GENERAL BIOLOGY MID EXAM

SUMMARY SEMESTER ONE

SESSION I : The Role of Chemistry in Biology

The Chemistry of Water

Intramolecular bond

H2O forms polar covalent bond

Covalent = bond that forms when non- metal bonds to
non- metal
Polar = there’s a big difference of electronegativity
*Electronegativity = the tendency of an atom in a bond
to attract electrons to itself.

Intermolecular bond

Hydrogen Bond

Slightly positive hydrogen molecules is attracted to

slightly negative oxygen of a nearby molecule

Due to Hydrogen Bond, water has this four properties that is vital for the Earth’s sustainability
for life :

1. Hydrogen bond = strong bond  strong adhesion & cohesion force

Cohesion = force of attraction between like substances due to mutual attraction.
Cohesive forces are associated with Van der Waals forces and hydrogen bonding
Adhesion = force of attraction between different substances
Strong cohesion bond  forming the water and dissolved nutrients into one long column
of fluid
 Strong cohesion bond  high surface tension  holds water structure when roots absorb
Strong adhesion bond  attach water to the xylem apoplast walls  provides upward force
against the gravity
Needle placed horizontally on water surface can float bcs the pressure it gave is weaker
than the surface tension.
2. Strong hydrogen bond  high specific heat
Specific heat = heat required to raise the temperature of the unit mass of a given
substance by a given amount.

High specific heat = Water absorbs a great deal of heat energy before its temperature rises
 water stabilizes Earth’s temperature by absorbing heat from warmer air and releasing
the stored heat to cooler air.

 At day, sea absorb and store huge amount of heat, meanwhile the temperature only rise a
bit
 At night, heat is released. Cooling the warm air

• Thus, the water that covers most of the earth areas keeps temperature fluctuations within
the limits that permit life.

3. Temperature lowers (heat energy decreases)  water molecule don’t have energy to
move, but still want to be intact, so it expand to its maximum structure ( crystalline
arrangement)  ice is less dense than water  floats atop water  separate and block
cool air to reach water bellows it  saves ocean organisms’ life.
4. Water = polar (hydrogen has a positive electrical charge and oxygen has a negative
charge)  heavily attracted to different molecule = wherever water goes it takes along
valuable chemical

Characteristic of Substances
According to water affinity
1. Hydrophilic – loves water
Importance in daily life: cellulose in the wall of plant help water moves up
2. Hydrophobic – hates water
Importance in daily life: lipid mainly construct cell membrane

According to pH
1. Acid = produce H+ (hydrogen ions), or H3O+ (hydronium)
2. Base = produce OH- (hydroxide ions)
Water = amphibious

 In basic solution  water act as acid  produce H3O+

 In acid solution  water act as base  produce OH-

2H₂O  H₃O⁺ + OH⁻

  Buffer in blood: carbonic acid (H2CO3) and bicarbonate anion (HCO3 -)
 When there’s acid substance (H3O+), bicarbonate ions (HCO3-) neutralize
H3O+ + HCO3-  H₂CO₃ + H2O
 When there’s basic substance (OH-)
OH- + H₂CO₃  HCO3- + H2O
Buffer = weak base/ acid + one of it’s salt  resist changes in pH

*water is a poor buffer tho, weak

Environmental Threat: Ocean acidification

Carbon: The Basis of Molecule Diversity

Molecular diversity happen due to variation in carbon skeleton (hydrocarbon and isomers)

Hydrocarbon
Hydrocarbon = consist only carbon and hydrogen
Isomers

Enantiomers
Importance of enantiomers in daily pharmaceutical life :
Example: Only S(+) ibuprofen that can block the access to the receptor side of the molecules so
that COX enzymes cannot be activated and produce prostaglandins (it promotes inflammation)
further (lock-and-key theory).

