SECTION "B" [25 Marks]

Q1. Classify proteins on the basis of functions with suitable examples. Write down the structural organization of secondary proteins. [3+3=6]

• The polypeptide chain coils into a right-handed helix.
• Each amino acid residue advances the helix by 1.5 Å (0.15 nm) and 100°.
• There are 3.6 amino acid residues per turn.
• Hydrogen bonds form between the -C=O of one residue and the -NH of the 4th residue ahead.
• The R-groups project outward from the helix.
• Example: alpha-keratin (hair, nails).

• The polypeptide chain is stretched into a zigzag configuration.
• Hydrogen bonds form between adjacent polypeptide strands running parallel or antiparallel to each other.
• Antiparallel beta sheets are more stable.
• R-groups alternate above and below the plane of the sheet.
• Example: Fibroin (silk), beta-keratin.

• A sharp turn that reverses the direction of the polypeptide chain.
• Typically involves 4 amino acid residues.
• Stabilized by a hydrogen bond between the 1st and 4th residue.
• Common at the surface of proteins.

• Segments with no regular repeating structure.
• Not truly random; have a defined structure in the native state.

Q2. Define enzyme, coenzyme, and isoenzyme. Explain factors that affect enzyme activity. [2+3=5]

1. Substrate Concentration: As substrate concentration increases, the reaction rate increases until all active sites are saturated (Vmax). The Michaelis-Menten equation describes this relationship. Km is the substrate concentration at half Vmax - a measure of enzyme-substrate affinity.
2. Temperature: Enzyme activity increases with temperature up to an optimum (~37°C in humans). Beyond the optimum, thermal denaturation of the protein structure causes rapid loss of activity. Q10 (temperature coefficient) = ~2 for most enzymes.
3. pH: Each enzyme has an optimal pH. Deviation from this pH alters the ionization state of active site residues, reducing activity. Example: Pepsin works best at pH 1.5-2.0; Trypsin at pH 7.8-8.7; most intracellular enzymes at pH 7.4.
4. Enzyme Concentration: At constant substrate, increasing enzyme concentration increases reaction rate proportionally (assuming substrate is in excess).
5. Inhibitors:
   • Competitive inhibition: Inhibitor resembles substrate and competes for the active site. Km increases, Vmax unchanged. Example: Malonate inhibiting succinate dehydrogenase.
   • Non-competitive inhibition: Inhibitor binds at a site other than the active site (allosteric site). Km unchanged, Vmax decreases. Example: Heavy metals (Hg2+, Pb2+).
   • Uncompetitive inhibition: Inhibitor binds only to the enzyme-substrate complex.
6. Cofactors and Coenzymes: Many enzymes require metal ions (Mg2+, Zn2+, Fe2+) or coenzymes for activity. Absence of these reduces or abolishes activity.
7. Allosteric Regulation: Allosteric enzymes have regulatory sites distinct from the active site. Binding of allosteric activators or inhibitors changes the enzyme's conformation and activity. Example: Phosphofructokinase-1 (PFK-1) is inhibited by ATP and activated by AMP.

Q3. Define neurotransmitter, write down the criteria for considering a substance as a neurotransmitter, and classify them. [1+2+2=5]

1. The substance must be synthesized in the presynaptic neuron.
2. It must be stored in synaptic vesicles in the nerve terminal.
3. It must be released from the presynaptic terminal in response to depolarization, in a calcium-dependent manner.
4. It must bind to specific receptors on the postsynaptic membrane and produce a defined response.
5. There must be a mechanism for its inactivation - either by enzymatic degradation (e.g., acetylcholinesterase), reuptake into the presynaptic terminal, or diffusion.
6. Application of the substance exogenously must mimic the effect of nerve stimulation.

