid envelope with specific viral glycoproteins (GP120) are
present.
★ These knob-like structures are responsible for binding to the target cell.

6
Ebola virus

★ Single-stranded RNA virus.

★ It has a lipid envelope outer to the capsid.
★ It has a polymerase enzyme which catalyses
RNA replication.
★ This is needed to make viral RNA for the new
viral particles and also for the transcription of
viral RNA

Tobacco mosaic virus

★ Single-stranded RNA virus

★ Genetic material is surrounded by the capsid.

λ Phage

★ It has a double-stranded circular DNA as the genetic material.

★ It has a head which is capsid, tail and tail fibres

7
Lytic and Latency

Once a virus enters into the host cell, there are two different routes of infection:

1. The lysogenic pathway

2. The lytic pathway

Latent - the state of non-virulent virus within the host cell

Lysogeny – the period when a virus is part of the reproducing host cell, but does
not affect the host adversely.

Lysogenic pathway

★ DNA viruses insert their DNA into the host cell

★ It is replicated every time when the host cell divides.
★ This inserted DNA is called provirus.
★ The viral gene causes a repressor protein to be produced.
★ So messenger RNA is not produced from the viral DNA.
★ The translation of the rest of the viral genetic material is impossible.
★ So the virus is said to be latent.
★ But when the host is damaged, the virus in the lysogenic pathway is activated.
★ The amount of repressor protein decreases and the virus enters into the lytic
pathway and becomes virulent.

8
Lytic pathway

★ Sometimes, the viral genetic material is replicated independently of the host

cell DNA soon after it enters into the host cell.
★ Mature viruses are made and eventually the host cell bursts, releasing large
numbers of new virus particles.
★ These particles invade other cells.
★ The virus is now disease-causing (virulent) and the process of replicating and
killing cells is known as lytic pathway.

9
The more complex life cycle- life cycle of retrovirus

★ The genetic material of retrovirus is RNA.

★ This viral RNA is converted into viral DNA by the enzyme reverse transcriptase.
★ This viral DNA enters into the host cell nucleus and is inserted into the host cell
DNA.
★ The host transcriptase enzyme makes viral mRNA and new viral genome RNA.
★ New viral material is synthesized and the new viral particles leave the cell by
exocytosis.

10
Bacterial disease-Tuberculosis

★ It is an infectious disease caused by the bacterium- Mycobacterium

tuberculosis. (airborne bacteria)
★ The bacteria produce a thick waxy outer layer which protects them from
enzymes and macrophages.
★ They are very resistant to antiseptics and disinfectants.
★ Mainly acquired by droplet infection.

★ When an infected person coughs or sneezes the droplets containing

bacterium spread in air.
★ When a healthy person inhale this contaminated air the person will get the
infection
★ It is an opportunistic infection.

11
 ★ TB bacteria enters the body (lung tissue).
★ Causes inflammatory response from the host body.
★ The macrophage become activated and engulf them
★ The bacteria reproduce in the lung , damaging the lung tissue by its toxins.
★ This causes coughing and increases the transmission of the disease.
★ Macrophages enter the alveoli in large numbers and engulf bacteria by
phagocytosis.
★ In response to infection a mass of tissue forms which is called granuloma.
★ Granuloma is anaerobic and contain dead bacteria and macrophages in the
middle are called tubercles
★ The infection is controlled after three to eight weeks and the lung heals.
★ But these bacteria survive and breed inside the macrophages in the tubercle
as they have a thick waxy coat. (latent TB)
★ The thick waxy coat makes the bacterium very difficult to break.
★ When the immune system is weakened the tubercles break and release TB
bacteria out.
★ This re-infects the body. (secondary infection/ active TB).
★ The lungs are progressively damaged which eventually leads to death.

12
Symptoms of TB

★ Persistent Coughing
★ Blood in sputum
★ Shortness of breath
★ Loss of appetite leading to weight loss.
★ Fever and fatigue

Why this infection can result in these symptoms

★ Alveoli have been destroyed by the tubercle

★ Destroyed lung tissue has reduced the surface area of the lung.
★ Breathing problems due to reduced gas exchange
★ The coughing is due to irritation because of the dead tissue
★ Blood coughed up is due to damage of lung blood vessels

How these symptoms leads to death

★ Breathing problems
★ Blood in sputum / coughing up blood
★ Mycobacterium also target T cells and reducing
the production of antibodies
★ So TB causes suppression of immune system
★ Leads to organ failure, brain damage,
opportunistic infection such as pneumonia

Opportunistic infection:- an infection caused by pathogens that usually do not

cause disease in a healthy organism with a healthy immune system.

13
Causes of spread and prevalence of TB

★ Mutated bacteria may evade the immune system –makes the vaccine less
effective.
★ The decreased availability of vaccination.
★ Development of antibiotic resistant TB bacteria due to misuse of antibiotics.
★ Increased travel and migration of infected people.
★ High population density.

Ingesting food containing these organisms is unlikely to lead to the

development of TB.

Kills bacteria in stomach by hydrochloric acid and gastric juice

14
HIV AND AIDS

★ Gp120 on (HIV) binds to (CD4) receptors on the cell surface of the helper T cells.
★ Virus (envelope) fuses with (cell surface) membrane of the helper T cell
★ These are also taken in by phagocytosis in macrophage

15
Once inside the cell

★ The single stranded RNA of the virus is converted into double stranded DNA by
reverse transcriptase enzyme.
★ The double stranded DNA incorporated into the genome of the host cell.
★ The integrated viral DNA is called provirus.
★ The provirus never leaves the host genome.
★ The virus will be latent if the infected T4 cells are not activated.
★ A secondary infection activates T4 lymphocytes.
★ The host’s RNA polymerase transcribes the proviral DNA into RNA.
★ This RNA can function both as mRNA for the synthesis of viral proteins and as a
genome for a new virus.

16
HIV infection to death of the patient

★ Glycoprotein / gp120 on virus binds with CD4 receptors on (surface)

membrane of lymphocytes / T helper cell
★ Viral RNA enters the lymphocyte and produces viral DNA by reverse
transcriptase .
★ Viral DNA become part of host cell DNA by integrase
★ Viral proteins are synthesized and form new viruses
★ Lymphocytes are destroyed when new viruses bud out of the cell.
★ T killer cells also destroy heavily infected T helper cells / lymphocytes.
★ Role of T helper cells in immune response is to produce cytokines, activate B
cells / killer cells
★ This lowers immunity to other diseases
★ Death is caused by opportunistic disease like TB or pneumonia.

HIV positive but no AIDS

★ HIV is a slow virus and after infection there may not be any symptoms until
years.
★ Replication of the virus and cell destruction occurs only after the activation of
T4 cells.
★ There are some flu-like symptoms for several weeks after becoming infected.
★ At this stage the person is HIV positive but does not have AIDS.

17
Phases of HIV infection

★ T helper cell count decreases because:

★ Virus attaches to CD4 surface receptors;
★ Virus genetic material enters T helper cell;
★ Virus genetic material produces new virus particles;
★ When the new virus bud out helper T cell lyses;
★ T killer cells attack infected T helper cells

Data about HIV infections are often estimates

★ HIV infection does not always produce symptoms ;

★ Provirus / latency
★ Test needed to detect symptomless HIV ;
★ only people who suspect they may have contracted HIV would have a test ;
★ Some people would not want to be tested / impossible to test everyone.
★ Symptoms are common to other diseases ;
★ New cases arising/ patients dying all the time
★ New strains of virus arising ;

18
A mixture of many new drugs needed for HIV treatment

★ HIV has many new / protein coats /in infected person

★ Some strains are resistant to a particular drug
★ These would survive if only one drug was used.
★ Mixture of drugs has more chance of getting rid of all strains
★ Rapid rate of multiplication of virus leads to rapid rate of mutation.
★ Drugs used together because of mutation

19
 A2 BIOLOGY
SEM TER THREE 2021
Student N es
12s8

IMMUNE R PONSE
Invading the body
Learning objectives:
I. Know the major routes pathogens may take when entering the body
II. Understand the role of barriers in protecting the body from infection,
including skin, stomach acid, and gut and skin flora
III. Understand the non-specific responses of the body to infection, including
inflammation, lysozyme action, interferon and phagocytosis
IV. Understand the roles of antigens and antibodies in the body’s immune
response including the involvement of plasma cells, macrophages and
antigen-presenting cells
V. Understand the differences between the roles of B cells (B memory and B
effector cells), and T cells (T helper, T killer and T memory cells) in the host’s
immune response
VI. Understand how individuals may develop immunity (natural, artificial, active
and passive)
VII. Understand how the theory of an ‘evolutionary race’ between pathogens and
their hosts is supported by evasion mechanisms shown by pathogens
VIII. Understand the difference between bacteriostatic and bactericidal antibiotics

1
2
Barriers to entry

Pathogens are transmitted in a variety of ways

★ Inhalation: when an infected person coughs or sneezes, the droplets

expelled from the respiratory tract contain pathogens. Part of the water from
these droplets evaporates leaving very small droplets full of pathogens which
will remain suspended in the air for a long time. When these droplets are
inhaled by a healthy person, he will be infected.
★ Vectors: a living organism that transmits infection from one host to another
is known as a vector.
★ Fomites: inanimate objects like hospital towels and beddings and someone
else cosmetics that carry pathogens from one host to another
★ Inoculation: a pathogen can be inoculated into the body directly through a
break in the skin. It can be through a contaminated needle or a knife,
damaged skin, infected animal bite
★ Ingestion : many of the pathogens that cause the gut diseases are
transmitted by faecally contaminated food or drink.
★ Direct contact: mainly skin diseases and sexual diseases

3
 Epithelial defences:

★ Skin – an impenetrable layer strengthened by a fibrous protein keratin.This forms

a physical barrier.
★ Sebum- an oily substance produced by the skin.This contains chemicals that
inhibit the growth of microorganisms.
★ Skin flora- produces substances that inhibit the growth of other microorganisms.
★ Epithelial layers of the internal tubes of nose, respiratory system and reproductive
system produce defensive secretions.
★ Many produce mucus that trap microorganisms and cilia move the mucus away
to the stomach .
★ Mucus contain lysozymes which are capable of destroying microbial cell wall
★ Pls study

Role of skin as a barrier

★ The epidermis of the skin provides a physical barrier to invading pathogens.

★ Contain fibrous protein keratin on the skin epidermis forms a physical
barrier.
★ The outermost compact closely packed cells prevent the entry of pathogens.
★ Secretions of the gland act as a chemical barrier to pathogens.
★ Sebum and sweat- these oily secretions make the skin acidic and inhibit
bacterial growth.
★ Sebaceous glands also secrete lysozyme- a natural antibiotic- destroys
bacterial cell wall and lyse bacteria.

4
Skin and gut flora

★ The normal growth of bacteria on skin and in the gut is called skin flora or
gut flora.
★ These bacteria are adapted to live in acidic conditions and it is not harmful to
the body.
★ They are called commensal bacteria.
★ These bacteria compete with invading bacteria for food/nutrients and space
and outcompete the harmful bacteria.

Stomach and first line defense

★ Gastric juice in the stomach contains Hydrochloric Acid.

★ This destroys the bacteria present in the food or saliva.
★ Toxins and pathogens are removed physically by vomiting.

Skin flora protect the body from infection

★ Skin flora prevent growth of or kill pathogens.

★ Competition for space and nutrients and outcompete pathogens.
★ Release chemicals such as enzymes to prevent the growth of microbes.
★ Lipids have antimicrobial effect which inhibit microbial growth.

5
Immunity to Infection

Infection: A microorganism is present inside a tissue

Immunity : the ability of an organism to resist infection

★ The immune response is the complex series of responses of the body to the
entry of a foreign antigen. It involves the activity of lymphocytes and
phagocytes
★ An antigen is a substance that is foreign to the body and stimulates an
immune response.
★ An antibody is a glycoprotein (immunoglobulin) made by plasma cells
derived from B-lymphocytes, secreted in response to an antigen; the variable
region of the antibody molecule is complementary in shape to its specific
antigen.

6
Non-specific immune response

★ The body reacts to a foreign matter and the response is not dependent on
the specific pathogen
★ They are either by lysozymes , inflammation, phagocytosis, and interferon
production.

Inflammation

★ Tissue damage
★ Mast cells release mediators such as histamine, kinins, prostaglandins etc.
★ Histamine leads to vasodilation.
★ So more blood flows towards the area. The area become red and hot (more
phagocytes and platelets arrive at the site of wound and heat speeds up
phagocytosis and skin cell division)
★ Increases the permeability of the capillary wall.
★ Increases tissue fluid formation and leads to local oedema.
★ Attract more WBC to the infected area.
★ Engulf pathogens and foreign bodies.
★ Dead monocytes and pathogens may form pus.

7
Phagocytosis

★ Microorganism binds to phagocytic cell ;

★ Microorganism is engulfed by phagocytic cell
★ By forming a vacuole / phagosome
★ A lysosome fuses with the phagocytic vacuole.
★ The enzymes break down the pathogen.
★ The phagocyte then presents the pathogen’s antigens.
★ It sticks the antigens on its surface to activate other immune system
★ So it’s also called an antigen-presenting cell.

8
Antimicrobial protein- interferon

★ Provides non specific response against viruses.

★ Virus infected cells produce interferon.
★ Provide innate defense against viruses and help activate macrophages.
★ It diffuses to the surrounding cells and prevents the virus from multiplying.
★ Limits the formation of new viruses by inhibiting viral protein synthesis.
★ Interferon prevents attachment of virus to other host cells
★ So that other cells cannot be infected when they burst out of infected cell

Lysozyme action

★ Has role in non-specific response

★ It destroys bacterial cell walls and lyse bacteria
★ And helps to prevent infection

9
Specific immune response

Cells of the immune system

10
T helper cells

★ T lymphocytes involved in cell mediated immunity;

★ T helpers cells produce chemical cytokine which aid B lymphocyte cloning
and produce plasma cells.
★ Plasma cells produce antibodies.
★ Activate killer T cells to kill virus infected cells.

B Cells

★ B lymphocytes produce antibodies/involved in humoral response;

★ Macrophages present antigens;
★ (specific) B lymphocytes bind to antigen; increase in numbers by mitosis;
★ produce plasma cells (which make antibodies);
★ antibodies bind to and clump virus;
𝑠𝑡 𝑛𝑑
★ memory cells produced by 1 exposure /cloned on 2 exposure;

11
Humoral immunity- Primary immune response

The immune response that is occurring on the first exposure to an antigen, with
specific antibodies appearing in the blood after a multiple day latent period.

When a new pathogen enters into the body, the immune system takes little time to
mount a response

Stages of humoral response

1. Antigen presentation
2. Activation of T helper cell
3. Activation of B cell
4. Production of plasma cells
5. Antibody production

Antigen presentation

★ A piece of biological material is engulfed by a macrophage.

★ Protein fragments from the material become attached to proteins in the cell.
★ Added to the cell surface membrane of the macrophage and displayed as
non-self antigen.
★ These macrophages are
antigen-presenting cells (APCs)
★ These act as a signal to alert the
immune system.

12
Activation of T helper cell

★ T helper cell with complementary shaped receptors on its surface binds to

the antigen on the surface of the APCs.
★ T helper cells are activated, and divides to produce a clone of active T helper
cells and T memory cells.
★ Memory cells remain in the body for months or years.

Activation of B cells

★ B cells bind to non self antigen and become APCs.

★ APCs bind with active clone T cells that are presenting the same antigen.
★ T helper cells release cytokines and stimulate the division and differentiation of
B cells.
★ B cells divide and form two clones of cells
called B effector cells and B memory cells.
★ B effector cells:- differentiate to produce
plasma cells which release antibodies into
the blood and last only for a few days.
★ B memory cells:- enabling an individual to
respond more quickly to the same antigen
in the future and remain in the body for
months or years

13
The production of sufficient antibody producing cells takes about 10-17 days.

This production of antibody producing cells is the primary immune response.

During this time period the person is likely to suffer the symptoms of the infection

14
Memory cells

These cells remain circulating in the body for a long time.

If the same antigen is reintroduced a few weeks or months after the first infection,
memory cells divide rapidly and develop into plasma cells and more memory cells.

Role of memory cells

★ On further exposure to the same microorganism.

★ Antigen recognised by memory cells.
★ Greater production of antibodies in a short time period.

Production of plasma cells

★ In humoral (immune) response

★ Phagocytosis by phagocytes
★ macrophages become antigen-presenting cells APCs
★ B cells also become antigen-presenting cells
★ T helper cells release cytokines for B cell activation
★ B cells forming clones (to form B effector cells) ;
★ B effector cells differentiate into plasma cells.

There is an extensive network of rough endoplasmic reticulum in the cytoplasm

(green) for the production of antibody molecules, which plasma cells secrete into
blood or lymph by exocytosis.

The mitochondria (blue) provide ATP for protein synthesis and the movement of
secretory vesicles.

15
Structure of antibody

★ Molecules that are synthesized by an animal in response to the presence of

foreign substances (antigens).
★ Each antibody is a protein molecule – immunoglobulin.
★ Consists of two heavy chains and two light chains (quaternary structure) .
★ These chains are held together by
disulfide bonds.
★ Has a constant and variable part.
★ Variable part acts like a key where the
antigen can bind.
★ Constant region is for it to attach on
phagocytes
★ Hinge region provides flexibility so
that more than one antigen can bind

16
Antigen

★ Molecules which can cause antibody formation.

★ All cells possess antigens in their cell surface membrane which act as
markers.
★ They are usually proteins or glycoproteins.
★ Body can distinguish foreign antigen and make antibodies against that.

Why is there a delay before the level of antibodies starts to rise?

★ Development of specific immunity

★ Antigen has to attach to B cells ;
★ T (helper) cells are needed in the activation of B cells;
★ T (helper) cells have to be activated before they can activate B cells
★ Cloning of B cells has to take place ;
★ B cells have to differentiate into plasma cells ;
★ Antibody production is by plasma cells

17
 Cell mediated immune response

Role of killer T cells

★ T killer cells with complementary receptors bind to the antigen present on the body
cell.
★ T killer cells divide to form an active clone by cytokines from T helper cells.
★ T killer cells release enzymes that create pores on the membrane of the infected cell.
★ Ions and water flow into the infected cell
which swells and bursts.
★ Pathogen is released and are destructed
by macrophages

18
Primary and secondary immune response

Primary immune response

★ When a pathogen enters the body for the first time the antigens on its
surface activate the immune system.
★ The non-specific immune response is activated first and then activates the
specific immune response.
★ The primary response is slow because there aren’t many B cells that can
make the antibody needed to bind to the antigen.

Secondary immune response

★ If the same pathogen enters the body again, the immune system will produce
a quicker, stronger immune response — the secondary response
★ T memory cells divide into the correct type of T cells to kill the cell carrying
the antigen.
★ B memory cells divide into plasma cells that produce the right antibody to
the antigen.

19
Immunity can be active or passive

★ Natural active immunity:- The immunity which results from natural

infection of the body and the production of antibodies by the immune
system.
★ Natural passive immunity:- Immunity which results from passing naturally
from a mother to her baby via the placenta, in the colostrum and in the milk.
★ Artificial passive immunity:- immunity which results when antibodies
formed in one individual are extracted and injected into another individual
★ Artificial active immunity:– immunity induced by the use of a small
amounts of antigen (vaccine) to trigger an active immune response

20
Why don't maternal antibodies give organisms long-lasting protection?

★ It is natural passive immunity

★ The specific immune response has not occurred
★ No T helper / T killer / B memory cells made.
★ And they have been broken down by the kidneys.

How can a person develop artificial active immunity?

★ Artificial active immunity can be developed by vaccination

★ A dead pathogen is put into person .
★ This stimulates the specific immune response.
★ This pathogen is engulfed by macrophage by phagocytosis.
★ Activate T helper cell.
★ Activated T helper cells activate B cells by cytokines.
★ Produce memory cells for secondary infection

21
A2 BIOLOGY
SEM TER THREE 2021
Student N es
12s8

Antibi i
Learning objectives

I. 6.12 understand how the theory of an ‘evolutionary race’ between pathogens

and their hosts is supported by evasion mechanisms shown by pathogens

II. 6.13 understand the difference between bacteriostatic and bactericidal

antibiotics

III. 6.14 CORE PRACTICAL 14 Investigate the effect of different antibiotics on

bacteria.