SESSION II : Biological Macromolecules and Lipid

Macromolecules = carbohydrates, protein, nucleic acid, lipid

Polymers = built by monomers linked by covalent bonds, similar in every end so can continue to
bond on either end= carbohydrates, protein, nucleic acid
Polymer formation:

And vice versa for breaking down a polymer, hydrolysis = water breakage, the bond between
monomers is broken by addition of water molecule

 Importance of polymers break down in daily life: digestion = polymers must be broken
down into monomers first by enzymes so it can be digested

Carbohydrates

Monosaccharides
Monosaccharides classification based on the location of carbonyl group: Aldose (aldehyde sugar)
or Ketose (ketone sugar).
Disaccharides
2 monosaccharides joined by a glycosidic linkage (a covalent bond formed by a dehydration
reaction)

; Maltose = glucose + glucose

; Sucrose = glucose + fructose
; Lactose = glucose + galactose

Polysaccharides
Thousand monosaccharides joined by a glycosidic linkage

Function of polysaccharides are determined by the monomers and position of glycosidic linkage

1. Storage function
a. Plant: starch = glucose + glucose linked by α
Surplus sugar stored in the form of starch, later can be withdrawn by hydrolysis
reaction. Starch have two structure : branched (e.g.: amylopectin) and unbranched
(e.g.: amylose)

b. Animal
Store in the form of glycogen (branched), mostly found in liver, and muscle cells.
When demand of sugar increases, hydrolysis in glycogen  glucose released. Usually
in human, glycogen storage depletes about a day.
2. Structural function
a. Plant: cellulose = glucose + glucose linked by β

Cellulose = major component of plant’s cell wall. Always straight/ unbranched

 Human cannot digest cellulose bcs don’t have cellulose enzyme like cow, horse,
sheep do. But cellulose fiber is still needed by the digestive system to abrades the
wall of digestive tract – keep food moving through the gut and push the waste out of
the body and also stimulates mucus production to smoothen the passage
Cellulose fibre can be found in fruits, vegies, grains
b. Animal: chitin = glucose with nitrogen appendage + glucose with nitrogen appendage
linked by β
Used by insects to build their exoskeleton

Proteins

… + … above  Amino acid  amino acid+ amino acid linked by peptide bond  polymer 
uniquely shaped, twisted, folded, coiled polymers = functional protein  precise sequence
dictate by DNA

20 types of amino acid based on the R group:

The function of protein is based on the kind and sequence of the side chain and its specific
structure

DNA dictate the primary structure

Primary structure = sequence of the amino acid

Secondary structure = coiled primary structure, varies between α and β helix based on where the
hydrogen bonds are

Tertiary structure = overall polymers (total of the secondary structure) folded bcs of the
interactions of the side chains

Queartenary structure = Association of >2 tertiary structure + non polypeptide components

The shape of a protein is critical to its function because it determines whether the protein can
interact with other molecules.

*protein can denaturate due to high temperature, pH, salt concentration, etc.  protein loses it’s
structure  unfunctional

Nucleic Acid
5 carbon sugar (pentose) + nitrogenous base  nucleoside

5 carbon sugar (pentose) (which differs between RNA and DNA)+ nitrogenous base + sugar
phosphate group (backbone) nucleotide  nucleotide + nucleotide linked by phosphodiester
linkage  polynucleotides = nucleic acid  2 types of nucleic acid : RNA (ribonucleic acids)
and DNA (deoxyribonucleic acids)

Nitrogenouse base :
Purines Pyrimidine
DNA Cytosine, Thymine
Guanine, Adenine
RNA Cytosine, Uracil
*purines = 2 rings of carbon + nitrogen atoms
*pyrimidine = 1 ring of carbon + nitrogen atom

