BIOL 3461 Exam 3 Study Guide drive

What is a transition state (X‡) in an enzymatic reaction?

A high free energy, short-lived, unstable state with at least one partial bond.

Do enzymes change the overall ΔG or Keq of a chemical reaction?

No, they only lower the activation energy (ΔG‡).

How do enzyme substrate (ES) binding affinities compare between the transition state and the substrate?

Enzymes bind the transition state much more tightly than the substrate (KT << KS).

What factors contribute to the destabilization of the ES complex?

Entropy loss, structural strain (induced fit), desolvation, and electrostatic repulsion.

What is the primary difference between the lock-and-key and induced-fit models?

Induced fit involves conformational changes upon binding that favor forming the transition state.

What are transition-shift analogs (TSAs)?

Stable molecules resembling the transition state that bind tightly and act as competitive inhibitors.

What do statins inhibit as transition-state analogs?

HMG-CoA reductase to lower cholesterol.

What enzyme is targeted by Tamiflu as a transition-state analog drug?

Viral neuraminidase.

What does a full arrowhead vs. a half arrowhead represent in curved-arrow notation?

Full arrowhead = movement of an electron pair; half arrowhead = a single electron.

Define nucleophile and electrophile in chemical catalysis.

Nucleophile is electron-rich and donates a pair; electrophile is electron-poor and accepts a pair.

What is a near-attack complex (NAC) in proximity and orientation catalysis?

Reacting atoms within ~3.2 Å and ±15° of the bonding angle.

What type of catalysis involves a temporary covalent bond between an active-site nucleophile and the substrate?

Covalent catalysis.

Which amino acid side chains frequently act as nucleophiles in covalent catalysis?

Ser, Cys, His, Lys, and Asp.

What does general acid-base catalysis involve during a reaction?

Proton transfer in the transition state by an active-site residue or water.

Why is Histidine exceptionally common in general acid-base catalysis?

Its pKa is near 6, close to physiological neutral pH.

What is the primary role of metal ion catalysis in enzyme active sites?

Stabilizes charged transient structures and makes strong nucleophiles.

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

An unusually short (

Which serine proteases are primarily involved in protein digestion?

Trypsin, chymotrypsin, and elastase.

What determines the substrate specificity of trypsin, chymotrypsin, and elastase?

The shape and charge of the substrate-binding pocket.

What amino acid residues does trypsin cleave on the C-side of?

Arg or Lys.

What amino acid residues does chymotrypsin cleave on the C-side of?

Phe, Tyr, and Trp.

What amino acid residues does elastase cleave on the C-side of?

Small, neutral residues like Ala, Gly, and Val.

If an enzyme makes n cut sites in a protein, how many peptide fragments are produced?

n + 1 peptides.

What are the three residues of the catalytic triad in chymotrypsin?

Asp102, His57, and Ser195.

What is the function of the oxyanion hole in serine proteases?

It stabilizes the tetrahedral oxyanion intermediate using backbone N-H groups.

What causes the 'burst kinetics' observed in serine protease reactions?

The first step (acylation) is fast, while the second step (deacylation) is slow.

What is the primary difference in catalytic residues between serine proteases and aspartic proteases?

Serine proteases use a catalytic triad; aspartic proteases use two catalytic aspartate residues.

What pH range are aspartic proteases generally active in?

Acidic pH.

How does HIV-1 protease achieve catalytic activity structurally?

As a homodimer where each monomer contributes one catalytic aspartate.

What are the key steps in the GAPDH catalytic mechanism?

Cys attack, NAD+ oxidation to a thioester, and phosphorolysis by Pi yielding 1,3-BPG.

How do protein kinases regulate enzymes through covalent modification?

They add a phosphate group to target residues like Ser, Thr, or Tyr.

What is zymogen activation?

The irreversible activation of an inactive enzyme precursor via specific proteolytic cleavage.

What are isozymes?

Enzymes with different subunit compositions that catalyze the same reaction with distinct tissue properties.

How does protein kinase A (PKA) use modulatory regulatory proteins for activation?

Regulatory subunits inhibit catalytic subunits until cAMP binds and releases them.

What characterizes the velocity versus substrate concentration curve of allosteric regulatory enzymes?

A sigmoidal (S-shaped) curve due to cooperativity.

What is the difference between homotropic and heterotropic allosteric effectors?

Homotropic effectors are the substrate itself; heterotropic effectors are different molecules.

What is the distinction between K systems and V systems in allosteric regulation?

K systems change K0.5; V systems change Vmax.

How do activators and inhibitors affect the sigmoidal v vs [S] curve?

Activators shift the curve left; inhibitors shift the curve right.

What are the two primary models of cooperativity in oligomeric enzymes?

The MWC (concerted) model and the KNF (sequential) model.

What is the primary physiological role of myoglobin versus hemoglobin?

Myoglobin stores O2 in muscle; hemoglobin transports O2 in blood.

What iron oxidation state is required for myoglobin and hemoglobin to bind O2?

Ferrous iron (Fe2+).

Which amino acid residue acts as the 5th coordination ligand to the heme iron?

His F8 (proximal histidine).

What structural changes occur in hemoglobin when O2 binds to the heme group?

Fe moves into the heme plane, triggering a quaternary T to R transition.

What stabilizes the T state (deoxy) of hemoglobin?

A network of intersubunit salt bridges.

What is the Bohr effect in hemoglobin regulation?

Low pH lowers O2 affinity and stabilizes the T state, promoting release in tissues.

How does 2,3-bisphosphoglycerate (BPG) affect hemoglobin's oxygen-binding affinity?

It binds in the central cavity, stabilizing the T state and lowering O2 affinity.

Why does fetal hemoglobin have a higher O2 affinity than maternal hemoglobin?

It has fewer positive charges in the BPG cavity, leading to weaker BPG binding.