IV. 6.15 know how an understanding of the contributory causes of

hospital-acquired infections has led to codes of practice regarding antibiotic

prescription and hospital practice that relate to infection prevention and

control

1
Antibiotics

★ Chemical produced by microorganisms that kills / inhibits the growth of

bacteria

★ Widely used in the treatment and prevention of infectious diseases.

Classification of antibiotics

According to mode of action antibiotics can be classified into two:-

Bactericidal antibiotics :- kill the bacteria (penicillin)

Bacteriostatic antibiotics:- prevent the multiplication of bacteria. (erythromycin)

Interfere with bacterial protein synthesis , DNA replication etc.

2
 ★ Bactericidal and bacteriostatic work depends on the dose given

★ At high doses, bacteriostatic antibiotics often kill a lot of the bacteria

★ Bactericidal antibiotics do not kill all of the bacteria.

★ They kill most of the bacteria within a given frame.

Methods of action of antibiotics

Ways in which antibiotics interfere with bacterial cell growth and division are the

following.

I. inhibit bacterial cell wall synthesis:

prevent the formation of peptidoglycan layer.

Results in weak wall which leads to cell lysis

II. inhibit protein synthesis:

Affect only prokaryotic cell as it binds only with 70s ribosome

Enzymes and other essential proteins are not produced.

III. Disrupt cell membrane:

Changes the cell membrane permeability which leads to cell lysis.

IV. inhibit nucleic acid synthesis, replication and transcription:

Prevents cell division

V. Inhibit specific enzymes:

3
4
Broad spectrum and narrow spectrum antibiotics

★ Broad spectrum antibiotics:

★ refers to an antibiotic that acts against a wide

range of disease-causing bacteria.

★ It may even destroy the useful bacteria.

Narrow spectrum antibiotics:

★ is effective against specific families of bacteria

Factors in the effectiveness of any antimicrobial drug include:

The concentration of the drug in the area of the body infected

The local pH

Whether either the pathogen or the host tissue destroy the antibiotic

The susceptibility of the pathogen to the particular antibiotic used.

5
 Ways in which hospital codes of practice have influenced the

prescription of antibiotics

Use only when necessary (not for viral infection)

Patients should finish the course

Using narrow spectrum antibiotics

Not use just in case infection occurs

Use appropriate antibiotics for the infection.

Rotating the antibiotics

6
 Ways in which hospital codes of practice can reduce the rate at which

antibiotic resistance is increasing.

Appropriate antibiotics should be given to patients ;

Educating patients about taking antibiotics / taking the full course of antibiotics

Hand washing, screening ;

Creating drug resistant bacteria

Mutation can occur during bacterial reproduction.

These mutations may make the cell wall impermeable to the drug or produce

enzymes that may break down the antibiotic.

As a result of natural selection, advantageous mutations become more common

and the bacterial population becomes increasingly resistant to the drug.

7
 Evolutionary race between pathogens and host

Humans evolve mechanisms to combat pathogens and pathogens evolve new

methods of overcoming our immune system.

Pathogens life cycle is faster than ours and their population size is greater.

Because of the faster reproductive cycle new mutations occur quite regularly in
pathogens.

This mutation may help the pathogen to survive

Immune system is one of the selection pressures acting on pathogens.

This selection pressure may lead to the evolution of pathogens that can evade the
immune system.

We are using new medicines and pathogens keep evolving resistance to these
drugs.

Antibiotic resistant pathogens may produce enzymes which break down the
antibiotic.

The presence of antibiotics also is a selection pressure.

Some are selected for and some are selected against.

Those which are selected for are grown and reproduced.

The frequency of the allele for resistance will increase within the bacterial
population.

Advantageous allele passed vertically and it is vertical evolution.

Advantageous alleles may pass from one bacterium to another through conjugation
and is called horizontal evolution.

8
Hospital acquired infections

★ Also called nosocomial infection.

★ It is an infection whose development is

favored by the hospital environment.

Examples include MRSA (methicillin-resistant

Staphylococcus aureus) and Clostridium difficile.

MRSA is a multi resistant bacterium.

Measures to control and prevent hospital acquired infections

★ Isolation of patients

★ Hand washing by staffs and visitors

★ Gloves and aprons worn

★ Screening of patients for superbug infections on arrival

★ Removal of jewellery / removal of outdoor clothing

★ Appropriate disposal of dressings / needles / laundry.

★ Sterilisation of bedding and equipment

9
 A2 BIOLOGY
SEM TER THREE 2022
Student N es
12s8

FORENSICS
Learning objectives
I. know how DNA can be amplified using the polymerase chain reaction (PCR)
II. know how gel electrophoresis can be used to separate DNA fragments of
different length
III. understand how DNA profiling is used for identification and determining
genetic relationships between organisms (plants and animals)
IV. understand how to determine the time of death of a mammal by examining
the extent of decomposition, stage of succession, forensic entomology, body
temperature and degree of muscle contraction

1
Polymerase Chain Reaction

★ It is the method of amplifying DNA.

★ DNA to be amplified is mixed with a good supply of the four different
nucleotides, primers, DNA polymerase and a buffer in a PCR tube and placed in
a thermal cycler.
★ Raise the temperature to 95oC.
★ Break hydrogen bonds between nitrogen bases and form single stranded DNA.
★ Lower the temperature to 50-60oC ;
★ This allows primers to bind or anneal to DNA at the complementary sequence at
start ;
★ Then the mixture is heated to 75oC;
★ Free nucleotides lined up by DNA polymerase along template strands to
produce new strands of DNA ;
★ Repeats the cycle for 30 times to get enough samples

2
Primers

★ A short length of DNA that has a base sequence complementary to the start of
the part of the DNA to be copied.
★ It joins to the beginning of the separated DNA strands
before copying can begin.
★ Primer is needed to begin synthesis of the complementary
strand.
★ It is 20 base pairs long

Question:- How many cycles of the PCR would be needed to produce 128
molecules of DNA from a single DNA molecule?

Properties of the enzyme in PCR

★ The enzyme DNA polymerase is heat stable (obtained from thermophilic

bacterium)
★ The optimum temperature for the enzyme is 75oC
★ Synthesises a new strand of DNA complementary to the template strand.
★ synthesis occurs in one direction
★ Primer is needed to begin synthesis of the complementary strand.

3
This enzyme is valuable for PCR for two reasons.

★ It is not destroyed by the denaturation step, so it does not have to be replaced

during each cycle.
★ Its high optimum temperature means that the temperature for the elongation
step does not have to be dropped below that of the annealing process, so
efficiency is maximised.

DNA polymerase from human is not used

★ Human enzymes will not work at high temperature or above 37oC

★ So denaturation /change in shape of active site occurs at temperatures in PCR

DNA Profiling

Analysing the patterns in the non-coding areas of the DNA and use them to identify
individuals

Forensic science- application of science to crime scene

Analysing the DNA

★ In DNA sequencing we analyse individual strands of DNA or individual genes.

★ This gives us a pattern of bases that code for a particular protein in the cell.
★ In DNA profiling we analyse the patterns in the non-coding areas of DNA .
★ These regions often contain variable numbers of repeated DNA sequences
and are known as variable number tandem repeats (VNTRs).
★ Only identical twins share all their VNTR sequences.
★ yolo

4
 ★
● Micro-satellites: It has 2 to 6
bases repeated 5 to 100 times
● Mini-satellites: It has 10 to 100
base sequence repeated 50 to
several hundred times

The theory used in DNA profiling

★ DNA profiling assumes every individual’s DNA is unique / different apart from
identical twins
★ DNA profiling analyses the introns / non-coding blocks
★ These non-coding DNA are hyper variable
★ Large number of introns are present
★ Many combinations at each locus/ huge variations in the number of repeats.
★ The probability that any two individuals have the same pattern of DNA is
unlikely

5
Main steps in DNA profiling

★ Obtain samples from the crime scene and suspects

★ Isolate and purify the DNA from tissue sample such as blood and saliva
★ Increase the number of DNA using PCR
★ Cut the DNA using restriction enzymes to get DNA fragments
★ Use gel electrophoresis to separate DNA fragments
★ Compare the DNA profile from the crime scene to patterns from suspects

6
How DNA could be prepared for analysis by gel electrophoresis

★ Extracting the DNA from body tissue like blood

★ Use polymerase chain reaction / PCR to amplify DNA.
★ Use restriction enzymes and produce DNA fragments.

DNA probe: A length of single stranded DNA with a specific

nucleotide sequence and it is labelled. The probe will attach
to the complementary sequence in a gene.

Gel electrophoresis

★ A technique used to separate the molecules based on their size.

★ Extracting the DNA from body tissue such as blood
★ Use polymerase chain reaction / PCR to amplify DNA.
★ Use restriction enzymes and produce DNA fragments.
★ These fragments are put into an electrical cell or tank containing agarose
gel, which acts as a supporting medium.
★ When electricity is applied the fragments move according to their size and
Smallest fragments move faster.
★ DNA is negatively charged so it moves towards the positive pole.
★ After gel electrophoresis DNA fragments are arranged according to their size
on the gel plate.

7
 ★ Then they are carefully transferred onto absorbent paper, which is placed
on top of the gel.
★ The paper is then heated to separate the two strands from one another.
★ Short sequences of single-stranded DNA called probes are added.
★ They have base sequences complementary to the VNTR regions.
★ The probes also contain a radioactive phosphorus isotope.
★ So when the paper is placed on an X-ray film, the radiation emitted by the
probes makes the film go dark.
★ So, we end up with a pattern of dark stripes on the film matching the
positions that the DNA fragments reached on the agarose gel.
★ Alternatively, the probes may be labelled with a fluorescent stain that
shows up when ultraviolet light is shone onto them

Uses of DNA profiling

★ Identifying the genetic relationship between organisms.

★ Detecting the presence of defective genes- thalassemia, CF
★ Identifying a guilty individual with a high degree of certainty.
★ Paternity test.

8
DNA profile and number of specific organism

★ Compare the (DNA) banding patterns / profiles.

★ Compare the number / position of bands.
★ The number of different sets of bands / profiles will equal the number of
organisms

9
DNA profiles can be compared to see how similar the pattern of bands on the gel is
— a match could help identify a person or determine a genetic relationship

Paternity Testing:

Children inherit half their chromosomes from each parent and thus should possess
a combination of parental fragments

In other words, all fragments produced in the child should also be produced by
either the mother or father

10
Identification and classification of organisms

★ The DNA patterns obtained in DNA profiling are unique to individuals.

★ But we can use the similarity of patterns to identify relationships between
individuals and even between species.
★ To identify the link between species the coding part of the DNA is used.

DNA barcodes

★ Looking at short genetic sequences from a part of the genome common to a

particular group of organisms.
★ Example: a region of the mitochondrial cytochrome oxidase 1 gene containing
648 bases is used as the standard barcode for most of the animal species.
★ It is not possible to use this region to identify plants because they evolve too
slowly to give sufficient differences between species.
★ Here two gene regions in chloroplasts are used to produce standard
barcodes for plants.

The more closely-related two individuals are, the more similar their DNA profiles will be
(e.g. more bands will match

11
 Question:- The diagram shows DNA profiles, from an adult female, an adult male
and each of four children.

Which of the children have both of

these adults as their parents? (1)

child 1 & child 2

child 1 & child 3
child 2 & child 3
child 2 & child 4

Determining time of death

Forensic evidence is usually combined with the evidence of witness and circumstantial
evidence to produce a best estimate of time of death.

A number of changes occur in the body of any mammal when it has died.

We can use these changes to help estimate the time of death.

A series of chemical changes begin to take place in the body after death in an orderly
manner until the body disintegrates.

Each stage has its own rate of time.

It can be estimated by the following factors:

● The temperature of the body

● Degree of rigor mortis
● State of decomposition
● Entomological evidence
● Succession on corpse

12
 Temperature of the body

★ Core temperature is measured via rectum or through abdominal stab by using a

chemical thermometer or thermocouple probe.
★ The cooling of the body gives a sigmoid curve.
★ The body is kept warm by the energy transferred during metabolic reactions such
as cellular respiration.
★ After death, the metabolic reactions which have warmed the body begin to slow
and eventually stop.
★ Energy is transferred from the surface of the body into the surroundings by
radiation, conduction and evaporation of water.
★ This cools the body- algor mortis.
★ The body temperature stays almost stable for a time before decreasing steadily to
room temperature.
★ Due to these changes, the temperature of
the body will give some indication of how
long the person has been dead

It is necessary to measure the body temperature and ambient temperature

as soon as possible

★ Core body temperature drops after death.

★ Rate of drop of temperature depends upon ambient temperature.
★ Ambient temperature fluctuates over time.
★ Measure the temperature sooner after death.
★ This provide more accurate time of death

13
Factors affecting the rate of cooling

★ Clothing:- Clothing would trap the heat so slows down cooling

★ Found in water:- speeds up cooling. Water is a better conductor of heat than air
★ Found indoors:- slows down cooling
★ Air movement:- speeds up cooling
★ Size of the body:-
○ larger size – surface area is large so slows down cooling.
○ smaller size-speeds up
★ Fat content:- more fat- fat act as insulator so slows down
★ Surface area to volume ratio:- smaller people will cool faster because they
have a large surface area to volume ratio than larger people

Estimated time of death for Clothing, position and air movement

Clothing

★ For the clothed body the estimate was too short compared to naked body
★ Because of clothing, the body would cool more slowly.
★ Clothing would trap the heat.

Position

★ For the body curled up the estimate was too short compared to stretched
body (died longer ago)
★ Because body would cool more slowly
★ As the exposed surface area was smaller

Air movement

★ For the moving air the estimate was too long compared to still air.(died later)
★ In moving air body would cool faster

14
Why the ambient temperature and the core temperature of the body are used
to determine the time of death of a person

★ The temperature of the body changes with time after death.

★ The core temperature depends upon the ambient temperature.
★ Other post-death changes like muscle contraction / insect life cycles /
decomposition etc. depend on ambient / body temperature.

Why are these data needed to estimate the time of death?

★ Body temperature decrease after death

★ Ambient temperature affects the change in body temperature
★ Body / ambient temperature affects other post death changes like rigor mortis.
★ Heavier / larger body will lose heat slower because surface area is smaller/ fat is
a (heat) insulator
★ The time of making the measurements is needed to work backwards from .
★ A naked body will lose heat faster
★ Body in water will lose more heat (than body in air)
★ Several pieces of information are used to estimate
time of death

15
Rigor mortis

★ Stiffening of the body after death.

★ It begins in the face and neck, progresses down the body and spreads
steadily to the larger muscles of the body.
★ On an average rigor mortis starts about 2 to 4 hours after death and takes
between 6 to 8 hours to take full effect.

The events occur after death leading to rigor mortis

★ Muscle cells are starved of oxygen and stop oxygen dependent reactions.
★ Anaerobic respiration leads to lactic acid accumulation.
★ pH falls and inhibits enzyme activities.
★ No ATP available.
★ Bonds between the muscle proteins become fixed.
★ Proteins can no longer move over one another.

Environmental factors that influence the rate of progress of rigor

mortis in a muscle immediately after death.

★ physical damage
★ immersion in water
★ (external) temperature
★ Burning
★ Electrocution
★ reference to {clothing}
★ wind / air movements

16
The factor which determine how quickly rigor mortis begins

★ The amount of ATP stored in muscles at the time of death.

○ If the level of ATP is less at the time of death, rigor mortis starts very
quickly.
★ Temperature of the person and the temperature of their surroundings.
○ Rigor mortis occurs more quickly at higher temperatures because the
chemical reactions in the body are faster.

Need to consider rigor mortis in several muscles of a body when estimating

the time of death.

★ Not all muscles reach full rigor at the same time .

★ Small muscles contract before large muscles.
★ Small muscle reaches full rigor before large muscle.
★ Full contraction does not last very long.
★ Large muscles might be still contracting while small muscles are relaxing.

17
State of decomposition

★ Body temperature and the degree of muscle contraction in a body are useful
in the first 48 hours.
★ For bodies found longer than 48 hours, forensic experts use the state of
decay.
★ Most bodies follow a similar pattern as they decay.
★ Breaking down the walls of the gut and then the surrounding cells by the
enzymes of the digestive system.
★ Then the lysosomes from the dead body cells rupture and release lysozyme
which break down cells.
★ These processes make the body a more suitable habitat for the organisms
responsible for further decay
★ Tissue is destroyed through bacterial proliferation soon after death
(putrefaction).
★ Bacteria that are in the respiratory tract and gastrointestinal tract are
responsible for this.
★ Autolysis is increased by mild heat and slowed by intense heat.

★ The speed of decomposition is variable and depends on the temperature of

the body and level of exposure
★ The warmer the body the faster the rate of decay. This is because the speed
of chemical reactions increases with increase in temperature.
★ Level of exposure - a buried body will decompose more slowly than a body
left in the open air.This is because the body on the surface is more available
to insects and other decomposers.

18
Signs of decomposition

★ Greenish discoloration of abdomen due to draining out of blood (36 hrs)

★ Spreads across rest of the body (36-72 hrs)
★ Discoloration darkens to reddish green (36-72 hrs).
★ Discoloration darkens to purple black (72 hrs).
★ Body bloated with gases (𝐻2𝑆 , 𝐶𝑂2 , 𝐶𝐻4) (one week).

★ Gas is released, body deflates and shrinks (more than week)

Forensic entomology

★ It is the use of insects and arthropods that feed on decaying remains.

★ Estimate the time of death using the age and development of maggots.
★ The fly, blow flies are attracted to a corpse very soon after death.
★ They lay their eggs on the corpse.
★ Their development follows a set of predictable cycles and known time.

19
 ★ Insects found in dead body can help to identify time of death
★ Maggots of different species usually take a fixed number of days to pupate.
★ This can be used to determine the age of the body.
★ For this maggots are taken from the body and allowed to grow and record
the time taken to pupate.

How maggots are useful

★ The stage of development at the ambient temperature can give an estimate

of age and hence time since the eggs were laid and hence the time of death
★ The time taken for eggs to hatch gives an indication of when the eggs were
laid and hence the time of death.
★ The age of the maggot, and hence when the eggs were laid can be
determined by measuring the fully extended length of the maggot and the
ambient temperature
★ Assumptions made to make this method useful:
○ Temperature has been fairly constant
○ Flies found the body to lay eggs soon after death

20
Succession on corpse

★ The human body supports a very rapidly changing ecosystem from the fresh
state to the dry bones.
★ Different stages of decomposition are attractive to different species of
insects.
★ Normally eggs are laid in wounds or at the openings of the body like nose,
mouth etc.
★ Prevailing conditions determine the community of the species that first
occupy the body.
★ Community of the species changes with succession.
★ The community of species present when the body is found allows the stage
of succession to be determined and time of death estimated.
★ As the body decomposes it undergoes changes
★ This may make it more attractive to other species.
★ The flies which feed on the body also bring about changes in it
★ That also makes it attractive to other species.
★ Decomposition follows a predictable sequence, so do the insect species
found over time

★ Insects can also help determine if a body has been removed.

