Chapter 1:

-​ Organization of Matter
●​ Atoms: Basic unit of matter; consists of protons, neutrons, and electrons.
●​ Molecules: Formed by chemical bonding between atoms (e.g., H₂O, CO₂).
●​ Macromolecules: Large, complex molecules (e.g., proteins, nucleic acids,
carbohydrates, lipids).
●​ Organelles: Specialized structures in cells (e.g., nucleus, mitochondria).
●​ Cells: Basic unit of life; prokaryotic (bacteria, archaea) or eukaryotic (plants, animals,
fungi, protists).

-​ Strong and Weak Chemical Bonds

●​ Strong Bonds (Covalent Bonds):
○​ Atoms share electrons (e.g., C–C, C–H, C=O).
○​ Require significant energy to break.
○​ types of strong chemical bonds: ionic, non polar covalent and polar covalent
●​ Weak Bonds (important for biomolecular interactions):
○​ Hydrogen Bonds: Interaction between partially positive hydrogen and an
electronegative atom (O, N). Important for protein and DNA stability.
○​ Ionic Bonds: Attraction between oppositely charged ions (e.g., Na⁺ and Cl⁻).
○​ Van der Waals Interactions: Weak attractions between nonpolar molecules.
○​ Hydrophobic Interactions: Nonpolar molecules aggregate to avoid water.

-​ Bulk and Main Trace Elements

●​ Bulk Elements (Major components of biomolecules): C, H, O, N, P, S.
●​ Trace Elements (Essential in small amounts): Fe, Zn, Cu, Mn, Se, I, Mo, Co.

-​ Shapes of Chemical Bonds Involving Carbon

●​ Single Bond (C–C, C–H, C–O): Tetrahedral (109.5°).
●​ Double Bond (C=C, C=O): Planar (120°).
●​ Triple Bond (C≡C): Linear (180°).
●​ Carbon Hybridization:
○​ sp³ (tetrahedral)
○​ sp² (trigonal planar)
○​ sp (linear)
 -​ Functional Groups
●​ Hydroxyl (-OH): Alcohols, polar, forms H-bonds. Found in carbohydrates and alcohols
●​ Carbonyl (-C=O): Aldehydes and ketones, important in sugar structure.
●​ Carboxyl (-COOH): Acidic, found in amino acids and fatty acids.
●​ Amino (-NH₂): Basic, found in amino acids.
●​ Sulfhydryl (-SH): Forms disulfide bonds in proteins.
●​ Phosphate (-PO₄³⁻): Found in nucleotides (DNA, RNA, ATP).
●​ Methyl (-CH₃): Hydrophobic, affects gene expression.

-​ Cell Structures
1. Animal and Plant Cell Structure

●​ Similarities:
○​ Plasma membrane (phospholipid bilayer).
○​ Nucleus (stores DNA).
○​ Endoplasmic reticulum (protein/lipid synthesis).
○​ Golgi apparatus (modifies and ships proteins).
○​ Mitochondria (ATP production).
●​ Plant-Specific:
○​ Cell wall (cellulose for rigidity).
○​ Chloroplasts (photosynthesis).
○​ Large central vacuole (storage, turgor pressure).

2. Prokaryotic Cell Structure

●​ No nucleus (DNA in nucleoid region).

●​ No membrane-bound organelles.
●​ Cell wall (peptidoglycan in bacteria).
●​ Ribosomes (protein synthesis).
●​ May have flagella or pili for movement.

-​ General Molecular Composition of a Typical Cell

●​ Water (~70%): Universal solvent, key for biochemical reactions.
●​ Proteins (~15%): Enzymes, structural components.
●​ Lipids (~10%): Membrane structure, energy storage.
 ●​ Carbohydrates (~3%): Energy source (glucose), structural (cellulose, chitin).
●​ Nucleic Acids (~1%): DNA (genetic material), RNA (protein synthesis).
●​ Ions & Small Molecules (~1%): Na⁺, K⁺, Ca²⁺, ATP, signaling molecules.

Chapter 2:

I. Functions of Water
1.​ Solvent for Biochemical Reactions
○​ Water dissolves many biomolecules (e.g., salts, proteins, nucleic acids) due to its
polarity.
○​ It enables transport of nutrients and waste in organisms.
2.​ Temperature Regulation
○​ High specific heat capacity allows water to absorb/release heat with minimal
temperature change, stabilizing body and environmental temperatures.
○​ High heat of vaporization enables cooling via sweat evaporation.
3.​ Reactant and Product in chemical Reactions
○​ Hydrolysis: Water breaks down molecules (e.g., ATP hydrolysis releases
energy).
○​ Condensation/ Dehydration: Water is released during macromolecule formation
(e.g., peptide bond formation in proteins).
4.​ Structural and Mechanical Support
○​ Water provides turgor pressure in plant cells.
○​ It acts as a cushion in joints (synovial fluid) and the brain (cerebrospinal fluid).

II. Properties of Water

Water's properties arise from hydrogen bonding and polarity:

-​ hydrogen Bond is a result on difference in electronegativity between a hydrogen atom

and another atom
-​ hydrogen bond has a short life span
1.​ Polarity
○​ Water has a partial negative charge on oxygen and partial positive charges
on hydrogen.
○​ This enables hydrogen bonding with other molecules.
2.​ Cohesion and Adhesion
○​ Cohesion: Water molecules stick to each other due to H-bonding (e.g., surface
tension).
○​ Adhesion: Water interacts with other polar surfaces (e.g., capillary action in
plants).
 3.​ High Specific Heat Capacity
○​ Water resists temperature changes, maintaining stable environments.
4.​ High Heat of Vaporization
○​ It takes significant energy to evaporate water, allowing organisms to cool
efficiently.
5.​ Ice is Less Dense than Liquid Water
○​ Ice has an open lattice structure due to maximized H-bonds, making it float and
insulating water bodies.
6.​ Solvent Properties
○​ Water dissolves polar and charged substances but not nonpolar molecules.

