Biochemistry (Lecture)  Cytosol – fluid portion of the cytoplasm (without

the organelles)
Biochemistry
CLASSES OF ORGANISM
Biologically important molecules
A comparison of Prokaryotes and Eukaryotes
 Its composition and structure Organelle Prokaryotes Eukaryotes
 The chemical reactions they undergo NUCLEUS No definite Present
nucleus; DNA is
Characteristics of a living organism present but not
separate from the
1. Living organism has the capacity to self-replicate. rest of the cell.
2. Living organism has the capacity to extract and CELL Present Present
transform energy from their environment. MEMBRANE
3. Each component part of a living organism has a MITOCHONDRIA None; enzymes Present
specific purpose of a function. for oxidation
4. Living organism is highly complicated and reactions located
organized. on plasma
membrane.
Chemical Composition of Living Matter ENDOPLASMIC None Present
RETICULUM
RIBOSOMES Present Present
BIOCHEMICAL CHLOROPLASTS None; Present in green
SUBSTANCES photosynthesis plants
(if present) is
localized in
chromatophores.
BIOINORGANIC BIOORGANIC
SUBSTANCES SUBSTANCES
are substances are substances Organelle Function
that do not that contain NUCLEUS Location of main genome; site of
contain carbon. carbon. most RNA and DNA synthesis.
MITOCHONDRION Site of energy-yielding oxidation
reactions; has its own DNA.
CHLOROPLAST Site of photosynthesis in green
plants and algae; has its own DNA.
Water – 70% -Proteins – 15%
Inorganic Salts – -Lipid – 8% ENDOPLASMIC Continuous membrane throughout
5% [Ca, K, Fe] -Carbohydrate – RETICULUM the cell; rough part studded with
2% ribosomes (the site of protein
-Nucleic Acid - synthesis).
2% GOLGI APPARATUS Series of flattened membranes;
involved in secretion of protein
Hierarchy of Molecular Organization of Cells from cells and in reactions that link
sugars to other cellular
Level 1: Monomeric Unit – Nucleotides, Amino Acid,
components.
Sugar LYSOSOMES Membrane-enclosed sacs containing
Level 2: Macromolecule – DNA, Protein, Cellulose hydrolytic enzymes.
PEROXISOMES Sacs that contain enzymes involved
Level 3: Supramolecule – Chromosome, Plasma in the metabolism of hydrogen
Membrane, Cell Wall peroxide.
CELL MEMBRANE Separates the cell contents from the
Level 4: The Cell and Its Organelles outside world; contents include
organelles (held in place by the
Universal Features of Living Cells cytoskeleton) and the cytosol.
1. Nucleus / Nucleoloid – contains genetic material, CELL WALL Rigid exterior layer of plant cells.
control center of the cell, membrane-bounded. CENTRAL VACUOLE Membrane-enclosed sac (plant cell).
2. Plasma Membrane – lipid bilayer, selectively
permeable.
3. Cytoplasm – holds organelles, within the plasma
membrane but outside the nucleus.
Processes That Regulates Cell Contents Water
- Principal component of most cells
Diffusion – net movement of solute particles from a region - Its solvent properties is largely determined by
of higher solute-concentration to a region of lower solute its polar nature
concentration. - (insert symbol of partial negative charge)
Osmosis – net movement of water from a region of lower POLARITY: Separation of Charges
solute-concentration to a region of higher solute
concentration. Hydrogen Bond – strongest of the intermolecular forces
-to make the solution more diluted, more quantity involving neutral species
of solvent. - Most important for Hydrogen compounds of N,
O, and F.
Osmotic Pressure – pressure that must be exerted on a Concept Acid Base
solution to prevent it from taking water, when it separated Arrhenius Increases H3O+ in Increases OH- in
from pure water by a semi-permeable membrane. aqueous solution aqueous solution
Bronsted-Lowry Donates proton Accepts proton
Solution Solute Water Effect on Effect
Lewis Accepts electron Donates electron
Concentrati Moveme Plant Cell on
pair pair
on nt Anim
al
Cell Arrhenius
Isotonic Inside = No net Flaccid As is
Outside moveme
nt
Hyperto Inside<Outs Outside Plasmolyz Shrin
nic ide the cell ed ks
Hypoton Inside>Outs Inside Turgid Swell
ic ide the cell s; Bronsted-Lowry
may
burst