★ There may be species of insects found on a body that would not naturally
occur in that location.
★ Ex. A particular species of insect is normally found in woods.
★ If the same species is present on the body which is indoors ,it has been
moved some time after the death

21
Estimating the time of death

★ Using the life cycle stage of the insects as these will change with time after
death
★ Using the state of decomposition as the changes occur in a certain order
★ Using ambient temperature as the rate of insect development /
decomposition / rigor / core temperature depends on temperature ;
★ because (core / ambient) temperature affects enzyme activity
★ using core temperature as this changes with time after death ;
★ Using extent of rigor which follow a set pattern ;
★ Using the effect of position / covering / size on body temperature ( if it is
curled the rate of cooling will be slow, if it is naked body rate of cooling would
be faster;)
★ Combining several pieces of information to arrive at estimate ;

22
A2 BIOLOGY
SEM TER FOUR 2022
Student N es
12s8

Cellular respiration
Learning objectives:
I. (7.1) understand the overall reaction of aerobic respiration as splitting of the
respiratory substrate to release carbon dioxide as a waste product and reuniting
hydrogen with atmospheric oxygen with the release of large amounts of energy
II. understand that respiration is a many-stepped process, with each step controlled
and catalyzed by a specific intracellular enzyme Names of specific enzymes are not
required.
III. (7.2) understand the roles of glycolysis in aerobic and anaerobic respiration,
including the phosphorylation of hexoses, the production of ATP by substrate level
phosphorylation, reduced coenzyme, pyruvate and lactate Details of intermediate
stages and compounds are not required.
IV. (7.3) understand the role of the link reaction and the Krebs cycle in the complete
oxidation of glucose and formation of carbon dioxide ( CO₂ ) by decarboxylation,
ATP by substrate level phosphorylation, reduced NAD and reduced FAD by
dehydrogenation (names of other compounds are not required) and that these
steps take place in mitochondria, unlike glycolysis which occurs in the cytoplasm
V. (7.4) understand how ATP is synthesized by oxidative phosphorylation associated
with the electron transport chain in mitochondria, including the role of
chemiosmosis and ATP synthase
VI. (7.5) understand what happens to lactate after a period of anaerobic respiration in
animals
VII. (7.6) understand what is meant by the term respiratory quotient (RQ)

1
What is cellular respiration?

It is the process by which the energy from food molecules is transferred to ATP.

The substance that is broken down is respiratory substrate.

The main respiratory substrate used by cells is glucose.

C₆H₁₂O₆ + 6O₂ → 6CO₂ +6H₂O + ATP

Glucose + oxygen → carbon dioxide + water + energy

An outline of aerobic respiration

★ Aerobic respiration occurs in two phases - glycolysis and Krebs's cycle

★ Glycolysis does not need oxygen
★ Here the respiratory substrate is broken down and the molecule is prepared
for the entry into the second stage.
★ Krebs cycle needs oxygen.
★ The link reaction moves the product of glycolysis to the Krebs cycle and the
electron transport chain.

2
Glycolysis

★ Phosphorylation of glucose to activate the glucose

and also make it unable to pass through the
membrane
★ ATP is used to phosphorylates glucose
★ Formation of fructose a 6C sugar
★ This split into two three-carbon sugar phosphates
/GALP
★ It is then converted to pyruvate by dehydrogenation
★ Produces reduced NAD and 2 ATP for each sugar
phosphate.
★ This occurs in the cytoplasm.
★ hello

If oxygen level is very low in the cell, pyruvate

remains there in the cytoplasm and is converted
into either ethanol (in plants and yeast) or lactate
(in mammals) with no additional ATP produced.

Link reaction

★ Pyruvate (3C) crosses the mitochondrial

membrane from cytoplasm.
★ It is converted into Acetyl CoA (2C) by the
release of CO₂ and H which reduce NAD.
★ It occurs in the presence of
decarboxylase and dehydrogenase
enzymes.

3
Kreb’s cycle

★ Acetyl CoA combines with a 4C compound to form a 6C compound.

★ CO₂ is formed by decarboxylation
★ This form 5C and then to 4C compound
★ Dehydrogenation produces reduced NAD.
★ ATP formed by substrate level phosphorylation
★ 4C compound is used to regenerate 6C compound (which allows cycle to
continue

4
Suggest what would happen in the Krebs cycle if acetyl CoA became
unavailable

★ Cycle would stop.

★ 4 carbon compound would accumulate
★ 6 carbon compound would not be synthesised
★ Reduce the production of ATP

5
The electron transport chain and oxidative phosphorylation

★ Oxidative phosphorylation takes place in the electron carriers which are

present in the cristae of mitochondria.
★ The hydrogen ions from reduced NAD or FAD are transported along a series
of carriers.
★ This combines with oxygen and forms water.
★ When electrons pass between the carriers, energy is transferred.
★ This energy is used by the cell and transfer to chemiosmotic channel to
convert ADP and Pi to ATP

6
Oxidative phosphorylation

★ NADH binds to protein complexes on the inner membrane of mitochondria.

★ This splits into NAD⁺ electron and Hydrogen ion
★ NAD⁺ returns to Krebs cycle, electron enters into electron transport chain
★ While electrons move through ETC, energy released is used to pump
Hydrogen ions into intermembrane space
★ Concentration of Hydrogen ions increases in the intermembrane space
★ It diffuses through chemiosmotic channel on the inner membrane
★ The diffusion provides energy to activate ATP Synthase
★ ATP Synthase phosphorylate ADP to ATP
★ Final electron acceptor Oxygen removes electron from the ETC and binds
with Hydrogen ion, forming water

7
 ★ Some metabolic poisons target the electron carriers in oxidative
phosphorylation, preventing them from passing on electrons.
★ This stops electrons moving down the electron transport chain, which stops
chemiosmosis.
★ Reduced NAD and reduced FAD are no longer oxidized, so NAD⁺ and FAD⁺
aren’t regenerated for the Krebs cycle
★ Causing the Krebs cycle to stop.
★ ATP synthesis in the cell ends up hugely reduced, so there’s not enough ATP
to fuel ATP-requiring cellular processes like the contraction of heart muscle.
★ This can be fatal for the organism.

8
How a high concentration of hydrogen ions (H+) is maintained in the
intermembrane space.

Reduced NAD binds to the protein complex, the electron from the reduced NAD
passes along the electron transport chain on the inner membrane of mitochondria.
The hydrogen ions are actively pumped into the inter membrane of mitochondria
using the energy released by the movement of electrons.

9
The role of the hydrogen ion concentration gradient in releasing energy

★ H⁺ ions follow diffusion gradient

★ This causes an energy change or makes energy available.
★ ATP is formed
★ This occurs on stalked particles ;
★ ATP is energy source for biological processes

How NAD⁺ is formed

★ Reduced NAD release electrons when it bind with protein complex on the
inner mitochondrial membrane
★ Electrons go to carrier ETC
★ H⁺ moved into intermembrane space
★ study

Fate of reduced NAD in aerobic respiration

★ Reduced NAD from glycolysis enters into mitochondria

★ Moves to inner membrane of the mitochondrion
★ Electrons transferred to electron transport chain
★ Hydrogen ions pumped into inter membrane space
★ Becomes oxidized /NAD / NAD⁺
★ NAD⁺ returns to Krebs cycle
★ pls

Explain the link between formation of ATP and H⁺ ions

★ When H⁺ diffuse through ATP synthase down an electrochemical gradient

energy is released
★ This energy is used to activate ATP synthase.
★ ATP synthase help to join ADP and Pi
★ This process is called chemiosmosis

10
Total number of ATP molecules produced from one glucose molecule

Anaerobic respiration

In the absence of oxygen-

★ No electrons can leave the respiratory chain

★ NADH cannot unload any hydrogen to the
respiratory chain.
★ So there is no NAD in the cell.
★ Enzymes of the Krebs cycle cannot work.
★ The whole respiration stops.

11
 ★ Lactate in the blood is transported to the liver.
★ Lactate is converted to pyruvate
★ This involves production of reduced NAD
★ Pyruvate is then oxidized to enter into Krebs cycle ;
★ This requires extra oxygen
★ Carbon dioxide and water are produced.

Exercise and musculo-skeletal system

★ During muscle contraction muscle cells uses anaerobic respiration.

★ Glycolysis produces lactic acid and it is poisonous.
★ As the pH falls, it neutralizes the negatively charged groups in the active site
of enzymes.
★ The substrate may no longer bind to the active site.
★ This stops the functioning of enzymes which leads to muscle fatigue and
cramp.

12
Getting rid of lactate after exercise

★ More oxygen is needed to remove the accumulated lactic acid.

★ This extra volume of oxygen needed is called oxygen debt or excess post
exercise oxygen consumption, EPOC.
★ Much of the lactate is converted back to pyruvate and which is oxidized
directly to CO₂ and H₂O.
★ The rest is transported to liver, converted back to glucose and then to
glycogen and stored in muscle tissue
★ Oxygen consumed to bring physiological variables to resting level

How heart muscle cells make ATP when less oxygen is available

★ Anaerobic respiration by glycolysis ;

★ Glucose is phosphorylated and produce NADH
★ During the formation of pyruvate, 2 ATP molecules are formed per glucose
molecule.
★ Need to regenerate oxidized NAD
★ For pyruvate to be converted to lactate.

13
An increase in the surface area of the inner membrane of mitochondria will
affect the synthesis of ATP in the muscle tissue of an athlete.

★ Contain cristae ;
★ It is the site of oxidative phosphorylation ;
★ Cristae contain electron transport chain ;
★ Electrons passed along carriers ;
★ Hydrogen ions moved to intermembrane space ;
★ Proton gradient is produced ;
★ Hydrogen ions move through chemiosmotic channel
★ This contains ATP synthase.
★ More ATP is synthesized

Respiratory substrates

★ Lipids – an excellent source of energy because a lipid molecule contains a

higher proportion of hydrogen (than a carbohydrate molecule)
★ therefore more reduced NAD / FAD is produced
★ therefore more hydrogen (ions) to accumulate in the intermembrane space /
to produce a proton gradient / to pass through ATP synthase channels / for
chemiosmosis / for oxidative phosphorylation})
★ They can be hydrolysed by lipase to give fatty acids and glycerol.
★ The glycerol is phosphorylated and enters the glycolytic pathway as GALP.
★ A single fatty acid can produce a large amount of ATP.
★ The complete oxidation of fat produces a large amount of usable energy.
★ Protein is not usually used as a respiratory substrate.
★ If the supply of both carbohydrates and lipids are very low the amino acid
which make up the peptide chains must be deaminated and is used.

14
 Respiratory quotients

★ The relationship between the amount of carbon dioxide produced and oxygen
used when different respiratory substrates are used in cellular respiration.
★ The amount of oxygen used and carbon dioxide produced during cellular
respiration change depending upon the level of activity of organisms and the type
of food being respired.
★ Respiratory quotient helps to understand what type of foods are being oxidized in
the body at a particular time.
★ It can be produced by measuring the amounts of carbon dioxide produced and
oxygen used by an organism in a given time period.

○ RQ＝1, carbohydrate is being used (the O₂ used and CO₂ released are equal)
○ RQ＝0.7, fats
○ RQ＝0.9, protein
○ RQ ≤ 1, combination of carbohydrate and lipid
○ RQ ≥ 1, anaerobic respiration

When the fatty acid oleic acid (from olive oil) is respired aerobically, the
equation is:

C₁₈H₃₄O₂ + 25.5O₂ → 18CO₂ + 17H₂O + energy

For the aerobic respiration of oleic acid:

𝐶𝑂₂ 18
𝑅𝑄 = 𝑂₂
= 25.5
= 0. 7

15
A2 BIOLOGY
SEM TER FOUR 2022
Student N es
12s8

MUSCL
Learning objectives
I. (7.9) know the way in which muscles, tendons, the skeleton and ligaments
interact to enable movement, including antagonistic muscle pairs, extensors
and flexors
II. (7.10) (i) know the structure of a mammalian skeletal muscle fibre
III. (ii) understand the structural and physiological differences between fast and
slow twitch muscle fibres
IV. (7.11) understand the process of contraction of skeletal muscle in terms of
the sliding filament theory, including the role of actin, myosin, troponin,
tropomyosin, calcium ions (Ca²⁺), ATP and ATPase

1
Tissues of the skeletal system

Bones

★ It is a living tissue.
★ Contains living cells called osteocytes.
★ Osteocytes are surrounded by matrix.
★ Matrix contains tiny crystals of calcium phosphate and fibres of collagen.
★ Calcium phosphate provides strength to bones to provide support.
★ Oxygen and nutrients are supplied by blood vessels

Cartilage

★ Flexible connective tissue.

★ Cartilage contains living cells called chondrocytes which
secrete matrix.
★ Does not contain calcium and so it is more flexible.
★ Ends of the bones are covered with cartilage.
★ Cartilage reduces friction and acts as a very good shock absorber.

Ligaments

★ These are made of protein collagen.

★ Fibres are arranged in layers.
★ Collagen provides strength and provides some elasticity.
★ Help to hold bones in position.
★ Allows movement at the joint

2
Tendons

★ Muscles are attached to bones by tendons.

★ Made of collagen arranged in parallel bundles.
★ Less stretchy than ligaments.
★ If the tendon is stretchy, the work done by the muscles would be wasted.
★ The contraction of the muscle would stretch the tendons without moving the
bones.
★ Provides little shock absorption.

3
Structure of synovial joint

★ The ends of the articulating bones are covered by a layer of smooth cartilage.
★ Cartilage reduces friction between the bones and acts as a shock absorber.
★ The bones are held in position by ligaments made of collagen fibres.
★ Collagen fibres form a capsule around the bones and limit the movement
and prevent dislocation.
★ The capsule is lined with synovial membrane which is waterproof.
★ Synovial membrane secretes synovial fluid into synovial cavity. Synovial fluid
is formed from blood plasma.
★ The fluid contains phagocytes. It helps in lubricating the joint, providing
nutrients and reducing friction between bones.

4
Muscle

★ Specialised tissue.
★ Largely made up of proteins.
★ Consists of large numbers of very long cells called muscle fibres.
★ Muscle fibres are bounded together by connective tissue.
★ Three main types:- striated, smooth and cardiac.

5
Structure of a muscle fibre

★ A single muscle fibre is made up of a bundle of smaller fibres- myofibrils.

★ These myofibrils are lying parallel to each other.
★ A muscle fibre contains cytoplasm called sarcoplasm, an internal membrane
system called sarcoplasmic reticulum and a cell surface membrane called
sarcolemma.
★ Inward extension of sarcolemma- T tubules- allow impulse to move deeper
into the cell

6
Sarcomere

★ A myofibril consists of repeating units called sarcomeres.

★ Sarcomere is the contractile unit of a myofibril.
★ These appear as light and dark bands under the microscope.
★ These are composed of long fibrous proteins namely actin and myosin.
★ Myosin forms the thick filament and actin forms the thin filament.
★ The head of the myosin makes it appear thick.
★ A sarcomere is the region between two dark lines called Z lines.
★ The Z line forms the borders of the sarcomere.
★ Surrounding the Z line is the region of the I band.
★ I band- a zone of thin filaments that is not superimposed by thick filaments.
(actin only).
★ An A band contains the entire length of a single myosin filament.
★ H band is the zone of thick filaments that is not superimposed by the thin
filaments (only myosin).

7
Structure of actin

★ Actin filament is made up of two chains of actin monomers

★ It is composed of three parts namely actin, tropomyosin and troponin.
★ Actin :- contains myosin binding site and myosin head attaches to it, and helps in
contraction by the sliding movement.
★ Tropomyosin :- prevents the myosin heads from attaching onto actin when the
muscle is relaxed.
★ Troponin :- combine with calcium ion causing the tropomyosin to change shape
and unblock the binding site

Structure of myosin

★ A myosin molecule is made up of two long polypeptide chains twisted together.

★ A myosin molecule is elongated with a globular head at
the end.
★ The head can act as ATPase enzyme.
★ Many myosin molecules form the thick myosin filament.
★ It has many heads projecting away from the main
molecule.
★ The head can form a cross-bridge with actin.
★ When attached to actin, a myosin head can change
shape and slide the actin further along the myosin

8
Sliding filament theory of muscle contraction

★ A nerve impulse arrives at the neuromuscular junction.

★ Calcium ions are released from the sarcoplasmic reticulum.
★ Calcium ions attach to troponin.
★ Troponin changes shape and shifts the position of tropomyosin.
★ Exposes myosin binding site on actin.
★ Myosin binds to actin.
★ ADP and Pi are released from myosin head.
★ Myosin head nod forward and actin slide over myosin.
★ A new ATP attaches to myosin head.
★ Myosin head detaches from actin.
★ ATP hydrolyzed to ADP and Pi causing myosin to regain its normal shape.
★ Process continues as long as calcium ions are present

9
Interaction between troponin and tropomyosin when a skeletal muscle
fibre contracts

★ Calcium ions bind to troponin ;

★ Troponin changes shape and this displaces tropomyosin away from myosin
binding sites on actin
★ study

Constant impulses along motor neurons cause cramps

★ Calcium ions are released from

sarcoplasmic reticulum
★ Continued stimulation leads to high
concentration of calcium ions
★ Calcium ions bind to troponin
★ Shift the position of tropomyosin
★ This leads to muscle contraction
★ well

Comparison of two sarcomeres in a relaxed and a contracted muscle

Relaxed muscle:

★ Actin and myosin lie side by side.

★ H zone and I band are at the maximum width.

Contracted muscle:

★ Actin and myosin interact.

★ Actin pulled towards the centre of myosin.
★ Sarcomeres shrink.
★ Ends of actin filaments overlap
★ H zone disappear and I band become very narrow

10
The diagram below shows the arrangement of actin and myosin myofilaments in part
of an extended muscle.

Complete the diagram below to show accurately the arrangement

of actin and myosin when the muscle is contracted. (3)

1. all fibres same length and width as original ;

2. Z lines closer together ;

3. more overlap of actin and myosin ;

Number of myofibrils?

11
The role of calcium ions and ATP in muscle contraction

★ Sarcoplasmic reticulum contain calcium ions ;

★ Calcium ions bind to troponin ;
★ So tropomyosin moves exposing binding sites for myosin
★ ATP is needed to remove calcium ions from sarcoplasm to sarcoplasmic
reticulum
★ ATP provides energy for changing shape of myosin
★ ATP is required to break cross bridges
★ ATP for synthesis of neurotransmitter

Antagonistic muscle

★ Muscles occur in pairs and work against each other.

★ These are important in bringing the muscle back to its normal state.
★ Contraction of one produces force which pulls the other and causes it to
lengthen.
★ Muscles cannot extend themselves
★ They need an opposing muscle to extend
★ Antagonistic muscle allows control of movement

12
Extensors:- muscles which cause a joint to extend.

Flexors :- muscles which cause a joint to bend.

How tendons and antagonistic muscles cause the lower leg to move in the direction
shown by the arrow in the diagram below

★ Extensor muscles contract

★ Leg is straightened
★ Flexor muscle relaxes
★ These muscles working in opposition, when one
contracts the other relaxes
★ Flexor is stretched
★ Tendons attach muscles to bones

13
Types of muscle fibres

There are mainly two types of muscle fibres – fast and slow twitch

14
Fast twitch fibres (white fibre)

★ These are adapted for short bursts of explosive action.

★ They are adapted to undergo very rapid and powerful contraction.
★ They generate ATP quickly from Creatine phosphate.
★ The energy need is met by anaerobic respiration.
★ Only glycolysis, no Krebs cycle. They have a relatively low amount of
myoglobin content and mitochondria.
★ They are rich in enzymes required for anaerobic respiration.
★ More myofibrils are packed into fast twitch fibres because little space is
taken up by mitochondria.
★

Slow twitch fibres (red muscle)

★ These are adapted to function over long periods of time.

★ These are mainly present in those muscles which are having relatively low levels
of activity.
★ They respire aerobically to avoid the build up of lactic acid.
★ Glucose is the fuel molecule. Glucose breaks down via glycolysis and Krebs cycle.
★ Plenty of mitochondria are there in these fibres.
★ Contain a good blood supply and myoglobin to serve as an oxygen store.
★ The rich blood supply and high levels of myoglobin gives the muscle a deep red
colour.
★ Extensive network of capillaries supply glucose.
★ So they can continue to produce ATP for as long as oxygen is available.