III. Concepts of Polarity and Solubility

●​ Polar Molecules / Hydrophilic ("Water-loving")
○​ Have partial charges or ionic groups (e.g., alcohols, sugars, salts).
○​ Readily dissolve in water via H-bonding or ion-dipole interactions.
●​ Nonpolar Molecules / Hydrophobic ("Water-fearing")
○​ Lack charge separation (e.g., lipids, hydrocarbons).
○​ Do not dissolve in water and instead aggregate due to the hydrophobic effect.
●​ Amphipathic Molecules
○​ Have both polar (hydrophilic) and nonpolar (hydrophobic) regions.
○​ Form micelles (e.g., detergents) or bilayers (e.g., cell membranes).

IV. Types of Hydrogen Bonds

1.​ Water-Water Hydrogen Bonds
○​ Each water molecule forms up to 4 hydrogen bonds, creating its unique
properties.
2.​ Water-Protein/Nucleic Acid Hydrogen Bonds
○​ Stabilize protein folding and DNA double helix.
3.​ Water-Small Molecule Hydrogen Bonds
○​ Assist in solubility of compounds (e.g., glucose dissolves in water due to OH
groups forming H-bonds).

V. Acid-Base Concepts
1. pH Scale
 ●​ pH = -log[H⁺], measures acidity/basicity of a solution.
●​ Acidic (pH < 7): High [H⁺] (e.g., stomach acid, pH ~2).
●​ Neutral (pH = 7): Pure water.
●​ Basic (pH > 7): Low [H⁺] (e.g., blood, pH ~7.4).

2. Acids and Bases

●​ Acid: Proton donor (e.g., HCl → H⁺ + Cl⁻).

●​ Base: Proton acceptor (e.g., NH₃ + H⁺ → NH₄⁺).

3. Buffers

●​ Definition: Solutions that resist pH changes when acids or bases are added.
●​ Mechanism: Maintain pH by shifting equilibrium (e.g., bicarbonate buffer system in
blood: H₂CO₃ ⇌ H⁺ + HCO₃⁻).

4. pKa

●​ pKa = -log(Ka), where Ka is the acid dissociation constant.

●​ Lower pKa → Stronger acid (more dissociation).
●​ Higher pKa → Weaker acid.

VI. Henderson-Hasselbalch Equation

Used to calculate pH of buffer solutions:

pH=pKa+log⁡([A−][HA])pH=pKa+log([HA][A−]​)

Where:

●​ [A⁻] = Concentration of conjugate base.

●​ [HA] = Concentration of weak acid.

Applications:

●​ Determines pH stability in biological systems.

●​ Helps design buffers for biochemical experiments.

Summary Table
Concept Key Points
 Functions of Water Solvent, temperature regulation, biochemical
reactions, structural support

Properties of Water Polarity, cohesion/adhesion, high heat

capacity, ice density, solvent ability

Solubility Concepts Polar = hydrophilic (soluble), nonpolar =

hydrophobic (insoluble), amphipathic = both

H-Bonds Water-water, protein-water, nucleic acid-water

pH & Acidity pH = -log[H⁺], acids donate H⁺, bases accept

H⁺

Buffers Resist pH changes (e.g., bicarbonate in

blood)

pKa Acid strength indicator

Henderson-Hasselbalch Calculates pH of buffer systems

chapter 3:

I. General Structure of an Amino Acid

Amino acids are the building blocks of proteins, each consisting of:

1.​ A central (α) carbon (chiral, except glycine).

2.​ An amino group (-NH₂) (acts as a base).
3.​ A carboxyl group (-COOH) (acts as an acid).
4.​ A unique R-group (side chain) that determines properties.
5.​ A hydrogen atom (-H).

General Formula:

H2N−CH(R)−COOHH2​N−CH(R)−COOH

At physiological pH (~7.4), amino acids exist as zwitterions, where the amino group is
protonated (-NH₃⁺) and the carboxyl group is deprotonated (-COO⁻).
II. Properties and Specificities of the 20 Amino Acids
Amino acids are classified into five groups based on their R-group properties:

1. Nonpolar (Hydrophobic) Amino Acids

●​ Characteristics: Nonpolar side chains, usually found in protein cores.

●​ Mnemonic: GAVLIMP FW

Amino Acid Abbr. R-group Special Feature

Glycine Gly (G) -H Smallest, achiral

Alanine Ala (A) -CH₃ Simple, hydrophobic

Valine Val (V) -CH(CH₃)₂ Branched-chain

Leucine Leu (L) -CH₂CH(CH₃)₂ Branched-chain

Isoleucine Ile (I) -CH(CH₃)CH₂CH₃ Two chiral centers

Methionine Met (M) -CH₂CH₂SCH₃ Sulfur-containing,

start codon (AUG)

Proline Pro (P) Cyclic (-CH₂CH₂CH₂-) Rigid, disrupts

α-helices

Phenylalanine Phe (F) -CH₂-Benzene Aromatic,

hydrophobic

Tryptophan Trp (W) -CH₂-Indole Largest amino acid,

absorbs UV (280 nm)

2. Polar, Uncharged Amino Acids

●​ Characteristics: Hydrophilic, form hydrogen bonds.

