Biochemistry

1st semester | Lectures & PPT | Doc DG

LECTURE 1 - CARBOHYDRATES
- Few hundred units to 50,000 units
Carbohydrates  Storage: starch, glycogen
 Most abundant class of bioorganic molecules on earth  Structure: cellulose, chitin (shells),
 2% of the human body fibers
 Acidic (commonly inside the
 Also known as “CHO”
body): hyaluronic, hemparin
 Plants produce carbohydrates through photosynthesis
o Plants release & get carbon, water, and solar
Classification of Monosaccharides
energy
 A polyhydroxy aldehyde or polyhydroxy ketone; a
compound that yields these two upon hydrolysis

Functions:

 CHO oxidation provides energy

 CHO storage (glycogen) provides a short-term Classification According to Functional Group
energy reserve
 CHO supplies carbon atoms for the synthesis of
(PLN)
 CHO forms part of the structural framework of DNA
and RNA
 CHO are structural components of cell membranes
 CHO functions in a variety of cell-cell, and cell-
molecule recognition processes.

Classification Based on Molecular Size

o Monosaccharide
- single PHA (polyhydroxy aldose) or PHK
(polyhydroxy ketose)
- Simplest group of carbohydrates
 e.g glucose, fructose, galactose
o Disaccharide
- 2 monosaccharide units bonded together
- Often added as sweeteners
 e.g sucrose, lactus, maltose,
cellobiose Aldoses: sugars with aldehyde functional group on carbon #1
o Oligosaccharide (glucose, galactose, ribose, glyceraldehyde)
- 3-10 monosaccharide units bonded together
Ketoses: sugars with ketone functional group on carbon #2
(glycosidic linkage = covalent linkage
(fructose)
between sugar molecules)

Biochemically Important Monosaccharides

 e.g trisaccharide raffinose, o Glyceraldehyde and Dihydroxy acetone
tetrasaccharide stachyose, o Glucose
pentasaccharides o Galactose
o Polysaccharide o Fructose

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o Ribose » general empirical structure for carbohydrates is

(CH2O)n
Dietary Conditions » building blocks of all carbohydrates are simple sugars
 Simple Carbs called monosaccharides
- Refined: processed foods, unhealthy
» The carbohydrates can be structurally represented in
 Most micronutrients/fibers are
removed any of the three forms:
- Natural: not processed, healthy o Open chain structure
 With micronutrients/fibers  long straight-chain
o Hemi-acetal structure
 Complex Carbs
- Hardest to breakdown sugar  1st carbon of the glucose condenses
with the -OH group of the 5th
- Very healthy, causing the most balanced
carbon to form a ring structure.
blood sugar amount of all the carbs
o Haworth structure
 Net Carbs
 it is the presence of the pyranose
- Total carbs – fibers = Net carbs
ring structure
- All carbs except fiber
Properties of Carbohydrates
 Physical Properties
o Stereoisomerism: compound shaving the
same structural formula but differ in spatial
configuration.
 Example: Glucose has two isomers
with respect to the penultimate
carbon atom. They are D-glucose
and L-glucose.

o Optical Activity: s the rotation of plane-

polarized light forming (+) glucose and (-)
glucose.

o Diastereo isomers: the configurational

changes with regard to C2, C3, or C4 in
Reactions of Monosaccharides glucose
o Oxidation to produce acidic sugars  Example: Mannose, galactose
o Reduction to produce sugar alcohols
o Glycoside Formation o Annomerism: the spatial configuration with
o Phosphate Ester Formation respect to the first carbon atom in aldoses
o Amino Sugar Formation and the second carbon atom in ketoses.

 Chemical Properties
o Osazone formation: carbohydrate
Notes: derivatives when sugars are reacted with an
excess of phenylhydrazine
 A minimum number of carbon in a  eg. Glucosazone
monosaccharide is 3 o Benedict’s test: Reducing sugars when
 CHO = Carbon, Hydrogen, Oxygen heated in the presence of an alkali get
converted to powerful reducing species
known as enediols. When Benedict’s reagent
solution and reducing sugars are heated
From Doc DG’s Notes together, the solution changes its color to
orange-red/ brick red.
» carbohydrates are a group of naturally occurring
carbonyl compounds (aldehydes or ketones)
o Oxidation: Monosaccharides are reducing
» carbohydrates that are soluble in water and sweet in sugars if their carbonyl groups oxidize to
taste are called “sugars” give carboxylic acids. In Benedict’s test, D-