15
 Difference between fast twitch and slow twitch muscle fibre
Fast twitch muscle fibre Slow twitch muscle fibre
Anaerobic Aerobic
Lactate production No lactate production
Few mitochondria Many mitochondria
Less ATP produced More ATP produced
More creatine phosphate Less creatine phosphate
Less myoglobin More myoglobin
Low capillary density High capillary density
More glycogen Less glycogen
More easily fatigued Less easily fatigued
White/more pale Red/darker
Contract rapidly Contract slowly
Larger capacity of sarcoplasmic reticulum Smaller capacity of sarcoplasmic reticulum

Fast twitch muscle fibres fatigue quickly

★ ATP supply limited

★ Due to anaerobic respiration lots of lactate is produced.
★ This reduces pH.
★ This affects enzymes and prevents muscle contraction

The mean speeds for the marathon are less than the 100 m sprint

★ Marathon distance is greater

★ More aerobic respiration is needed to reduce the production of lactate
★ Anaerobic respiration is not efficient enough
★ Lactate levels cannot be sustained over this distance
★ Marathon runners use slow twitch fibres

16
A2 BIOLOGY
SEM TER FOUR 2022
Student N es
12s9

COORDINATION OF CARDIAC CYCLE AND ECG

Learning objectives:

7.12 know the myogenic nature of cardiac muscle

(ii) understand how the normal electrical activity of the heart coordinates the heartbeat,
including the roles of the sinoatrial node (SAN), the atrioventricular node (AVN), the bundle
of His and the Purkyne fibres

(iii) understand how the use of electrocardiograms (ECGs) can aid in the diagnosis of
abnormal heart rhythms

7.13 (i) be able to calculate cardiac output

(ii) understand how variations in ventilation and cardiac output enable rapid delivery of
oxygen to tissues and the removal of carbon dioxide from them, including how the heart
rate and ventilation rate are controlled and the roles of the cardiovascular control centre
and the ventilation centre in the medulla oblongata

7.14 understand the role of adrenaline in the fight or flight response

7.16(i) understand what is meant by the terms negative feedback and positive feedback
control

(ii) understand the principle of negative feedback in maintaining systems within narrow
limits

7.17 understand what is meant by the term homeostasis and its importance in maintaining
the body in a state of dynamic equilibrium during exercise, including the role of the
hypothalamus in thermoregulation

1
Myogenic stimulation of the heart

★ Stimulation generated from within the cardiac muscle and no external

stimulation is needed
★ This brings about depolarisation

The sequence of muscular contraction in the heart is coordinated and the

movement of blood through the heart is controlled

Depolarisation initiates at Sinoatrial node / SAN

This depolarisation passes through the wall of atria and causes atrial systole.

AV valve opens and blood is pushed into the ventricles.

The impulse is received by AVN

AVN conducts the impulse to the walls of the ventricles through a bundle of His and
Purkyne fibres.

Ventricular systole occurs from the apex of the heart.

So that blood is squeezed upwards towards the main arteries.

During ventricular systole atrio-ventricular valves closed and prevent blood flow to
atria

Semilunar valves opened by high pressure in ventricle

Blood is forced into the pulmonary artery and aorta.

During diastole pressure in ventricles decreases

This closes semilunar valves

2
The role of the SAN in controlling heartbeats

★ Initiates heartbeat by wave of excitation / depolarisation

★ This initiates the heartbeat and determines heart rate

How the SAN ensures that oxygenated blood enters the aorta.

★ SAN initiates electrical activity over atria

★ This causes atria to contract and forcing the oxygenated blood into the left

ventricle

★ Electrical activity from SAN is received by AVN then travels through a bundle

of His and Purkyne fibres to the walls of the ventricle.

★ This causes left ventricle to contract and forcing blood into aorta

Stroke volume:- the volume of the blood pumped out by the left ventricle.

Cardiac output:- the volume of blood pumped out in 1 minute

Cardiac output= stroke volume×heart rate

3
ECG : the electrocardiogram

★ The contraction of the cardiac muscle generates electrical currents in the

body fluids around the heart.

★ This current can be detected on the body surface using recording electrodes.

★ Electrical activity of the heart can be recorded by ECG.

★ These measurements are called lead polarity.

★ It is represented by characteristic waves such as P, Q, R, S and T.

An ECG shows waves of electrical activity in the heart over a period of time /

during cardiac cycle

4
ECG

★ The P wave represents Atrial Systole.

★ SAN generates electrical impulse/wave of excitation/electrical signals which

causes depolarisation of atria and atrial systole occur

★ The QRS wave represents the ventricular systole.

★ AVN transmits the electrical impulse which passes through Bundle of His and

Purkinje fibers to the ventricle

★ Ventricular depolarisation occurs and causes ventricular systole

★ The T wave represents ventricular repolarization, relaxation.

★ This causes ventricular diastole.

★ PR interval represents the time taken for the impulse to conduct from SAN

across the atria to ventricles through AVN.

★ Interval between two P waves is the heart rate.

★ ST is the period where ventricles are relaxed.

★ The T wave coincides with the ventricular diastole.

★ ECGs are used to diagnose CVDs.

5
How an ECG can be used to calculate a person’s heart rate

★ It shows electrical activity of the heart

★ One heart beat is from one P wave / QRS complex / T wave to the next

★ Count the number of these in a set time or how long from one set of

electrical activity to the next

★ Obtain heart rate by dividing beats by time

The ECG below was recorded at rest

This person had a resting heart rate of 74 beats per minute.

Calculate the time taken for this ECG. Show your working

74 Beats= 60sec

10 beats= x sec

1 beat = 0.81 sec / 60 ÷ 74

For 10 beats 8.1 seconds

6
An ECG is a test that can be used to check the heart’s rhythm and electrical activity.
Sensors attached to the skin are used to detect the electrical signals produced by
the heart each time it beats. The graph below shows part of a trace from a healthy
person at rest.

(ii) Calculate the heart rate of the person in beats per minute (bpm).

Time for 1 beat= 0.8sec (P to P (0.22-1.02)/ R to R (0.45-1.25)interval)

Heart rate=60/0.8=75bpm

How ECGs can aid the diagnosis of CVDs and other heart conditions

★ The depolarisation in the heart causes tiny little electrical changes on the
surface of the skin.
★ Electrodes attached to the skin measure these changes.
★ Doctors compare their patients’ ECGs with a normal trace.
★ This helps them to diagnose any problems with the heart’s rhythm.
★ This may indicate cardiovascular disease (heart and circulatory disease) or
other heart conditions (e.g. muscle damage or the AVN not conducting
properly)
★ Increased frequency of ECG peaks suggests that there is increase in heart
rate
★ A change in the distance between two parts of ECG suggests that there is
change in cardiac cycle.
★ Longer time between Q and T suggests that the heart takes longer to recover
between heart beats.

7
Normal ECG

This is fibrillation — a really irregular heartbeat.

It can result in anything from chest pain and fainting to lack of pulse and death.

This heartbeat is too fast — around 120 beats per minute. It’s called tachycardia.

At rest it shows that the heart isn’t pumping blood efficiently

The 5th heartbeat on this ECG is an ectopic heartbeat — an ‘extra’ heartbeat.

It is caused by an earlier contraction of the atria

8
Describe the effect of the ectopic beat on heart activity and suggest an
explanation for this effect

★ Changes the depolarisation of heart

★ Peak is reversed
★ Peak is earlier than expected
★ No change in pressure in pulmonary artery
★ Because little blood in ventricles
★ Missed normal wave after E / longer gap before next wave
★ Missed (effective) contraction after E
★ Early depolarisation leaves ventricle insensitive ;
★ The wave of depolarisation is prevented
★ The ventricle is in refractory period

During exercise there is little change to the lengths of the P wave, QRS
complex, or T wave. Describe and explain how the distance between
consecutive P waves would differ in a person taking exercise.

Shorter/closer together. Due to less time between atrial systole and ventricular
systole/ventricular systole and ventricular diastole/ventricular systole and atrial
systole

9
A person visited his doctor for a health check.

The doctor obtained an ECG trace to show the electrical activity of the person’s
heart.

The diagram shows part of this trace.

Twelve months later, the same person visited his doctor with symptoms of stress.

The doctor obtained another ECG trace.

The diagram shows part of this trace.

The doctor diagnosed that the person was suffering from stress.

Analyze the data in both ECG traces to comment on this diagnosis

★ heart rate is faster so person may have stress (1)

★ there are other reasons for an increased heart rate (1) Eg: exercise / drugs /
smoking /
★ BMI / fitness / diet / atherosclerosis
★ difference in heart rate may or may not be significant (1)
★ need to repeat ECG to confirm diagnosis (1)

10
Homeostasis

Maintaining a state of dynamic equilibrium through responses of the body to

external and internal stimuli.

The process of maintaining a constant internal environment

Negative feedback mechanism

The receptors detect a change in condition.

This results in effectors being stimulated to restore the equilibrium.

A change in one direction causes a change in the opposite direction to ensure a

constant value / set point / narrow range of values

Positive feedback mechanism

The receptors detect a change in condition.

This results in effectors being stimulated to increase the effect that has triggered
the response.

The effectors respond to further increase the level away from the normal level.

A change in one direction causes a change in the same direction

Example : Platelets become activated and release a chemical — this triggers more
platelets to be activated,

Regulation of the heart rate- The tissue in the heart that controls resting heart rate -
SAN

Heart beat is controlled by SAN

★ The heart rate has to be adjusted according to the demand of blood in our
body.
★ It is mainly done by nervous and chemical control systems.
★ Conditions around the blood stream are changing.
★ But homeostatic response maintain constant condition

11
Variations in Heart Rate

Animals need to alter their heart rate to respond to internal stimuli, e.g. to prevent
fainting due to low blood pressure or to make sure the heart rate is high enough to
supply the body with enough oxygen.

Heart rate is controlled unconsciously by the cardiovascular control centre in the

medulla oblongata.

The cardiovascular control centre controls the rate at which the SAN fires — the
SAN generates electrical impulses that cause the atria to contract, which sets the
rhythm of the heartbeat

Chemical receptors and pressure receptors detect stimuli in the blood

The sympathetic nervous system helps to increase the heart rate during exercise.

The parasympathetic nervous system helps to decrease the heart rate after
exercise.

12
Changing cardiac output

Cardiac output is changed mainly by two ways:

(1) Regulation of heart rate

★ Nervous control of heart rate

★ Hormonal control of heart rate

(2) Regulation of stroke volume

★ The end diastolic volume

★ The average aortic pressure
★ The strength of ventricular contraction

Nervous control

★ Include sympathetic and parasympathetic nervous systems.

★ Parasympathetic nerves arise from the cardiovascular control center in the
medulla oblongata.
★ This makes up a portion of the vagus nerve.
★ These fibers make contact with SAN and AVN.
★ When stimulated these nerve endings release acetylcholine.
★ Acetylcholine decreases the activity of both SAN and AVN.
★ This results in a reduction in heart rate.
★ Sympathetic nerve fibers reach the heart by means of cardiac accelerator
nerves.
★ These nerves innervate both SAN and ventricles.
★ SNS act on beta adrenergic receptors on SAN
★ Endings of these fibers release norepinephrine.
★ This increases heart rate and contraction

13
Hormonal control of the heart

★ When you are stressed, the sympathetic nerve stimulates the adrenal

medulla to release the hormone adrenaline.

★ It was carried around the body in blood.

★ Adrenaline stimulates the cardiovascular center in the brain.

★ This binds to the receptors in the target organ SAN.

★ Increases the impulses in the sympathetic neurons which supply to the heart.

★ Adrenaline increases the frequency of excitation and heart rate increases.

★ This helps to supply extra oxygen and glucose for muscles and brain.

How the heart rate can be increased by nervous control during exercise

★ Change in CO2 / pH / lactate / O2 level /temperature

★ Detected by chemoreceptors / thermoreceptors /stretch receptors

★ Present in aortic body / carotid body and hypothalamus / skin

★ Send impulse to medulla / cardiovascular center

★ Stimulate sympathetic / accelerator nerve

★ Send impulse to SAN

★ Also to atria / heart muscle walls / skeletal muscles / tendons

14
Regulation of stroke volume

Stroke volume is regulated by three variable:

The end diastolic volume (EDV)

The average aortic blood pressure

The strength of ventricular contraction

EDV: end-diastolic volume (blood left in ventricles after diastole)

★ increase in EDV →increase in stroke volume.

★ The increase in EDV leads to lengthening of cardiac fibers.

★ Lengthening improves the force of contraction.

★ Result in an increased pumping of blood per beat.

★ The variable that influences EDV is the rate of venous return to the heart.

★ Increase in venous return leads to increase in EDV and the stroke volume.

15
An increase in resting BP

★ Detected by carotid baroreceptors.

★ Sensory nerves carry impulse to the Cardiovascular control center.

★ Stimulate parasympathetic nerves.

★ Carry impulse to heart.

★ Reduce heart rate and BP

When a person starts exercise

★ Adrenaline is released.

★ Dilate blood vessels.

★ BP falls a little.

★ Reduces the stretch of baroreceptors and almost stop responding.

★ Do not stimulate CCC.

★ Send signals along sympathetic nerve fibres.

★ Increases HR and BP

Vigorous muscular activity and Bainbridge Reflex

★ If there is an increase in venous blood, BP in the vena cava increases.

★ Increases the number of impulses from baroreceptors.
★ These impulses are transmitted by sensory nerves to cardioacceleratory
center.
★ CAC is stimulated and transmits impulse via SNS to SAN, AVN and cardiac
muscle.
★ Release noradrenaline.
★ Stimulate SAN and Reduce the delay at AVN.
★ This increases HR.
★ This reflex pathway is known as Bainbridge reflex.
★ This regulates venous pressure in the heart.

16
How the cardiovascular center, in the medulla oblongata, affects the SAN
during exercise

Increased impulses to SAN via sympathetic nervous system

This stimulates more frequent depolarisation in SAN.

Increases heart rate / cardiac output.

Suggest how increase in blood flow is brought about by noradrenaline

Noradrenaline acts as neurotransmitter

This increases SAN activity

This increase heart rate and cardiac output

Describe the changes in the heart that bring about an increase in cardiac
output during sprint

★ Heart rate increases

★ Stroke volume increases

★ Activity of SAN increases

★ AVN time delay decreases

★ More blood returning to the heart causes heart muscle to stretch

★ Ventricles contract with greater force.

17
Variations in Breathing Rate

When you exercise your muscles contract more frequently, which means they use

more energy.

To replace this energy your body needs to do more aerobic respiration.

So it needs to take in more oxygen and breathe out more carbon dioxide.

The body does this by:

Increasing breathing rate and depth — to obtain more oxygen and to get rid of

more carbon dioxide.

Increasing heart rate — to deliver oxygen (and glucose) to the muscles faster and

remove extra carbon dioxide produced by the increased rate of respiration in

muscle cells

18
The Medulla Oblongata Controls Breathing Rate

The medulla oblongata has areas called ventilation centers. There are two

ventilation centers — the inspiratory center and the expiratory center. They control

the rate of breathing

Control of ventilation- Negative feedback

★ Inspiration inflates lungs.

★ Stretch receptors in the bronchial tree are stimulated.

★ Send more impulses to the expiratory center via the vagus nerve.

★ Temporarily inhibits inspiration.

★ Internal intercostals muscle contract.

★ External intercostal muscles relax.

★ Elastic recoil of the lung tissue occurs and expiration takes place.

★ Bronchial tree is no longer stretched.

★ Stretch receptors are no longer stimulated.

★ Expiratory center becomes inactive.

★ Inspiration begins.

★ The cycle is repeated throughout the lifetime

19
Increase in the level of carbon dioxide

★ Chemoreceptors in the carotid and aortic bodies are stimulated.

★ Send nerve impulse to the inspiratory center.

★ Send impulse to external intercostal muscles and diaphragm via external

intercostal and phrenic nerves.

★ Rate of contraction of diaphragm and external intercostal muscle increases.

★ Increases the rate of inspiration.

Explain how the atmosphere near a volcano can lead to an increase in

breathing rate.

★ Concentration of carbon dioxide in the alveoli is higher

★ So concentration of carbon dioxide in the blood is higher

★ pH of blood falls due to increased CO2

★ CO2 / pH levels in blood detected by chemoreceptors in carotid body and

aortic body

★ Impulse send to respiratory center in medulla

★ Sends more impulses along neurons to intercostals muscles / diaphragm

Suggest how an increase in breathing rate can help to reduce the

concentration of carbon dioxide in a person walking away from a volcano

★ Inhaled air has a lower CO2

★ CO2 concentration in blood is higher than in the alveoli

★ So CO2 moving down concentration gradient / out of blood

★ CO2 lost to atmosphere through exhaling

20
How an increased heart rate results in increased uptake of oxygen by the

blood in the lungs

There is more blood passing through the capillaries surrounding the alveoli

So diffusion gradient is maintained

Faster diffusion of oxygen into blood occurs.

Thermoregulation

★ An increase in temperature sets into motion the process which decreases it.

★ A decrease in temperature sets into motion the process which increases it .

★ Anyway, it returned to its normal state.

★ The optimum point is the set point.

★ The system is self adjusting.

★ Corrective mechanism bringing the change in temp. normal.

★ There will be receptors, effectors and control centers for coordination.

21
Set point: the temperature at which a person feels comfortable.

Regulation of core body temperature is by involuntary response.

Thermoreceptors in the hypothalamus detect change in core temperature.

It is very sensitive to temperature fluctuations.

Two regions are there in hypothalamus- heat loss centre and heat gain centre

Heat loss centre is activated by increase in temperature and heat gain centre by
decrease in temperature.

When body temperature rises

★ Metabolic rate decreases

★ Arterioles in skin dilate, shunt vessels constrict.

★ Increases blood flow to skin and increases heat loss via conduction,

convection and radiation.

★ Stimulate sweat gland to produce sweat.

★ Increase in evaporation decreases heat.

★ Hair flattens and reduce insulation.

★ Decreased muscular activity

22
When Body temperature falls

★ Metabolic rate increases.

★ Arterioles in skin constrict.

★ Decreases blood flow to skin.

★ Decreased heat loss via conduction, convection and radiation.

★ Inhibit sweating and reduce heat loss via evaporation.

★ Hair raised so increased insulation.

★ Increased muscular activity.

★ Shivering

Maintaining a constant body temperature when an animal in a cold

environment

★ Thermoreceptors in the skin are stimulated.

★ Send nerve impulses to hypothalamus / thermoregulatory centre

★ Arterioles constricts and shunt vessels dilate so less blood flow to skin

★ Hair erector muscles contract to trap air

★ Less heat loss by radiation / convection

★ Heat generated by shivering / muscle contraction

★ Less sweating by inhibition of sweat glands

★ Less heat loss by evaporation

23
Gymnasts will generate a lot of heat during activity. Explain how changes in

blood flow in the skin will help to control body temperature.

★ More blood flows near the skin surface

★ Due to vasodilation / dilation of arterioles

★ Vasoconstriction of shunt vessels

★ More blood to capillaries

★ More heat lost via radiation

24
25
A2 BIOLOGY
SEM TER FOUR 2022
Student N es
12s9

NERVOUS SYSTEM
NEURONS STRUCTURE & FUNCTION

Learning objectives:
I. (8.1) know the structure and function of sensory, relay and motor neurons,
including Schwann cells and myelination
II. (8.2) understand how the nervous system of organisms can cause effectors
to respond to a stimulus
III. (8.3) know the structure and function of a spinal reflex arc, including gray
matter and white matter of the spinal cord
IV. (8.4) understand how a nerve impulse (action potential) is conducted along
an axon, including changes in membrane permeability to sodium and
potassium ions
V. (8.5) understand the role of myelination in saltatory conduction
VI. (8.6) (i) know the structure and function of synapses in nerve impulse
transmission, including the role of neurotransmitters and acetylcholine
VII. (8.7) understand how the effects of drugs can be caused by their influence on
nerve impulse transmission, illustrated by nicotine, lidocaine and cobra
venom alpha toxin, the use of L-DOPA in the treatment of Parkinson’s
disease and the action of MDMA (ecstasy)

1
The basic structure of a nervous system

★ Nervous system is made up of interconnected neurons.

★ Neurons- individual cells and each one has a long nerve fiber.
★ Nerves- bundles of nerve fibers
★ Neurons carry impulses from receptor cells to effector cells (muscles/glands)
★ In vertebrates, the central nervous system consists of the brain and spinal
cord.
★ Sensory neurons carry impulses from receptor cells about the internal and
external environment to the CNS.
★ The motor neurons carry impulses from the CNS to the effector organs.

