Biochemistry End-of-Year 2012 (2) — Past Paper OmpathStudy

Bchem EOY 2012 (2) — Past Paper Questions & Answers University of Nairobi, Level I Examinations 2011/2012 — HBC 100 / UPC 100 / VBC 100: Biochemistry. This paper carries no printed answer key; model answers below are written from standard biochemistry references, not copied from a marking scheme. --- Section A: Essay Questions (Attempt any THREE) — 30 Marks Question 1 With full details, describe the conversion of palmitoyl-CoA to myristoyl-CoA. Model answer: This is one round of the β-oxidation spiral, shortening the 16-carbon palmitoyl-CoA by two carbons to the 14-carbon myristoyl-CoA. Oxidation: Acyl-CoA dehydrogenase removes two hydrogens from the Cα–Cβ bond, forming a trans-Δ²-enoyl-CoA and reducing FAD to FADH₂ (which feeds electrons into the ETC via ETF). Hydration: Enoyl-CoA hydratase adds water across the double bond, forming L-3-hydroxyacyl-CoA. Oxidation: 3-hydroxyacyl-CoA dehydrogenase oxidizes the hydroxyl to a keto group, forming 3-ketoacyl-CoA and reducing NAD⁺ to NADH. Thiolysis: β-ketothiolase cleaves the bond between Cα and Cβ using a new CoA-SH, releasing acetyl-CoA and the shortened myristoyl-CoA (C14). Net: Palmitoyl-CoA + FAD + NAD⁺ + CoA-SH → Myristoyl-CoA + FADH₂ + NADH + Acetyl-CoA. --- Question 2 The titration curve of amino acid alanine shows the ionization of the two functional groups with pKa values of 2.34 and 9.96 corresponding to carboxylic acid and protonated amino groups respectively, on addition of 0.1M NaOH. (i) Draw the titration curve indicating the various ionic species at particular pH values. (ii) Calculate and explain the meaning of "isoelectric pH". (iii) Mention three things that can be derived from the titration curve. Model answer: (i) The curve (pH on y-axis vs. equivalents of NaOH on x-axis) starts at low pH with alanine fully protonated (⁺H₃N–CH(CH₃)–COOH, net charge +1). As NaOH is added, the first buffering plateau occurs around pH 2.34 (pKa1) as the carboxyl group is titrated, giving the zwitterion (⁺H₃N–CH(CH₃)–COO⁻, net charge 0) at the first equivalence point. Further NaOH titrates the amino group, plateauing near pH 9.96 (pKa2), ending with the fully deprotonated species (H₂N–CH(CH₃)–COO⁻, net charge −1) at the second equivalence point. (ii) Isoelectric pH (pI) = average of the two pKa values flanking the neutral (zwitterion) species: pI = (2.34 + 9.96)/2 = 6.15 . This is the pH at which the amino acid carries no net charge (exists predominantly as the zwitterion) and therefore doesn't migrate in an electric field. (iii) From the titration curve one can derive: the pKa values of each ionizable group (read at the midpoint of each buffering region); the isoelectric point (pH at the inflection between the two pKa's, where net charge = 0); and the buffering regions/capacity of the amino acid (flattest parts of the curve, near each pKa, where the solution best resists pH change). --- Question 3 (a) Outline the criteria used to classify compounds as neurotransmitters. (b) Mention three ways by which action of neurotransmitters can be terminated. (c) Name the two compounds used in synthesis of acetylcholine and the enzyme catalyzing this reaction. Model answer: (a) Criteria for classifying a compound as a neurotransmitter: It must be synthesized in the presynaptic neuron (or its precursors/synthesizing enzymes must be present there). It must be stored in synaptic vesicles and released in a calcium-dependent manner upon depolarization. Exogenous application to the postsynaptic cell must reproduce the same effect as physiological nerve stimulation. A specific receptor for the substance must exist on the postsynaptic membrane. A mechanism must exist to terminate its action (reuptake, enzymatic degradation, or diffusion). (b) Ways neurotransmitter action is terminated: Enzymatic degradation (e.g. acetylcholinesterase breaking down acetylcholine; MAO/COMT breaking down catecholamines). Reuptake into the presynaptic neuron via specific transporters (e.g. serotonin, dopamine, norepinephrine reuptake). Simple diffusion away from the synaptic cleft. (c) Acetylcholine is synthesized from choline and acetyl-CoA , catalyzed by the enzyme choline acetyltransferase (ChAT) . --- Question 4 (a) Briefly explain the role of the following enzymes in DNA replication: (i) DNA helicases (ii) DNA polymerase I (iii) DNA ligase. (b) Explain why DNA replication proceeds with very high fidelity. (c) The scheme shows a gene expression system. Use the genetic code to fill the missing information and name processes x and y. (d) Which genetic disorder is associated with inability to repair DNA damage by UV radiation? Describe the biosynthesis of testosterone in the testis. Model answer: (a)(i) DNA helicases unwind the parental double helix ahead of the replication fork, breaking the hydrogen bonds between base pairs using ATP hydrolysis. (ii) DNA polymerase I (in bacteria) removes the RNA primers from Okazaki fragments and fills the resulting gaps with DNA, using its 5'→3' exonuclease and p