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glucose is oxidized to D-gluconic acid thus, Some of their major functions include:
glucose is considered a reducing sugar.
 accessible energy to fuel cellular reactions: they are
o Reduction to alcohols: the C=O groups in the most abundant dietary source of energy
open-chain forms of carbohydrates can be (4kcal/gram) for all living beings.
reduced to alcohols by sodium borohydride,  chief energy source/ instant sources of energy:
NaBH4, or catalytichydrogenation (H2, Ni, glucose is broken down by glycolysis/ Kreb’s cycle
EtOH/H2O). The products are known as to yield ATP.
“alditols  It is stored as glycogen in animals and starch in
plants.
 Properties of Monosaccharides  Stored carbohydrates act as an energy source instead
 Most monosaccharides have a sweet taste of proteins
(fructose is sweetest; 73% sweeter than  form structural and protective components, like in
sucrose). the cell wall of plants and microorganisms.
 They are solids at room temperature.  intermediates in the biosynthesis of fats and proteins.
 They are extremely soluble in water: –  aid in the regulation of nerve tissue and is the energy
Despite their high molecular weights, the source for the brain
presence of large numbers of OH groups  get associated with lipids and proteins to form
makes the monosaccharides much more surface antigens, receptor molecules, vitamins, and
water-soluble than most molecules of antibiotics.
similar MW.  Formation of the structural framework of RNA and
 Glucose can dissolve in minute amounts of DNA
water to make a syrup (1 g / 1 ml H2O)  linked to many proteins and lipids important in cell-
cell communication and interactions in the cellular
Classification of Carbohydrates environment
o Monosaccharide  In animals, they are an important constituent of
 often called simple sugar (cannot hydrolyze) connective tissues
 colorless, crystalline solid  Carbohydrates that are rich in fiber content help to
 soluble in water and insoluble in a non-polar prevent constipation. Also, they help in the
solvent modulation of the immune system.
 the general formula is Cn(H2O)n or
CnH2nOn
 classified according to the number of carbon
atoms present

o Oligosaccharides
 The general formula of disaccharides is
Cn(H2O)n-1 and that of trisaccharides is
Cn(H2O)n-2 and so on.

o Polysaccharides
 also called “glycans”
 they are primarily concerned with two
important functions: Structural functions and
the storage of energy

Functions
 Carbohydrates are widely distributed molecules in
plant and animal tissues
 In plants and arthropods, carbohydrates form the
skeletal structures,
 food reserves in plants and animals.
 They are an important energy source required for
various metabolic activities, the energy is derived by
oxidation.

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LECTURE 2 - LIPIDS
Chemical Reactions of Triacylglycerols
Lipids
 Diverse group of organic compounds: fats, oils,
hormones, & membrane components
 Does not appreciably interact with water Hydrolysis Water
 Insoluble in water >Hydrogenation Additional H atom
 Soluble in a nonpolar organic solvent >Oxidation Releases Oxygen
Fatty Acids transform to a
Saponification
Classification Based on Biochemical Function soap-like form
» Based on characteristics o Membrane Lipids
o Energy Storage Lipids - Structural component
- Lipids stored for use when energy demand is - Mainly consists of Lipids, Carbohydrates, &
high Protein
 Triacylglycerols/ Triglyceride - Barrier to the passage of polar molecules
(glycerol & fatty acids) and ions
 Fats = solid or semi-solid at - Membranes are 2 layers of thick sheath-like
room temp. (from animals) structures
 Oils= liquid at room temp. - Formed by a non-covalent assemblage of
(from plants) lipids and proteins
 Pure fats =odorless, colorless,
& tasteless 3 Major Types of Membrane Lipids:

 Phospholipids
- Glycerophospholipids: 2 F.A & 1 P.G
 Lecithins
 Cephalins
- Sphingophospholipids: 1 F.A & 1 P.G
attached to sphingosine molecule
 Sphingomyelins
 Sphingoglycolipids
 Cholesterol
Dietary Considerations and Triacylglycerols

DIETARY CONSIDERATIONS Transport Across Cell Membranes

BAD FAT GOOD FAT » Passive Transport
- Automatic
- No energy needed
DIETARY CONSIDERATIONS
OMEGA 3 OMEGA 6 - From high to low concentration
 Diffusion
» Active Transport
DIETARY CONSIDERATIONS
ESSENTIAL FATTY ACIDS FAT SUBSTITUTES
- Uses energy to allow protein bonds
- ATP = Adenosine Triphosphate
» Fat Substitutes/ Artificial Fats: - Lower to higher concentration
- Not natural, yet better to consume. » Facilitated Transport
- Low in calories & fats, because it is not a - Use protein to enter
lipid - Protein = facilitate molecule
» 2 Essential Fatty Acids
- Linoleic & Linolenic
- Needed in the human body obtained from
o Emulsification Lipids
dietary sources
- Can’t be synthesized within the body - Stabilize and disperse water-insoluble
» Omega 3 is better than Omega 6 materials in an aqueous solution
- Lipid emulsifying agent:

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 Bile Acids – break down fats & oils; excrete - Contain ester that can undergo hydrolysis =
through digestive tracks bubbles =to breakdown to smaller units
 e.g Cholic Acid & Deoxycholic Acid
 Bile – secreted by the liver, stored in the
gallbladder, & released into the small
intestine during digestion

o Messenger Lipids
 Regulatory lipids that act in the tissue where they
are synthesized or at other locations after transport
via the bloodstream
 Hormones are biochemical substances
produced by a ductless gland that has a
messenger function
 Steroid Hormones
 From glands & Cholesterol
 Sex Hormones: secondary sex
characteristics
 Estrogen
 Androgen
 Progestins
 Adrenocorticoids: regulate biochemical
processes
 Mineralocorticoids
 Glucocorticoids

 Eicosanoids
MEDIATION OF THE  Triglycerides
FOLLOWING  Waxes
 Sphingolipids & Phospholipids
- The inflammatory response
- The production of pain and
fever
- The regulation of BP
- The induction of blood clotting
- The control of reproductive
functions
- The regulation of sleep/wake
pattern
 Prostaglandins
 Thromboxanes
 Leukotrienes

Name Fatty Acids of Biological Importance

o Protective Coating Lipids
 Water-insoluble, water-repellent lipids with o Structural Notation:
protective-coating and lubricant functions o Common Name: given name by scientists
 Biological Waxes o Structure:

Classification Based on Saponifiability Notes:

o Saponifiable
- Ability to create soap

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depending upon the alcohol group present

(glycerol or sphingosine)

» Derived Lipids
 Hydrolysis product of simple and compound
lipids
Physical Properties of Fatty Acids
 Include fatty acid, glycerol, sphingosine and
» Water-solubility steroid derivatives
» Melting Point  Steroid derivatives are phenanthrene
- structures that are quite different from lipids
made up of fatty acids

o Non-saponifiable Functions
- Does not have an ester o role in the structure of cell membrane and organellar
- Cannot be hydrolyzed membranes
 Steroids & Prostaglandins o important roles in the normal functions of a cell
 Cholesterol, Bile acid, & Eicosanoids o Energy Storage
o Making Biological Membranes
o Insulation
From Doc DG’s Notes o Protection e.g protecting plant leaves from drying up
Lipids o Buoyancy
o Acting as hormones
 They are energy-rich organic molecule
 Soluble in organic solvents like alcohol, chloroform, o Provides the hydrophobic barrier that permits
acetone, benzene partitioning of the aqueous contents of the cell and
 Made of the elements Carbon, Hydrogen, and subcellular structures.
Oxygen, but have a much lower proportion of water o Lipids are major sources of energy in animals and
than other molecules such as carbohydrates. high lipid-containing seeds
 Lipids are not polymers—they lack a repeating o Activators of enzymes eg. glucose-6-phosphatase,
monomeric unit stearyl CoA desaturase and ω-monooxygenase, and
 They are made from two molecules: Glycerol and β-hydroxybutyric dehydrogenase (a mitochondrial
Fatty Acids. enzyme) require phosphatidylcholine micelles for
 Fatty acids consist of an acid group at one end of the activation
molecule and a hydrocarbon chain, which is usually
denoted by the letter ‘R’.
LECTURE 3 - PROTEINS

Classification/ Types of Lipids Proteins

» Simple Lipids  Most abundant biological macromolecules/ substance
 Fats and oils which yield fatty acids and in nearly all cells, next to the water
glycerol upon hydrolysis  15% of a cell’s overall mass
 Waxes, which yield fatty acids and long-  Half of the cells’ dry mass
chain alcohols upon hydrolysis.  Composed of C, H, O, N, & most S
 Part of our food intake
» Complex Lipids  There are good proteins and not-so-good protein
 Phospholipids, which yield fatty acids,  High protein = weight loss (e.g tofu, corn, cashew
glycerol, amino alcohol sphingosine, nuts, mung beans)
phosphoric acid, and nitrogen-containing
 Naturally occurring & branch of polymer which
alcohol upon hydrolysis. They may be
monomer units are amino acids
glycerophospholipids or
 Primary protein structure = sequence of Amino Acid
sphingophospholipid depending upon the
Chain
alcohol group present (glycerol or
sphingosine)  Most versatile organic molecule; diff sizes, form
 Glycolipids, which yield fatty acids, small peptides to large polymers
sphingosine or glycerol, and a carbohydrate  Covalently linked by peptide bonds
upon hydrolysis. They may also be
glyceroglycolipids or sphingoglycolipid