Dialysis – biochemical method of method of separation Base Conjugate Acid

and purification by selective passage of ions and molecules NH3 NH4+
through a semi-permeable membrane. OH- H2O
Surface Tension – tendency of a surface of a liquid to
contract making it look like a stretch membrane. Acid Conjugate Base Conjugate
-surface molecules feel an unbalanced attraction Base Acid
and are pulled inward. HCl Cl- NH3 NH4+
HBr Br- OH- HOH
Water and Acid Equilibria HNO3 NO3- H2O H3O+
HC2H3O2 C2H3O2- CO32- HCO3+
Comparison of Ionic, Polar, and Non-Polar Bonding
Comparison: Strong and Weak Acids and Bases
Ionic Bonding – ions [(+) cation, (-) anion] STRONG WEAK
-complete transfer of electrons Acid Base Acid Base
-full ionic charges HClO4 NaOH HCOOH NH3
-Na+Cl- HI Ca(OH)2 HNO2 (CH3)2NH2
-metal + non-metal HNO3 KOH CH3COOH
HCl CsOH HCN
Covalent Bonding HBr LiOH HF
→ Polar H2SO4 Ba(OH)2
- Unequal sharing of electrons
- Partial ionic charges Autoionization of Water
- Two different non-metals - Water is amphoteric
→ Non Polar - In pure water, a few molecules act as bases and
- Equal sharing of electrons a few acts as acids
- No charges
- Two identical non-metal
 INTERMOLECULAR FORCES

Dissociate Ionize – remove H

Interacting Molecules / Ions

Are polar NO Are ions YES Are polar

molecules involved? molecules and
involved? ions both
present?
YES

NO Are hydrogen
NO
atoms bonded to
N, O, or F atoms? YES

YES
NO

Dispersion Dipole Hydrogen Ion- Ionic

Forces - Bonding Dipole Bonding
dipole Forces
Forces
1. Calculate the pH of 0.06 mol/L HCl.
Given:
Dissociation of Weak Acids
- When a weak acid (HA) is dissolved in water:

Monoprotic Acid
- Gives off one proton (only one H+ to be released).
Polyprotic Acid
2. Calculate the pOH of 0.02 M NaOH. - Yields more than one H+ per molecule
Given: - Ka1 > Ka2 > Ka3….
- When dissociation constants are far apart in
polyprotic acids, the dissociation of each proton
may be considered independent from each other.
3. - Eg. H3PO4 (Phosphoric Acid)
K – equilibrium constant