2
Structure of a neuron

★ Axon:- Extremely long and thin nerve fiber which carries impulses away from
the cell body.
★ Dendron:- the bushy, branching extensions of a neuron that receive
messages and conduct impulses towards the cell body
★ Cell body is usually compact and enclosed by a plasma membrane.
○ Contain Nissl’s granules; a group of RER and ribosomes. (synthesis of
neurotransmitter)
★ Myelin sheath :-thick insulating material along the length of axon.
○ It is produced by specialized supporting cells called Schwann cells.
○ This wrapped many times around the axon.
★ Gaps between the membranes of each Schwann cell are called nodes of
Ranvier.
○ This is the gaps in myelin sheath where action potentials are
transmitted.
★ Impulse jumps from one nodes of Ranvier to the next (saltatory effect)
★ Break down of myelin sheath – multiple sclerosis

3
Axon membrane:- s uc re d o n on

★ Cell membrane is made up of

phospholipid- which restricts ion
movement
★ Sodium potassium pump- helps to
pump ions
★ Protein gates- help in the diffusion of ions.
★ Voltage-gated channels- They are membrane proteins that open and close
depending on the electrical potential (or voltage) across the membrane.

Importance of myelin sheath

★ Made up of lipids together with some proteins

★ Protects the nerve from damage.
★ Speeds up the transmission of impulse. (saltatory effect)
★ Prevent leakage of the current as it travels down the axon (insulator)

4
Role of nodes of Ranvier

★ The small, uncovered areas of axon between Schwann cells are called nodes of
Ranvier
★ Depolarisation occurs at these nodes.
★ This causes impulse to jump from node
to node (saltatory conduction)
★ This speeds up transmission of impulse
★ There’s nothing holding me back

Types of neuron

★ Multipolar- one axon and many dendrites.

★ Unipolar-have one cytoplasmic extension
★ Bipolar- have one axon and one dendrite

5
Sensory neuron :- Bip ne

★ Transmits impulses from sense organ to CNS

★ Cell body in the center of cell / axon
★ It is myelinated
★ Has long Dendron and short axon

Motor neuron :- Mul la

★ It transmits impulses from CNS to effector

★ Cell body at end of cell
★ Short dendrites / many dendrites from cell body
★ Long axon
★ Myelinated

Relay neuron

★ Transmitting impulses between sensory and

motor neurone
★ Short axons
★ No myelination

6
Reflex arc

★ The simplest type of nervous response is a reflex arc.

★ A reflex arc is the pathway along which impulses are transmitted from a
receptor to an effector without involving ‘conscious’ regions of the brain
★ If a reflex involves the spinal cord but not the brain it is known as a spinal
reflex
○ Receptor: to detect stimulus
○ Sensory neuron: receive stimulation from receptor to CNS
○ Relay neuron: carry messages across synapse, from sensory to motor
neuron
○ Motor neuron: carry impulses from relay neuron to effector
○ Effector: carry out response after receiving a message from motor
neuron.
○ Synapse: a junction between two neurons synaptic transmission
involves chemicals called neurotransmitters

7
 Type of neuron
Feature
Sensory Motor Relay

Found only in the CNS

Cell terminates at the effector

Presynaptic membrane not

found in the CNS

Impulse moves away from the

receptor

Factors affecting the speed of nerve impulse

Diameter of the nerve fiber

★ The thicker the fiber the more speedy the transmission.

★ As the axon diameter increases the speed of conduction increases
★ Speed of transmission depends on resistance
of axoplasm
★ This resistance is related to the diameter of
the axon.
★ The greater /larger the diameter of the axon
the less the resistance.

Presence or absence of myelin sheath

★ Myelinated nerve fiber carry impulses much

faster than non myelinated one.

8
 CONDUCTING IMPULSE
Resting potential

★ Resting membrane potential is maintained by sodium potassium pumps.

★ It pumps Na⁺ ions out and K⁺ ions into the nerve fiber using ATP.
★ For every three Na⁺ ions that are pumped out only two K⁺ ions are pumped
into the nerve.
★ This establishes concentration gradients for sodium ions and potassium ions
★ K chanel pumps K⁺ out of the membrane.
★ At rest the axon membrane is freely permeable to K⁺ than Na⁺.
★ As the concentration of K⁺ ions increases, these diffuse back out of the cell.
★ Actively pumped out Na⁺ cannot diffuse back.
★ Outside of the membrane becomes positively charged and the inside
becomes negatively charged.
★ Inside of the cell is left slightly negative relative to the outside at -70mV.
★ The membrane is polarized.

9
Explain why maintaining a resting potential requires ATP

★ because ATP is used by the sodium-potassium pump to move sodium ions

and potassium ions across the cell membrane to establish concentration
gradients for sodium ions and potassium ions

10
Action potential

★ When a stimulus is applied, the permeability of the membrane to sodium

ions increases.
★ Sodium ion voltage gated channels open
★ Na⁺ ions diffuse into the neuron.
★ Inside becomes more positive than outside. (depolarisation)
★ If the stimulus reaches the threshold level more sodium ion channels open
★ An action potential occurs.
★ When the action potential reaches its peak, sodium ion gated channels close
slowly and potassium ion gated channels open slowly. (+35 / +40mV)
★ Sodium ions stop moving into the cell but potassium ions diffuse out.
★ Potential difference starts to drop.

11
 Repolarisation

★ The sodium ion gated channels close.

★ Potassium ion gated channels open.
★ Membrane becomes more permeable to potassium.
★ More potassium ions diffuse out of the neuron down the electrochemical gradient.
★ The outward movement of potassium ions removes positive charge from inside the
axon to the outside.
★ Membrane approaches resting potential.
★ LOL

Hyperpolarization

★ Potassium ion gated channels slow to close

★ Overshoot / too many potassium ions diffuse out of neuron
★ Potential difference becomes
more negative than resting
potential

12
Refractory period

★ No (new) action potential/nerve impulse be produced in this time;

★ Impulse/action potential can only move in one direction
★ Channels are recovering / Na⁺ closed at repolarisation & K⁺ closed during
hyperpolarization;
★ The hyperpolarized membrane is in a refractory period and cannot fire.

Absolute refractory period: Soon after the action potential the nerve fiber is
completely inexcitable. So cannot propagate another impulse.

Relative refractory period: After the absolute refractory period a stimulus above
the threshold level sets up another action potential.

13
Threshold level

The threshold potential is the critical level to which the membrane potential must
be depolarized in order to initiate an action potential.

★ Action potentials are only generated if the potential difference reaches a

value between −60mV and −50mV.
★ This value is the threshold potential.

All or none law

★ The size of the action potential is always the same.

★ No matter how the stimulus size is.
★ But the frequency will be changed.

14
15
Summation

When a stimulus is weak, only a small bit of neurotransmitter is released. This may
not be enough to stimulate an action potential.

Spatial summation : excitatory potentials from many different presynaptic

neurons cause the postsynaptic neuron to reach its threshold and fire.

Temporal summation : a single presynaptic neuron fires many times in

succession, causing the postsynaptic neuron to reach its threshold and fire.

A second stimulus had no effect on the potential difference during the first action potential

★ The neurone has not reached the resting potential

★ And sodium ion channels are closed

16
Impulse transmission through synapse

★ Synaptic cleft:- Space between the presynaptic

and postsynaptic cell
★ Postsynaptic cell:- May be a neuron, muscle cell,
or endocrine cell
★ Neuromuscular junction:- Synapse between a
motor neuron and a skeletal muscle cell

Transmission through synapse

★ An action potential reaches the presynaptic membrane.

★ Depolarises the membrane.
★ Calcium ion channels open.
★ Calcium ions diffuse into the pre synaptic knob.
★ Presynaptic vesicles containing the
neurotransmitter migrate and fuse with the
presynaptic membrane.
★ The neurotransmitter is released into the synaptic
cleft and diffuses across the synapse.
★ The neurotransmitter binds to specific receptors on
the postsynaptic membrane.
★ The neurotransmitter is broken down by enzymes.
★ These products diffuse back into the presynaptic
knob.
★ They are resynthesized to the neurotransmitter.
★ More mitochondria are present in the synaptic knob
for the synthesis of neurotransmitters.

17
The sequence of events that occurs at the synapse after a neurotransmitter
has been released

★ Diffuses across gap and binds to receptors on postsynaptic membrane

★ Sodium gated-channels open and Na⁺ travels through
postsynaptic membrane
★ This causes a depolarisation
★ An action potential is set up in postsynaptic membrane
★ Provides temporal or spatial summation
★ This allows one way flow of information
★ Neurotransmitter is broken down by enzyme which make
receptors available again
★ Reabsorbed through presynaptic membrane

The roles of synapses

★ Synapses ensure one-way transmission

★ This is because only the presynaptic knob has vesicles containing
neurotransmitters and the postsynaptic membrane contains receptors for
the neurotransmitter to bind.
★ Synapses allow integration of impulses
★ Allowing nerve impulse to diverge and converge

18
The neurotransmitter- acetylcholine(ACh)

★ It is an excitatory neurotransmitter.
★ The synapses that use acetylcholine as the transmitter substance are known as
cholinergic synapses.
★ The arrival of the action potential on the presynaptic membrane causes calcium
ion voltage-gated channels to open.
★ calcium ions diffuse into the cytoplasm of the presynaptic neuron.
★ The influx of calcium ions stimulates vesicles containing ACh to move to the
presynaptic membrane and fuse with it.
★ releasing Ach into the synaptic cleft by exocytosis.
★ It diffuses across the synapse
★ ACh molecules temporarily bind with the complementary shaped receptors on
the postsynaptic membrane.
★ Sodium ion gated channels open
★ Sodium ions diffuse into the postsynaptic neuron.
★ This depolarizes the membrane.
★ The synaptic cleft contains an enzyme,
acetylcholinesterase, which catalyzes the
hydrolysis of ACh molecule into acetate and
choline
★ They are taken back into the presynaptic knob
and recombined to Ach using ATP.

19
Neurotransmitter

★ A chemical released from presynaptic neuron

★ It diffuses across the synaptic gap
★ It affects postsynaptic neuron

Types of neurotransmitter

I. Excitatory:- These neurotransmitters make the postsynaptic membrane

more excitable and more likely to generate nerve impulse.
II. Inhibitory:- These neurotransmitters make the postsynaptic membrane less
excitable and less likely to transfer nerve impulse

Anesthetic drug prevents the patient feeling pain

★ Some may binds to sodium (ion) channels

★ So less influx of sodium ions into neuron
★ Less / no depolarisation
★ No action potentials generated
★ No impulses to brain

(OR)

★ Calcium ion channels are blocked.

★ So no calcium ions enter pre synaptic knob
★ Vesicles do not fuse with presynaptic membrane
★ Less neurotransmitter release
★ Reduced binding to receptors on the postsynaptic membrane
★ reduced depolarisation and no action potentials to brain

20
The effect of drugs on the nervous system

21
The effect of nicotine on nerve impulse transmission

★ Nicotine mimics the effect of acetylcholine and binds to specific receptors

(nicotinic receptors)in the postsynaptic membrane.
★ It triggers an action potential in the postsynaptic membrane.
★ The receptor remains unresponsive to more stimulations for some time.
★ Nicotine increases the heart rate and blood pressure.
★ It also triggers the release of a neurotransmitter in the brain called
dopamine.
★ If the level of nicotine is high, it causes the receptors to block.

22
Lidocaine

★ It is a drug used as a local anesthetic.

★ Lidocaine molecules block voltage gated sodium ion channels.
★ Prevents the generation of action potential in the sensory nerves.
★ This prevents the feeling of pain.
★ Lidocaine also reduces or prevents early or extra action potentials from the
pacemaker region. Thereby prevent irregular heart beat.
★ Here it blocks the sodium ion channel and raises the depolarization
threshold.

Cobra venom (alpha-cobratoxin)

★ It is a substance made by several species of cobra.

★ It binds reversibly to acetylcholine receptors in postsynaptic membrane and
neuromuscular junction
★ This prevents the impulse transmission across the synapse.
★ So muscles are not stimulated to contract and leads to paralysis.
★ If the toxin reaches the muscles involved in breathing it causes death.
★ But at a low level, it relaxes the muscles of the trachea and bronchi so can be
used in the treatment of asthma attacks.

23
Parkinson’s disease

★ Associated with the death of a group of dopamine secreting neurons in the brain.
★ Results in the decreased level of Dopamine in the brain.
★ Dopamine is associated with the control of movement and emotional response.

Symptoms of parkinson's:

➢ Stiffness of muscles
➢ Tremor of muscles
➢ Slowness of movement
➢ Poor balance
➢ Walking problems
➢ Depression
➢ Speech problems
➢ Swallowing difficulty

L-Dopa

★ L-Dopa can reach brain and converted to dopamine in brain

★ This increases dopamine levels in the brain
★ Parkinson’s disease has low dopamine levels
★ So the treatment reduces symptoms of Parkinson’s disease.

24
Clinical depression

★ Serotonin is a neurotransmitter linked with feelings of

reward and pleasure.
★ Low levels of neurotransmitter serotonin in the synapse
★ So reduced depolarisation of postsynaptic membrane
★ Fewer impulses / action potentials in postsynaptic
membrane / neuron

Action of MDMA (ecstasy)

★ MDMA inhibits reabsorption of serotonin into the neuron.

★ Increases the level of serotonin in the synapse.
★ It binds to and blocks the reuptake proteins on the presynaptic membrane.
★ MDMA also triggers the release of serotonin from presynaptic neurons.
★ This means that serotonin levels stay high in the synapse and cause
depolarisation of the postsynaptic neurons in parts of the brain that control
mood.

Symptoms of clinical depression:

➢ Prolonged feeling of sadness

➢ Anxiety
➢ Hopelessness
➢ Loss of interest
➢ Restlessness
➢ Insomnia
➢ Thoughts of death

25
A2 BIOLOGY
SEM TER FOUR 2022
Student N es
12s9

HORMON AND GENE EXPR SION

Learning objectives:
I. (7.22) understand how genes can be switched on and off by DNA transcription
factors, including the role of peptide hormones acting extracellularly and
steroid hormones acting intracellularly
II. (8.13) Understand how coordination in animals is brought about through
nervous and hormonal control

1
Switching on and off of a gene by DNA transcription factors including hormones

Transcription factor:- It is a protein / hormone that switch on / activates a Gene and

synthesise mRNA

DNA transcription

★ RNA polymerase attaches to the promoter region of DNA and starts

transcription.
★ Attachment of RNA polymerase is mediated by transcription factors. (a group
of proteins).
★ Only after the attachment of transcription factors, RNA polymerase can bind.
★ Here it form transcription initiation complex(assembly of transcription factors
and RNA polymerase on promoter DNA)
★ After the formation of this complex, the double helical structure unwinds.
★ Transcription of template strand occurs.
★ Some transcription factors are present in all the cells.
★ Some are synthesized in a particular type of cell or at a particular stage of
development
★ Most are created in an inactive form.
★ Activation of transcription factors are either by hormones, growth factors or
regulatory molecules.
★ If the transcription factors are inactive genes remain switched off.
★ Activator molecules stimulate the binding of transcription initiation complexes.
★ Repressor molecules attached to the promoter region of DNA or to the
transcription factors and prevent the formation of transcription initiation
complex and there by transcription (gene is switched off)

2
What are hormones?

★ Hormones are organic chemicals produced in endocrine glands and released

into the blood.
★ They are responsible for one of the main forms of chemical control in animals.
○ It has a target cell to act.
○ It is specific for a target.
○ Small and soluble organic molecules.
○ Effective in low concentration.
★ Hormones are usually either peptide or steroid

Endocrine
Endocrine

3
The Endocrine glands
★ They are found around the body usually in association with other organ systems.
★ The glands have a rich blood supply with plenty of capillaries.
★ The exocrine glands produce secretions and are released into small ducts.
★ But the endocrine glands release their secretions directly into the bloodstream.
★ The pituitary:- GH, TSH, FSH, LH, ACTH, MSH, oxytocin, Prolactin
★ The hypothalamus:- ADH, growth hormone releasing hormone
★ The thyroid:- thyroid hormones- controlling growth and metabolism.
★ The parathyroid:-homeostatic control of calcium metabolism
★ The pancreas:- exocrine as well as endocrine
★ Exocrine- digestive enzymes
★ Endocrine- produces insulin and glucagon involved in homeostatic control of blood
sugar
★ Adrenal glands:- adrenaline- fight or flight responses
★ Aldosterone:- homeostatic control of the osmotic balance of the body
★ The kidneys:- hormones involved in the production of RBC and vitamin D
metabolism.
★ The ovaries:- produce the female sex hormones
★ The testes:- produce male sex hormones

4
Hormone release systems

★ Some hormones are released as a result of direct stimulation of the endocrine

gland by nerves.
★ Adrenal medulla of the adrenal gland releases adrenaline when it is stimulated
by the sympathetic nervous system.
★ Many hormones are released from the endocrine glands in response to
another hormone in the blood.
★ Pituitary gland in the brain secretes several hormones that directly stimulate
other endocrine glands.
★ Changes in the blood can also stimulate the release of hormones.
★ yolo

The pituitary gland

★ The pituitary gland in the brain produces and releases secretions.

★ These secretions affect other endocrine glands.
★ The pituitary gland is under the control of hypothalamus.
★ The hypothalamus contains neurosecretory cells.
★ These are nerve cells that produce secretions from the ends of axons.
★ One group of these cells produces substances
(releasing inhibiting factors) that stimulate or inhibit
the release of hormones from the anterior pituitary.
★ The other group of cells produces secretions that are
stored in the posterior pituitary and are released later
as hormones.

5
The hormones of Pituitary

Anterior lobe

★ Thyroid stimulating hormone (TSH)

○ Controls the secretion of thyroxin from the
thyroid gland.
○ please
★ Growth hormone (GH)
○ Stimulates the growth of body cells.
○ Increases the buildup of proteins
○ do
★ Follicle stimulating hormone (FSH)
○ It stimulates the ovaries to produce oestrogen (females)
○ Stimulates the development of ova in the menstrual cycle.
○ It stimulates the testes to produce sperm (males)
○ study
★ Adrenocorticotropic hormone (ACTH)
○ Controls the secretion of hormones from the adrenal cortex and the
adrenal glands.
○ before
★ Luteinizing hormone (LH)
○ Stimulates ovulation
○ Formation of corpus luteum in females.
○ Prepares the uterus for implantation
○ Stimulates the testes to produce testosterone in males
○ test
★ Prolactin
○ Stimulates and maintains the production of milk by the mammary gland

6
Posterior lobe

★ Antidiuretic hormone (ADH)

○ Decreases the urine volume by affecting the kidney tubules.
○ Causes arteries to constrict after haemorrhage.
○ This prevent excess blood loss and raising blood pressure
○ yay
★ Oxytocin
○ Stimulates the muscles of the uterus to contract during labour.
○ Stimulates the contraction of cells in the mammary tissue so that milk is
squeezed out when an infant suckles.

How do hormones have their effects?

Some hormones act by binding to specific receptors on the cell surface membrane of
the target cell.

★ Steroid hormones:- these are lipid soluble and These can enter the cell
through phospholipid bilayer.

Examples: Oestrogen and testosterone

★ Peptide hormones:- these are not lipid soluble and they bind to receptors on
the cell surface membrane. They release second messenger

Examples: adrenaline, insulin, glucagon and ADH

7
Peptide hormone:- Sec m en m an

★ A hormone molecule reaches the target cell.

★ Binds to specific receptor protein on the surface of plasma membrane.
★ Receptor protein is associated with a molecule of adenylate cyclase.
★ Binding of the hormone to the membrane releases a second messenger.
★ In most cases cyclic AMP is the second messenger
★ This triggers a series of enzyme controlled reactions.
★ CAMP binds to other chemicals which pass into the nucleus and act as DNA
transcription factors.

8
Steroid hormone

★ This passes through the cell surface membrane and binds to receptor protein
in the cytoplasm.
★ Form a hormone–receptor complex.
★ This complex passes to the cell nucleus and hormones switch on some genes
and stimulate transcription.
★ mRNA enters into the cytoplasm translated to new protein.

Hormonal vs nervous response

Hormonal control Nervous control

Hormonal coordination is chemical Nervous coordination is electrical

response is slow response is fast

longer term action short term action

action is widespread action is localised

9
10
A2 BIOLOGY
SEM TER FOUR 2022
Student N es
12s9

THE EFFECT OF DRUGS ON THE NERVOUS

SYSTEM
Learning objectives:
I. Understand how the effects of drugs can be caused by their influence on
nerve impulse transmission, illustrated by nicotine, lidocaine and cobra
venom alpha toxin, the use of L-DOPA in the treatment of Parkinson's
disease, and the action of MDMA (ecstasy).
II. Understand how imbalances in certain naturally occurring brain chemicals
can contribute to ill health, including dopamine in Parkinson's disease and
serotonin in depression, and to the development of new drugs.