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 20 essential amino acids = building blocks of Protein Non-Polar 1 amino group Glycine
(H2N) Alanine
1 carboxyl g. Valine
(COOH) Leucine
Non-polar side Isoleucine
chain Proline
> hydrophobic Phenylalanine
when Methionine
incorporated to Tryptophan
 Three components: Amino G., Carboxyl G., R group some proteins
 Polar Neutral 1 amino group Serine
1 carboxyl g. Cysteine
1 polar-neutral Threonine
side chain Asparagine
> neither acidic Glutamine
nor basic Tyrosine

Polar Acidic 1 amino group Aspartic Acid

2 carboxyl g. Glutamic Acid
1 c.g attached to
side chain bearing
(-) charge
> lost its acidic
hydrogen atom
Polar Basic 2 amino group Histidine
1 carboxyl g. Lysine
Amino Acids = amino group + acid group 1 a.g attached to Arginine
side chain bearing
 700 naturally occurring P, only 20 standard A.A.
(+) charge
> also have
accepted proton,
One letter Three letter Amino Acid
nitrogen atom; a
code code
basic behavior
A Ala Alanine
R Arg Arginine
Essential Amino Acids
D Asp Aspartic Acid
» Needed in protein synthesis
N Asn Asparagine
» Obtained by dietary sources
C Cys Cysteine
» Body cannot synthesize an adequate amount
E Glu Glutamic Acid
» 9 for adults; 1 for child growth
Q Gln Glutamine
G Gly Glycine
Histidine Phenylalanine
H His Histidine
Isoleucine Threonine
I Ile Isoleucine Leucine Tryptophan
L Leu Leucine Lysine Valine
K Lys Lysine Methionine Arginine
M Met Methionine
F Phe Phenylalanine Dietary Proteins
P Pro Proline Complete Dietary Contains all the essential amino acids
S Ser Serine Proteins in the same relative amount the body
T Thr Threonine needs
W Trp Tryptophan
Y Tyr Tyrosine It may or may not contain all the
V Val Valine non-essential AA
Incomplete Does not contain an adequate amount
Four Categories of Standard Amino Acids Dietary Proteins of 1 or more essential A.A
Catergory Definition Examples Limiting Amino The missing in IDP

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Acids  All proteins contain the elements carbon, hydrogen,

Missing essential A.A, present in an oxygen, nitrogen and sulfur some of these may also
inadequate amount contain phosphorus, iodine, and traces of metals like
Complementary Joint A.A to complete dietary ion, copper, zinc and manganese.
Dietary Proteins proteins  A protein may contain 20 different kinds of amino
acids. Each amino acid has an amine group at one
2/ more IDP combined to provide an end and an acid group at the other and a distinctive
adequate amount of all essential A.A side chain.
 The backbone is the same for all amino acids while
General Structural Characteristics of Proteins the side chain differs from one amino acid to the
» Peptide Chain next.
- Protein = peptide chain in which at least 40
amino acid residues are present Primary Protein A sequence of a
- Monomeric: only 1 peptide chain Structure chain of amino acids
- Multimeric: more than 1 peptide chain
- Nature of the peptide bond = pentapeptide determines the
- Peptide bonds = link A. A together in the further levels of
peptide chain organization of
- Oligopeptide = 10-20 protein molecules.
- Polypeptide = 100 and up
» Chemical Composition Secondary Protein Local folding of the Alpha Helix
Structure polypeptide chain - coiled (1 strand)
- Simple: only amino acids are present
into helices/sheets
- Complex: have non-amino acid entities
 Conjugated – 1/more non-A. A present
Formed by regular
in addition to 1/more peptide chain
repeated patterns of Beta Pleated Sheet
 Prosthetics – non-A. A present to the
H-bond formation (B-helix)
conjugated group
between backbone - right-handed coiled
atoms (2) strand
Types of Conjugated Proteins:
o Hemoproteins = heme unit - H-bonding is
 Hemoglobin: carrier of O2 in blood between strands
 Myoglobin: oxygen binder in muscles (inter-strand)
o Lipoproteins = lipid
 LDL & HDL: lipid carrier Intra-strand = within
o Glycoproteins = carbohydrates
 Gamma globulin: antibody
 Mucin: lubricant in mucous secretions
 Interferon: antiviral protection Tertiary Protein The 3D folding
o Phosphoproteins = phosphate group Structure pattern of a protein
 Glycogen phosphorylase: enzyme in due to side chain
glycogen phosphorylation interactions
o Nucleoproteins = nucleic acid Produced by
 Ribosomes: site for protein synthesis interactions between
in cells A. A residues
 Viruses: self-replicating; infectious Quarternary A Protein consisting
complex Protein Structure of more than one
o Metalloproteins = metal ion amino acid chain
 Iron-ferritin: storage complex for iron
Protein Denaturation
o Breaking down proteins in extreme conditions
Protein Structure o Structure determines the function of proteins
 The linear sequence of amino acid residues in a o Amount of heat determined motion
polypeptide chain determines the three-dimensional o Open a whole new chain for bonding
configuration of a protein
 The structure of a protein determines its function. Classification of Proteins

