Seminar exam questions
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116 Terms
QS1
Collagen PTMs
Hydroxylation and glycosylation; carboxylation is not the collagen modification asked for.
Vitamin for prolyl/lysyl hydroxylases
Vitamin C.
Vitamin for glutamate carboxylase
Vitamin K.
Vitamin K antagonist rodenticide
Impaired gamma-carboxylation of glutamate in clotting factors; bleeding/coagulopathy.
Valine at its isoelectric point
Zwitterion: NH3+–CH(CH(CH3)2)–COO−. Below pI, net positive; does not migrate toward positive anode.
3. What is the name of form B?
Answer: Zwitterion (dipolar ion).
It contains both a positively charged NH₃⁺ group and a negatively charged COO⁻ group, giving an overall net charge of zero.
4. Does form A move towards the anode?
Answer: NO.
Form A is positively charged, so it moves towards the cathode (negative electrode), not the anode (positive electrode).
Glycated haemoglobin
Reflects average glycaemic exposure over the lifespan of circulating erythrocytes; not a serum haemoglobin measurement.
Ubiquitin question
C: ubiquitin attaches to lysine residues; polyubiquitination often marks proteins for proteasomal degradation.
Phosphorylation/dephosphorylation
Kinases generally transfer phosphate from ATP; phosphatases remove it. Regulation is reversible and signal-dependent.
QS2
Protein structure matching
Primary = sequence (B); secondary = local regular structure (D best approximate); tertiary = full 3D fold (no
precise option); quaternary = subunit assembly (A). The options are imperfect.
Amino acids at neutral pH
A: predominantly zwitterions (dipolar ions).
Optically inactive amino acid
A: glycine.
Chirality
C: alpha carbon bonded to four distinct groups.
Glutamyl-cysteinyl-glycine
Glutathione (GSH); gamma-glutamyl linkage; antioxidant and peroxide detoxification.
Alpha helix
Statements 1 and 5 true. Side chains point outward; proline disrupts alpha helices.
Peptide migration
At pH 2: positive, toward cathode. At pH 11: negative, toward anode. At pI: no net migration.
Mad cow disease
E: prions.
QS3
Coenzyme vs metal
Coenzymes are organic cofactors, often vitamin-derived; Mn2+ is a metal cofactor, not a coenzyme.
Enzyme-substrate association
A: temporary association.
Saturation plateau
A: enzyme active sites saturated with substrate.
Allosteric inhibitor
A: binds outside the catalytic site.
Catalysis
E: enzymes lower activation energy; do not alter reaction equilibrium constants.
PMSF serine protease inhibition
A: irreversible covalent inhibition.
Competitive inhibition
Apparent Km increases; Vmax unchanged. In Lineweaver–Burk plot lines intersect at y-axis.
Km and enzyme speed
Km alone cannot identify the fastest enzyme: it reflects substrate concentration at half Vmax, not Vmax or kcat
QS4
Bilirubin transport
Unconjugated bilirubin circulates bound to albumin; bilirubin is conjugated in liver.
Heme degradation
Heme —heme oxygenase→ biliverdin (green) —biliverdin reductase→ bilirubin (yellow).
Hemoglobin dissociation
Increased pH or decreased CO2 shifts oxygen dissociation curve left.
Lead and ferrochelatase
Inhibits Fe2+ incorporation into protoporphyrin IX, impairing heme synthesis.
Direct bilirubin elevation
Biliary obstruction is the listed classic cause.
QS5
Lactate formation
Pyruvate + NADH + H+ → lactate + NAD+; regenerates NAD+ for glycolysis.
Glycolysis location
Cytosol, not mitochondria.
Hexokinase and glucokinase
Both use ATP and produce glucose-6-phosphate. Glucokinase has higher Km; hexokinase is inhibited by G6P.
Pyruvate kinase deficiency in dogs
Reduced erythrocyte ATP can cause haemolysis and anaemia; the haemoglobin oxygen-dissociation curve
may change with 2,3-BPG.
Seminar 1
Q: What enzymes add and remove phosphate groups from proteins?
A: Protein kinases add phosphate groups; protein phosphatases remove them.
Q: Which amino acid side chains are commonly phosphorylated?
A: Serine, threonine and tyrosine
Q: What molecule donates phosphate during protein phosphorylation?
A: ATP.
Q: Which amino acids are hydroxylated in collagen?
A: Proline and lysine.
Q: Which vitamin is required for collagen hydroxylation?
A: Vitamin C.
Q: Which vitamin is required for glutamate carboxylation in coagulation factors?
A: Vitamin K.
Q: Which post-translational modifications are important for collagen?
A: Hydroxylation and glycosylation.
Q: What is the consequence of ubiquitination for proteins targeted for degradation?
A: Recognition and degradation by the proteasome.
Q: What is the nonenzymatic attachment of glucose to proteins called?
A: Glycation.
Q: How is glycosylation different from glycation?
A: Glycosylation is enzyme-mediated; glycation is nonenzymatic.
Q: What is the result of phosphorylation of tyrosine?
A: A phosphate group is attached to the phenolic hydroxyl group of the tyrosine side chain.
Q: What is the role of vitamin K antagonists in coagulation?
A: They impair vitamin K-dependent carboxylation of clotting factors, increasing bleeding risk.
Seminar 2
Q: What is the primary structure of a protein?
A: Its amino acid sequence.