1
 ★ The brain uses a number of different neurotransmitters.
★ An imbalance in these transmitters can result in both mental and physical
symptoms.
★ Treating diseases which are caused by such imbalances means transferring
drugs across the blood-brain barrier.
★ These are very tightly joined together:
★ This makes it difficult for bacteria to cross into the brain and cause
infections.
★ The blood-brain barrier also makes it difficult for therapeutic drugs to enter
the brain.
★ Drugs that do affect the brain are usually active at the synapses.
★ wow

The effect of drug on synapse

★ Drugs may affect the synthesis and storage of neurotransmitters.

○ Example – L–dopa:- converted into dopamine and increasing the
concentration of dopamine.
★ May affect the release of neurotransmitters from the presynaptic
membrane.
★ May affect the interaction between the
neurotransmitters and the receptors on
the postsynaptic membrane.
★ Some may prevent the reuptake of
neurotransmitters back into the presynaptic
membrane.
★ May inhibit the enzymes which break down
the neurotransmitters in synaptic cleft

2
The effect of nicotine on nerve impulse transmission:

★ Nicotine mimics the effect of acetylcholine.

★ It binds to specific receptors (nicotinic receptors) in the
postsynaptic membrane.
★ It triggers an action potential in the postsynaptic membrane.
★ The receptor remains unresponsive to more stimulations for
some time.
★ Nicotine increases the heart rate and blood pressure.
★ It also triggers the release of a neurotransmitter in the brain
called dopamine.
★ If the level of nicotine is high, it causes the receptors to block.

3
Lidocaine

★ It is a drug used as a local anesthetic.

★ Lidocaine molecules block voltage gated sodium ion channels.
★ Prevents the generation of action potential in the sensory nerves.
★ This prevents the feeling of pain.
★ Lidocaine also reduces or prevents early or extra action potentials from the
pacemaker region. Thereby preventing irregular heartbeat.
★ Here it blocks the sodium ion channel and raises the depolarization
threshold.

Cobra venom (alpha-cobratoxin)

★ It is a substance made by several species of cobra.

★ It binds reversibly to acetylcholine receptors in postsynaptic membrane and
neuromuscular junction
★ This prevents the impulse transmission across the synapse.
★ So muscles are not stimulated to contract and leads to paralysis.
★ If the toxin reaches the muscles involved in
breathing it causes death.
★ But in low levels, it relaxes muscles of the
trachea and bronchi so can be used in the
treatment of asthma attacks.

4
Parkinson’s disease

★ Associated with the death of a group of dopamine

secreting neurons in the brain (substantia nigra).
★ Results in the decreased level of Dopamine in the
brain.
★ Dopamine is associated with the control of movement and emotional responses

Symptoms of parkinson's:

➢ Stiffness of muscles ➢ Walking problems

➢ Tremor of muscles ➢ Depression

➢ Slowness of movement ➢ Speech problems

➢ Poor balance ➢ Swallowing difficulty

Levodopa (L-Dopa)

★ Levodopa (L-dopa) is a precursor to dopamine

★ L-Dopa can cross blood-brain barrier and reach brain and are converted to
dopamine This increases dopamine levels in the brain
★ Parkinson’s disease has low dopamine levels
★ So the treatment reduces symptoms of Parkinson’s disease.
★ Supplying the brain with
L-dopa allows the
remaining cells to make as
much dopamine as
possible

5
Dopamine agonists

★ These are chemicals that mimic the effect of dopamine.

★ They bind to dopamine receptors in brain synapses.
★ This trigger action potentials
★ They are often used at the beginning of the disease when they are most
effective.

Monoamine oxidase B (MAOB) inhibitors

★ MAOB is an enzyme that breaks down dopamine in the brain synapses.

★ MAOB inhibitors reduce the destruction of the dopamine made by the cells.
★ This leads to depolarization in the postsynaptic neuron

6
Clinical depression

★ Serotonin is a neurotransmitter linked with feelings of reward and pleasure.

★ Low levels of neurotransmitter serotonin in the synapse
★ So reduced depolarisation of postsynaptic membrane
★ Fewer impulses / action potentials in postsynaptic membrane / neuron

Symptoms of clinical depression:

➢ Prolonged feeling of sadness

➢ Anxiety
➢ Hopelessness
➢ Loss of interest
➢ Restlessness
➢ Insomnia
➢ Thoughts of death

7
Action of MDMA (ecstasy)

★ MDMA inhibits reabsorption of serotonin into neurons.

★ Increases the level of serotonin in the synapse.
★ It binds to and blocks the reuptake proteins on the presynaptic membrane.
★ MDMA also triggers the release of serotonin from presynaptic neurons.
★ This means that serotonin levels stay high in the synapse
★ Cause depolarization of the postsynaptic neurons in parts of the brain that
control mood.

Effect of SSRI

★ SSRI binds to reuptake proteins

★ serotonin is not reabsorbed from the synapse
★ So there is a high level of serotonin
★ Serotonin continues to bind to receptors in
postsynaptic membrane

Tricyclic antidepressants (TCAs)

★ Increasing the levels of serotonin and

noradrenaline in the brain.

Monoamine oxidase inhibitors

★ They inhibit the enzymes which usually

cause the breakdown of
neurotransmitters in the synapses of the brain.

8
Illegal drugs and the brain

★ Ecstasy (MDMA: 3,4-methylenedioxy-N-methylamphetamine )

★ It acts as a stimulant, increasing the heart rate.
★ The short-term effects of the drug are to change mood and make people feel
sociable, full of energy, warm and empathetic,
★ The drug affects the serotonin synapses of the brain.
★ Ecstasy blocks the serotonin reuptake transport system.
★ Serotonin cannot be returned to the presynaptic knob
★ The synapses are completely flooded with serotonin.
★ Sometimes all of the serotonin in the presynaptic knob is moved out into the
synapse which affects the postsynaptic membrane
★ High levels of serotonin stimulating the release of more dopamine

★ Ecstasy causes physical changes, such as increased heart rate.

★ It causes problems in the body's thermoregulatory system.
★ There may be no desire to drink, which can lead to hyperthermia
(overheating) with raised blood pressure and irregular heartbeat.
★ Ecstasy can also affect the hypothalamus so that it secretes more antidiuretic
hormone (ADH).
★ This stops the kidneys from producing urine.
★ This can lead to problems if someone keeps drinking water in an attempt to
stay hydrated and cool down.
★ They retain so much water that osmosis destroys their cells.

9
A2 BIOLOGY
SEM TER FOUR 2022
Student N es
12s9

THE BRAIN
Learning objectives:
I. (8.14) know the location and main functions of the cerebral hemispheres,
hypothalamus, pituitary gland, cerebellum and medulla oblongata of the
human brain
II. (8.15) understand how magnetic resonance imaging (MRI), functional
magnetic resonance imaging (fMRI), positron emission tomography (PET) and
computed tomography (CT) are used in medical diagnosis and the
investigation of brain structure and function

The basic pattern of a vertebrate brain

★ The vertebrate brain has three distinct regions

★ Forebrain, midbrain and hindbrain

1
The brain is made up of a combination of grey matter and white matter

★ Grey matter – cell bodies of neurons

★ White matter – nerve fibres
★ Receives information from sensory organs
★ Interpretation / coordination of information
★ Transmits impulses to effector

Parts of human brain

2
Cerebrum – la s r o t r i

★ At the front of the brain / frontal lobes / fore brain

★ Controls voluntary action like thought / learning / intelligence / memory /
personality / emotion/Speech / language

Cerebellum – li l in

★ located at the back under the cerebrum.

★ Responsible for movement, balance, posture.
★ Often takes over learned activities.

Medulla - co c t e r ot p a c

★ At top of spinal cord / hindbrain / below pons

★ Controls involuntary action
★ Involved in homeostatic control
★ Simple reflex centre (sneezing)

3
Hypothalamus

★ Osmoregulation, maintaining body temperature and synthesis of hormones

of posterior pituitary gland.
★ Coordinate the autonomic nervous system.
★ Monitors chemistry of blood.
★ Provides link between brain and endocrine glands

Cerebrospinal fluid

★ Medium of transport between the blood and neurons.

★ Provide nourishment to the cells of the brain and spinal cord.
★ Carry away wastes.
★ Provides lubrication.

Coordination movement is controlled by part of the brain labelled

A cerebral hemisphere
B cerebellum
C medulla oblongata
D hypothalamus

4
SPINAL CORD

★ This is the way by which brain communicate with the body to coordinate
functions of the body
★ The spinal cord is a tube made up of a core of grey matter surrounded by
white matter.
★ Spinal cord runs out from the base of the brain (the medulla oblongata)
through the vertebrae.
★ It is approximately 43-45 cm long.

∘ Sensory receptor- sensory nerve fibre- dorsal root-spinal cord-spinal nerve-brain

∘ Brain - motor fibres in the spinal cord -motor neurons

5
6
REFLEX ARC

★ The simplest type of nerve pathway in the body, known as a reflex arc.
★ Reflex arc controls unconditioned reflexes. (blinking if an object
approaches the eye)
★ Reflex arc involves a receptor, a motor neuron and a sensory neuron.
★ The reflex arc may simply involve sensory and motor neurons.
★ But there is often a small third relay neuron situated in the CNS.
★ The function of the reflex arc is to cause an appropriate response to a
particular stimulus as rapidly as possible.
★ This avoids the time delay that occurs if the conscious centres become
involved.
★ Two different types of reflexes
○ Spinal reflex
○ Cranial reflex (pupil reflex)

7
Spinal reflexes

8
 The peripheral nervous system

9
 ★ The role of peripheral nervous system is nervous coordination
★ The changes in the internal or external environment is detected by sensory
receptors and are carried to the CNS.
★ The instructions from the CNS must be carried to the effector
★ The motor nerves are of two main types- the voluntary nervous system and
autonomic nervous system.
★ The voluntary nervous system: motor neurons function as a result of
conscious thought.
★ The autonomic nervous system: this is involuntary in action.
★ This involves motor neurons that the conscious areas of the brain do not
control.
★ The autonomic nervous system is again divided into sympathetic nervous
system and parasympathetic nervous system
★ There are anatomical and functional differences between them

10
Sympathetic and parasympathetic nervous system

Preganglionic neuron

★ Cell body is located within the CNS

★ It emerge from the brainstem or spinal cord and make
a synaptic connection in ganglia

Postganglionic neuron

★ It has a cell body originating in the ganglion.

★ It is generally non myelinated and terminates on
effector organs.

Compare the structure of sympathetic and parasympathetic nervous system

★ Both contain myelinated preganglionic fibres that leave the CNS and synapse
in a ganglion with unmyelinated post ganglionic fibres
★ In the sympathetic nervous system, the preganglionic fibres are short and
the post ganglionic fibres are long.
★ In the parasympathetic nervous system, the preganglionic fibres are long and
post ganglionic fibres are very short.

11
Functional differences between the sympathetic and parasympathetic
nervous system

★ The sympathetic nervous system produces noradrenaline at the synapses.

★ Usually produce a rapid response in the target organ system.
★ The sympathetic nervous system will dominate when a person is physically
active or under physiological stress.
★ Thus stimulate the organs to cope with the stress you experience.

★ Parasympathetic nervous system produces acetylcholine in the synapse.

★ It usually has a slower or inhibitory effect on the organ system.
★ Parasympathetic system maintains the normal functioning of the body.
★ This restores calm after a stressful situation.

12
Studying human brain

★ Using animal models

★ Using surgery and imaging techniques

Computed Tomography (CT)

★ Narrow beam of X-Rays passes through the patient’s head.

★ The rays are collected on the other side of the head and measure the
strength.
★ If the density of the tissue increases the strength of the signal decreases.
★ It gives information about the type of tissue in the brain.
★ Shows brain structure.
★ It helps to find out diseases such as cancer, stroke and oedema.
★ Blood has a different density from brain tissue so it shows up as a lighter
colour on a CT scan
★ It will not show brain activity.
★ They will give only frozen images
★ A scan will show the extent of the bleeding and its location in the brain.
★ CT scans are potentially dangerous because they use X-rays
★ X-rays can cause mutations in DNA, which may lead to cancer

Tumour appears white in scan:

★ These are growing cells and their density is high.

★ So most of the waves are absorbed or blocked by
these cells

13
MRI Scan

★ Align protons in the water molecules using magnetic fields.

★ When the fields are switched off, the proton gives out a little energy.
★ This can be detected.
★ Record the energy given out by protons.
★ Build up a sequence of thin pictures of the types of tissues inside the brain.
★ Build up a 3D image of the inside of the head.

★ MRI shows much finer images than CT scans.

★ They are produced using magnetic fields and
radio waves to image the soft tissues.
★ Hydrogen atoms are the most commonly imaged
element (because so much of the body is made up of water and hydrogen
atoms produce a particularly strong MRI signal )
★ Different tissues respond differently to the magnetic field depending on the
amount of water in the structure.

Medical diagnosis

★ MRI scans can also be used to diagnose medical problems because they
show damaged or diseased areas of the brain, e.g. a brain tumour
★ Tumour cells respond differently to a magnetic field than healthy cells, so
they show up as a lighter colour on an MRI scan.
★ A scan will show the exact size of a tumour and its location in the brain.
★ Doctors can then use this information to decide the most effective treatment.
★ Also help doctors to work out what brain functions may be affected by the
tumour

14
Functional magnetic resonance imaging (fMRI)

★ fMRI can allow brain activity to be seen in real time

★ fMRI uses radio waves / magnetic field
★ Increase supply of oxygenated blood in active areas
★ Oxyhaemoglobin reflects/does not absorb fMRI signals.
★ Active area of the brain absorbs less energy than a less active area.

PET scans/ Positive emission tomography

★ This is also used to form 3D images of the inside of the body including the
brain.
★ The great advantage of PET scan is that they can show how parts of the brain
are actually working.
★ The patient is injected with a radiotracer (radioactive isotope) which is
similar to glucose.
★ It will be carried to all the cells just like glucose.
★ From the area of accumulation, the radiotracer gives off radiation.
★ These radiations are detected and are converted
into images.
★ More active areas respire more and need
increased supply of glucose.
★ PET scans combined with CT and MRI scans to
produce a very detailed image to help with
diagnosis.

15
 Describe how positron emission tomography (PET) could be
used to identify the part of the brain involved.

★ isotope {that emits positrons / is incorporated into glucose}

(1) Accept suitable named isotope e.g. carbon-11 or
oxygen-15,radioactive material in glucose
★ more active neurons with increased respiration will require
increased supply of glucose/will {absorb/use} more glucose
★ positrons (emitted from glucose) produce gamma rays that
detected and are converted into an image (1)

fMRI and CT

CT Scan fMRI

Gives brain image at a point in time Brain activity can be viewed directly over a period of time

CT takes only still image fMRI takes moving images

Safer than CT as it is not using X rays

Identify active areas by greater oxygen uptake or by the

presence of more oxyHb

Suggest why functional magnetic resonance imaging (fMRI) is considered

better than CT for studying brain function.(2)

★ View brain activity directly by fMRI.

★ (MRI identifies active areas by greater blood, greater oxygen uptake or
presence of more oxyhaemoglobin in these areas)
★ See brain activity over a period of time CT gives still image
★ fMRI is safer as it does not use X rays and In fMRI no need to use special dye

16
CT Scan and MRI

CT Scan MRI

Both give 2D / 3D images

Images for both are at one point in time

Image resolution is low in CT Image resolution is high in MRI

Identifies only larger structures Identifies smaller structures

Uses X-Rays Uses radio waves or magnetic field

Not noisy Noisy

Less expensive More expensive

Surgery

★ A local anaesthetic is given to the person.

★ Surgeons are asking questions by stimulating some parts of the brain.
★ The patient is able to tell about their feelings when he stimulates a particular
region.
★ Give the functions of the brain.

17
A2 BIOLOGY
SEM TER FOUR 2022
Student N es
12s9

OSMOREGULATION
Learning objectives:
I. (7.18) know the gross and microscopic structure of the mammalian kidney
II. (7.19) understand how urea is produced in the liver from excess amino acids
(details of the ornithine cycle are not required) and how it is removed from
the bloodstream by ultrafiltration
III. (7.20) understand how solutes are selectively reabsorbed in the proximal
tubule and how the loop of Henle acts as a countercurrent multiplier to
increase the reabsorption of water
IV. (7.21) understand how the pituitary gland and osmoreceptors in the
hypothalamus, combined with the action of antidiuretic hormone (ADH),
bring about negative feedback control of mammalian plasma concentration
and blood volume

Osmoregulation

★ It is the maintenance of the osmotic potential in the tissues of a living

organism within narrow limits by controlling water and salt concentration.
★ In mammals, the main organ involved in homeostatic control of the water
balance of the body is the kidneys.
★ Liver is also involved in homeostasis by breaking down excess amino acids
and removal of toxins.

1
The liver, protein metabolism and homeostasis

★ The liver plays an important role in deamination of excess amino acids in

protein metabolism.
★ The liver cells (hepatocytes) deaminate excess amino acids.
★ They remove the amino group and convert it first into ammonia.
★ This ammonia is very toxic.
★ Ammonia is then converted to urea which is less toxic and can be excreted
by the kidneys.
★ The ammonia produced in the deamination of protein is converted into urea
by a series of enzyme controlled reactions known as the ornithine cycle.
★ The remainder of the amino acid can be used in aerobic respiration or be
converted into lipids for storage.

Deamination

2
Osmoregulation in mammals

★ Osmoregulation in mammals is brought

about by the kidneys.
★ The kidneys are a pair of organs capable
of producing urine.
★ This is hypertonic to the body fluids (more
concentrated than the body fluid)
★ This makes it possible to conserve water.
★ This has allowed mammals to spread into most of the land environments.
★ study

The kidneys

★ Kidneys are a pair of dark reddish brown organs attached to the back of the
abdominal cavity.
★ They are surrounded by a thick layer of fat for protection from mechanical
damage.
★ The two main roles of the kidney – osmoregulation and excretion
★ They control the water potential of the blood plasma that passes through
them.
★ They remove urea and excess
salts and water to form urine.

3
The basic structure of a mammalian kidney

A section through the kidney shows it is made up of the following structures:

★ Fibrous capsule: an outer membrane that protects the kidney.

★ Cortex: this has a rich capillary network and is very dark in color. It contains
the Malpighian bodies of all the nephrons.
★ Medulla : this region is made up of loops of Henle from the nephrons,
collecting ducts and blood vessels.
★ Pyramid: a collection of tubules, collecting ducts and blood vessels
★ Pelvis: the a funnel shaped central chamber where urine arrives from the
collecting ducts
★ Ureter: a tube that carries urine to bladder
★ Renal artery: supplies the kidney with blood from the heart via the aorta
★ Renal vein: returns blood to the heart via vena cava

4
Structure of a nephron
The nephron is the functional unit of the kidney. A narrow tube closed at one end
with two twisted regions separated by a long hair pin loop.

Each nephron is made up of:

★ Bowman’s capsule: cup shaped and the closed end at the start of the nephron.
★ It contains a mass of blood capillaries called glomerulus.
★ The Bowman’s capsule and Glomerulus together are called the Malpighian
body.
★ Inner layer of Bowman’s capsule is made up of cells called podocytes.
★ The basement membrane acts as a molecular filter.
★ Each glomerulus is supplied with blood by a branch of the renal artery called an
afferent arteriole.
★ The capillaries of the glomerulus rejoin to form an efferent arteriole.
★ The efferent arterioles lead to form a network of capillaries.
★ Blood from these capillaries flows into a branch of the renal vein

5
★ Proximal convoluted tubule: a series of loops surrounded by blood
capillaries. The cells lining this tubule are covered with microvilli. This
increases the surface area through which substances can be absorbed.
★ Loop of Henle: a long hairpin loop that extends from the cortex into the
medulla of the kidney and back again. It is surrounded by blood capillaries.
★ Distal convoluted tubule: a series of loops surrounded by blood capillaries.
But fewer capillaries than the proximal convoluted tubule.
★ Collecting duct: a tube into which a number of distal convoluted tubules
empty. It becomes increasingly wide as it empties into the pelvis of the kidney.