Comparison: Strong and Weak Acids *the lower the equilibrium constant, the higher the
STRONG ACID WEAK ACID difficulty in removing hydrogen
Strong acids are molecules Weak acids are molecules
that completely dissociate that partially dissociate into
into their ions when it is in ions in aqueous solution.
water.
pH of a strong solution is pH of a weak acid solution
very low. is about 3 – 5.
Acid dissociation constant Acid dissociation constant Buffer Solutions – resist drastic changes in pH upon
is a higher value. is a lower value. addition of small to moderate amounts of strong acids or
Release all the H+ ions to Do not release all H+ ions. strong bases.
the solution. Buffer = Weak Acid (HA) + Conjugate Base (A-)
General Equation: (H+)
Case 1: Addition of Strong Acid (HCl)
Case 2: Addition of Strong Acid Base (NaOH)
Henderson-Hasslebalch Equation Uses
 To control pH of optimum reaction conditions
 To prepare buffer solution of known pH
 To calculate the degree of dissociation of weak
acid-conjugate base pairs at a particular pH
Ka = dissociation constant
1. What is the pH of a buffer that is 0.12 M in lactic
acid [CH3CH(OH)COOH, or HC3CH5O3] and O.10 M
in sodium lactate [CH3CH(OH)COONa, or
NaC3H5O3]? For lactic acid, Ka=1.4X10-4.
Given:
[HA]=0.12 M
[A-]=0.10 M
Ka=1.4X10-4
2. Calculate the pH of a 0.500 L buffer solution
composed of 0.700 M formic acid (HCOOH, Ka =
1.77 x 10-14) and 0.500 M sodium formate
(HCOONa).
a. Calculate the pH after adding 50.0 mL of a
1.00 M NaOH solution.
Solution for a:
 We need to determine the moles of formic acid
and sodium formate after the NaOH was added.
We first calculate the amounts before the addition
of the NaOH:
HCOOH  (0.700 mol/L) (0.500 L) = 0.350 mol
HCOONa ---> (0.500 mol/L) (0.500 L) = 0.250 mol
 Now, determine the moles of NaOH:
NaOH ---> (1.00 mol/L) (0.0500 L) = 0.0500 mol
 NaOH reacts in a 1:1 molar ratio with HCOOH:
HCOOH ---> 0.350 mol − 0.0500 mol = 0.300 mol
HCOONa ---> 0.250 mol + 0.0500 mol = 0.300 mol
 Calculate the new pH:
Buffer Solutions: Criteria
 Suitable pKa for the buffer.
 No interference with the reaction or with the
assay.
 Suitable ionic strength for the buffer.
 No precipitation of reactants or products due to
preference of the buffer.
 Non biological nature of the buffer.
Buffering Capacity
 The effectiveness of the buffer solutions.
 Trend:  concentration of both weak acid and
conjugate base,  buffering capacity.
Protein
 Came from the Greek word “proteios”
 Most abundant molecules in the cells
 9 000 (human cell)
 100 000 (human body)
 Composition: C, H, N, O, S
Amino Acids: Classifications
 Nonpolar amino acids – contains 1 amino group,
1 carboxyl group, and a nonpolar side chain.
 Hydrophobic – not attracted to water molecules
and it can be found in the interior of proteins,
where there is no polarity.
 Polar Amino Acid – hydrophilic
Types:
- Polar neutral
- Polar acidic
- Polar basic
Amino Acids: Nonpolar L – Left (Levo)
D – Right (Dextro)
 Glycine (Gly, G)
 Alanine (Ala, A) Amino Acids: Acid-Base Properties
 Valine (Val, V)
 Leucine (Leu, L)
 Isoleucine (Ile, I)

Amino Acids: Polar (Neutral)

 Contains polar but neutral side chain

Polar (Acidic, Basic)

Acidic Basic
Contains a carboxyl group Contains an amino group as
as part of the side chain. a part of the side chain. Protonation: Addition of H+ protonate
Deprotonation: removal of H+
Amino Acids: Essential
Amino Acids: Zwitterion
 Needed in the human body that must be obtained
 The neutral form of an amino acid does not really
from dietary sources
exists.
 The salt is the neutral form of amino acid.
 Arginine  Methionine
 This form exists at pH 6.00
 Histidine  Phenylalanine
 Isoleucine  Threonine
 Leucine  Tryptophan
 Lysine  Valine

Amino Acids: Complete Dietary Protein

Food Source Amino Acid Deficiency

Soy None
Wheat, rice, oats Lysine
Corn Lysine, Tryptophan
Beans Methionine, Tryptophan
Peas Methionine
Almonds, Walnuts Lysine, Tryptophan

Chirality

 The (alpha)-carbon is chiral

 Reason: Four different groups are attached to the
(alpha)-carbon atom
 Consequence: on amino acids – all of the 19
standard amino acids are chiral (except lysine). Amino Acids: Zwitterion
 Achiral
 pH Acid Groups Amino Groups
Low (Acidic) Protonated COOH Protonated NH3
Neutral Deprotonated Protonated N+H3 Primary Structure
COO-
 H refers to the sequence of amino acids
High (Basic) Deprotonated Deprotonated NH2
COO-

Organic Chemistry: Amide Bond

Peptide Bond: Features

Isoelectric Point (pI)  Partial double bond character
 pH at which an amino acid solution has no net  Rigid and planar
charge  Bonds between the (alpha)-carbon and the
 There is an equal number of positive and negative (alpha)-amino or (alpha)-carboxyl groups can be
charges. fully rotated.