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» Based on Structure Messenger proteins:

- Fibrous Proteins (insoluble): strand insulin & glucagon,
 Keratin – found in wool, feathers, hormones, Human
fingernails, hooves, silk growth hormone
 Collagens – tendons, bones, Contractile For all forms of
connective tissues movement
 Elastins -found in blood vessels &
ligaments
Actin & Myosin
 Myosins – found in muscle tissues
Structural Confer stiffness and
 Fibrin -found in blood clots
rigidity
- Globular Proteins (soluble): circle
 Insulin - controls glucose metabolism Collagen & Keratin
 Myoglobin – involved in oxygen Transmembrane Controls in & out of
storage in muscles molecules and ions in
 Hemoglobin – involved in oxygen the cell
transport in blood
 Transferrin – involved in iron transport
in blood Storage Bind and store small
 Immunoglobulins – involved in molecules for future
immune system responses use

» Based on Composition Ferritin - iron storage

- Simple Proteins: fibrous & globular Myoglobin
- Conjugated Proteins: combined with non- Regulatory On& off switch
protein moiety
- Derived proteins: degraded product of Regulates biochemical
simple and conjugated processes
 Primary
 secondary
Nutrient Nutrition in protein

» Based on Function Casein in milk

Ovalbumin in egg
Catalytic Proteins Acts as catalysts
white
Called as “enzymes”
Buffer Controls acid-base
Metabolic reactions
balance in body fluid
Defense “immunoglobulin or
antibodies”
Hemoglobin
Transmembrane
Bind to foreign
Fluid-balance Helps maintain the
substances to help
fluid balance between
combat invasion on the
blood and surrounding
body
tissue
Central to the immune
Found in capillary beds
system function
of the circulatory
Transport Carries/ binds with
system:
other molecules to
transport
Albumin
Messenger Transmit signals to Globulin
coordinate biochemical
processes between diff
From Doc DG’s Notes
cells, tissues, organs

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Roles of the Essential Amino Acids - also important for energy production,
immune function, and the production of
o Phenylalanine collagen and elastin
- a precursor for the neurotransmitters o Histidine
tyrosine, dopamine, epinephrine, and - used to produce histamine, a
norepinephrine. neurotransmitter that is vital to immune
- plays an integral role in the structure and response, digestion, sexual function, and
function of proteins and enzymes and the sleep-wake cycles.
production of other amino acids - critical for maintaining the myelin sheath, a
o Valine protective barrier that surrounds your nerve
- one of three branched-chain amino acids, cell
meaning it has a chain branching off to one
side of its molecular structure. Protein Structure and Functions
- helps stimulate muscle growth and
regeneration and is involved in energy Proteins
production  most versatile macromolecules in living systems and
o Threonine serve crucial functions in essentially all biological
- a principal part of structural proteins such processes.
as collagen and elastin, which are important  They function as catalysts, transport and store other
components of the skin and connective molecules such as oxygen, provide mechanical
tissue. support and immune protection, generate movement,
- plays a role in fat metabolism and immune transmit nerve impulses, and control growth and
function differentiation.
o Tryptophan
Several key properties enable proteins to participate in
- often associated with causing drowsiness
such a wide range of functions:
- needed to maintain proper nitrogen balance
and is a precursor to serotonin, a 1. Proteins are linear polymers built of monomer units
neurotransmitter that regulates your appetite, called amino acids. The construction of a vast array of
sleep and mood macromolecules from a limited number of monomer building
o Methionine blocks is a recurring theme in biochemistry. Does protein
- plays an important role in metabolism and function depend on the linear sequence of amino acids? The
detoxification function of a protein is directly dependent on its three-
- also necessary for tissue growth and the dimensional structure. Remarkably, proteins spontaneously
absorption of zinc and selenium, minerals fold up into three-dimensional structures that are determined
that are vital to your health by the sequence of amino acids in the protein polymer. Thus,
o Leucine proteins are the embodiment of the transition from the one-
- Like valine, leucine is a branched-chain dimensional world of sequences to the three-dimensional
amino acid that is critical for protein world of molecules capable of diverse activities.
synthesis and muscle repair
- It also helps regulate blood sugar levels, 2. Proteins contain a wide range of functional groups.
stimulates wound healing, and produces These functional groups include alcohols, thiols, thioethers,
growth hormones carboxylic acids, carboxamides, and a variety of basic groups.
o Isoleucine When combined in various sequences, this array of functional
- The last of the three branched-chain amino groups accounts for the broad spectrum of protein function.
acids, isoleucine is involved in muscle For instance, the chemical reactivity associated with these
metabolism and is heavily concentrated in groups is essential to the function of enzymes, the proteins that
muscle tissue. catalyze specific chemical reactions in biological systems.
- also important for immune function,
hemoglobin production, and energy 3. Proteins can interact with one another and with other
regulation biological macromolecules to form complex assemblies.
o Lysine The proteins within these assemblies can act synergistically to
- plays major roles in protein synthesis, generate capabilities not afforded by the individual component
hormone and enzyme production, and the proteins. These assemblies include macro- molecular
absorption of calcium machines that carry out the accurate replication of DNA, the