Amino Acid Abbr. R-group Special Feature

Serine Ser (S) -CH₂OH H-bond donor, in

active sites

Threonine Thr (T) -CH(OH)CH₃ Two chiral centers,

H-bonds
Cysteine Cys (C) -CH₂SH Forms disulfide
bonds (Cys-Cys)

Asparagine Asn (N) -CH₂CONH₂ Amide of aspartate

Glutamine Gln (Q) -CH₂CH₂CONH₂ Amide of glutamate

Tyrosine Tyr (Y) -CH₂-Benzene-OH Aromatic,

phosphorylated

3. Acidic (Negatively Charged) Amino Acids

●​ Characteristics: Contain carboxyl groups, negatively charged at pH 7.

Amino Acid Abbr. R-group Special Feature

Aspartate Asp (D) -CH₂COO⁻ pKa ~3.9, ionizable

Glutamate Glu (E) -CH₂CH₂COO⁻ pKa ~4.2,

neurotransmitter
(glutamate)

4. Basic (Positively Charged) Amino Acids

●​ Characteristics: Protonated at physiological pH, positively charged.

Amino Acid Abbr. R-group Special Feature

Histidine His (H) -CH₂-Imidazole pKa ~6.0, buffers at

physiological pH

Lysine Lys (K) -CH₂CH₂CH₂CH₂NH₃⁺ pKa ~10.5, strong

base

Arginine Arg (R) -CH₂CH₂CH₂NHC(NH pKa ~12.5, strongest

₂)⁺NH₂ base

III. Concept of Enantiomers (L- vs. D-Amino Acids)

●​ Chirality: All amino acids (except glycine) have chiral α-carbons, meaning they exist as
enantiomers (L and D forms).
 ●​ L-Amino Acids: The biologically relevant form found in proteins.
●​ D-Amino Acids: Rare, found in bacterial cell walls and some antibiotics.

Why L-Amino Acids?

●​ L-forms have early enzyme specificity.

IV. Amino Acids as Buffers

●​ Amino acids can act as buffers due to their ionizable groups.
●​ They have two (or three) pKa values corresponding to:
1.​ Carboxyl (-COOH): pKa ~2
2.​ Amino (-NH₃⁺): pKa ~9-10
3.​ Ionizable R-group (if present, e.g., Asp, Glu, His, Lys, Arg).

1. Titration of an Amino Acid (Example: Glycine)

●​ At low pH, both COOH and NH₃⁺ are protonated (+ charge).

●​ At pI (isoelectric point), net charge = 0 (zwitterion).
●​ At high pH, both COO⁻ and NH₂ are deprotonated (- charge).

2. Henderson-Hasselbalch Equation for Amino Acid Buffers

pH=pKa+log⁡([A−][HA])pH=pKa+log([HA][A−]​)

●​ Helps determine buffering range.

●​ Best buffering occurs near pKa values.

3. Importance of Buffering Amino Acids

●​ Histidine (pKa ~6): Important for maintaining intracellular pH.

●​ Glutamate and Aspartate (pKa ~4): Contribute to enzyme active site charge.
●​ Lysine and Arginine (pKa ~10-12): Stabilize negatively charged biomolecules.

Summary Table
Concept Key Points

Amino Acid Structure Central carbon, amino (-NH₂), carboxyl

(-COOH), R-group
 Nonpolar AAs Hydrophobic, found in protein cores

Polar AAs Hydrophilic, form hydrogen bonds

Acidic AAs Negatively charged at pH 7

Basic AAs Positively charged at pH 7

Enantiomers L-AAs used in proteins, D-AAs in bacteria

AAs as Buffers Ionizable groups maintain pH stability

chapter 4:

I. Levels of Protein Structure

Proteins have a hierarchical organization, categorized into four levels:

1. Primary Structure

●​ Definition: The linear sequence of amino acids in a polypeptide chain, held together by
peptide bonds.
●​ Peptide Bond Properties:
○​ Covalent bond between α-carboxyl (-COO⁻) of one amino acid and α-amino
(-NH₃⁺) of another.
○​ Planar and rigid due to partial double-bond character (resonance).
○​ Trans configuration is favored (except in proline).
○​ No free rotation around the peptide bond.

2. Secondary Structure

●​ Definition: Localized folding patterns stabilized by hydrogen bonds between

backbone atoms.
●​ Types of Secondary Structures:
1.​ Alpha (α) Helix
■​ Right-handed coil stabilized by H-bonds between C=O (n) and N-H
(n+4).
■​ R-groups extend outward.
■​ Disruptors: Proline (rigid), Glycine (too flexible), bulky/charged side
chains.
2.​ Beta (β) Pleated Sheet
 ■​ Extended structure stabilized by H-bonds between adjacent strands.
■​ Can be parallel (same direction) or antiparallel (opposite direction,
stronger H-bonds).
■​ R-groups alternate above and below the sheet.
3.​ Beta Turns (β-bends)
■​ Reverse turns that connect β-strands.
■​ Usually Proline (induces kink) and Glycine (small, flexible).
4.​ Omega Loops
■​ Irregular, flexible regions, often found on protein surfaces.

3. Tertiary Structure

●​ Definition: The 3D folding of a single polypeptide, stabilized by:

○​ Covalent Bonds: Disulfide bonds (-S-S-) between cysteines.
○​ Non-Covalent Interactions:
■​ Hydrogen bonds (polar groups).
■​ Ionic bonds (charged R-groups).
■​ Hydrophobic interactions (nonpolar R-groups cluster in protein core).
■​ Van der Waals forces (weak, short-range interactions).

