FMGE Bio Chemistry Syllabus

Define an enzyme and the terms substrate, active site, and cofactor.

An enzyme is a biological catalyst (usually protein) that lowers activation energy without being consumed. The substrate is its reactant; the active site is where catalysis occurs; cofactors are non-protein helpers (metal ions or organic coenzymes) required for activity.

What do Km and Vmax represent in Michaelis-Menten kinetics?

Vmax is the maximal reaction velocity when the enzyme is saturated with substrate. Km (Michaelis constant) is the substrate concentration at half Vmax; a low Km indicates high affinity of the enzyme for its substrate.

Compare competitive and noncompetitive enzyme inhibition in terms of Km and Vmax.

Competitive inhibitor binds the active site: Vmax unchanged, Km increased (overcome by excess substrate). Noncompetitive inhibitor binds elsewhere: Vmax decreased, Km unchanged. Uncompetitive: both Km and Vmax decreased.

Give two classic examples of irreversible enzyme inhibitors and their targets.

Aspirin irreversibly acetylates cyclooxygenase (COX). Organophosphates irreversibly inhibit acetylcholinesterase. Penicillin irreversibly inhibits bacterial transpeptidase. These form covalent bonds, permanently inactivating the enzyme.

What is the net ATP and NADH yield of glycolysis per glucose, and where does it occur?

Glycolysis occurs in the cytoplasm and converts glucose to 2 pyruvate, yielding a net of 2 ATP (4 produced − 2 used) and 2 NADH per glucose. It is the only pathway that can run anaerobically.

Which are the three irreversible (regulatory) enzymes of glycolysis?

Hexokinase/glucokinase, phosphofructokinase-1 (PFK-1, the rate-limiting and committed step), and pyruvate kinase. These catalyze the large-negative-ΔG, essentially irreversible steps that are bypassed in gluconeogenesis.

What is gluconeogenesis and which four enzymes bypass the irreversible glycolytic steps?

Gluconeogenesis is synthesis of glucose from non-carbohydrate precursors (lactate, glycerol, glucogenic amino acids), mainly in liver/kidney. Bypass enzymes: pyruvate carboxylase, PEP carboxykinase (PEPCK), fructose-1,6-bisphosphatase, and glucose-6-phosphatase.

What are the two phases and products of the Pentose Phosphate Pathway (HMP shunt)?

Oxidative phase (irreversible) generates NADPH and ribose-5-phosphate (rate-limiting enzyme glucose-6-phosphate dehydrogenase). Non-oxidative phase reversibly interconverts sugars. It supplies NADPH for biosynthesis/antioxidant defense and ribose for nucleotides.

Why does G6PD deficiency cause hemolytic anemia?

G6PD is needed to make NADPH, which maintains reduced glutathione that protects RBCs from oxidative damage. With deficiency, oxidative stress (drugs, fava beans, infection) denatures hemoglobin into Heinz bodies, causing hemolysis.

Name the key enzymes of glycogen synthesis and breakdown.

Glycogenesis: glycogen synthase (rate-limiting; adds UDP-glucose via α-1,4 bonds) plus branching enzyme. Glycogenolysis: glycogen phosphorylase (rate-limiting; releases glucose-1-phosphate) plus debranching enzyme.

How do insulin and glucagon reciprocally regulate glycogen metabolism?

Insulin activates glycogen synthase (dephosphorylated active) promoting storage. Glucagon/epinephrine raise cAMP, activating protein kinase A, which phosphorylates and activates glycogen phosphorylase and inactivates glycogen synthase, promoting breakdown.

What is the net yield of the Citric Acid (Krebs) cycle per acetyl-CoA?

Per acetyl-CoA: 3 NADH, 1 FADH2, 1 GTP (or ATP), and 2 CO2 released. It occurs in the mitochondrial matrix and is the central hub for oxidation of carbohydrate, fat, and protein-derived acetyl-CoA.

Which enzymes are the major regulatory/rate-limiting points of the Krebs cycle?

Citrate synthase, isocitrate dehydrogenase (the key rate-limiting step), and α-ketoglutarate dehydrogenase. They are inhibited by high ATP/NADH and activated by ADP/Ca2+, linking the cycle to energy demand.

Where does fatty acid β-oxidation occur and what does each cycle produce?

In the mitochondrial matrix. Each β-oxidation cycle removes a 2-carbon acetyl-CoA and produces 1 FADH2 and 1 NADH. The carnitine shuttle (CPT-1, rate-limiting) transports long-chain fatty acids into mitochondria.

Where does fatty acid synthesis occur and what are its key requirements?

In the cytoplasm. It requires acetyl-CoA (via citrate shuttle), NADPH (from the HMP shunt), and the multienzyme fatty acid synthase. Acetyl-CoA carboxylase (forms malonyl-CoA) is the rate-limiting, biotin-dependent enzyme.

Outline triacylglycerol (TAG) metabolism: synthesis and mobilization.