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transmission of signals within cells, and many other essential

processes.

4. Some proteins are quite rigid, whereas others display

limited flexibility. Rigid units can function as structural
elements in the cytoskeleton (the internal scaffolding within
cells) or in connective tissue. Parts of proteins with limited
flexibility may act as hinges, springs, and levers that are
crucial to protein function, to the assembly of proteins with
one another and with other molecules into complex units, and
to the transmission of information within and between cells

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LECTURE 4 – ENZYMES & VITAMINS

Enzymes 2 types of Enzyme Action Models

 Is a compound, usually a protein that acts as a o Lock-Key Model
catalyst for the biochemical reaction. - NO ADJUSTMENTS
- Catalyst = increases the speed of reactions - “One key for a particular part”
 Without enzymes, biochemical reactions cannot - Substrate with the matching shape can fit
proceed - A particular substrate to a particular enzyme
 Most enzymes are globular proteins (spherical)
 Undergo all reactions of proteins (Denaturation) o Induced-Fit Model
 Increases reaction through structure due to physical - CAN ADJUST
interaction - Active sites have flexible shapes to accept a
 The chemical reactions that keep us alive – our variety of related substrates
metabolism – rely on the work that enzymes carry - Change the shape of the active site for the
out. substrate to fit an enzyme, forming an enzyme-
substrate complex
Enzyme Structures:
 Simple – only composed of protein (Apoenzyme) Enzyme Specificity
 Conjugated – nonprotein part (Cofactor)  Absolute Specificity
 Holoenzyme – apoenzyme with cofactors - One enzyme to catalyze a specific reaction

• A cofactor may be either a coenzyme—an organic  Group Specificity

molecule, such as a vitamin—or an inorganic metal - Only acts on a specific functional group
ion; some enzymes require both. - Ex. Hydroxyl G. and Amino G.
• A cofactor may be either tightly or loosely bound to
the enzyme. If tightly connected, the cofactor is  Linkage Specificity
referred to as a prosthetic group - Acts only on specific bonds (Ex. Phosphate
Ester bond)
6 Classes Based on the Type of Reaction they Catalyze
 Stereochemical Specificity
- Acts only on a specific stereoisomer

Factors Affecting the Rate of Enzyme Activity

o Temperature
-  temp =  rate
- Until reached the optimum temp (37) then
slowly goes down
- If reached higher than 37= denaturation
o pH
-  pH = faster reaction rate
- Until reached the optimum pH(7-7.5pH) then
slowly goes down

o Concentration of Substrate
Models of Enzyme Action -  substrate concentration =  reaction rate
 Enzymes Active Site - Until reached the max reaction rate then
- An enzyme’s Region where substrate molecules maintained
bind and undergo a chemical reaction
o Concentration of Enzyme
-  enzyme concentration =  reaction rate
- Continuously rising

 Enzymes-Substrate Complex
- The formation formed when an enzyme binds
with the substrate

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 Extremophile = a microorganism, especially an Archaean, • Lipases – a group of enzymes that help digest fats in the
that lives in conditions of extreme temperature, acidity, gut.
alkalinity, or chemical concentration. • Amylase – helps change starches into sugars. Amylase is
 Extremozyme = an enzyme, often created by archaea, found in saliva.
which are known prokaryotic extremophiles that can
function under extreme environments. • Maltase – also found in saliva; breaks the sugar maltose
Enzyme Inhibition
- Substances that bind to an enzyme and stop/slow normal
catalytic activity

o Competitive Enzyme Inhibitor

 Binds to active site; temporarily blocks
reaction and substrates from occupying
 Ex. Statin

o Non-Competitive Enzyme Inhibitor

 Rival; a molecule binds together with the
substrates in active sites and one on the non-
active site
 Ex. Cyanide

o Irreversible Enzyme Inhibitor

 Changes the shape of the active site via a into glucose. Maltose is found in foods such as potatoes,
covalent bond pasta, and beer.
 Permanently prevent substrates from • Trypsin – found in the small intestine, breaks proteins
occupying down into amino acids.