6
The kidney performs three main functions in its osmoregulatory role.

★ These are ultrafiltration, selective reabsorption and tubular secretion.

★ Each kidney is made up of microscopic tubules called nephrons.
★ There are two main types of nephrons- Cortical nephrons and
Juxtamedullary nephrons.
★ Cortical nephrons are found mainly in the renal cortex.
★ They have a loop of Henle that only just reaches into the medulla
★ Juxtamedullary nephrons have long loops of Henle that penetrate right
through the medulla.
★ They are efficient in producing concentrated urine.

7
Ultrafiltration

★ This is the first stage in osmoregulation.

★ This is due to very high blood pressure in the glomerular capillaries and
structure of the Bowman’s capsule and glomerulus. (capillary walls are made
up of endothelial cells with pores between them)
★ Diameter of the afferent arteriole is greater than the efferent arteriole.
★ This builds up hydrostatic pressure within the glomerulus
★ The high pressure squeezes the blood out through the pores in the capillary
wall.
★ Almost all the contents of the plasma can pass out (forced out) of the
capillary except the blood cells (they are large) and largest plasma proteins.
★ Most of the filtrate is later reabsorbed into the blood.

8
Detail of the endothelium of a glomerular capillary and Bowman’s capsule.

9
Selective reabsorption

★ By ultrafiltration it removes a lot of water with glucose, salt and other

substances from the blood along with urea.
★ Glucose, water, salt and other inorganic ions are needed by the body.
★ The main function of the kidney tubule is to return most of what has been
removed during ultrafiltration back into the blood.

★ Many microvilli- increases the surface area for selective reabsorption as

they have many membrane proteins.
★ Many mitochondria-provide energy for sodium– potassium (Na⁺–K⁺) pump
proteins in the outer membranes of the cells.
★ Co-transporter proteins in the membrane facing the lumen- diffusion of
glucose and amino acid

10
Proximal tubule

★ Reabsorbs 80% of the glomerular filtrate into the blood.

★ The cells lining this tubule are covered with microvilli.
★ There will be more membrane proteins which increases the surface area for
the reabsorption.
★ These cells also contain large numbers of mitochondria.
★ It provides energy for the active transport of substances during reabsorption.
★ By active transport, sodium ions are returned to blood.
★ From the lumen of the tubule sodium ions diffuse into the cells lining the
tubule through special carrier proteins.
★ Along with sodium ions, glucose ,amino acids and chloride ions are also
carried (co-transport)
★ Water also follows down the water potential gradient.
★ These substances enter into intracellular spaces from the cells of the tubule.
★ From there it diffuses into the extensive network of capillary.
★ The continuous movement of blood through the capillary maintains a
concentration gradient.
★ When it reaches the loop of Henle, the filtrate is isotonic to the tissue fluid
surrounding the tubule.
★ The amount of reabsorption in the proximal tubule is always the same.

11
 ★ In the proximal tubule, quite a lot of urea is reabsorbed too.
★ Urea is a small molecule which passes easily through cell membranes.
★ Its concentration in the filtrate is considerably higher than that in the
capillaries, so it diffuses passively through the cells of the proximal
convoluted tubule and into the blood.
★ Uric acid and creatinine are not reabsorbed.
★ Creatinine is actively secreted by the cells of the proximal convoluted tubule
into its lumen.

12
Relative concentrations of five substances in different parts of a nephron

Proximal convoluted tubule: (P)

★ all the glucose is reabsorbed by active transport / use of energy / use of ATP
★ urea concentration rises as water is reabsorbed
★ sodium ions absorbed because concentration does not increase (despite less
water)

Loop of Henle: (L)

★ urea concentration rises

★ sodium ion concentration rises in descending limb
★ water reabsorbed from descending limb by osmosis
★ sodium ion concentration falls in ascending limb
★ Loop of Henle act as countercurrent multiplier and create a concentration
gradient by the active transport of sodium ions out of the ascending limb

Distal tubule and collecting duct: (C)

★ urea and sodium ion concentration rise as water is reabsorbed by osmosis

★ Here ADH affects permeability of membrane to water

13
The Loop of Henle

★ The descending limb is permeable to water, whereas the ascending limb is

not.
★ The loop of Henle is in close contact with a network of capillaries.
★ Together they create a water potential gradient between the filtrate and the
medullary tissue fluid.
★ So water can be reabsorbed from the distal tubule and the collecting duct.
★ Due to this water potential gradient mammals produce urine which is more
concentrated than their blood.
★ The cells that line this region of the loop actively transport sodium and
chloride ions out of the fluid in the loop, into the tissue fluid.
★ This decreases the water potential in the tissue fluid and increases the water
potential of the fluid inside the ascending limb.
★ The biological system that uses active transport to establish and maintain a
concentration gradient is countercurrent multiplier

14
The distal tubule

★ It is permeable to water, but the permeability varies with the level of ADH
(Antidiuretic hormone)
★ If there is not enough salt in the body, sodium can be actively pumped out of
the tubule with chloride ions
★ Then water leaves by diffusion.

The collecting duct

★ The permeability of the collecting duct is affected by ADH.

★ Water moves out of the collecting duct as it passes through the medulla.
★ Because medulla contains high levels of sodium and chloride ions.
★ So urine becomes more concentrated.
★ Water can be removed along the whole length of the collecting duct.
★ So kidneys can produce very hypertonic urine when it is necessary to
conserve water for the cells.

15
Osmoregulation

★ Osmoregulation is the control of the water potential of body fluids.

★ This regulation is an important part of homeostasis and involves the
hypothalamus, posterior pituitary gland and the kidneys.
★ The water potential of the blood is constantly monitored by specialized
sensory neurons in the hypothalamus, known as osmoreceptors.
★ In response to the stimulus from these receptors, ADH is produced by the
hypothalamus and secreted into the posterior lobe of the pituitary and are
stored there.
★ ADH increases the permeability to water of the distal tubule and the
collecting duct

16
How ADH increases water reabsorption in the collecting duct

★ ADH binds to specific receptors on the cell surface membrane

★ It triggers a cascade of reactions that result in the formation of cAMP as the
second messenger.
★ The enzymes are activated
★ The cells contain ready-made vesicles with aquaporins on the membrane.
★ The vesicles migrate towards the cell surface membrane.
★ These vesicles fuse with the membrane and aquaporins become inserted
into the membrane.
★ Increasing the permeability of the membrane to water

Osmoregulation
17
 Osmoregulation

The high water potential of the blood is Increases the permeability of the
constantly monitored by osmoreceptors membrane of distal tubule and the
in the hypothalamus collecting tube to water.

ADH is produced by the hypothalamus Vesicles migrate towards the cell surface
and secreted into the posterior lobe of membrane, fuse with it and become
the pituitary and are stored inserted into the membrane

ADH binds to specific receptors on the The cells contain ready-made vesicles
cell surface membrane that have many aquaporins in their
membranes

Triggers a cascade of reactions that The enzymes are activated by the arrival
result in the formation of cAMP as the of ADH
second messenger

18
If water is in short supply/ sweat a lot/ eat a very salty meal, the concentration of
inorganic ions in the blood rises

★ Increase in the concentration of inorganic ions in plasma

★ This increase is detected by osmoreceptors in the hypothalamus.
★ The impulse will be sent to the posterior pituitary which constantly releases
stored ADH into the blood.
★ ADH binds to the receptors on the cell surface
membrane of the kidney tubules.
★ This increases the permeability of the distal tubules
and the collecting duct to water.
★ Water leaves the tubule by osmosis into the
surrounding capillary network.
★ Blood plasma receives more water from the filtrate.
★ A small volume of concentrated urine is produced.

Increase in water potential or decrease in ion concentration:

★ Osmoreceptors in the hypothalamus detect the increase in water potential.

★ This stimulates the pituitary gland to reduce the release of ADH.
★ This decreases the permeability of the distal
tubule and the collecting duct to water and urea.
★ Less water is reabsorbed back into the blood from
the collecting duct.
★ More dilute urine is produced and water potential
of the blood decreases.

19
QUESTIONS:-

1. Explain the role of the nephron in osmoregulation.

★ as blood concentration increases osmoreceptors / hypothalamus detects
change
★ pituitary gland release ADH
★ increase permeability of collecting duct reabsorbed from collecting duct /
into blood
★ less urine /more concentrated urine
★ increases water level / reduces blood concentration
★ (so that) hypothalamus not stimulated / pituitary releases less ADH / negative
feedback idea

20
 2. A kangaroo rat is a mammal that lives in hot desert regions of America.
(i) In kangaroo rats, the tissue surrounding the collecting duct contains
a high concentration of ions. Explain how this feature enables kangaroo
rats to survive in the desert. (3)

★ water reabsorbed / water into blood (1)

★ osmosis (1)
★ concentrated urine / less water in urine / less urine (1)

3. The table lists three molecules. It also gives their concentrations in the
glomerulus, the Bowman’s capsule and the bladder. Explain the difference
between the concentration of each substance in the glomerulus and in the
bladder. (4)

★ protein large (molecule) (1)

★ cannot enter Bowman’s capsule / cannot leave blood / cannot pass through
glomerulus / basement membrane / capillaries (1)
★ glucose (re)absorbed / glucose into blood / glucose into capillaries (1)
★ proximal convoluted tubule / by active transport / diffusion (1)
★ urea concentration higher / increased (1)
★ because water (re)absorbed / water into blood / water into capillaries / urea
excreted / urea added to urine (1)

21
 A2 BIOLOGY
SEM TER FOUR 2022
Student N es
12s9

Ph oreception in plants
Learning objectives:
I. Understand how phytochrome, auxin (IAA) and gibberellins bring about
responses in plants, including their effects on transcription

Phytochrome

★ Phytochrome is a blue green pigment that exists in two interconvertible

forms.
★ Plants detect light using photoreceptors called phytochromes (the leaves,
seeds, roots and stem).

1
 Plants detect light using Photoreceptors

★ Plants detect light using photoreceptors called phytochromes (the leaves,

seeds, roots and stem).
★ Phytochromes are molecules that absorb light.
★ They exist in two states — the Pr state absorbs red light (P660) and the Pfr
state absorbs far-red light (P730).
★ Phytochromes are converted from one state to another when exposed to
light:
○ Pr is quickly converted into Pfr when it’s exposed to red light.
○ Pfr is quickly converted into Pr when it’s exposed to far-red light.
★ Pfr is slowly converted into Pr when it’s in darkness.
★ Daylight contains more red light than far-red light, so more Pr is converted
into Pfr than Pfr is converted to Pr.
★ The differing amounts of Pr and Pfr control the responses to light by
regulating the transcription of genes involved in these responses.

2
 Phytochrome and seed germination

★ Pfr stimulates seed germination.

★ Germination occurs at a faster rate at warmer temperatures.
★ Germination occurs when long durations of light are available.

Flash of light and seed germination

★ Flash of red light stimulates seed germination.

★ A flash of far red light inhibits seed germination.
★ A sequence of red and far red light. Here the last flash determines seed
germination.
○ Red- far red- red …………… stimulate germination
○ Red – far red - red – far red …………… inhibit germination

3
Photoperiodism

★ The response by an organism to changes in day length

★ Plants detect light using photoreceptors called phytochromes.
★ The detection of photoperiod takes place in the leaves.
★ A chemical messenger, florigen was made in response to changing levels of
phytochromes.
★ These are carried in the plant transport system to the flower bed.

4
Phytochrome and flowering

★ Phytochrome help for photoperiodism

★ Long day plants flowers only in summer
★ Flowering stimulated by Pfr example: poppies,lettuce
★ Short day plants flower only in autumn
★ Flowering stimulated by Pr example: chrysanthemum
★ Day neutral plants are unaffected by length of the day example: cucumber,
tomato.

★ Long day plants: Pfr left at the end of the short night. High levels of Pfr
promote flowering for LDPs.
★ As the nights are short, relatively little Pfr is converted to Pr. Low level of Pfr
or High level of Pr inhibits flowering.
★ Long day plants require a short period of unbroken darkness to flower.
★ It should not be longer than the critical period
★ Short day plants: All the Pfr will be converted to Pr by long night. Lack of Pfr
stimulates flowering in SDPs.
★ Short day plants require long periods of unbroken darkness to flower.
★ It should be longer than the critical period

5
Phytochrome and Greening

★ Exposure to sunlight stimulate Pfr

★ Promote the formation of chlorophyll and leaf
development
★ Inhibit the elongation of internodes

When the plants are in complete darkness

★ Pr is produced in darkness
★ Brings about the elongation of internodes
★ Yellowing of leafs
★ Elongation of stem
★ This is called etiolation
★ Pfr activates the protein needed for the initiation of
light regulated genes in young seedlings
★ This switches on the gene for the enzyme that produces chlorophyll.

If a number of plants are grafted together, but

only one is exposed to the correct lighting regime,
all will flower.

6
 When a leaf is exposed to a given
amount of light and dark

FT gene/ Flowering Locus T is activated.

FTmRNA is produced in the leaf

This mRNA moves from cell to cell to

the transport tissue through the
plasmodesmata

It travels from the leaves to the apex of

the shoot.

Genes associated with flowering are

activated

7
Phytochrome as a transcription factor

★ In the presence of light Pr is converted to Pfr

★ This Pfr enters into the nucleus where it binds to a transcription factor–
phytochrome interacting factor 3 (PIF3).
★ This factor only binds to Pfr and not to Pr.
★ This PIF3 only activates gene transcription and mRNA formation when it is
bound to Pfr

Process Effect of far red light Effect of far red light

Conversion of Promotes P730- P660 Promotes P660-P730
phytochrome
Germination of small Inhibits Promotes
seed
Flowering in long day Inhibits Promotes
plants
Flowering in short day Promotes Inhibits
plants

Leaf expansion Inhibits Promotes

8
An investigation was carried out to study the effects of different periods of light
and darkness on the flowering of cocklebur plants. The relative periods of light
and darkness and the results of this investigation are shown in the diagram
below.

Using your knowledge of

photoreceptors in plants, suggest
an explanation for the results of
this investigation. (4)

★ The results suggest that cocklebur is a short-day plant

★ Plants detect light using photoreceptors called phytochromes
★ In the dark, Pfr (slowly) reverts to Pr
★ These plants need a sufficiently long dark period to allow Pfr to reach critical
(low) concentration
★ High Pr promotes flowering / high Pfr inhibits flowering
★ Short period of light during darkness converts Pr back to Pfr

9
Synergy and antagonism

★ If the growth regulators work together, complementing each other and giving
a greater response- synergy
★ Auxins and gibberellins work synergistically in the growth of stems.
★ If the hormones have opposite effects- antagonism

Plant hormone Auxin

Growth and auxins

★ Powerful growth stimulants that are effective in very low concentration.

★ It is a diffusible chemical substance produced at the tip of young shoots
which stimulates growth.
★ Auxins stimulate the growth of shoots by cell elongation — this is where cell
walls become loose and stretchy, so the cells get longer.
★ It moves down from shoot to root by active transport.
★ If the tip of the stems are removed, root growth slows down and stops.

10
Role of auxins in the growth of plant shoot

★ Affect the ability of the plant cell wall to stretch.

★ IAA is made in the tip of the shoot and diffuses down towards the zone of
elongation
★ Binds to specific receptors on the cell membrane.
★ Active pumping of hydrogen ions into the primary cell wall.
★ Provide optimum pH.
★ Enzymes break the bonds between adjacent cellulose microfibrils and keep
the wall flexible.
★ The cells absorb water by osmosis and stretch and cells expand.
★ As the cell matures, IAA is destroyed by enzymes.

11
12
IAA is known to bind to transcription factors. Suggest how IAA can stimulate
cells to synthesize proteins.

★ IAA enters the cell

★ IAA in cytoplasm enters to nucleus
★ Binds to the promoter region of the DNA
★ Binds to transcription factor and forms a transcription initiation complex
★ This switch on gene and which is transcribed to mRNA
★ mRNA is translated to protein.

13
Phototropism

The growth response of a living organism in response to light direction is called

phototropism

★ Light causes the redistribution of auxin / IAA/

★ So high concentration of auxin is away from light
★ Auxin diffuses down into the zone of elongation of the shoot.
★ Binds to specific receptors on the cell membrane.
★ Active pumping of hydrogen ions into the primary cell wall.
★ Provide optimum pH.
★ Enzymes break the bonds between adjacent cellulose microfibrils and keep
the wall flexible.
★ The cells absorb water by osmosis and stretch and cells expand.
★ So the side away from light is longer and it bends towards light.

So that plants can photosynthesise more and as the roots grow away from light,
they move into the soil and can absorb water and minerals.

14
The tip of a plant shoot was placed on two agar blocks and light was shone from
one side. The tip was removed and the agar blocks were then placed on a shoot
without a tip, as shown in the diagram below.

Draw a diagram to show the shoot as it

would appear several hours later. (1)

15
Gibberellins

★ It is a group of plant hormones.

★ These act as growth regulators.
★ They affect the internode elongation, promote the growth of fruit and
stimulate seed germination.

Gibberellins and seed germination

★ Seeds absorb water and swell and the embryo is activated.

★ Embryo secretes gibberellins that diffuse into the aleurone layer.
★ It acts as transcription factor
★ They stimulate the formation of an enzyme, amylase.
★ This breaks down starch stores in cereal plants into glucose.
★ Glucose is available for respiration in the embryo

16
 A2 BIOLOGY
SEM TER FOUR 2022
Student N es
12s9

PHOTORECEPTION IN ANIMALS
Learning objectives:
I. (8.8) understand how the nervous systems of organisms can detect stimuli
with reference to rods in the retina of mammals, the roles of rhodopsin,
opsin, retinal, sodium ions, cation channels and hyperpolarization of rod
cells in forming action potentials in the optic neurons
II. (ii) understand how the pupil dilates and contracts
III. study

Photoreceptors are light receptors in your eye

★ Light enters the eye through the pupil.

★ The amount of light that enters is controlled by the muscles of the iris.
★ Light rays are focused by the lens onto the retina, which lines the inside of the
eye.
★ The retina contains photoreceptor cells — these detect light.
★ The fovea is an area of the retina where there are lots of photoreceptors.
★ Nerve impulses from the photoreceptor cells are
carried from the retina to the brain by the optic nerve
★ Where the optic nerve leaves the eye is called the
blind spot — there aren’t any photoreceptor cells, so
it’s not sensitive to light

1
Structure of human Eye

2
Structure of the Eye: Retina

★ The retina is the sensor or film of your eye.

★ Its layers do three things:
○ Provide blood and nutrients (choroid)
○ Absorb light and convert to an electrical signal (photoreceptors)
○ Transfer the signal to the brain (nerve cells)
★ Retina is a light-sensitive layer of cells at the back of the eye where an image
is formed

3
Photoreceptors convert light into an electrical impulse

★ Light enters the eye, hits the photoreceptors and is absorbed by

light-sensitive pigments.
★ Light bleaches the pigments, causing a chemical change.
★ This triggers a nerve impulse along a bipolar neuron.
★ Bipolar neurons connect photoreceptors to the optic nerve, which takes
impulses to the brain
★ The human eye has two types of photoreceptor — rods and cones.

Rod and cone

★ Rods are mainly found in the peripheral parts of the retina, and cones are
found packed together in the fovea.
★ Rods only give information in black and white (monochromatic vision), but
cones give information in colour (trichromatic vision).
★ There are three types of cones — red-sensitive, green-sensitive and
blue-sensitive

4
Photoreceptors: Rods

★ Rods are responsible for low light and peripheral vision

★ They are present everywhere in the retina except the fovea.
★ contain a pigment called rhodopsin that is sensitive to dim light.
★ Rods have no ability to detect colours.
★ The pigmented region is cylindrical in shape.
★ The outer segment of the rod cell contains a stack of flattened vesicles.
★ These membranes are packed with rhodopsin molecules.
★ A narrow constriction with a pair of cilia connects the outer segment to the
inner segment.
★ The inner segment contains nucleus, other organelles such as mitochondria,
golgi body and ribosomes
★ Extension of the inner segment synapses with the bipolar neuron.
★ Bipolar neuron synapses with ganglion neuron

5
 Photoreceptors: Cones

★ Cones are responsible for our fine detailed and colour vision in the bright
light.
★ Cones are clustered near the centre of the retina, called the fovea.
★ In cones the vesicles containing the pigments are fewer and are formed by
the outer membrane itself.
★ In cones the pigmented region is cone-shaped.
★ Contain the pigment iodopsin.