4. Quaternary Structure

●​ Definition: Arrangement of multiple polypeptide subunits into a functional protein

complex.
●​ Examples:
○​ Hemoglobin (α₂β₂) → Oxygen transport.
○​ Collagen (triple helix) → Structural support.

II. Polypeptides vs. Proteins

●​ Polypeptide: A single chain of amino acids (may or may not be functional).
●​ Protein: A functional biologically active molecule, which may consist of one or more
polypeptide chains.

Globular vs. Fibrous Proteins

Type Characteristics Examples

Globular Proteins Compact, spherical, soluble Hemoglobin, Enzymes

Fibrous Proteins Long, insoluble, structural Collagen, Keratin

III. Importance of Phi (ϕ) and Psi (ψ) Angles
●​ Definition: Rotation angles of bonds around the α-carbon:
○​ Phi (ϕ): Rotation between N—Cα.
○​ Psi (ψ): Rotation between Cα—C'.
●​ Importance:
○​ Govern protein folding and secondary structure formation.
○​ Ramachandran Plot shows allowed ϕ/ψ angles (excludes steric hindrance
regions).

IV. Structure of Key Structural Proteins

1. Keratin (Fibrous)

●​ Structure:
○​ α-keratin → Right-handed α-helices forming coiled-coil dimers.
○​ Held together by disulfide bonds (more bonds = stronger, e.g., hair vs. nails).
●​ Function: Found in hair, nails, skin.

2. Collagen (Fibrous)

●​ Structure:
○​ Triple helix of three polypeptides, rich in Gly-X-Y (X = Pro, Y =
Hydroxyproline).
○​ Cross-linked via lysine residues for strength.
●​ Function: Provides tensile strength in skin, tendons, cartilage.

Summary Table
Concept Key Points

Primary Structure Linear sequence of amino acids, peptide

bonds

Secondary Structure α-helix, β-sheet, β-turns, omega loops

Tertiary Structure 3D folding, stabilized by covalent &

non-covalent interactions

Quaternary Structure Multiple subunits forming functional proteins

 Polypeptides vs. Proteins Polypeptide = chain; Protein = functional unit

Globular vs. Fibrous Soluble (globular) vs. insoluble (fibrous)

Covalent Bonds Disulfide bridges (cysteine)

Non-Covalent Bonds H-bonds, ionic, hydrophobic, Van der Waals

Phi/Psi Angles Control folding, visualized by Ramachandran

plot

Keratin Coiled-coil α-helices, disulfide bridges

Collagen Triple helix, glycine-rich, cross-linked

Chapter 5:

I. Protein Folding and Denaturation

1. Concepts of Protein Folding

●​ Protein folding is the process by which a linear polypeptide chain assumes its
functional 3D structure.
●​ Folding follows the "Anfinsen's Dogma": the primary sequence determines the final
structure.
●​ Folding is driven by non-covalent interactions, including:
○​ Hydrogen bonds (stabilize α-helices, β-sheets).
○​ Ionic interactions (between charged residues).
○​ Hydrophobic interactions (bury nonpolar residues in the core).
○​ Van der Waals forces (weak interactions that fine-tune structure).

2. Protein Denaturation

●​ Denaturation = loss of 3D structure (and function) due to disruption of weak

interactions.
●​ Causes of Denaturation:
○​ Heat → Breaks hydrogen bonds.
○​ pH changes → Alters charge interactions.
○​ Chemical agents (urea, guanidinium chloride) → Disrupts hydrogen bonds.
○​ Detergents (SDS) → Disrupts hydrophobic interactions.
○​ Reducing agents (β-mercaptoethanol, DTT) → Breaks disulfide bonds.
3. Chaperones (Molecular Chaperones)

●​ Proteins that assist in correct folding and prevent aggregation.

●​ Types:
○​ Heat-shock proteins: induced at higher temperature
○​ peptidyl-prolyl cis-trans isomerases: isomerase the peptide bond involving
proline from trans to cis and vice versa. (Ribosomes)
○​ protein- disulfide isomerases : formation of disulfide bridges.

II. Post-Translational Modifications (PTMs)

After translation, proteins undergo modifications that alter their function, stability, or
localization.

Modification Description Example Proteins

Phosphorylation Addition of phosphate (Ser, Signaling proteins (e.g.,

Thr, Tyr) kinases)

Glycosylation Addition of carbohydrates Membrane proteins

Acetylation Addition of acetyl group (Lys) Histones (gene regulation)

Methylation Addition of methyl group (Arg, Histones (epigenetics)

Lys)

Ubiquitination Addition of ubiquitin → Marks Cyclins (cell cycle)

for degradation

Lipid modification Addition of lipid chains Membrane-anchored proteins

Proteolytic Cleavage Removal of peptide segments Insulin activation

III. Protein Analysis & Purification Techniques

-​ separation of a protein of interest form a complex mixture of of proteins and other
molecules
-​ cell breakage/ tissue homogenization, protein extraction
-​ protein purification: precipitation methods and chromatography methods

1. In Vitro Protein Synthesis

 ●​ Cell-free system that synthesizes proteins outside living cells.
●​ Requires:
○​ Ribosomes, tRNA, amino acids.
○​ ATP/GTP for energy.
○​ mRNA template.

2. Determination of Amino Acid Composition

●​ Hydrolysis: Breaks peptide bonds → Releases individual amino acids.