Synthesis (lipogenesis) esterifies glycerol-3-phosphate with three fatty acyl-CoAs, stored in adipose tissue. Mobilization (lipolysis) uses hormone-sensitive lipase (activated by glucagon/epinephrine, inhibited by insulin) to release free fatty acids and glycerol.

Classify the major plasma lipoproteins by function.

Chylomicrons carry dietary (exogenous) TAG. VLDL carries endogenous (hepatic) TAG. LDL delivers cholesterol to tissues ('bad'). HDL performs reverse cholesterol transport from tissues to liver ('good'). Density increases as protein content rises.

What are ketone bodies, when are they made, and which tissues use them?

Acetoacetate, β-hydroxybutyrate, and acetone, synthesized in liver mitochondria (ketogenesis) from acetyl-CoA during starvation, prolonged fasting, or uncontrolled diabetes. Used by brain, heart, and muscle as fuel. The liver cannot use them (lacks thiophorase/SCOT).

Distinguish glucogenic, ketogenic, and mixed amino acids.

Glucogenic amino acids yield pyruvate or TCA intermediates and can form glucose. Purely ketogenic: leucine and lysine (yield acetyl-CoA/acetoacetyl-CoA only). Both glucogenic and ketogenic: isoleucine, phenylalanine, tyrosine, tryptophan, threonine.

How is ammonia from amino acid catabolism disposed of, and where?

Excess nitrogen is converted to urea via the urea cycle in the liver (mitochondria + cytoplasm). The rate-limiting/committed step is carbamoyl phosphate synthetase I (CPS-I), activated by N-acetylglutamate. Urea is excreted by the kidneys.

What is one-carbon metabolism and which key carriers are involved?

Transfer of single-carbon units (methyl, methylene, formyl) for synthesis of purines, thymidylate, and methionine. Major carriers are tetrahydrofolate (THF, from folate) and S-adenosylmethionine (SAM), with vitamin B12 linking folate and methionine metabolism.

List the metabolic fates of the amino acid tyrosine.

Tyrosine (from phenylalanine) is the precursor of catecholamines (dopamine, norepinephrine, epinephrine), thyroid hormones (T3/T4), and melanin. Its catabolism defects cause alkaptonuria; phenylalanine hydroxylase deficiency causes phenylketonuria (PKU).

Where do the electron transport chain and ATP synthesis occur, and how is ATP made?

On the inner mitochondrial membrane. Electrons from NADH/FADH2 pass through complexes I-IV, pumping protons to create an electrochemical gradient. ATP synthase (complex V) uses the proton-motive force to phosphorylate ADP (chemiosmotic theory, Mitchell).

What is the approximate ATP yield from NADH and FADH2 via oxidative phosphorylation?

Each NADH yields ~2.5 ATP (older value 3) and each FADH2 yields ~1.5 ATP (older value 2), reflecting the protons pumped from their respective entry points (complex I vs complex II).

How is oxidative phosphorylation regulated, and what do uncouplers and inhibitors do?

Mainly by respiratory (acceptor) control—ADP availability drives the rate. Uncouplers (e.g., 2,4-DNP, thermogenin/UCP1) dissipate the proton gradient as heat so respiration continues without ATP. Inhibitors (cyanide, CO at complex IV; oligomycin at ATP synthase) block flow/ATP synthesis.

What is the biochemical basis of mitochondrial disorders, and how are they inherited?

Defects in the electron transport chain/oxidative phosphorylation impair ATP production, hitting high-energy tissues (brain, muscle, heart). mtDNA is maternally inherited and shows heteroplasmy with a threshold effect. Examples: MELAS, MERRF, Leber hereditary optic neuropathy (LHON).

Classify hormones by their chemical nature with examples.

Peptide/protein hormones (insulin, glucagon, GH); steroid hormones (cortisol, estrogen, testosterone, derived from cholesterol); amino acid derivatives (thyroid hormones, catecholamines). Lipid-soluble steroids/thyroid act via intracellular receptors; peptides act via cell-surface receptors.

Compare the cAMP and the IP3/DAG signal transduction pathways.

cAMP pathway: Gs-coupled receptor → adenylyl cyclase → cAMP → protein kinase A (e.g., glucagon, epinephrine via β). IP3/DAG pathway: Gq-coupled receptor → phospholipase C → IP3 (releases Ca2+) and DAG → protein kinase C (e.g., α-1 adrenergic). Both use second messengers.

What is the principle and a clinical application of ELISA?

ELISA (enzyme-linked immunosorbent assay) detects/quantifies an antigen or antibody using a specific antibody linked to an enzyme that generates a measurable color signal. Applications include HIV screening, hormone (hCG) and infectious-disease serology, and protein quantification.

What is the function of vitamin B12 and folate, and what deficiency do they share?

Both are coenzymes in one-carbon metabolism/DNA synthesis. Deficiency of either causes megaloblastic (macrocytic) anemia. B12 (cobalamin) additionally causes neurological damage (subacute combined degeneration); B12 deficiency also raises methylmalonic acid, distinguishing it from folate deficiency.