Feature Rods cones

Frequency in single retina About 120×10⁶ About 6 × 10⁶

Distribution Evenly spread throughout Tightly packed at fovea
retina except at fovea
Shape of outer segment Rod-shaped Cone-shaped
Light sensitive pigment Rhodopsin (affected by light of Iodopsin (affected by light
low intensities) of high intensities)
Synapse with bipolar cell Synapse in groups Synapse individually
Vision Unable to distinguish color Able to distinguish color

6
Rhodopsin

★ Rhodopsin is sensitive to dim light.

★ This pigment is necessary for night vision (Scotopic
vision).
★ Rhodopsin is synthesised with the help of vitamin A.
★ The pigment is also called visual purple.
★ Rhodopsin is made up of retinal and opsin
★ Light causes cis retinal to change into trans retinal.
★ So retinal and gets separated (bleaching)

Identify the statement that describes what happens to rhodopsin when photons of light
enter rod cells

rhodopsin is bleached producing opsin and cis-retinal

rhodopsin is bleached producing opsin and trans-retinal
rhodopsin is formed from opsin and cis-retinal
rhodopsin is formed from opsin and trans-retinal

7
Photoreception by rod cells

★ Light falls on rod cells.

★ Cis retinal is converted to trans retinal
★ Rhodopsin breaks down to retinal and opsin.
★ Opsin binds with rod cells.
★ Sodium ion channel in the outer segment closed.
★ Sodium influx to outer segments stops.
★ Inner segment continues to pump sodium ions out.
★ Inside of the cell becomes hyperpolarized.
★ Release of neurotransmitter glutamate stops.
★ Bipolar sodium ion channels open.
★ Cell membrane depolarised.

In the dark

★ Rhodopsin is formed and accumulates in the

dark.
★ Retinal is in the cis form.
★ In the dark, influx of sodium ions occurs
through the cation channel.
★ This produces a depolarization.
★ Triggers the release of neurotransmitters
glutamate (inhibitory)
★ In the dark it is released continuously.
★ Neurotransmitter binds to bipolar cell and
stops depolarization.

8
 Pupil reflex
★ The iris controls the amount of light entering the eye cavities.
★ The contraction of radial or circular smooth muscles located within the
iris permit changes in the pupil diameter.
★ It is involuntary and which still occurs in an unconscious person

9
Antagonistic muscles – t e p efl x

★ Circular muscles contract and radial muscles relax to constrict pupil

★ Radial muscles contract and circular muscles relax to dilate pupil
★ It is needed for fine control of aperture to allow pupil to be reset to a
different size according to varying light intensity
★ These muscles can only shorten
★ Antagonistic muscles have opposite effects
★ Contraction of one muscle set stretches the other

High light level

★ Strikes on photoreceptors on the retina.

★ Causes nerve impulse to pass along the optic nerve to CNS and a group of
coordinating cells in the midbrain.
★ Impulses from these cells are sent along parasympathetic motor neurons
to circular muscle.
★ Circular muscle contract and radial muscle relax.
★ Constricts pupil.
★ Reducing the amount of light entering the eye.
★ Preventing the damage of the retina.

10
Low light level

★ Fewer impulses to the coordination centre in the brain.

★ Impulses sent down to sympathetic motor neurons to the radial muscles.
★ Radial muscle contract.
★ Pupils dilate.
★ Allow more light to reach the retina.

11
 A2 BIOLOGY
SEM TER FOUR 2022
Student N es
12s9

HABITUATION
Habituation

Habituation is a form of learning

It is a reduced response to a repeated or harmless stimulus

How habituation is achieved?

★ Due to repeated stimulation

★ Calcium channels become less responsive.
★ Less calcium ions cross the presynaptic membrane.
★ Less neurotransmitters are released.
★ Less depolarization of the postsynaptic membrane.
★ No action potential in the motor neuron
to the effector.
★ No response from the effector.

1
Investigating habituation of a snail to stimulus

★ Allow snail to adjust to environment by giving 15 minutes before starting

★ Tap the the snail with a dampened cotton bud
★ Maintain the strength of stimulus by giving same force
★ Find out the time taken for the eye stalk to re emerge completely
★ Repeat the stimulus after response for 5 times
★ Repeat the experiment with different snail of the same gender;

Variables to be controlled

★ Temperature using temperature controlled room

★ Environmental factor such as background noise, humidity, light intensity (use
same surface or container for snail)
★ Species, age, gender
★ Previous handling of the snail /time to recover during experiment

Suggest how this habituation may be of benefit to a sea slug.

Animals can avoid wasting time and energy on unimportant or non threatening
stimuli - which are natural frequent stimuli.

2
Describe an investigation to determine whether habituation by the
birds occur in the presence of a scarecrow.

A scarecrow is a model of a human dressed in old clothes. Some farmers believe

that a scarecrow will frighten birds and the crops will not be eaten. However, some
scientists believe that habituation by the birds will occur and the crops will be
eaten.

★ Use scarecrows in a field.

★ Release 50 birds of the same species in the field.
★ Count the number of birds that fly away.
★ Repeat it many times and find out the mean number of birds that fly away.
★ Repeat this in another field of the same crop and light intensity.
★ Number of birds that fly away will decrease after every trial.

A sea slug uses a tube called a siphon to help with gas exchange. When the
siphon is touched, it is withdrawn into the body of the sea slug.Explain the
advantage of this behaviour (habituation) to the sea slug living in rough
water.

★ As the stimulus is harmless it is ignored.

★ Less withdrawal of siphon saves energy and has more energy for another
activity.
★ This allows gas exchange.

3
An investigation was carried out to study habituation in a group of people.

Each person wore a pair of headphones through which a short sound was
played once.

This sound made each person blink their eyes.

The degree of contraction of one muscle involved in blinking was recorded.

The mean degree of muscle contraction was calculated for the group.

This was repeated with the sound played 5 times, 10 times, 15 times and 20
times.

The mean results for the group were recorded.

Describe how this investigation could be extended to obtain valid and reliable
data on how the volume of the sound could affect habituation.

★ reference to different volume(s) used ;

★ idea that muscle contraction is measured for each number of times the
volume was repeated ;
★ idea of same type of sound ;
★ idea of control of one other abiotic variable e.g other noise , temperature,
rest period, interval between trials ;
★ idea of control of volunteers e.g. same age, gender, hearing ability ;

4
A2 BIOLOGY
SEM TER FOUR 2022
Student N es
12s9

GENE TECHNOLOGY
Learning objectives:
I. (8.17) know how drugs can be produced using genetically modified
organisms (plants, animals and microorganisms)
II. (8.18) understand how recombinant DNA can be produced, including the
roles of restriction endonucleases and DNA ligase
III. (8.19) understand how recombinant DNA can be inserted into other cells
IV. (8.20) know how microarrays can be used to identify active genes
V. (8.2) understand what is meant by the term bioinformatics
VI. (8.22) understand the risks and benefits associated with the use of
genetically modified organisms

Recombinant DNA

Recombinant DNA is DNA made by joining pieces from two or more different
sources.

An organism containing recombinant DNA is called a Genetically Modified

Organism.

1
An overview of gene transfer

★ There are many different ways in which a GMO may be produced.

★ The gene that is required is identified.
★ It may be cut from a chromosome using restriction enzymes or made from
mRNA by reverse transcriptase or synthesized from nucleotides.
★ Multiple copies of the gene are made using the technique known as the
polymerase chain reaction (PCR).
★ The gene is inserted into vectors (by the enzyme ligase ) such as plasmids,
viruses and liposomes which delivers the gene to the cells of the organism.
★ The vector takes the gene into the cells.
★ The cells that have the new gene are identified and cloned.

Explain the role of the enzymes involved in making recombinant DNA

★ Cut gene out of animal DNA using restriction enzyme

★ Amplification using DNA polymerase in PCR
★ Open the plasmid using same endonuclease to produce ‘sticky ends’
★ Hydrogen bonds formed between bases at ‘sticky ends’
★ Ligase is used to join gene to plasmid
★ Phosphodiester bond formed between adjacent mono nucleotides

2
 Restriction enzymes

★ These enzymes cut the sugar–phosphate backbone of DNA at specific places within
the molecule.
★ Each restriction enzyme binds to a specific target
site on DNA and cuts at that site.
★ Some restriction enzymes cut the DNA and leave
sticky ends.
★ Sticky ends attach to other compatible sticky ends by
forming hydrogen bond between the base pairs
★ whoa

Integrating the new gene into a vector

★ Usually bacterial plasmid is used as the vector to carry the DNA into a host
bacterial cell.
★ The circular DNA of the plasmid is cut open using the same restriction enzyme,
the one used to cut out the gene, so that the sticky ends are complementary.
★ The enzyme DNA ligase is used to link together the desired gene and the
plasmid.
★ The gene for the enzyme that produces the green fluorescent protein (marker
gene) is inserted into the plasmids.
★ This produces a closed circle of double-stranded DNA containing the new
gene.
★ This is now recombinant DNA.

Structure of the modified plasmid

○ It is a small circle of DNA

○ Containing bacterial genes and animal gene
○ Also contain marker gene

3
Why plasmids?

★ They are small and do not contribute much additional DNA to the host cell.
★ They replicate rapidly in the host cell and independently of the host cell.
★ They are easily taken up by bacterial cells.
★ It is easy to determine their DNA sequence.
★ They have a number of recognition sites so that different restriction enzymes
may be used.
★ They possess natural marker genes such as antibiotic resistance so can be
recognised easily

Vectors

★ Vectors transfer the required gene with any marker gene into the new cells.
★ A successful vector should target the right cell and ensure the desired gene is
incorporated into the host genetic material.
★ So the gene can be transcribed and translated to produce desired protein
★ Different ways by which required genes are transferred to the host cell:
○ Gene gun
○ Harmless virus
○ Liposome
○ microinjection

4
 ★ Gene guns: shoot DNA carried on very small gold or tungsten pellets into
the cell at high speed.
★ Harmless virus: remove the gene for viral replication and insert the
required gene and allow to infect an animal’s cell
★ Viruses can cause an immune response in some people in the same way as
pathogenic viruses.
★ So mostly focusing on non-viral vectors such as liposomes.
★ Liposomes cause fewer side effects and potential immune responses.
★ Liposome wrapping: the gene to be inserted is wrapped in liposomes. This
liposome fuses with the target cell membrane and passes through. Then
deliver the DNA into the cytoplasm
★ Microinjection: introducing DNA into a cell through a very fine
micropipette.
★ This is not very efficient because many cells have to be injected before one
accepts the DNA successfully.

5
Knockout organisms: silencing genes

★ In genetic modification scientists also remove or silence a gene.

★ In knockout organisms, scientists silence one or more genes, so they no
longer function.
★ For this insert a new gene with a marker gene similar to the gene to be
investigated, but which makes the original DNA sequence impossible to read.
★ So the original gene is silenced and cannot make a protein.
★ Knockout organisms can be used to identify the function of a gene.
★ It can also be used to investigate disease and test potential treatments.

(knock out genes that are known to be non functioning in human disease to create animal models of the disease)

Why Microorganisms in Genetic modification?

★ They are relatively easy and cheap to culture.

★ They reproduce rapidly.
★ So a transferred gene is copied very rapidly when the microorganism is
allowed to replicate in ideal condition.

6
Microorganism and human insulin

★ Isolate the gene responsible for the production of insulin.

★ Cut out with Restriction Endonuclease enzyme.
★ Join DNA with plasmid and produce recombinant DNA.
★ Introduce recombinant DNA to the host cell. (bacterial cell from which
plasmid is removed)
★ Host cell with recombinant DNA inserted into a continuous stirred tank
bioreactor.

7
 ★ Insulin can be produced using mRNA isolated from the beta cells of
human pancreas.
★ Reverse transcriptase produces cDNA from this mRNA.
★ DNA polymerase changes this single stranded cDNA into double stranded
DNA.
★ Cut this with restriction enzymes to leave sticky ends.
★ Cut the isolated bacterial plasmid also with the same restriction enzyme.
★ Join the DNA with the plasmid using DNA ligase enzyme to form
recombinant plasmids.
★ Insert the recombinant plasmid into the bacterium.
★ Culture the transformed bacterium.
★ These bacteria produce human insulin

8
 GENETICALLY MODIFIED ORGANISMS (GMO)
★ Introduction of genetic material to another organism leads to the
development of transgenic organisms.It is also called Genetically Modified
Organisms.
★ Genetic engineering:-
○ modern methods of creating new combinations of genes.
○ Alteration of genes

Transgenic plants

★ It is mainly for producing edible drugs such as vaccines.

★ The vector used to insert the gene is Agrobacterium tumefaciens.
★ This bacterium causes tumors in plants.
★ Invade through wounds.
★ Ti plasmid enters the host cell nucleus.
★ Causes abnormal growth.

9
 Edible vaccine

Transgenic animals

★ A transgenic animal is one whose genome has been changed to carry genes
from other species.
★ Transgenic animals are useful as
disease models and producers of
substances for human welfare

10
Production of protein using transgenic animals

★ Isolate the desired human gene which codes for the desired protein.
★ Introduce this gene into the genetic material of a fertilized egg of a
different animal species.
★ There is also a promoter sequence which makes sure the gene will be
expressed in the mammary gland of the lactating female.
★ The fertilized egg is then replaced inside a surrogate mother.
★ It grows into a whole animal that contains a copy of the gene in every cell.
★ The protein produced from the gene is normally purified from the milk of
the animal.
★ The number of animals can be increased by breeding or cloning.
★ Large animals give large volumes of milk and therefore human proteins.

Human antithrombin (used to treat people with a blood clotting disorder) has been produced from
genetically modified goats.

Examples of drugs from transgenic animals

★ Factor VII and Factor IX-

○ Important components of the human blood clotting process.
○ Theses are harvested from transgenic milk to treat Hemophilia
★ Alpha- 1 antitrypsin- protease inhibitor.
○ The absence of this leads to emphysema as lungs become elastic

11
Risk associated with the use of GMO

Genetic pollution:-

★ Crossing GM plants with conventional plants of the same species.

★ May be transferred to wild plants.
★ Natural genome is disturbed.

Developing antibiotic resistance in microbes:-

★ Antibiotic genes are used to identify GM bacteria.

GM plants may become resistant to herbicide:-

★ herbicide-resistant crops interbreed with wild plants it could create

‘superweeds’
★ Damage food chain and environment.
★ Farmers are forced to use selective herbicides

GM plants may not produce fertile seeds:-

★ For further farming the farmers have to depend on biotechnology

companies, which is too expensive.

★ Some people are worried about the long-term impacts of using GMOs.
There may be unforeseen consequences.
★ The modified plants may be a direct hazard to humans, domestic animals or
other beneficial animals, by being toxic or producing allergies
★ Some people think it’s wrong to genetically modify animals purely for human
benefit.

12
Benefits associated with the use of GMO

★ Agricultural crops can be modified so that they give higher yields or are
more nutritious.
○ These plants can be used to reduce the risk of famine and
malnutrition.
★ Crops can also be modified to have pest resistance, so that fewer pesticides
are needed.
○ This reduces costs (making food cheaper)
○ Reduces any environmental problems associated with using
pesticides.
★ Industrial processes often use enzymes.
○ These enzymes can be produced from genetically modified organisms
in large quantities for less money, which reduces costs.
★ Some disorders can now be treated with human proteins from
genetically engineered organisms instead of with animal proteins.
○ Human proteins are safer and more effective.
★ Vaccines produced in plant tissues don’t need to be refrigerated.
○ This could make vaccines available to more people, e.g. in areas where
refrigeration (usually needed for storing vaccines) isn’t available.
★ Producing drugs using plants and animals would be very cheap because
once the plants or animals are genetically modified they can be reproduced
using conventional farming methods.
○ This could make some drugs affordable for more people, especially
those in poor countries.

13
Some GM crops that are available to farmers are resistant to herbicides
(weedkillers). Other GM crops are resistant to diseases caused by viruses and
to damage by insects. Some people are for the use of GM crops because they
may be beneficial to ecosystems. Some people are against the use of GM
crops because they could harm ecosystems.

Discuss these opinions for and against the use of GM crops.

Points in favor of GM crops:

1. less insecticide / pesticide used

2. less bioaccumulation of pesticides / less evolution of resistance to pesticides
/ no pesticide remaining in soil / eq
3. pest resistant crops do not affect non-target species / pollinators
4. weedkiller kills weeds but not (GM) crops / easier to remove weeds / eq
5. less spread of viruses to other species / crops / eq

Points against GM:

6. gene transfer to other species / (cross) pollinate with other species / eq

7. outcompete native species / affect food chains / eq
8. reduction in insect populations
9. requires herbicide use / more use of herbicides

14
Gene therapy

Replacing a defective allele with a normal one.Genotype and the phenotype of the
target cells are altered.

Somatic cell therapy

★ Isolate the normal genes coding for the normal protein .

★ Introduce the genes into the cells
★ By using a vector such as a virus or liposome.
★ Insert it into the cell by using a nebulizer or injection.
★ The normal gene is transcribed and translated to normal protein
★ The treatment needs to be repeated due to cell replacement

(OR)

Germ-line therapy

★ Repairing the gene in a fertilized egg.

★ It is inherited.
★ The repaired gene would be copied into each of the daughter cells during
mitosis.

15
 MICROARRAYS AND BIOINFORMATICS
★ Microarray is a laboratory tool that allows scientists to detect thousands of
active genes at the same time. Identifying genes for-
○ Genetic modifications
○ Gene silencing
○ Identifying mutations which cause specific diseases
○ Analyzing patterns of genes and disease in a population

Using microarrays

★ When genes are active, mRNA is produced from active genes and are
translated to protein on the ribosome.
★ If there is a mutation in the gene a different mRNA will be formed.
★ A gene contains many DNA bases and there are many places where a
mutation can take place.
★ A microarray is a tool scientists usually use to show if a DNA sample from an
individual contains any mutation.
★ These DNA samples are known as DNA chips

16
Using microarrays

★ A DNA microarray is a slide with thousands of spots.

★ Each spot is in a specific location and contains a known DNA sequence.
★ Collect mRNA samples.
★ There will be a reference sample (known gene sequence) and an
experimental sample (from individuals with a particular disease).
★ Using reverse transcriptase convert mRNA into cDNA.
★ Label the known sample with a green fluorescent and the experimental
sample with a red fluorescent.
★ Mix the labeled samples together.
★ Then applied this on the microarray slide.
★ In the microarray slide they bind to the matching DNA probes
(hybridisation).
★ After hybridization, the microarray is scanned to measure the fluorescent
light produced by the different spots.
★ If both samples are expressing genes equally, the light will appear yellow.
★ If the experimental sample is expressing more than the control, the spot will
appear red.
★ If the sample is expressing less than the control, the spot will appear green.
★ The analysis of the data provides detailed information about gene profiles,
the causes of many diseases and the effectiveness of some treatments.

17
18
Bioinformatics

★ It is the development of the software and computing tools needed to

organize and analyze raw biological data.
★ This includes the development of algorithms, mathematical models and
statistical tests which can help us interpret the enormous quantities of data
that are generated.
★ We can process and use the information generated using microarrays and
other forms of DNA analysis using bioinformatics.
★ Using this scientists can learn more about the biology of many different
organisms

Describe how microarrays and bioinformatics could be used to investigate the

genetic basis of Parkinson’s disease.

★ Microarrays allow identification of active genes

★ The activity of many genes can be analyzed in a single sample simultaneously
by collecting information about genetic differences from many individuals
with or without Parkinson’s
★ Bioinformatics /computers/databases /algorithms used to analyze the data
★ to identify the differences between healthy and Parkinson’s disease
individuals

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