🧬 Biomolecules & Enzyme Kinetics

All living organisms are composed of organic macromolecules and inorganic constituents operating in a dynamic non-equilibrium steady state. Mastery of biomolecular thermodynamics and enzyme kinetics is essential for understanding physiological regulation and metabolic fluxes.

1. 🧪 Chemical Composition Analysis (Acid-Soluble vs Acid-Insoluble Pool)

When living tissue (e.g., liver or leaf) is ground in Trichloroacetic acid ( $C l_{3} C - C O O H$ ) and filtered through cheesecloth:

Fraction	State	Molecular Weight Range	Major Chemical Constituents
Filtrate (Acid-Soluble Pool)	Biomicromolecules / Cytoplasmic matrix	$18 - 800 Da$	Monosaccharides, Amino acids, Nucleotides, Mineral ions, Organic acids
Retentate (Acid-Insoluble Pool)	Biomacromolecules / Cellular organelles	$> 10, 000 Da$	Proteins, Polysaccharides, Nucleic Acids, Lipids

The Lipid Anomaly (High-Yield NEET Trap)

Lipids have molecular weights under $800 Da$ , yet they separate into the acid-insoluble retentate!

Reason: Lipids are not polymeric macromolecules; however, when cell membranes are disrupted during grinding, lipids aggregate into insoluble hydrophobic vesicles and micelles that cannot pass through the filter mesh.

2. 🥩 Amino Acids and Protein Architecture

🥩 Amino Acid Substituted Methane Architecture and pH-Dependent Zwitterion Equilibrium

2.1 Essential vs Non-Essential Amino Acids

Essential Amino Acids (Must be acquired via diet): $PVT TIM HALL ⟹ Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Arginine, Leucine, Lysine$
Aromatic Amino Acids: Tyrosine, Phenylalanine, Tryptophan.
Sulfur-Containing Amino Acids: Methionine, Cysteine.
Basic Amino Acids: Lysine ( $+ 1$ ), Arginine ( $+ 1$ ), Histidine.
Acidic Amino Acids: Glutamic acid ( $- 1$ ), Aspartic acid ( $- 1$ ).
Neutral Amino Acids: Glycine (simplest, optically inactive), Alanine, Valine.

2.2 Hierarchical Levels of Protein Structure

Level	Stabilizing Chemical Bonds	Structural Motifs	Classic Examples
Primary ( $1^{\circ}$ )	Covalent peptide bonds ( $- C O - N H -$ )	Positional linear sequence from N-terminus to C-terminus	Insulin (51 amino acids), Polypeptide chain
Secondary ( $2^{\circ}$ )	Intramolecular & Intermolecular Hydrogen bonds	$α$ -Helix (Right-handed, $3.6 residues/turn$ ), $β$ -Pleated Sheets	Keratin (hair), Collagen, Fibroin (silk)
Tertiary ( $3^{\circ}$ )	Hydrophobic interactions, Disulfide bridges ( $- S - S -$ ), Ionic bonds, Van der Waals	3D globular biological folding (Creates active catalytic clefts)	Myoglobin, Ribonuclease, Most enzymes
Quaternary ( $4^{\circ}$ )	Non-covalent subunit interactions	Multi-subunit spatial assembly	Hemoglobin ( $α_{2} β_{2}$ tetramer, $4 heme groups$ )

3. ⚡ Enzyme Catalysis & Michaelis-Menten Kinetics

Enzymes are biocatalysts that accelerate chemical reactions by lowering the activation energy ( $E_{a}$ ) without altering the overall thermodynamic equilibrium ( $Δ G^{\circ}$ ).

E + S ⇌_{k_{- 1}}^{k_{1}} ES \overset{k_{cat}}{\to} E + P

⚡ Enzyme Thermodynamics: Lowering Activation Energy ($E_a$) Barrier

3.1 The Michaelis-Menten Equation

v = \frac{V_{max} [S]}{K_{m} + [S]}

Where:

$v$ = Initial reaction velocity.
$V_{max}$ = Maximal velocity when all active sites are saturated with substrate.
$K_{m}$ (Michaelis Constant) = Substrate concentration $[S]$ at which the reaction velocity is half-maximal ( $v = \frac{V_{max}}{2}$ ).
Affinity Relationship: $K_{m} \propto \frac{1}{Enzyme Affinity for Substrate}$ (A smaller $K_{m}$ signifies higher catalytic affinity).

4. 🛑 Enzyme Inhibition Mechanisms

🛑 Competitive vs Non-Competitive Enzyme Inhibition Kinetics

Parameter	Competitive Inhibition	Non-Competitive Inhibition	Uncompetitive Inhibition
Binding Site	Catalytic active site	Allosteric site (E or ES)	ES complex exclusively
Substrate Overcome?	Yes (At high $[S]$ , inhibitor displaced)	No (Cannot be reversed by adding $[S]$ )	No
$V_{max}$ Effect	Unchanged	Decreased	Decreased
$K_{m}$ Effect	Increased	Unchanged	Decreased
Canonical Example	Malonate inhibiting Succinate Dehydrogenase; Statin inhibiting HMG-CoA reductase	Cyanide inhibiting Cytochrome c Oxidase ( $F e^{3 +}$ binding)	Lithium on inositol monophosphatase

5. 🧩 Enzyme Classification (IUBMB System: 6 Master Classes)

Memory Mnemonic: OTHLIL

Oxidoreductases / Dehydrogenases: Catalyze oxidation-reduction reactions ( $A_{red} + B_{ox} ⇌ A_{ox} + B_{red}$ ).
Transferases: Transfer functional groups other than hydrogen ( $S - G + S^{'} ⇌ S + S^{'} - G$ ).
Hydrolases: Cleave ester, ether, peptide, glycosidic, or $C - C$ bonds using water ( $H_{2} O$ ).
Lyases: Cleave bonds by mechanisms other than hydrolysis, leaving double bonds ( $C - C ⟶ C = C$ ).
Isomerases: Catalyze interconversion of geometric, optical, or structural isomers.
Ligases / Synthetases: Catalyze joining of two molecules coupled with ATP hydrolysis (e.g., DNA Ligase, Glutamine synthetase).

🧬 Biomolecules & Enzyme Kinetics ​

1. 🧪 Chemical Composition Analysis (Acid-Soluble vs Acid-Insoluble Pool) ​

2. 🥩 Amino Acids and Protein Architecture ​

2.1 Essential vs Non-Essential Amino Acids ​

2.2 Hierarchical Levels of Protein Structure ​

3. ⚡ Enzyme Catalysis & Michaelis-Menten Kinetics ​

3.1 The Michaelis-Menten Equation ​

4. 🛑 Enzyme Inhibition Mechanisms ​

5. 🧩 Enzyme Classification (IUBMB System: 6 Master Classes) ​