●​ Chromatography used to separate and quantify amino acids.

3. Edman Degradation (Protein Sequencing)

●​ Stepwise removal of N-terminal amino acids, identified by chromatography.

●​ Limited to ≤50 residues (longer proteins need cleavage into fragments).

IV. Protein Purification Methods

Chromatography techniques are used to separate proteins based on physical and chemical
properties.

Type of Chromatography Principle Application

Gel Filtration (Size Separates by size (larger Removing aggregates

Exclusion) proteins elute first)

Ion Exchange Separates by charge (anion Purifying charged proteins

vs. cation exchange)

Hydrophobic Interaction Separates by Membrane proteins

hydrophobicity (nonpolar
regions bind to hydrophobic
column)

Affinity Separates by specific His-tagged proteins,

binding interactions antibodies
(ligand-receptor,
antibody-antigen)

V. Protein Structure Determination

1. X-ray Crystallography

●​ Used to determine high-resolution 3D protein structure.

●​ Requires protein crystals exposed to X-rays, creating diffraction patterns analyzed for
structure.
●​ Limitations: Requires crystallization (not all proteins crystallize well).

2. Mass Spectrometry (MS)

●​ Identifies molecular mass of peptides/proteins.

●​ Can sequence proteins via tandem MS (MS/MS).

VI. Protein Electrophoresis & Blotting Techniques

1. SDS-PAGE (Sodium Dodecyl Sulfate Polyacrylamide Gel Electrophoresis)

●​ Separates proteins by size (denatured form).

●​ SDS (detergent):
○​ Coats proteins with uniform negative charge.
○​ Disrupts non-covalent bonds, unfolding proteins.
●​ Smaller proteins migrate faster in the gel.

2. Western Blot (Immunoblotting)

●​ Detects specific proteins using antibodies.

●​ Steps:
1.​ SDS-PAGE → Proteins separated by size.
2.​ Transfer → Proteins transferred onto a membrane.
3.​ Primary Antibody → Binds target protein.
4.​ Secondary Antibody + Enzyme → Produces detectable signal (e.g.,
chemiluminescence).

Summary Table
Concept Key Points

Protein Folding Driven by non-covalent interactions,

chaperones assist
 Denaturation Loss of structure (heat, pH, chemicals,
detergents)

Chaperones Hsp70, Chaperonins (GroEL/GroES)

Post-Translational Modifications Phosphorylation, glycosylation, acetylation,

ubiquitination

In Vitro Protein Synthesis Uses ribosomes, tRNA, ATP/GTP

Amino Acid Composition Analysis Hydrolysis + Chromatography

Edman Degradation Identifies N-terminal amino acids

Chromatography Methods Gel Filtration (size), Ion Exchange (charge),

Hydrophobic (polarity), Affinity (binding)

X-ray Crystallography Determines 3D structure at atomic resolution

Mass Spectrometry Measures molecular weight, can sequence

proteins

SDS-PAGE Separates proteins by size

Western Blot Detects specific proteins using antibodies

chapter 6:

I. Function and Mechanism of Enzymes

Enzymes are biological catalysts that speed up biochemical reactions without being
consumed in the process. They work by lowering the activation energy (ΔG‡) required for a
reaction, thus increasing the reaction rate.

-​ speed is determined by activation energy. Low = faster

1. Enzyme Mechanism

●​ Enzymes bind to substrates forming an enzyme-substrate (ES) complex.

●​ The enzyme stabilizes the transition state, lowering the activation energy (ΔG‡).
●​ After the reaction, products are released, and the enzyme is free to catalyze another
reaction.
II. Six Classes of Enzymes
Enzymes are categorized into six major classes based on the type of reaction they catalyze:

Enzyme Class Type of Reaction Example

1. Oxidoreductases Catalyze Lactate dehydrogenase

oxidation-reduction
reactions (transfer of
electrons).

2. Transferases Catalyze the transfer of Aminotransferase

functional groups (e.g.,
methyl, phosphate).

3. Hydrolases Catalyze hydrolysis Lipase, Protease

reactions (breaking bonds
with water).

4. Lyases Catalyze addition or Pyruvate decarboxylase

removal of groups (e.g.,
decarboxylation,
dehydration).

5. Isomerases Catalyze the rearrangement Glucose isomerase

of atoms within a molecule
(isomerization).

6. Ligases Catalyze the joining of two DNA ligase

molecules, usually with
energy from ATP.

III. Key Enzyme Terms and Concepts

1. Holoenzyme

●​ The active enzyme made up of an apoenzyme (protein) and a cofactor (non-protein

part).
●​ Complete functional enzyme capable of catalysis.

2. Cofactor
 ●​ A non-protein molecule required for enzyme activity.
●​ Can be inorganic ions (e.g., Mg²⁺, Fe²⁺, Zn²⁺) or organic molecules (e.g., vitamins,
coenzymes).

3. Coenzyme

●​ A specific type of organic cofactor that works with the enzyme to facilitate the reaction.
●​ Coenzymes are often derived from vitamins (e.g., NAD⁺, FAD, CoA).

IV. Types of Vitamins: Polar and Non-polar

Vitamins serve as coenzymes or precursors to coenzymes. They are divided into two types
based on their solubility:

1. Polar (Water-Soluble) Vitamins

●​ These vitamins dissolve in water and are often involved in enzyme catalysis as
coenzymes.
●​ Examples:
○​ Vitamin B complex (B₁, B₂, B₆, B₁₂).
○​ Vitamin C (ascorbic acid).

