BIOL 3461 Exam 3 Practice Packet 1

Which statement about the transition state (X‡) of a reaction is correct?

High free energy, short-lived, with at least one partial bond.

Compared with the uncatalyzed reaction, an enzyme changes which of the following?

Lowers activation free energy (ΔG‡).

Enzyme catalysis requires what relationship between KT and KS?

KT is much smaller than KS (tighter transition-state binding).

What is a transition-state analog (TSA)?

A stable molecule resembling the transition state that acts as a competitive inhibitor.

Which drug was described as based on the transition state of its target enzyme?

Tamiflu (viral neuraminidase inhibitor).

Which is NOT a way enzymes destabilize the ES complex to favor catalysis?

Binding the substrate as tightly as possible to maximize ES stability.

What is a near-attack complex (NAC)?

Reacting atoms within about 3.2 Å and within ±15° of the transition-state bonding angle.

In covalent catalysis, what does the enzyme do?

Uses an active-site nucleophile to form a temporary covalent bond with the substrate.

What is correct about a low-barrier hydrogen bond (LBHB)?

Heteroatoms are closer than 0.25 nm and have similar pKa values.

What is the catalytic triad of chymotrypsin?

His57, Asp102, and Ser195.

What forms the oxyanion hole of chymotrypsin?

Backbone N-H groups of Gly193 and Ser195.

Trypsin cleaves peptide bonds on the carbonyl side of which residues?

Lys or Arg, except when followed by Pro.

How many peptide fragments result when a polypeptide is cut 4 times by trypsin?

5 fragments.

Why does chymotrypsin show burst kinetics with an artificial ester substrate?

Fast acylation releases product first, followed by slower deacylation limiting the rate.

In the first step of the serine protease mechanism, His57 acts as what?

A general base that removes the proton from Ser195-OH.

How do aspartic proteases like pepsin differ from serine proteases?

They use two Asp residues and activated water with no covalent intermediate.

Why is pepsin active at acidic pH?

One active-site Asp must be protonated and the other deprotonated.

How is HIV-1 protease best described?

A homodimeric aspartic protease with a two-fold symmetric active site.

In the GAPDH mechanism, Cys-SH first reacts with GAP to form what?

A thiohemiacetal oxidized by NAD+ to a thioester.

Which enzyme regulation form is irreversible?

Zymogen (proenzyme) activation by proteolytic cleavage.

In protein kinase A, how is the catalytic (C) subunit activated?

cAMP binds the regulatory (R) subunit, releasing active C.

Acetylation of the ε-amino group of a Lys residue does what?

Neutralizes the positive charge by forming a neutral amide.

What is TRUE about regulatory (allosteric) enzymes?

They are usually oligomers showing sigmoidal v versus [S] curves.

How many residues remain in mature insulin after removing residues 31-65 from proinsulin (86 aa)?

51 residues.

What feature belongs to the MWC (concerted) model?

All oligomer subunits are in the same state (T or R) and switch together.

What statement about the KNF (sequential) model is correct?

Ligand binding induces conformational change passed to neighbors, allowing intermediate states.

How does a negative allosteric effector affect a K system enzyme?

Shifts curve right (higher K0.5) with unchanged Vmax.

How does a negative allosteric effector affect a V system enzyme?

K0.5 stays constant and Vmax decreases.

In the MWC model, what does a positive effector do?

Shifts T/R equilibrium toward R, lowering L.

How do myoglobin and hemoglobin differ?

Mb is a monomer with hyperbolic O2 curve; Hb is a tetramer with sigmoidal curve.

Which heme iron state binds O2, and what is its fifth ligand?

Fe2+, with His F8 as the fifth ligand.

In a patient with alkalosis, how does the hemoglobin O2 saturation curve shift?

Shifted left because O2 affinity is higher.

How does 2,3-bisphosphoglycerate (BPG) affect hemoglobin?

Binds central cavity between β subunits of deoxy-Hb, stabilizing T state.

Why does fetal hemoglobin have higher O2 affinity than adult Hb?

γ chains have Ser instead of His143, weakening BPG binding.

How does CO2 lower hemoglobin's O2 affinity?

Forms protons and carbamates that stabilize the T state.

How is hemoglobin's cooperative O2 binding best explained?

Features of both KNF and MWC models.

An organism using light for energy and CO2 for carbon is a what?

Photoautotroph.

Which description of catabolism is correct?

Oxidative degradation of nutrients to simple products, capturing energy as ATP/reduced carriers.

What is NADPH mainly used for?

A source of reducing power for biosynthetic (anabolic) reactions.

What are the final products of complete aerobic catabolism?

CO2 and H2O.

What is ΔG for PEP + ADP → pyruvate + ATP given PEP hydrolysis is -78 kJ/mol and ATP synthesis is +55 kJ/mol?

-23 kJ/mol.

Why can't catabolic and anabolic pathways be exact reverses?

Each direction must be favorable and independently regulated.

What is a pathway serving both catabolism and anabolism called?

Amphibolic.

What is fluxomics?

Quantitative study of metabolite flow through a metabolic network.

If an inhibitor blocks one enzyme in a linear pathway, what happens?

Upstream intermediates accumulate; downstream intermediates fall.

Which of the following is a ketose?

Fructose.

D-glucose and D-galactose differ only at C4. What are they?

Epimers.

Which pair are enantiomers?

D-glucose and L-glucose.

How many stereoisomers does an aldohexose have?

16.

In the Haworth projection of a D-sugar, where is the α anomer's hydroxyl?

Pointing down, opposite the CH2OH group.

D-glucose in solution exists in all mutarotation forms EXCEPT which one?

L-glucopyranose.

Reaction of C5 hydroxyl of glucose with C1 aldehyde forms what?

A pyranose ring containing a hemiacetal and new chiral anomeric carbon.

Why is sucrose not a reducing sugar?

Both anomeric carbons are tied up in the glycosidic bond.

What is lactose composed of?

Galactose β(1→4) glucose.

How do cellulose and amylose differ?

Cellulose has β(1→4) linkages forming fibers; amylose has α(1→4) linkages coiling into helices.

How do glycogen and starch (amylopectin) differ mainly?

Glycogen has a higher degree of branching.

What is notable about heparin?

It is a highly negatively charged GAG acting as an anticoagulant.

In an N-linked glycoprotein, where is the oligosaccharide attached?

The amide nitrogen of an Asn side chain.

Which feature describes the Gram-positive bacterial cell wall?

One membrane with a thick peptidoglycan layer.