Drugs that Inhibit Enzyme Activity • Lactase – also found in the small intestine, breaks lactose,
» Ace Inhibitors the sugar in milk, into glucose and galactose.

• Acetylcholinesterase – breaks down the neurotransmitter

Angiotensin-converting-enzyme inhibitors are a class acetylcholine in nerves and muscles.
of medication used primarily for the treatment of
high blood pressure and heart failure. They work by • Helicase – unravels DNA.
causing the relaxation of blood vessels as well as a
• DNA polymerase – synthesize DNA from
decrease in blood volume, which leads to lower blood
deoxyribonucleotides.
pressure and decreased oxygen demand from the
heart.

» Sulfa Drugs

Sulfonamides, or "sulfa drugs," are a group of

medicines used to treat bacterial infections.

» Penicillins

A group of antibiotics originally obtained from

Penicillium moulds, principally derived from fungi.
(P. chrysogenum and P. rubens)

Medical Uses of Enzymes

EXAMPLES OF SPECIFIC ENZYMES

There are thousands of enzymes in the human body, here are
just a few examples:

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Vitamins
 An organic compound included in the enzyme
structures
 Enzymes need vitamins to perform catalytic
functions
 Obtained from dietary sources

2 Major Classes

» Fat Soluble = A, D, E, K
» Water Soluble = B complex & C

Absorption

Transport

Storage

Excretion

Tonicity

Requirements

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LECTURE 5 – NUCLEIC ACID
- DNA, mRNA, tRNA are made up of chains of base pairs
Nucleic Acid of nucleic acids stretching from as few as three to
 Building blocks of living organisms millions
 Naturally occurring chemical compound that is - When those pairs combine in super long chains (DNA),
capable of being broken down to yield they make a shape called a double helix..
» phosphoric acid - RNA is the genetic material of certain viruses, but it is
» sugars also found in all living cells, where it plays an important
role in certain processes such as the making of proteins.
» mixture of organic bases (purines and
pyrimidines)
Nucleotides
 Nucleic acids determine the inherited characteristics
of every living thing.
o Building blocks of Nucleic Acids
 Composed of monomer nucleotides connected like
o Nucleic acids are polynucleotides
links in a chain to form nucleic acid polymers
» long chainlike molecules composed of a series
 Nucleotides consist of a nucleoside (the combination
of a pentose monosaccharide molecule and a of nearly identical building blocks called
nitrogenous base) and a phosphate group. nucleotides.
» Nucleoside = without an attached phosphate
group, the sugar attached to one of the bases
2 Types of Nucleic Acid:
(Pentose + Nitrogenous Grp.; adenine)
 Deoxyribonucleic Acid (DNA)
» Each Nucleotide consists of a nitrogen-
- Master blueprint for life
containing aromatic base attached to a pentose
 Ribonucleic Acid (RNA)
(five-carbon) sugar, which is in turn attached
- Both play a central role in every function of every living
to a phosphate group.
organism.
- The difference between RNA and DNA lies in a single o Sugar Phosphate Backbone = forming strands
nitrogenous base and a single atom of oxygen within a sugar o DNA & RNA are combination of pairs of N.A
molecule o
Four of five possible nitrogen-containing bases:

 adenine (A)
 guanine (G)
 cytosine (C)
 thymine (T)
 uracil (U)

- Adenine (A) & Thymine (T)  have 2 H. Bonds

- Guanine (G) & Cytosine (C) have 7 H. bonds

- A & G are categorized as purines

- C,T, & U are pyrimidines

Deoxyribonucleic Acid

• DNA is a polymer of the four nucleotides A, C, G,

and T; joined through a backbone of alternating
phosphate and deoxyribose sugar residues.
• The spans of A:T and G:C hydrogen-bonded pairs are
nearly identical, allowing them to bridge the sugar-
phosphate chains uniformly.
• This structure, along with the molecule’s chemical
stability, makes DNA the ideal genetic material.
• The bonding between complementary bases also
provides a mechanism for the replication of DNA and
the transmission of genetic information.