2. Non-polar (Fat-Soluble) Vitamins

●​ These vitamins dissolve in fat and are stored in the body’s fat tissues. They often act as
antioxidants or hormones.
●​ Examples:
○​ Vitamin A (retinol), Vitamin D, Vitamin E, Vitamin K.

V. Thermodynamic Concepts in Enzyme Kinetics

1. ΔGo’ (Standard Free Energy Change)

●​ The change in free energy of a reaction under standard conditions (298 K, 1 M

concentration of reactants and products, 1 atm).
●​ ΔGo’ < 0 → Exergonic (spontaneous).
●​ ΔGo’ > 0 → Endergonic (non-spontaneous).

2. ΔG (Gibbs Free Energy Change)

 ●​ The actual free energy change in a reaction at any given moment, depending on the
concentration of reactants and products.
●​ ΔG = ΔGo’ + RT ln([products]/[reactants]).

3. Kcat (Turnover Number)

●​ The maximum number of substrate molecules converted to product per enzyme

molecule per unit time (usually in seconds).
●​ A higher Kcat implies a faster enzyme.

4. Keq (Equilibrium Constant)

●​ The ratio of products to reactants at equilibrium.

●​ Keq > 1 → Reaction favors products (exergonic).
●​ Keq < 1 → Reaction favors reactants (endergonic).

5. Exergonic vs. Endergonic Reactions

●​ Exergonic: Release energy, ΔG < 0 (spontaneous).

●​ Endergonic: Require energy input, ΔG > 0 (non-spontaneous).

6. Activation Energy (ΔG‡)

●​ The energy barrier that must be overcome for a reaction to occur.

●​ Enzymes lower ΔG‡, allowing reactions to proceed faster.

VI. Enzyme-Substrate Interaction and Theories

1. Enzyme-Substrate Complex (ES)

●​ Formed when the enzyme binds to the substrate, facilitating the conversion to
products.

2. Catalytic Site (Active Site)

●​ The region of the enzyme where the substrate binds and the catalytic reaction occurs.
●​ Typically a small region, with a high degree of specificity for the substrate.

3. Lock and Key Model

●​ The enzyme's active site is an exact match to the substrate, like a key fitting into a
lock.
 ●​ Less flexible than the induced fit model.
●​ transition- state stabilization
●​ proximity effect depends on concentration of enzyme and substrate

4. Induced Fit Model

●​ The enzyme’s active site undergoes conformational changes when the substrate
binds, optimizing the fit.
●​ This model accounts for flexibility in enzyme-substrate interactions.

VII. Enzyme Mechanisms

1. Two Types of Enzyme Mechanisms

Enzymes catalyze reactions through various mechanisms, such as:

A. Acid-Base Catalysis

●​ The enzyme donates or accepts protons (H⁺) to stabilize transition states or

intermediates.
●​ Example: Chymotrypsin uses histidine to catalyze peptide bond hydrolysis.

B. Covalent Catalysis

●​ The enzyme forms a temporary covalent bond with the substrate or transition state,
helping to lower activation energy.
●​ Example: Serine proteases (e.g., trypsin) form covalent bonds with substrates during
catalysis.

VIII. Summary Table

Concept Key Points

Holoenzyme Active enzyme with cofactor/coenzyme

Cofactor Non-protein molecule required for enzyme

activity

Coenzyme Organic cofactors, often derived from

vitamins
 Polar Vitamins Water-soluble (e.g., B vitamins, Vitamin C)

Non-polar Vitamins Fat-soluble (e.g., Vitamin A, D, E, K)

ΔGo' Standard free energy change

ΔG Actual free energy change

Kcat Turnover number, enzyme efficiency

Keq Equilibrium constant

Activation Energy (ΔG‡) Energy barrier for reaction

Exergonic Release energy, spontaneous (ΔG < 0)

Endergonic Requires energy input, non-spontaneous (ΔG

> 0)

Enzyme-Substrate Complex (ES) Complex formed during catalysis

Catalytic Site Active site where substrate binds and

reaction occurs

Lock and Key Model Enzyme active site exactly matches substrate

Induced Fit Model Enzyme active site undergoes conformational

change upon binding

Acid-Base Catalysis Involves proton transfer to stabilize transition

states

Covalent Catalysis Formation of covalent bonds between

enzyme and substrate

chapter 7:

I. Michaelis-Menten Kinetics
1. Michaelis-Menten Equation

●​ Describes the relationship between the reaction rate (v) and the concentration of
substrate ([S]).
 ●​ Equation:​
v=Vmax[S]KM+[S]v=KM​+[S]Vmax​[S]​
○​ v = rate of the reaction (velocity).
○​ Vmax = maximum reaction velocity (rate when the enzyme is saturated with
substrate).
○​ KM = Michaelis constant, the substrate concentration at which the reaction rate is
half of Vmax.
○​ [S] = concentration of the substrate.
●​

2. Important Terms

●​ Vmax: The maximum rate of reaction, achieved when the enzyme is saturated with
substrate.
●​ Kcat (Turnover Number): The number of substrate molecules converted to product per
enzyme molecule per unit time (sec⁻¹).
●​ KM (Michaelis Constant): A measure of the enzyme’s affinity for its substrate.
○​ Low KM → High affinity (enzyme reaches half-maximal velocity at low substrate
concentration).
○​ High KM → Low affinity.