Example:
Valine

Peptide Conventions Used

Aspartic Acid  Directionality of peptide chain

 Parts of the peptide chain
1. Backbone
2. Substituents on the backbone

Dipeptide = 2 amino acids, 1 peptide bonds

Hexapeptide = 6 amino acids, 5 peptide bonds
Electrophoresis
Peptide Nomenclature: IUPAC Rules
 Predict the direction of the migration of lysine,
phenylalanine, and glutamic acid at pH = 5.5  Write the free amino acid group of the peptide
chain (N-terminal) to the left.
Levels of Protein Structure  Write the free carboxyl group of the peptide chain
 Primary Structure: Amino acid residues (C-terminal) to the right.
 Secondary Structure: (alpha) helix  Read it from the N-terminal to the C-terminal end.
 Tertiary Structure: Polypeptide chain  Replace the names of all the amino acid residues
 Quaternary Structure: Assembled subunits ending in -ine or ic-acid to -yl except the following:
1. Tryptophan – Tryptophyl
 2. Cysteine – Cysteinyl  Disulfide bonds – between two –SH groups on the
3. Glutamine – Glutaminyl same chain and different chains
4. Asparagine – Asparaginyl
 Retain the name of the rightmost amino acid Cysteine – AA
Cystine – Dimer
Example:
1. Glycine – Glycyl
Reducing agents: ammonium thioglycolate
2. Aspartic Acid – Aspartyl
Oxidating agents: potassiumbromate
Secondary Structure
Myoglobin – storage of oxygen (muscle)
 Hydrogen-bonded arrangement of the polypeptide
chain. - Single polypeptide chain
- Includes a prosthetic group -heme
Romachandram Diagram - Has 8 regions
- No β-pleated sheet regions
 Shows the allowed conformation for specific - The affinity of the free heme for CO is
protein sequences. 25000 times greater than its affinity for
oxygen.
1.
2. Quaternary Structure
3. Collagen helix
 Has 4 Fe2+
 Subunit – individual polypeptide chains that make
up a complete protein
 Keratin
 The chains interact noncovalently
 Electrostatic attractions
 Hydrogen bonds
 Parallel  Hydrophobic interactions
 Antiparallel
 Interchain: H-bond are formed between the Tetramer – 4 Dimer – 2
polypeptide backbones of separate polypeptide
Hemoglobin: Composition of Normal Adult Human
chains
 Intrachain: single polypeptide chain folding back
Form Composition Fraction of Source
on itself Total
Structure Characteristics Examples Hemoglobin
, cross- Tough, insoluble (Alpha) HbA 90% Adults
linked by disulfide productive keratin of HbF <2% Synthesized
bonds structures of hair, feathers during fetal
varying hardness and nails development
and flexibility HbA2 2 – 5% Synthesized in
Soft, flexible Silk fibroin adults but at
filaments low levels
Collagen Triple High tensile Collagen of HbA, c 3 – 9% Increased
Helix strength, without tendons, bone amounts can
stretch matrix be found in
patients with
diabetes
Tertiary Structure mellitus

