MBBS Bio Chemistry Syllabus

What is the general structure of an α-amino acid at physiological pH?

An α-amino acid has a central α-carbon bonded to an amino group, a carboxyl group, a hydrogen, and a variable R side chain. At physiological pH it exists as a zwitterion: the amino group is protonated ($\ce{-NH3+}$) and the carboxyl is deprotonated ($\ce{-COO^-}$).

How many standard amino acids are there, and how are they classified by side chain polarity?

There are 20 standard amino acids. They are classified as nonpolar/hydrophobic (e.g. Gly, Ala, Val, Leu), polar uncharged (e.g. Ser, Thr, Cys, Gln), acidic/negatively charged (Asp, Glu), and basic/positively charged (Lys, Arg, His).

Define the isoelectric point (pI) of an amino acid and how it is calculated for a neutral amino acid.

The pI is the pH at which the amino acid carries no net charge (exists as a zwitterion). For a simple amino acid with two ionizable groups, $\text{pI} = \frac{pK_{1} + pK_{2}}{2}$, averaging the $pK_a$ values flanking the neutral species.

Which amino acids are essential in humans?

The essential amino acids are Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Arginine (conditionally), Leucine, and Lysine. Mnemonic: "PVT TIM HALL."

What type of bond links amino acids in a protein, and what are its key structural features?

The peptide bond, an amide bond between the α-carboxyl of one amino acid and the α-amino of the next. It is planar and rigid due to partial double-bond (resonance) character, and is usually in the trans configuration.

Define the four levels of protein structure.

Primary: the linear sequence of amino acids. Secondary: local folding into α-helices and β-sheets stabilized by hydrogen bonds. Tertiary: the overall 3D fold of a single polypeptide. Quaternary: the assembly of multiple polypeptide subunits.

Compare the α-helix and β-pleated sheet secondary structures.

α-helix: a right-handed coil with $\approx 3.6$ residues per turn, stabilized by hydrogen bonds between the backbone C=O of residue $i$ and N–H of residue $i+4$. β-sheet: extended strands (parallel or antiparallel) hydrogen-bonded laterally between adjacent strands.

Which bonds and interactions stabilize tertiary protein structure?

Hydrophobic interactions (major driving force, burying nonpolar side chains), hydrogen bonds, ionic (salt) bridges, van der Waals forces, and covalent disulfide bonds ($\ce{-S-S-}$) between cysteine residues.

Define protein denaturation and name common denaturing agents.

Denaturation is the loss of secondary, tertiary, and/or quaternary structure (and thus function) without breaking peptide bonds. Agents include heat, extremes of pH, organic solvents, urea, detergents (SDS), and heavy metals.

What is the role of molecular chaperones in protein folding?

Chaperones (e.g. heat shock proteins like Hsp70, and chaperonins like GroEL/GroES) assist correct folding by preventing inappropriate aggregation of nascent or stress-denatured polypeptides; they do not specify the final fold but provide a favorable environment for it.

According to Anfinsen's dogma, what determines a protein's native three-dimensional structure?

The primary amino acid sequence determines the native folded structure. The native conformation is generally the thermodynamically most stable (lowest free energy) state accessible under physiological conditions.

What is an enzyme, and how does it accelerate a reaction in thermodynamic terms?

An enzyme is a biological catalyst (mostly protein; some are ribozymes). It speeds reactions by lowering the activation energy ($E_a$, $\Delta G^{\ddagger}$) of the pathway. It does not change the overall $\Delta G$ or the equilibrium position, only the rate.

State the Michaelis–Menten equation and define each term.

$$v_{0} = \frac{V_{max}[S]}{K_{m} + [S]}$$ where $v_0$ is initial velocity, $V_{max}$ is maximum velocity, $[S]$ is substrate concentration, and $K_m$ is the Michaelis constant (the $[S]$ at which $v_0 = \tfrac{1}{2}V_{max}$).

What does the Michaelis constant $K_m$ indicate about enzyme–substrate affinity?

$K_m$ is the substrate concentration giving half-maximal velocity. A low $K_m$ indicates high affinity (less substrate needed to reach half $V_{max}$); a high $K_m$ indicates low affinity.

Write the Lineweaver–Burk (double reciprocal) equation and state its use.

$$\frac{1}{v_{0}} = \frac{K_{m}}{V_{max}} \cdot \frac{1}{[S]} + \frac{1}{V_{max}}$$ It linearizes Michaelis–Menten data: the y-intercept is $\frac{1}{V_{max}}$, the x-intercept is $-\frac{1}{K_{m}}$, and the slope is $\frac{K_m}{V_{max}}$. It is used to determine kinetic constants and inhibition types.

Differentiate competitive, noncompetitive, and uncompetitive enzyme inhibition by their effects on $K_m$ and $V_{max}$.

