Question 1

Which amino acids are most likely to serve as the generic proton donor (1) and acceptor (2) in the chymotrypsin active site, as depicted in the reaction mechanism above?

Accepted Answer

Histidine and Serine

Question 2

In the reaction catalyzed by lactate dehydrogenase, what is the biochemical role of NADH?

Accepted Answer

NADH acts as a reducing agent, donating electrons to pyruvate.

Question 3

Given the table of enzyme kinetics, which enzyme-substrate pair is the most efficient, and why?

Accepted Answer

Fumarase with malate, because it has the highest kcat/KM value.

Question 4

If the kcat of urease for urea is $$1.0 	imes 10^4$ s$$^{-1}$$, what does this value represent?

Accepted Answer

The number of substrate molecules converted to product per enzyme molecule per second when the enzyme is saturated with substrate.

Question 5

A mutant form of lactate dehydrogenase (LDH) with Arg109 replaced by Gln shows only 25% of pyruvate binding and 0.07% of wild-type activity. Why is the activity so low despite significant pyruvate binding?

Accepted Answer

The mutation removes a positive charge needed to stabilize the transition state, reducing catalytic efficiency.

Question 6

In the context of enzyme inhibition, if trial B shows an increased slope but similar y-intercept compared to trial A in a Lineweaver-Burk plot, what type of inhibition is most likely present?

Accepted Answer

Competitive inhibition

Question 7

Which bond in raffinose is hydrolyzed by α-galactosidase in Beano®, and why does this aid digestion?

Accepted Answer

The α-1,6 bond between galactose and glucose, because humans lack the enzyme to break this bond.

Question 8

Amylopectin and glycogen are both polysaccharides used for sugar storage. What is the primary structural difference between them?

Accepted Answer

Glycogen has more frequent branching than amylopectin.

Question 9

Phospholipase A2 cleaves the fatty acid at position 2 of a phospholipid. What is the effect of this reaction on the plasma membrane?

Accepted Answer

It disrupts membrane integrity by producing lysophospholipids and free fatty acids.

Question 10

Rank the melting points of the following fatty acids from highest to lowest: (1) cis-Palmitoleic (16:1), (2) trans-oleic (18:1), (3) cis-linolenic (18:3), (4) arachidic (20:0), (5) palmitic (16:0). Justify your answer.

Accepted Answer

Arachidic \u003e palmitic \u003e trans-oleic \u003e cis-palmitoleic \u003e cis-linolenic; saturated and trans fats have higher melting points.

Question 11

Given the DNA sequence: ATG – GCT – GGC – TGG – CTT – ATA – GCA – GGG – TAT – GGC – TTT – GTA – TAA, what is the amino acid sequence of the encoded protein?

Accepted Answer

Met – Ala – Gly – Trp – Leu – Ile – Ala – Gly – Tyr – Gly – Phe – Val – Stop

Question 12

Based on the amino acid sequence above, would you predict this peptide to reside in the cytosol or plasma membrane, and why?

Accepted Answer

Cytosol, because it lacks a hydrophobic transmembrane domain.

Question 13

For a mutation to be inheritable, in which biopolymer must the mutation occur, and why?

Accepted Answer

DNA, because it is the genetic material passed to offspring.

Question 14

Actinomycin D is considered an intercalating agent. What is the definition of an intercalating agent?

Accepted Answer

A molecule that inserts between base pairs of DNA, distorting the double helix.

Question 15

What effect does actinomycin D have on the melting temperature of DNA, and why?

Accepted Answer

It increases the melting temperature by stabilizing base stacking interactions.

Question 16

Which of the following best explains how enzymes speed up reactions, as shown in a reaction coordinate diagram?

Accepted Answer

Enzymes lower the activation energy by stabilizing the transition state.

Question 17

In a multi-step enzyme mechanism, which catalytic strategy is most likely used by chymotrypsin?

Accepted Answer

Covalent catalysis and general acid-base catalysis

Biochemistry Exam II & III Study Guidance

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