3. Lineweaver-Burk Equation (Double-Reciprocal Plot)

●​ The Lineweaver-Burk plot is a linearized form of the Michaelis-Menten equation,

allowing easy determination of Vmax and KM from experimental data.
●​ Equation:​
1v=KMVmax[S]+1Vmaxv1​=Vmax​[S]KM​​+Vmax​1​
●​ It is represented as a double reciprocal plot with:
○​ The y-intercept = 1VmaxVmax​1​
○​ The x-intercept = −1KM−KM​1​

4. Sequential and Ping-Pong Mechanisms

●​ Enzyme-catalyzed reactions can follow different mechanisms:

○​ Sequential Mechanism: All substrates bind to the enzyme before the products
are released. Both substrates must bind to form a ternary complex.
■​ Ordered mechanism: Substrates bind in a defined order.
■​ Random mechanism: Substrates bind in any order.
○​ Ping-Pong Mechanism: The enzyme binds one substrate, reacts to form a
product, and then releases the product before binding the second substrate. The
enzyme is modified between the two reactions.
II. Enzyme Inhibition
Enzyme inhibitors are molecules that decrease enzyme activity by binding to the enzyme and
preventing the normal catalytic reaction.

1. Types of Enzyme Inhibition

Type of Binding Site Effect on Km Effect on Vmax Reversibility
Inhibition

Competitive Inhibitor Increases No effect on Reversible

Inhibition competes with KM(apparent) Vmax (at high
substrate for the substrate
active site concentration)

Non-competitiv Inhibitor binds to No effect on KM Decreases Reversible

e Inhibition an allosteric site Vmax
(not the active
site)

Uncompetitive Inhibitor binds Decreases Decreases Reversible

Inhibition only to the ES KM(apparent) Vmax
complex

Mixed Inhibitor binds to Increases Decreases Reversible

Inhibition both the KM(apparent) Vmax
enzymeand ES
complex

●​ ​
Competitive Inhibition:
○​ Effect: The inhibitor competes with the substrate for the active site, increasing
the apparent KM.
○​ Vmax is unchanged because if the substrate concentration is high enough, the
reaction can still reach the maximum rate.
●​ Non-competitive Inhibition:
○​ Effect: The inhibitor binds to a site other than the active site (allosteric site),
changing the enzyme's structure.
○​ KM remains the same, but Vmax decreases because the enzyme's catalytic
ability is reduced.
●​ Uncompetitive Inhibition:
○​ Effect: The inhibitor binds only to the enzyme-substrate (ES) complex,
preventing the formation of products.
○​ Both KM and Vmax decrease.
●​ Mixed Inhibition:
 ○​ Effect: The inhibitor binds to both the enzyme and enzyme-substrate complex.
It affects both the KM(increases it) and Vmax (decreases it).

III. Allostery and Cooperativity

1. Allosteric Enzymes

●​ Allosteric enzymes have multiple binding sites:

○​ Active site for substrate binding.
○​ Allosteric site for the binding of regulatory molecules (effectors).
●​ Binding of an effector to the allosteric site induces a conformational change in the
enzyme, which can enhance or inhibit enzyme activity.
○​ Allosteric activators increase enzyme activity.
○​ Allosteric inhibitors decrease enzyme activity.

2. Models of Cooperativity

●​ Cooperativity refers to the phenomenon where the binding of a ligand (e.g., substrate)
to one subunit of a multi-subunit enzyme affects the binding of additional ligands to other
subunits.
○​ Positive cooperativity: The binding of the first substrate enhances the binding
of subsequent substrates.
○​ Negative cooperativity: The binding of the first substrate reduces the affinity for
subsequent substrates.

Models of Cooperativity:

●​ Concerted Model (Monod-Wyman-Changeux Model): All subunits of the enzyme are

in one of two states, either active or inactive. Binding of a ligand to one subunit causes a
conformational change in all subunits.
●​ Sequential Model (Koshland Model): The enzyme exists in multiple conformational
states, and binding of a ligand to one subunit causes a local change in conformation,
affecting adjacent subunits.

IV. Regulation of Enzymes

1. Mechanisms of Enzyme Regulation
 ●​ Feedback Inhibition: The end product of a metabolic pathway inhibits an enzyme
earlier in the pathway.
○​ Example: In glycolysis, ATP inhibits phosphofructokinase, reducing the rate of
glucose metabolism when energy is abundant.
●​ Covalent Modification: Enzymes are regulated by the addition or removal of chemical
groups.
○​ Phosphorylation (addition of phosphate) is a common regulatory modification.
○​ Dephosphorylation (removal of phosphate) can activate or deactivate enzymes.
●​ Allosteric Regulation: As discussed, allosteric enzymes are regulated by the binding of
molecules at allosteric sites, leading to conformational changes that enhance or inhibit
activity.
●​ Proteolytic Activation: Some enzymes are synthesized as inactive zymogens
(proenzymes) and are activated by proteolytic cleavage.
○​ Example: Trypsinogen is activated to trypsin by cleavage of a peptide bond.
●​ Enzyme Synthesis and Degradation:
○​ Gene expression: Enzyme activity can be regulated by controlling the synthesis
of the enzyme itself.
○​ Proteasomal degradation: Enzymes can be marked for degradation by the
addition of ubiquitin, leading to their destruction by the proteasome.