Competitive: $K_m$ increases, $V_{max}$ unchanged (inhibitor binds active site, overcome by high $[S]$). Noncompetitive: $V_{max}$ decreases, $K_m$ unchanged (binds allosteric site). Uncompetitive: both $K_m$ and $V_{max}$ decrease (binds only the ES complex).

Give a clinical example of a competitive inhibitor and explain its mechanism.

Methanol/ethylene glycol poisoning treated with ethanol or fomepizole: ethanol competitively inhibits alcohol dehydrogenase, which has higher affinity for ethanol, preventing conversion of methanol to toxic formaldehyde/formic acid. Another classic example is allopurinol inhibiting xanthine oxidase.

Distinguish reversible from irreversible enzyme inhibitors, giving an example of each.

Reversible inhibitors bind non-covalently and can dissociate (e.g. statins inhibiting HMG-CoA reductase). Irreversible inhibitors form covalent bonds and permanently inactivate the enzyme (e.g. aspirin acetylating cyclooxygenase; organophosphates inhibiting acetylcholinesterase).

What is the overall reaction, location, and net ATP yield of glycolysis?

Glycolysis converts one glucose to two pyruvate in the cytosol. Net yield per glucose: $2\ \text{ATP}$ (4 produced − 2 invested) and $2\ \text{NADH}$. Net equation: $$\ce{Glucose + 2 NAD+ + 2 ADP + 2 P_i -> 2 Pyruvate + 2 NADH + 2 H+ + 2 ATP + 2 H2O}$$

Name the three irreversible (regulatory) enzymes of glycolysis.

(1) Hexokinase/glucokinase (glucose → glucose-6-phosphate), (2) phosphofructokinase-1 (PFK-1; fructose-6-phosphate → fructose-1,6-bisphosphate) — the rate-limiting/committed step, and (3) pyruvate kinase (phosphoenolpyruvate → pyruvate).

What is the most important allosteric regulator of PFK-1, and what activates and inhibits this enzyme?

Fructose-2,6-bisphosphate is the most potent allosteric activator of PFK-1. PFK-1 is also activated by AMP and inhibited by ATP and citrate (high-energy signals). This makes PFK-1 the key control point of glycolysis.

What are the fates of pyruvate under aerobic versus anaerobic conditions?

Aerobic: pyruvate enters mitochondria and is oxidatively decarboxylated by pyruvate dehydrogenase to acetyl-CoA. Anaerobic: pyruvate is reduced to lactate by lactate dehydrogenase, regenerating $\ce{NAD+}$ to sustain glycolysis: $$\ce{Pyruvate + NADH + H+ -> Lactate + NAD+}$$

Define gluconeogenesis: its purpose, main site, and major precursors.

Gluconeogenesis is the synthesis of glucose from non-carbohydrate precursors, occurring mainly in the liver (and renal cortex). Major precursors are lactate, glucogenic amino acids (e.g. alanine), and glycerol. It maintains blood glucose during fasting.

Which four key enzymes allow gluconeogenesis to bypass the irreversible steps of glycolysis?

(1) Pyruvate carboxylase (pyruvate → oxaloacetate, mitochondrial, requires biotin), (2) PEP carboxykinase (oxaloacetate → phosphoenolpyruvate), (3) fructose-1,6-bisphosphatase (rate-limiting), and (4) glucose-6-phosphatase (G6P → glucose, in liver/kidney ER).

What is the main function of the pentose phosphate pathway and its two products?

The PPP (hexose monophosphate shunt) operates in the cytosol to produce NADPH (for reductive biosynthesis and antioxidant defense) and ribose-5-phosphate (for nucleotide and nucleic acid synthesis). Its rate-limiting enzyme is glucose-6-phosphate dehydrogenase (G6PD).

Why is NADPH from the pentose phosphate pathway important in red blood cells, and what disease results from its deficiency?

NADPH maintains reduced glutathione, which protects RBCs from oxidative damage. G6PD deficiency reduces NADPH, causing oxidative hemolysis (hemolytic anemia, Heinz bodies, bite cells) especially after oxidant stress (fava beans, infections, primaquine, sulfa drugs).

Describe glycogenesis and the key enzymes involved.

Glycogenesis is glycogen synthesis. Glucose-6-phosphate → glucose-1-phosphate → UDP-glucose (via UDP-glucose pyrophosphorylase). Glycogen synthase adds glucose via $\alpha\text{-}1,4$ linkages (the regulated step), and branching enzyme creates $\alpha\text{-}1,6$ branch points.

Describe glycogenolysis and its key enzymes.

Glycogenolysis is glycogen breakdown. Glycogen phosphorylase (rate-limiting; uses pyridoxal phosphate) cleaves $\alpha\text{-}1,4$ bonds to release glucose-1-phosphate. Debranching enzyme removes $\alpha\text{-}1,6$ branch points. Glycogen phosphorylase is activated by phosphorylation (via glucagon/epinephrine).

How do insulin and glucagon reciprocally regulate glycogen metabolism?