• Excitatory: Glutamate, Acetylcholine, Dopamine, Norepinephrine, Serotonin
• Inhibitory: GABA (major inhibitory NT of CNS), Glycine (major inhibitory NT of spinal cord), Dopamine (in some pathways)

Q4 (Short Notes) [3×3=9]

a. Reactions of Glycolysis with Rate-Limiting Enzymes

• Preparatory phase (steps 1-5): consumes 2 ATP
• Pay-off phase (steps 6-10): generates 4 ATP + 2 NADH

• Hexokinase (Km ~0.1 mM) is inhibited by product glucose-6-phosphate.
• Glucokinase (liver, Km ~10 mM) is induced by insulin.

• Most important regulatory enzyme of glycolysis.
• Activated by: AMP, ADP, Fructose-2,6-bisphosphate, Pi.
• Inhibited by: ATP (high energy charge), Citrate.

• Activated by: Fructose-1,6-bisphosphate (feed-forward activation).
• Inhibited by: ATP, Alanine, Acetyl-CoA.

b. Thalassemia

• Adult hemoglobin (HbA) = α2β2 tetramer.
• α-globin genes: located on chromosome 16 (2 genes per haploid genome, total 4 genes).
• β-globin gene: located on chromosome 11 (1 gene per haploid genome, total 2 genes).
• α-Thalassemia: mainly caused by gene deletions.
• β-Thalassemia: mainly caused by point mutations affecting transcription, splicing, or translation of β-globin mRNA.

• Decreased synthesis of one globin chain leads to relative excess of the other.
• Unpaired excess chains form intracellular precipitates → oxidative damage → hemolysis and ineffective erythropoiesis.

• β-Thalassemia Major (Cooley's anemia): Homozygous (β0/β0 or β+/β+). Severe microcytic hypochromic anemia. Requires regular blood transfusions. Hepatosplenomegaly, bone marrow expansion causing facial deformities ("chipmunk facies"), growth retardation.
• β-Thalassemia Intermedia: Moderate anemia; blood transfusions not regularly required.
• β-Thalassemia Minor (trait): Heterozygous (β0/β or β+/β). Mild or no anemia; red cell abnormalities (microcytosis, hypochromia) present. Usually asymptomatic. Protects against malaria.

• Silent carrier (-/αα): completely asymptomatic.
• α-Thalassemia trait (--/αα or -α/-α): mild microcytic anemia.
• HbH disease (--/-α): moderately severe hemolytic anemia. Excess β-chains form β4 tetramers (HbH).
• Hydrops fetalis / Hb Bart's (--/--): all 4 α genes deleted; lethal in utero. Excess γ-chains form γ4 tetramers (Hb Bart's) with very high O2 affinity.

c. Myasthenia Gravis

• In ~85% of cases: IgG autoantibodies against nicotinic acetylcholine receptors (nAChR) at the postsynaptic membrane of the NMJ.
• In ~5-10%: antibodies against MuSK (muscle-specific kinase), important for clustering of AChRs.
• Antibody-receptor binding leads to:
  1. Receptor internalization and degradation (reduced receptor number).
  2. Complement-mediated destruction of the postsynaptic membrane.
  3. Functional block of receptor activation.
• Result: Reduced acetylcholine-mediated depolarization → muscle weakness.

• Fatigable muscle weakness - worse with repetitive use, better with rest.
• Ocular muscles most commonly affected first: ptosis (drooping eyelid), diplopia (double vision).
• Can progress to dysphagia, dysarthria, limb weakness.
• Myasthenic crisis: respiratory muscle involvement → life-threatening respiratory failure.

• Edrophonium (Tensilon) test: short-acting acetylcholinesterase inhibitor transiently improves weakness.
• Serum anti-AChR antibodies (positive in ~85%).
• Repetitive nerve stimulation: decremental response.
• CT chest: thymoma present in ~15% of patients.

• Acetylcholinesterase inhibitors (Pyridostigmine) - increase ACh in synapse.
• Immunosuppressants (Prednisolone, Azathioprine).
• Plasmapheresis / IV Immunoglobulin in crisis.
• Thymectomy.