Carbon sugar

*only differs in existence of Oxygen on the second carbon in the ring

Gene expression
DNA  RNA  Protein

1. Transcription: to make mRNA from sense (5' to 3') DNA. Happens @nucleus,
mitochondria, plastid.
a. Initiation: unwind the double helix structure because of RNA polymerase enzyme
b. Elongation: nucleotides are added to the growing RNA chain  producing mRNA
c. Termination: end of the transcription process bcs receiving stop signal from the
amino acid

mRNA is modified:
mRNA goes to ribosom

2. Translation: to produce polypeptide from mRNA

a. Initiation: rRNA and tRNA interact with mRNA
b. Elongation: rRNA unite amino acid together, and the tRNA bring anticodon to be
paired with mRNA’s codon polypeptide chain
c. Termination: come to stop codon

DNA:

Structure: Double Helix, complementary anti-parallel

The structure of DNA accounts for its function of transmitting genetic information

RNA:

Structure: Single Helix

Types :

1. mRNA
2. tRNA
3. rRNA

Lipids
Lipids is not a polymers bcs it have a unique starting molecule that is different from the subunits.
So, lipids only grow in one direction.

Lipids are hydrophobic bcs it is linked by nonpolar covalent bond

Categorized based on the fatty acid it has, lipids is divided into 3 major group:
Steroids
Do not contain fatty acid

Phospholipids (Diglyceride)
2 fatty acid + glycerol linked by esther linkage

Major constituent of cell membrane, discussed more detail in session 4

Fats (Triglyceride)
3 fatty acid + glycerol linked by esther linkage

Categorize into 2 based on the existence of double bond

 Single bond  Saturated fatty acid  saturated fat; animal fats like lard, butter. Solid at
room temp
 Double bond(s)  unsaturated fatty acid  unsaturated fat; plant and fish fats like olive
oil, cod oil. Liquid at room temp

SESSION III : CELL STRUCTURE AND FUNCTION

Types of cell
based on the cell
nucleus clarity

Prokaryotic Eukaryotic

Bacteria &
Fungi Animal Plant
Archaea

Eukaryotic have all what prokaryotic have

Prokaryotic Cell

 Cell wall & plasma membrane

 Cytosol
 Ribosom but not yet membrane bound
 Unbound chromosome (nucleoid)  no nucleus

Eukaryotic Cell
a. Animal Cell

b. Plant Cell

Plant Cell Animal Cell

Nucleus
 Contain most of the cell’s gene
Contain nucleolus and chromatin
*DNA + protein  Chromatin  when the cell prepares to divide chromatin condenses  form
discrete chromosomes
*nucleolus is the site of synthesis of ribosomal RNA (rRNA)
Enclosed by nuclear envelope: divided into inner and outer membrane that each built from lipid
bilayer
Envelope is perforated by pore structure that regulaltes the entry and exit of molecules from
nucleus
Before enclosed by envelope, nucleus is enclosed by nuclear lamina composed of protein to
maintain nucleus shape
Ribosom
Made from ribosomal RNA and protein
Function: synthesize protein
There’s free ribosom in cytosol, and bound to endoplasmic reticulum or to nuclear envelope
Endiplasmic Recituculum
Smooth ER (without ribosom) functions: Rough ER functions:
 Synthesize lipid (including steroids  Connected to nucleus envelope
(sex hormone)  Secrete glycoproteins
 Metabolizes carbohydrates  Distributes transport vesicles
 Detoxifies drugs and poisons  Membrane factory
 Stores calcium ions
Golgi Apparatus
Have ball like shape things in the end= cisternae  transport materials to transport vesicles
Synthesize lisosom