Insulin activates glycogen synthase (dephosphorylation) and inhibits phosphorylase, promoting glycogen synthesis. Glucagon/epinephrine activate phosphorylase and inhibit synthase (via cAMP-dependent phosphorylation), promoting glycogen breakdown. Phosphorylation activates phosphorylase but inactivates synthase.

What is the overall function of the citric acid (Krebs) cycle, its location, and the molecule that enters it?

The citric acid cycle oxidizes acetyl-CoA to $\ce{CO2}$ in the mitochondrial matrix, capturing energy as reduced coenzymes. Acetyl-CoA (2 carbons) condenses with oxaloacetate (4 carbons) to form citrate (6 carbons), the first step catalyzed by citrate synthase.

State the energy yield (per acetyl-CoA) of one turn of the citric acid cycle.

Per turn: $3\ \text{NADH}$, $1\ \text{FADH2}$, $1\ \text{GTP}$ (or ATP), and $2\ \ce{CO2}$ released. Through oxidative phosphorylation this corresponds to roughly $10\ \text{ATP}$ per acetyl-CoA.

Name the three regulatory (irreversible) enzymes of the citric acid cycle.

Citrate synthase, isocitrate dehydrogenase (the rate-limiting step), and the α-ketoglutarate dehydrogenase complex. They are inhibited by high ATP/NADH and activated by ADP/$\ce{Ca^2+}$ (signals of low energy).

Where does fatty acid β-oxidation occur, and how are long-chain fatty acids transported into this compartment?

β-oxidation occurs in the mitochondrial matrix. Long-chain fatty acyl groups are carried across the inner mitochondrial membrane by the carnitine shuttle (carnitine palmitoyltransferase I and II). CPT-I is the rate-limiting step and is inhibited by malonyl-CoA.

What are the products of one round of fatty acid β-oxidation, and the energy yield from palmitate?

Each cycle shortens the fatty acyl chain by 2 carbons, producing 1 acetyl-CoA, 1 FADH2, and 1 NADH. Complete oxidation of palmitate ($\ce{C16}$) yields about $106\ \text{ATP}$ net (8 acetyl-CoA, 7 FADH2, 7 NADH, minus 2 ATP for activation).

Where and from what is fatty acid synthesis carried out, and what is its committed regulatory step?

Fatty acid synthesis occurs in the cytosol using acetyl-CoA, NADPH, and the multienzyme fatty acid synthase. The committed/rate-limiting step is acetyl-CoA → malonyl-CoA by acetyl-CoA carboxylase (requires biotin; activated by citrate and insulin, inhibited by palmitoyl-CoA and glucagon).

What are ketone bodies, where are they made, and when are they produced?

Ketone bodies are acetoacetate, β-hydroxybutyrate, and acetone, synthesized in liver mitochondria (ketogenesis) from acetyl-CoA. They are produced during prolonged fasting, starvation, or uncontrolled diabetes when fatty acid oxidation exceeds the citric acid cycle's capacity, and serve as fuel for brain and muscle.

Describe the structure and main storage function of triacylglycerols (triglycerides).

A triacylglycerol is a glycerol backbone esterified to three fatty acids. It is the major storage form of energy, stored in adipose tissue, because the highly reduced, anhydrous fatty acids yield more than twice the energy per gram of carbohydrate or protein.

What enzymes mobilize and synthesize triacylglycerols, and how are they hormonally regulated?

Lipolysis: hormone-sensitive lipase (and adipose triglyceride lipase) hydrolyzes stored TAG, releasing free fatty acids and glycerol; it is activated by glucagon/epinephrine (cAMP) and inhibited by insulin. Synthesis (esterification) is promoted by insulin in the fed state.

List the major classes of lipoproteins in order of increasing density and decreasing triglyceride content.

Chylomicrons (lowest density, highest TG) < VLDL < IDL < LDL < HDL (highest density, highest protein, lowest TG). As density increases, the protein content rises and triglyceride content falls.

State the primary function of each major lipoprotein class.

Chylomicrons transport dietary (exogenous) triglycerides from the intestine. VLDL transports endogenous (liver-made) triglycerides. LDL delivers cholesterol to peripheral tissues ("bad" cholesterol). HDL performs reverse cholesterol transport, carrying cholesterol from tissues back to the liver ("good" cholesterol).

What is the role of lipoprotein lipase (LPL) and which apolipoprotein activates it?

Lipoprotein lipase, located on capillary endothelium, hydrolyzes triglycerides in chylomicrons and VLDL to release free fatty acids for uptake by tissues. It is activated by apolipoprotein C-II on the lipoprotein surface.

Outline the regulation and rate-limiting step of cholesterol synthesis.

Cholesterol is synthesized in the cytosol/ER from acetyl-CoA. The rate-limiting step is HMG-CoA reductase converting HMG-CoA to mevalonate. It is inhibited by cholesterol and statins, inhibited by glucagon (phosphorylation), and activated by insulin. This is the target of statin drugs.