Q: What is the secondary structure of a protein?
A: Local regular structures such as alpha helices and beta sheets.
Q: What is the tertiary structure of a protein?
A: Its overall three-dimensional conformation.
Q: What is the quaternary structure of a protein?
A: The association of multiple polypeptide subunits.
Q: Which amino acid is optically inactive?
A: Glycine.
Q: What is the predominant ionic form of amino acids at neutral pH?
A: Zwitterions (dipolar ions).
Q: What is the tripeptide gamma-glutamyl-cysteinyl-glycine?
A: Glutathione.
Q: What is unusual about the glutamate–cysteine bond in glutathione?
A: It is a gamma-glutamyl isopeptide bond.
Seminar 3
Q: Which protease acts in the acidic stomach?
A: Pepsin.
Q: Which amino acids does trypsin preferentially cleave after?
A: Lysine and arginine.
Q: Which residues does chymotrypsin preferentially cleave after?
A: Phenylalanine, tyrosine and tryptophan.
Q: What does a protease hydrolyze?
A: Peptide bonds.
Seminar 4
Q: When is Vmax reached?
A: When the enzyme is saturated with substrate.
Q: What is Km in Michaelis–Menten kinetics?
A: The substrate concentration at which initial velocity equals half of Vmax.
Q: What happens to Vmax and apparent Km in competitive inhibition?
A: Vmax remains unchanged; apparent Km increases.
Q: What is an irreversible inhibitor?
A: An inhibitor that permanently inactivates the enzyme under the conditions considered.
Q: What complex forms when an enzyme first binds its substrate?
A: The enzyme–substrate complex.
Q: Where does an allosteric inhibitor bind?
A: At a regulatory site distinct from the active site.
Seminar 5
Q: What is the main purpose of converting pyruvate to lactate?
A: Regeneration of NAD+ so glycolysis can continue.
Q: Which enzyme catalyzes pyruvate ↔ lactate?
A: Lactate dehydrogenase.
Q: How much net ATP does glycolysis yield per glucose?
A: 2 ATP.
Q: What happens to NADH during pyruvate reduction to lactate?
A: NADH is oxidized to NAD+.
Seminar 6
Q: Which enzyme complex converts pyruvate to acetyl-CoA?
A: Pyruvate dehydrogenase complex.
Q: What type of reaction converts pyruvate to acetyl-CoA?
A: Oxidative decarboxylation.
Q: Where does the citric acid cycle occur in eukaryotic cells?
A: Mitochondrial matrix.
Q: How many NADH and FADH2 are formed per acetyl-CoA oxidized in the citric acid cycle?
A: 3 NADH and 1 FADH2.
Q: How many GTP equivalents are generated per turn of the citric acid cycle?
A: 1 GTP.
Q: Does phosphorylation activate or inactivate pyruvate dehydrogenase?
A: Inactivates it.
Q: Does dephosphorylation activate or inactivate pyruvate dehydrogenase?
A: Activates it.
Q: What are reactions that replenish citric acid cycle intermediates called?
A: Anaplerotic reactions.
Q: How does a high NADH/NAD+ ratio affect alpha-ketoglutarate dehydrogenase?
A: It inhibits the enzyme.
Seminar 8
Q: What are the three amino acids of glutathione?
A: Glutamate, cysteine and glycine
Q: What is reduced glutathione abbreviated as?
A: GSH.
Q: What is oxidized glutathione abbreviated as?
A: GSSG.
Q: Which enzyme uses GSH to reduce hydrogen peroxide?
A: Glutathione peroxidase.
Q: Which enzyme regenerates GSH from GSSG?
A: Glutathione reductase.
Q: Which reducing equivalent is needed to regenerate glutathione?
A: NADPH.
Q: Why is the pentose phosphate pathway important in red blood cells?
A: It supplies NADPH for antioxidant protection.
Seminar 10
Q: Where are ketone bodies synthesized?
A: Liver mitochondria.
Q: From what precursor are ketone bodies synthesized?
A: Acetyl-CoA.
Q: Name the three ketone bodies.
A: Acetoacetate, beta-hydroxybutyrate and acetone.
Q: Which ketone body spontaneously decarboxylates to acetone?
A: Acetoacetate.
Q: Can the liver use ketone bodies as fuel?
A: No; the liver lacks the enzyme needed for ketone body utilization.
Q: Can red blood cells use ketone bodies?
A: No; they lack mitochondria.
Q: Can the brain use ketone bodies during prolonged fasting?
A: Yes.
Q: Can muscles use ketone bodies without oxygen?
A: No; ketone utilization requires mitochondrial aerobic metabolism.
Q: What does elevated beta-hydroxybutyrate in dairy cows suggest?
A: Increased fat mobilization and ketogenesis, often associated with negative energy balance
Seminar 11
Q: Which amino acid is the precursor of adrenaline?
A: Tyrosine.
Q: Which amino acid is the precursor of serotonin?
A: Tryptophan.
Q: Which amino acid is the precursor of GABA?
A: Glutamate.
Q: Which amino acid is the precursor of nitric oxide?
A: Arginine.
Q: What does glutamate decarboxylase produce?
A: GABA and CO2.
Q: What does arginase produce from arginine?
A: Ornithine and urea.
Q: What is the major urinary breakdown product of creatine/phosphocreatine?
A: Creatinine.
Q: Which enzyme phosphorylates creatine?
A: Creatine kinase.