Lysosom
Sac filled with hydrolytic enzymes (lisosomal enzymes) to digest macromolecules
 Endocytosis : pinositosis (digesting small molecules), fagositosis (digesting big
molecules)
 Exocytosis
 Autophagy: programmed own organelles eating bcs it is broken, functioning poorly
 Autolysis: malfunction, when lysosome leaks out from digestive system and destroy the
cell itself
Vacuole
a. Food Vacuole: Store food
b. Contactile v. = Pump excess water out of freshwater protists cells.
c. Central v. = hold organic compound (pigment, essential oil), and water
Mitochondria
Sites of cellular respiration  produce ATP using oxygen
Inner membrane folded into cristae
Folded so it provides more mitochondrial matrix surface area for enzymes that synthesize ATP
Peroxisomes
 break down fatty acids to be used for forming membranes and as fuel for respiration
 produce catalase enzymes to break down H2O2 (toxic) into H2O + O2
 Cytoskeleton
The cytoskeleton is a network of filaments and tubules that extends throughout all of the material
in a cell except for the nucleus.
Function : supports the cell, gives it shape, organizes and tethers the organelles, and has roles in
molecule transport, cell division and cell signaling.
Components:
 Microfilament: made from actin. Function: pulling two daughter cells apart in
cytokinesis, allow cells to contract and relaxation
 Intermediate Filaments: maintain the cell’s shape, bear tension, and provide structural
support to the cell.
 Microtubules: form flagella – propel cell to move, forming the spindle apparatus
Plasma membrane
the boundary of the living cells
Cell wall Extracellular matrix
Made of cellulose fibers + other Made up of glycoproteins such as collagen,
polysaccharides + protein proteoglycans, and fibronectin
Maintain cell shape, prevents excessive water To bind to receptor proteins in the plasma
uptake membrane called integrins
Function: regulate a cell’s gene behaviour by
communicating with a cell through integrins
Chloroplast
Contains chlorophyll, thylakoids (disk), stroma
(internal fluid)

Endomembrane system: regulates protein traffic and performs metabolic functions in cells

= components that are either continuous or connected via transfer by vesicles

Cell – Cell Junction
Physical interaction between neighbouring cell

a. Plant: plasmodesmata = channel that perforates cell wall to transfer water and small
solutes (and sometimes proteins and RNA)
b. Animal
1. Gap junction = similar to plasmodesmata
2. Tight junction
Prevent extracellular fluid to enter by tightly pressing the
plasma membrane

; tight junction between skin cells make us watertight

3. Desmosome (anchoring junction)

Button- like, only attach, no transfer fluid

SESSION IV : CELLULAR MEMBRANE AND TRANSPORT

Cellular membrane: Act as the boundary that separates the living cell from its surrounding.
Regulating cell’s molecular traffic by select and control passage of substance. Selectively
permeable boundary.

Plasma membrane structure:

Majorly built by phospholipid but the ones who determines the membrane specific function is the
protein

Phospholipid = amphipathic (have both hydrophobic and hydrophilic side) hydrophilic side from
phosphate group and hydrophobic side from lipid.

Easily pass through the membrane, dissolve in the lipid bilayer: hydrophobic (nonpolar)
molecules; hydrocarbon, O2, CO2

Ions and polar molecules do not cross the membrane easily.

Formed from unsaturated fatty acid  more liquid

Formed from saturated fatty acid  more viscous

*Cholesterol act as fluidity buffer,

when cold – tails saturated/ packed  cholesterol get in the way
when hot – tails unsaturated  but cholesterol hold them together

*Peripheral protein: does not perforates through the phospholipid bilayer, only bound indirectly
by interactions with integral proteins or directly by interaction with lipid polar head

*Integral protein: perforates through phospholipid bilayer either halfway or completely through
(called transmembrane protein).

Major function of membrane protein:

1. Transport (discussed further below)

2. Enzymatic activity
With the active side to the outside solution, protein that act as enzyme receive molecules
and change it into desired product
3. Signal transduction
The external messenger (signalling molecule) may cause the protein to change shape and
allowing it to relay message to the inside cells.

4. Cell- cell recognition (the glycoprotein)

5. Intercellular joining
Forming junction (gap, tight, anchoring)

More long lasting than cell- cell recognition with

glycoprotein

6. Attachment to cytoskeleton and ECM

 Linked by non covalent bond

To maintain cell shape and stabilizes the location of

certain membrane proteins

To coordinate between intracellular and extracellular

changes.

