Biochemistry - MCQ Practice Questions

Cooperative binding (positive cooperativity) occurs when binding of one substrate molecule increases affinity for subsequent molecules, a classic example of allosteric regulation as seen in hemoglobin.

GAA codes for Glutamic acid (Glu), GUA codes for Valine (Val). This is a non-conservative substitution of a charged to hydrophobic residue.

Serine proteases (like trypsin, chymotrypsin) form an acyl-enzyme intermediate through a nucleophilic attack by the active site serine residue.

Apparent Km = Km(1 + [I]/Ki) = 2(1 + $\frac{1}{0}$.5) = 2(1 + 2) = 6 mM. Competitive inhibition increases apparent Km without changing Vmax.

Tertiary structure requires secondary structure elements. Secondary structures (α-helix, β-sheet) fold into tertiary structure; one cannot exist without the other.

Ca²⁺ is required for enzymatic activity and is not consumed in the reaction, making it a cofactor. Many proteases require metal ions as structural or catalytic cofactors.

In non-competitive inhibition, both Km and Vmax are affected proportionally. On a Lineweaver-Burk plot (1/v vs 1/[S]), this results in lines with different slopes that intersect on the y-axis.

When Km >> [S], the Michaelis-Menten equation simplifies to v = (Vmax/Km)[S], making the reaction essentially first-order. The enzyme has low affinity for substrate under these conditions.

Negative cooperativity occurs when substrate binding to one subunit decreases the affinity of other subunits for substrate, resulting in a hyperbolic (rather than sigmoidal) binding curve.

Turnover number (kcat) is the number of substrate molecules converted to product per enzyme molecule per unit time when the enzyme is fully saturated. It equals Vmax/[E]total.

Serine proteases have an extended substrate-binding site composed of multiple subsites (S1, S1', S2, etc.) that recognize and bind extended substrate peptides. The catalytic triad (Ser-His-Asp) performs the actual catalysis.

Aminoacyl-tRNA synthetases achieve high fidelity through a two-step selection process: initial selection during aminoacylation and a second proofreading step (editing) that hydrolyzes incorrectly charged tRNA-amino acid complexes before they leave the enzyme.

GroEL/GroES in prokaryotes forms a barrel-like structure that creates an isolated environment for protein folding. GroEL binds unfolded proteins using ATP hydrolysis, providing conformational assistance distinct from Hsp70's role in preventing aggregation.

IRE1α is a transmembrane protein with both kinase and RNase (endonuclease) domains. Upon ER stress (detected by dissociation from BiP), it autophosphorylates and uses its RNase domain to splice XBP1 mRNA, a key transcription factor in the UPR.

The SCF (Skp1-Cullin1-F-box protein) complex, specifically SCF-β-TrCP, recognizes phosphorylated IκB and polyubiquitinates it for proteasomal degradation. This is a key regulatory step in the NF-κB inflammatory signaling pathway.

Transition state theory proposes that enzymes achieve catalysis by stabilizing the transition state more effectively than the substrate ground state. The differential stabilization lowers the activation energy barrier, accelerating the reaction.

Glycine (every third residue) provides flexibility, proline stabilizes the polyproline II helix conformation, and hydroxyproline (formed by post-translational modification) stabilizes the triple helix through additional hydrogen bonding.

PFK exhibits allosteric regulation where AMP/ADP (signals of low energy) activate the enzyme, while ATP/citrate (signals of high energy/biosynthesis) inhibit it by binding to allosteric sites, changing enzyme conformation.

Ornithine transcarbamylase (OTC) catalyzes the condensation of carbamoyl phosphate (formed by CPS I) with ornithine to form citrulline, the second step of the urea cycle. OTC deficiency is the most common urea cycle disorder.

Alcohol dehydrogenase contains catalytic zinc that coordinates the hydroxyl group of ethanol/aldehyde substrate, activating it for hydride transfer to NAD+, and structural zinc that maintains protein stability.