V. Summary Table
Concept Key Points

Michaelis-Menten Equation Describes the relationship between reaction

rate (v), substrate concentration ([S]), Vmax,
and KM

Vmax Maximum reaction velocity

KM Michaelis constant, substrate concentration at

half-maximal velocity

Kcat (Turnover Number) Number of substrate molecules converted to

product per enzyme molecule per unit time

Lineweaver-Burk Equation Linearized form of Michaelis-Menten

equation, allows calculation of Vmax and KM

Enzyme Inhibition Types: competitive, non-competitive,

uncompetitive, mixed
 Allostery Regulation of enzyme activity via allosteric
sites

Cooperativity Models Concerted and sequential models of

cooperativity

Regulation of Enzymes Feedback inhibition, covalent modification,

proteolytic activation, synthesis/degradation

chapter 8:

I. General Structure of a Monosaccharide

Monosaccharides are the simplest form of carbohydrates, consisting of a single sugar unit. They
can be classified into aldoses and ketoses, depending on the functional group they contain.

1. Basic Structure of Monosaccharides

Monosaccharides have the general formula (CH₂O)n, where n ≥ 3. They consist of:

●​ A carbon backbone (a chain of carbon atoms).

●​ At least one hydroxyl group (-OH) attached to each carbon (except for the carbonyl
group).
●​ A carbonyl group (C=O), which determines whether the sugar is an aldose or a
ketose.
○​ Aldoses: The carbonyl group is an aldehyde (-CHO) located at the end of the
molecule.
○​ Ketoses: The carbonyl group is a ketone (C=O) located in the middle of the
molecule.

2. Aldoses vs. Ketoses

●​ Aldoses:
○​ Contain an aldehyde group (-CHO) as the functional group.
○​ Examples: Glucose, Galactose.
●​ Ketoses:
○​ Contain a ketone group (C=O) within the molecule.
○​ Examples: Fructose, Ribulose.
II. Functions of Carbohydrates
Carbohydrates serve a variety of crucial biological functions in living organisms, including:

1. Energy Source and Storage

●​ Monosaccharides like glucose provide an immediate source of energy for cells through
glycolysis and cellular respiration.
●​ Polysaccharides like glycogen (in animals) and starch (in plants) serve as storage
forms of glucose for future energy needs.

2. Structural Role

●​ Cellulose (a polysaccharide) provides structural support to plant cell walls, giving them
rigidity.
●​ Chitin provides structure to the exoskeletons of arthropods and the cell walls of fungi.

3. Signaling and Recognition

●​ Carbohydrates are often attached to proteins and lipids on the cell surface, forming
glycoproteins and glycolipids. These play key roles in cell recognition, signaling, and
immune responses.

4. Glycoconjugates: covalent linkage between a saccharide and protein,

peptide, or lipid. Also called glycoprotein and glycolipid

●​ Carbohydrates are important precursors for the synthesis of nucleotides, amino acids,
and lipids.

III. Concepts Related to Monosaccharides

1. Enantiomer

●​ Enantiomers are non-superimposable mirror images of each other.

○​ For monosaccharides, enantiomers differ in the spatial arrangement of atoms
around one or more asymmetric carbon atoms. They have chiral carbons and
form enantiomers
○​ D enantiomers of saccharides are more common
○​ Example: D-glucose and L-glucose are enantiomers. They are mirror images of
each other and cannot be superimposed on each other.
○​
2. Epimer

●​ Epimers are stereoisomers that differ in the configuration at only one chiral center
(asymmetric carbon) in their structure.
○​ Epimers have the same molecular formula but differ in the orientation of atoms
at one specific carbon atom.
○​ Example: D-glucose and D-galactose are epimers, differing at carbon 4.

IV. Monosaccharide Structure and Stereochemistry

1. Fischer Projections

●​ The Fischer projection is a two-dimensional representation of a molecule, commonly

used to depict the configuration of chiral centers in monosaccharides.
●​ The horizontal lines represent bonds coming out of the plane of the paper, and the
vertical lines represent bonds going into the plane.
●​ The chiral centers are typically represented at the intersections of lines, with hydroxyl
groups or hydrogensattached to each chiral center.

2. Haworth Projections

●​ The Haworth projection is a way of depicting the cyclic form of monosaccharides

(such as glucose) when they are in their ring structure.
○​ For aldoses (e.g., glucose), the aldehyde group reacts with a hydroxyl group
to form a pyranose (six-membered ring).
○​ For ketoses (e.g., fructose), the ketone group reacts with a hydroxyl group to
form a furanose (five-membered ring).
○​ In the Haworth structure, the carbon atoms involved in the ring formation are
numbered, and substituents like hydroxyl groups are shown relative to the
plane of the ring (either above or below the plane).

V. Summary Table of Important Concepts

Concept Definition/Explanation

Monosaccharide Structure Simple sugars with general formula (CH₂O)n;

contain carbonyl group (aldehyde or ketone)
and hydroxyl groups.
Aldoses Monosaccharides with an aldehyde group
(-CHO), such as glucose.

Ketoses Monosaccharides with a ketone group

(C=O), such as fructose.

Enantiomer Stereoisomers that are non-superimposable

mirror images of each other.

Epimer Stereoisomers that differ at only one chiral

center.

Fischer Projection A 2D representation of a monosaccharide,

highlighting chiral centers.

Haworth Projection A 3D representation of the cyclic form of

monosaccharides.

VI. Summary of Carbohydrate Functions

Function Explanation

Energy Source Monosaccharides (e.g., glucose) are used in

glycolysis for energy production.

Energy Storage Polysaccharides (e.g., glycogen, starch) store

glucose for future energy.

Structural Support Cellulose and chitin provide rigidity and

structure in plants and animals.

Signaling Glycoproteins and glycolipids play roles in

cell signaling and recognition.

Precursor to Biomolecules Carbohydrates serve as building blocks for

lipids, nucleic acids, and proteins.