Passive transport doesn’t require energy, following gradient

Channel mediated is simply a tunnel that allows specific molecules or ions

- Aquaporins = only allow water
- ion channel / gated channel bcs only moves in response to a stimulus

Carrier mediated = the protein change shape to translocate the molecule

Carrier mediated : ion pump = an elegtronegative pump is a transport protein that generates
voltage across a membrane. ; sodium kalsium pump in animal, proton pump in plant

Active = move solutes against the gradient, need energy (ATP)

Cotransport occurs when active transfer of a solute indirectly drives transport of other substances
Endocytosis:

1. Phagocytosis (cellular eating) = big molecule

2. Pinocytosis (cellular drinking) = liquid
3. Receptor- mediated endocytosis

SESSION V: CELL REPRODUCTION

Binary Fission
Simpler than mitosis, happen in prokaryotic.

Duplication of chromosome  nucleus cariokynesis  cytoplasm divided (cytokinesis) 

division into two daughter cells

Mitosis
 G1: The cell increases in mass in
preparation for cell division.

S: DNA synthesize (DNA replication,

primer binding, elongation,
termination, …)

G2: The cell synthesizes proteins and

continues to increase in size.

- Nuclear envelope still present

- Cell chromosome has duplicate,
but still in chromatin form.

1. Prophase: sister chromatids formed, nuclear envelope disappear, spindle formed

begin to move apart
2. Prometaphase: microtubule attach at kinetochore, pulling it away. other non
kinetochore microtubule pushing against each other to elongate the cell.
*kinetochore: protein compexes associated with centromers.
3. Metaphase: chromosomes at equator line
 4. Anaphase: sister chromatids parted to opposite ends, the cell elongate as the
nonkinetochor microtubule lengthen.
5. Telophase: 2 daughter nuclei form in the cells, nuclear envelopes start to form,
chromosome less condensed, spindle microtubules depolymerised from the end with
kinetochore with it
6. Cytokinesis : division of cytoplasm. In animal cell, by forming a cleavage furrow. In
plant cell by forming a cell wall plate in the middle between nucleus a and b

Regulation of karyotic cell cycle

The frequency of cell division varies with the type of cell; skin cells and liver cells differ

Cancer cell manage to escape the usual controls on the cell cycle

Molecules in cytoplasm is suspected to drive cell reproduction

Regulatory protein : Cyclin, + cyclin- dependent kinases (Cdks)  MPF (maturation promoting
factor)
Factors that determines growth:

1. Internal
; Cells will not begin anaphase until all chromosomes are properly attached to the spindle
at the equator line, to assures that daughter cells will have correct number of
chromosomes.
2. Outside: Chemical
Addition of stimulate makes cells divide
3. Outside: Physical
Most cell exhibit anchorafe dependence to divide (they must be attached to a substratum)

Meiosis
Human have 23 pairs of chromosomes (22 pairs autosom, 1 pair gonosom), each pair are called
homologous chromosomes. Each pair are the same length, shape, and carry genes controlling the
same inherited characters

In DNA synthesize  each chromosome is replicated  two identical sister chromatids

Sister chromatids are used in cell division, like in cell replacement, whereas homologous
chromosomes are used in reproductive division, like making a new person. Sister chromatids
are genetically the same. That is, they are identical copies of one another specifically created for
cell division. Homologs are not identical though each carries the same genes in the same order,
but the alleles for each trait may not be the same.
Sex chromosomes determine gender of individual, called x and y. Female  homologous pair of
X chromosomes (XX), male XY. Remaining 22 pairs are called autosomes
Meiosis 2 similar to mitosis
Genetic variation occurs due to:

1. Independent assortment of chromosomes

2n, n= 23, 2n = 8,388,608 chromosomes combination possibility
2. Crossing over
In humans, an average of one to three crossover events occurs per chromosome
3. Random fertilization
One ovum fertilized with many sperms that carry also 8 million possibilities, produces a
zygote with 8million2 = 70 trillion diploid combinations