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radiation, or the action of chemical

DNA Chemical Structure carcinogens.
o James D. Watsons and Francis H.C. Crick (1953) - DNA can also be cleaved and degraded by
proposed a 3-d structure for DNA on low- enzymes called nucleases.
resolution X-ray crystallographic data
 Methylation
o Erwin Chargaff’s observation - Special enzymes called DNA
- naturally occurring DNA, the amount of T methyltransferases are responsible for this
equals the amount of A and the amount of methylation; they recognize specific
G equals the amount of C. sequences within the DNA molecule so
that only a subset of the bases is modified.
o Watson and Crick, postulated that two strands of
polynucleotides coil around each other, forming a  Nucleases
double helix. - Enzymes that hydrolytically cleave the
phosphodiester backbone of DNA.
o The two strands, though identical, running - Endonucleases cleave in the middle of
opposite directions as determined by the chains, while exonucleases operate
orientation of the 5′ to 3′ phosphodiester bond. selectively by degrading from the end of
the chain
DNA Biological Structure
 Mutation
• Naturally occurring DNA molecules can be circular - Anions such as bisulfite can deaminate
or linear. cytosine to form uracil, changing the genetic
• The genomes of single-celled bacteria and archaea message by causing C-to-T transitions.
(the prokaryotes), as well as the genomes of - Exposure to acid causes the loss of purine
mitochondria and chloroplasts (certain functional residues, though specific enzymes exist in
structures within the cell), are circular molecules. cells to repair these lesions.
• In addition, some bacteria and archaea have smaller - Exposure to UV light can cause a variety of
circular DNA molecules called plasmids that lesions that are mutagenic if not repaired.
typically contain only a few genes. - Halogens such as chlorine and bromine are
• In all cells, DNA does not exist free in solution but often mutagenic.
rather as a protein-coated complex called chromatin. - Similarly, nitrous acid which then leads to
• In prokaryotes, the loose coat of proteins on the DNA changes in base pairing and mutation.
helps to shield the negative charge of the
phosphodiester backbone.
• Chromatin also contains proteins that control gene
expression and determine the characteristic shapes of
chromosomes.  Super Coiling
- is partially responsible for the great
compaction of DNA that is necessary to fit it
Biochemical Properties within the confines of the cell.
 Denaturation (heating) - The DNA in one human cell would have an
- Heating DNA in solution easily breaks extended length of between two and three
these hydrogen bonds, allowing the two meters, but it is packed very tightly so that it
strands to separate can fit within a human cell nucleus that is 10
 Renaturation (hybridization/annealing) micrometers in diameter.
- The two strands may re-associate when the
solution cools, reforming the starting DNA  Sequence Determination
duplex - Methods to determine the sequences of
bases in DNA were pioneered in the 1970s
 Chemical Modification by Frederick Sanger and Walter Gilbert,
- After a DNA molecule has been assembled, whose efforts won them a Nobel Prize in
it may be chemically modified—sometimes 1980.
deliberately by special enzymes called - The Gilbert-Maxam method relies on the
DNA methyltransferases and sometimes different chemical reactivities of the bases,
accidentally by oxidation, ionizing

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while the Sanger method is based on the  Transfer RNA

enzymatic synthesis of DNA in vitro. - Transfer RNA (tRNA) carries individual
amino acids into the ribosome for assembly
Ribonucleic Acid into the growing polypeptide chain.
- The tRNA molecules contain 70 to 80
• RNA is a single-stranded nucleic acid polymer of the nucleotides and fold into a characteristic
four nucleotides A, C, G, and U joined through a cloverleaf structure.
backbone of alternating phosphate and ribose sugar - The nucleotide sequence is converted into a
residues.
protein sequence by translating each three-
• It is the first intermediate in converting the
base sequence (called a codon) with a specific
information from DNA into proteins essential for the
protein.
working of a cell. Some RNAs also serve direct roles
in cellular metabolism.
• RNA is made by copying the base sequence of a
section of double-stranded DNA, called a gene, into a
piece of single-stranded nucleic acid. This process,
called transcription, is catalyzed by an enzyme called
RNA polymerase.

RNA Chemical Structure

 Whereas DNA provides the genetic information for the

cell and is inherently quite stable, RNA has many roles
and is much more reactive chemically.

 Messenger RNA
- The 5′-triphosphate residue is further
esterified, forming a structure called a cap. At
the 3′ ends, eukaryotic mRNAs typically
contain long runs of adenosine residues
(polyA) that are not encoded in the DNA but
are added enzymatically after transcription.
- Eukaryotic mRNA molecules are usually
composed of small segments of the original
gene and are generated by a process of
cleavage and rejoining from an original
precursor RNA (pre-mRNA) molecule, which
is an exact copy of the gene (as described in
the section Splicing).
- In general, prokaryotic mRNAs are degraded
very rapidly, whereas the cap structure and the
polyA tail of eukaryotic mRNAs greatly
enhance their stability.

 Ribosomal RNA
- Ribosomal RNA (rRNA) molecules are the
structural components of the ribosome.
- The rRNAs form extensive secondary
structures and play an active role in
recognizing conserved portions of mRNAs and
tRNAs. They also assist with the catalysis of
protein synthesis.
- In the prokaryote E. coli, seven copies of the
rRNA genes synthesize about 15,000
ribosomes per cell.

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