 Conformations of side chain

 Positions of any prosthetic (non-protein) Hemoglobin: Forms
 Arrangement of helical and pleated sheets
 T form (Taut or tense form)
sections with respect to one another
 R form (Relaxed form)
Interactions  Deoxygenated – tight
 Oxygenated – relaxed
 Side chain hydrogen bonds
 Hydrophobic interactions
 Electrostatic attraction – acidic, basic
Hemoglobin: Oxygen binding curve Classes
Simple Enzyme Conjugated Enzyme
 The plot of Y measured at different partial Protein only (amino acid Nonprotein part + protein
pressures of oxygen (pO2) chains) part
 p50
 Partial pressure of oxygen needed to achieve half- Structure:
saturation of the binding sites.  Apoenzyme: protein part of a conjugated enzyme
 Cooperative binding  Cofactor: Nonprotein part of a conjugated enzyme
 Holoenzyme: biochemically active conjugated
p50 (mmHg) Function enzyme
Myoglobin 1 Storage Substrate
Hemoglobin 26 Transport  The reactant in an enzyme-catalyzed reaction,
 The substance upon which the enzyme “acts”.
Graph: Asymptotic, Sigmoidal
Enzymes: Six Major Classes
Hemoglobin: Allostenic Effects Classes Reaction catalyzed
 A conformational change in one subunit induces a Oxydoreductases Oxidation-reduction
change in another subunit. Transferases Functional group transfer
reactions
Factors shifting curve to the right Hydrolases Hydrolysis reaction
 Lower pH (more acidic) Lyases Reactions involving
 High temperature addition or removal of
 High PCO2 groups from double bonds
 High 2,3 – BPG called Bohr effect Isomerases Isomerisation reactions
Ligases Reactions involving bond
Protein: Hydrolysis formation coupled with ATP
 This happens when a protein or smaller peptide in hydrolysis.
a solution of strong acid or strong base is heated.
Enzyme: Nomenclature
Denaturation  Suffix –ase identifies it as an enzyme
 Partial or complete disorganization of a protein’s Examples:
characteristic 3-dimensional shape. - Urease
 It does not affect the primary structure of a - Sucrose
protein. - Lipase
 Effects:  Exception: The suffix –in is still found in the
1. Loss of biochemical activity names of some digestive enzymes
2. Loss of water solubility Examples:
- Trypsin
- Chymotrypsin
Denaturing Agents Mode of Action
- Pepsin
Heat Disrupts hydrogen bond
 Type of reaction
Microwave radiation Disrupts hydrogen bond
- Oxidase: catalyzes an oxidation reaction
Ultraviolet radiation Disrupts hydrogen bond
- Hydrolase: catalyzes a hydrolysis reaction
Violent whipping Elongates globular shapes
 Identity of substrate
Detergent Affects hydrophobic
- Glucose oxidase
interactions
- Pyruvate oxidase
Organic solvents Affects R-group interactions - Succinate dehydrogenase
Strong acids/bases Disrupts hydrogen bond  General nature of substrate: lipase
Salts of heavy metal Affects –SH groups  Systematic Name
Reducing agents Affects –SH groups Example: ATP, creatine phosporotransferase
(EC 2-7-3-2)
ENZYMES - Transferases
 Proteins that act as a catalyst for biochemical - Transferring phosphorus-containing groups
reactions. - Phospotransferases with a nitrogenous group as
 Most enzymes are globular proteins. acceptor
 It undergo all the reactions of proteins including - Creatine kinase
denaturation. - Divided into 6 major classes
- Developed by IUBMB
Oxidoreductases
Selected Subclasses Type of reaction catalyzed
Oxidases Oxidation of a substrate
Reductases Reduction of a substrate
Dehydrogenases Introduction of double bond
(oxidation) by formal
removal of two H atoms
from substrate, the H being
accepted by a coenzyme
Oxidation: O Reduction: H
Transferases
Selected Subclasses Type of reaction catalyzed
Lipases Hydrolysis of ester linkages
in lipids
Proteases Hydrolysis of amide
linkages in proteins
Nucleases Hydrolysis of sugar-
phosphate ester bonds in
nucleic acids
Carbohydrases Hydrolysis of glycosidic
bonds in carbohydrates
Phosphatases Hydrolysis of phosphate-
ester bonds
Hydrolases
Selected Subclasses Type of reaction catalyzed
Transminases Transfer of amino group
between substrate
Kinases Transfer of a phosphate
group between substrate
Lyases
Selected Subclasses Type of reaction catalyzed
Dehydratases Removal of H2O from
substrate
Decarboxylases Removal of CO2 from
substrate
Deaminases Removal of NH3 from
substrate
Hydratases Addition of H2O to a
substrate
Isomerases
Selected Subclasses Type of reaction catalyzed
Racemases Conversion of D to L isomer,
or vice versa
Mutases Transfer of a functional
group from one position to
another in the same
molecule.
Ligases
Selected Subclasses Type of reaction catalyzed
Synthetases Formation of new bond
between two substrate,
with participation of ATP
Carboxylases Formation of new bond
