CSIR NET Life Sciences Molecules And Their Interaction Relevant To Biology Syllabus

Give the Henderson-Hasselbalch equation.

pH = pKa + log([A-]/[HA]), where [A-] is the conjugate base concentration and [HA] is the weak acid concentration.

What is a buffer and when is its buffering capacity maximal?

A buffer is a solution of a weak acid and its conjugate base that resists pH change on adding acid or base. Capacity is maximal when pH = pKa (equal concentrations of acid and conjugate base).

Define pH and give the pH of a neutral aqueous solution at 25 C.

pH = -log[H+]. At 25 C, neutral water has [H+] = 1 x 10^-7 M, so pH = 7.

State the relationship between Gibbs free energy, enthalpy, and entropy.

deltaG = deltaH - T*deltaS. A reaction is spontaneous (exergonic) when deltaG < 0.

What does the standard free energy change deltaG zero prime relate to the equilibrium constant Keq?

deltaG zero prime = -RT ln(Keq). A large Keq gives a large negative deltaG zero prime (favorable reaction).

What are colligative properties and what do they depend on?

Properties depending only on the number of solute particles, not their identity: boiling point elevation, freezing point depression, vapor pressure lowering, and osmotic pressure.

Give the van't Hoff equation for osmotic pressure.

Osmotic pressure pi = iMRT, where i = van't Hoff factor, M = molar concentration, R = gas constant, T = absolute temperature.

Define reaction order and give the rate law for a first-order reaction.

Reaction order is the sum of exponents of concentration terms in the rate law. First order: rate = k[A], with units of k in s^-1 and an exponential decay of [A] over time.

What is the net ATP and NADH yield of glycolysis per glucose?

Net 2 ATP (4 produced, 2 consumed), 2 NADH, and 2 pyruvate per glucose molecule.

Name the three irreversible (regulatory) enzymes of glycolysis.

Hexokinase, phosphofructokinase-1 (PFK-1, the key control step), and pyruvate kinase.

Where does oxidative phosphorylation occur and what is its overall function?

It occurs at the inner mitochondrial membrane. Electrons from NADH/FADH2 pass through the electron transport chain, pumping protons to create an electrochemical gradient that ATP synthase uses to make ATP.

State the chemiosmotic theory (Mitchell's hypothesis).

Energy from electron transport is used to pump protons across the inner mitochondrial membrane, creating a proton-motive force (electrochemical gradient) that drives ATP synthesis as protons flow back through ATP synthase.

What is the approximate ATP yield from complete oxidation of one glucose molecule (modern estimate)?

About 30-32 ATP total (glycolysis + pyruvate oxidation + citric acid cycle + oxidative phosphorylation).

What is a coupled reaction in metabolism?

A thermodynamically unfavorable (endergonic) reaction is driven by linking it to a favorable (exergonic) reaction, typically ATP hydrolysis, so the combined deltaG is negative.

What is a group transfer reaction and give a biological example?

A reaction transferring a functional group from one molecule to another; e.g., kinases transfer a phosphoryl group from ATP to a substrate (phosphoryl group transfer).

What are biological energy transducers? Give examples.

Systems that convert one form of energy into another usable form, e.g., ATP synthase (proton gradient -> chemical energy in ATP), chloroplasts (light -> chemical energy), and muscle (chemical -> mechanical energy).

State the Michaelis-Menten equation and define Vmax and Km.

v = (Vmax[S]) / (Km + [S]). Vmax is the maximal rate at saturating substrate; Km is the substrate concentration at half Vmax and reflects enzyme-substrate affinity (lower Km = higher affinity).

How do competitive and noncompetitive inhibitors affect Km and Vmax?

Competitive: increases apparent Km, Vmax unchanged (relieved by excess substrate). Noncompetitive: Vmax decreases, Km unchanged.

What does a Lineweaver-Burk (double-reciprocal) plot show?

A plot of 1/v versus 1/[S] giving a straight line: y-intercept = 1/Vmax, x-intercept = -1/Km, slope = Km/Vmax. Used to determine kinetic constants and inhibition type.

Define allosteric regulation of enzymes.

Regulation in which an effector molecule binds at a site other than the active site, changing enzyme conformation and activity; allosteric enzymes typically show sigmoidal (cooperative) kinetics.

What is feedback (end-product) inhibition?

The final product of a metabolic pathway inhibits an early (often the first committed) enzyme, preventing overaccumulation of product and conserving resources.

Name four mechanisms enzymes use to catalyze reactions.

Acid-base catalysis, covalent catalysis, metal-ion catalysis, and catalysis by proximity and orientation (and transition-state stabilization).

Contrast the lock-and-key and induced-fit models of enzyme action.

Lock-and-key: the active site is a rigid, exact complement to the substrate. Induced-fit (Koshland): substrate binding induces a conformational change in the enzyme to optimally fit and catalyze the reaction.

What are isozymes (isoenzymes)? Give an example.

Different molecular forms of an enzyme that catalyze the same reaction but differ in structure, kinetics, or tissue distribution; e.g., lactate dehydrogenase (LDH) exists as five isozymes (combinations of H and M subunits).

What does a Ramachandran plot display, and which regions are favored?

It plots backbone dihedral angles phi (C-N rotation) versus psi (C-C rotation) for each residue. Favored (allowed) regions correspond to the right-handed alpha-helix and beta-sheet; most other combinations are sterically forbidden.

Give the defining hydrogen-bonding pattern and rise of the right-handed alpha-helix.

Each backbone C=O hydrogen bonds to the N-H four residues ahead (i to i+4); ~3.6 residues per turn, rise ~0.54 nm per turn (0.15 nm per residue).

Compare A-, B-, and Z-DNA helices.

B-DNA: right-handed, most common physiological form, ~10 bp/turn. A-DNA: right-handed, shorter/wider, found in dehydrated/RNA-DNA hybrids, ~11 bp/turn. Z-DNA: left-handed, zigzag backbone, occurs in GC-rich alternating sequences, ~12 bp/turn.

Define protein domains, motifs, and folds.

A motif (supersecondary structure) is a small recurring arrangement of secondary structures (e.g., helix-turn-helix, beta-hairpin). A domain is an independently folding, often functional unit. A fold is the overall 3D arrangement/topology of secondary structures.

Describe the cloverleaf secondary structure of tRNA and its key functional sites.

tRNA folds into a cloverleaf with the acceptor stem (3' CCA end that carries the amino acid), the D arm, the anticodon arm (anticodon reads the mRNA codon), and the TψC arm; it folds into an L-shaped 3D structure.

What is microRNA (miRNA) and how does it regulate gene expression?

miRNA is a small (~22 nucleotide) non-coding RNA that base-pairs with complementary sequences (usually in the 3' UTR) of target mRNAs, causing translational repression or mRNA degradation via the RISC complex.

Compare the antiparallel beta-sheet with the parallel beta-sheet.

In an antiparallel sheet, adjacent strands run in opposite directions giving straight, well-aligned (more stable) hydrogen bonds; in a parallel sheet, strands run the same direction giving bent, angled hydrogen bonds and it is typically less stable.