between a substrate and
CO2, with participation of
ATP
Models of Enzyme Action
Active Site
 Place where substrate binds to enzyme
 Some enzymes have more than one active site
Enzyme Substrate Complex
 Intermediate reaction species formed when
substrate binds with the active site
Lock-and-Key
 Induced Fit
Factors That Affect Enzyme Activity
1. Temperature
 Optimum temperature for human enzymes is 37°C
(body temperature)
 Increased temperature (high fever) leads to
decreased enzyme activity
2. pH
 Most enzymes have optimal activity in the pH
range of 7.0 – 7.5
Exception:
- Pepsin: Optimum pH = 2.0
- Trypsin: Optimum pH = 8.0
Substrate Concentration
 Trend: At a constant enzyme concentration, the
enzyme activity increases as substrate
concentration increases.
Enzyme Concentration
 Trend: At a constant substrate concentration,
enzyme activity increases as the enzyme
concentration increases.
Enzyme Inhibition
 Enzyme Inhibitor: A substance that slows down
or stops the normal catalytic function of an
enzyme by binding to it.
Modes of Inhibition
Irreversible Reversible
Permanent Temporary
Inactivates enzymes by May or may not alter the
forming a strong covalent conformation of enzymes.
bond with the enzyme’s
active site.
 frequent doses. periodic doses.
Reversible Relationship to Function as Do not function as
1. Competitive: Its addition competes with the enzymes coenzymes. coenzymes.
substrate for the same active site.
2. Non competitive: Its inhibitor can bind either Vitamin C
the free enzyme or the ES complex  Co-substrate in the formation of structural protein
3. Uncompetitive: Its inhibitor can bind to the collagen.
ES complex but not to the free enzyme.  Involved in metabolism of certain amino acids.
 100 mm / day saturates all body tissues
Examples
Competitive Non competitive Uncompetitive Vitamin B
Atorvastatin Lead in Shikimate
and simvastatin ferrochelatase Pathway – A 7 –  Thiamine  Nilacin
step metabolic  Riboflavin (two  Pantotheic Acid
route; used by forms)
bacteria, fungi,  Vitamin B6 (three  Folate
algae, parasites, forms)
and plants for  Vitamin B12  Biotin
biosynthesis of
aromatic amino
acids. Water-Soluble: Vitamin B
B Vitamin Coenzymes Groups
Vitamins Transferred
 Organic compounds Thiamin Thiamin Carbon dioxide
 Must be obtained from dietary sources pryphosphate (TPP) (carboxyl group)
 Essential for proper functioning of the body Riboflavin Flavin monucleotide Hydrogen atoms
 Two classes: Water soluble and Fat soluble (FMN)
Falvin adenine
dinucleotide (FAD)
Vitamis: Two Classes Niacin Nicotinamide adenine Hydrogen atoms
Water-Soluble Vitamins Fat-Soluble Vitamins dinucleotide (NAD+)
Thiamin Vitamin A Nicotinamide adenine
Riboflavin Vitamin D Dinucleotide
Niacin Vitamin E phosphate (NADP+)
Vitamin B6 Vitamin K Pantothenic Coenzyme A (CoA) Acyl groups
Folate acid
Vitamin B12 Vutamin B6 Pyridoxal-5’- Amino groups
Pantothenic Acid phosphate (PLP)
Biotin Pyridoxine-5’-
Vitamin C phosphate (PNP)
Pyridoxamine-5’-
Vitamins: Two Classes phosphate (PMP)
Water-Soluble Fat-Soluble Biotin biotin Carbon dioxide
Vitamins (B Vitamins (A, D, E, (carboxyl group)
Vitamins and K) Folate Tetrahydrofolate One-carbon
Vitamin C) (THF) groups other
Absorption Directly into the First enter into than CO2
blood. the lymph system. Vitamin B12 methylcobalamin Methyl groups,
Transport Travel without May require hydrogen atoms
carriers. protein carriers.
Storage Circulate in the Found in the cells
water-filled parts associated with
of the body. fat.
Excretion Kidneys remove Tend to remain
excess in urine. fat-storage sites.
Toxicity Not likely to reach Likely to reach
toxic levels when toxic levels when
consumed from consumed from
supplements. supplements.
Requirements Needed in Needed in
Fat Soluble Vitamins

Lipid-soluble vitamins and their functions

Vitamin Function
Vitamin Serves as the site of the primary
A photochemical reaction in vision.
Vitamin Regulates calcium (and phosphorus)
D metabolism.
Vitamin Serves as an antioxidant; necessary for
E reproduction in rats and may be necessary for
reproduction in humans.
Vitamin Has a regulatory function in blood clotting.
K

Vitamin A
 Vision
 Regulating cell differentiation
 Maintenance of the healthy of epithelial tissues via
epithelial tissue differentiation
 Reproduction and growth

Vitamin E
 Antioxidant – protects against oxidation of other
compounds


Vitamin D Vitamin K
 It controls correct ratio of calcium and  Active in the formation of proteins involved in
phosphorus for bone mineralization (hardening). regulating blood clotting.
 As a hormone it promotes calcium and
phosphorus absorption in intestine – calcitriol.