Biochem Unit 2 Homework

Product formation contributes how much to Km?

Very small amount

When [S] = Km, what is V₀?

V₀ = ½ Vmax

What happens to Vmax and Km when Enzyme is doubled?

• Vmax doubles

• Km is the same

What happens to Vmax and Km when Substrate is doubled?

• Vmax doesn’t double (still increases)

• Km doubles

What is the roles of each thing in Catalytic Triad?

• Ser = nucleophile (deprotonated)

• His = accepts proton from ser (protonated)

• Asp = stabilizes positive His and help tune its reactions

What is the substrate-specificity pocket?

Recognizes right substrate side chain and positions target bond for cleavage

What does the oxyanion hole do?

Stabilizes negatively charged tetrahedral intermediate through hydrogen bonding

How does primary and secondary active transport work?

• Primary - ATP

• Secondary - moves with ion

What is a secondary messenger?

Produced in the cell and carries signal from receptor pathway to intracellular targets

What is signal amplification?

1 activated receptor activates many G protein

What is desensitization?

Pull receptor inside and blocks G-protein activation

What is adaptation?

Remove secondary messenger and cell adapts by going back to baseline

What does trans-autophosphorylation do?

Creates phosphotyrosine docking sites. Proteins with phosphotyrosine binding domains (SH2) can bind these sites, assembling a signaling complex and propagating the signal

What happens when Keq »» Q ?

Reactions is far from equilibrium in forward direction, Delta G negative

Maintaining a high ATP:ADP ratio increases thermodynamic force because…

Lower ADP lowers Q, and a smaller Q makes delta G more negative

Why is it misleading to say ATP is hydrolyzed first and simply “releases” energy for the kinase? What does the kinase actually transfer?

The kinase couples the reactions by transfering ATP’s terminal phosphoryl group directly to ACC. ATP is not hydrolyzed in a separate step that releases energy for the kinase to use later. So ATP’s favorable free energy change helps drive ACC phosphorylation

Why can FAD participate in one-electron steps whereas NAD⁺ normally accepts two electrons together as a hydride. Connect your answer to the flavin and nicotinamide ring systems.

FAD’s extended conjugated isoalloxazine ring can delocalize and stabilize an unpaired electron, allowing a semiquinone intermediate and sequential one-electron chemistry.

NAD⁺ has a more localized nicotinamide redox center and normally accepts a hydride (2 e- and H+) rather than a stable one-electron intermediate

Acceptor MINUS Donor

Acceptor MINUS Donor

When delta E is negative, what is delta G?

Positive

Explain how rapid consumption of oxaloacetate and a high NAD⁺:NADH ration influence the actual delta G and favored direction

Removing oxaloacetate lowers the product term in Q, and abundant NAD⁺ with relatively less NADH also lowers Q for the forward reaction. Both make RTlnQ more negative, shifting the delta G toward the forward direction

Why does succinate dehydrogenase use an enzyme-bound flavin instead of NAD⁺ as its electron acceptor?

• An enzyme-bound flavin can be tuned by its protein environment to a higher reduction potential

• Flavins can also support one electron chemistry that NAD

What does it mean when a molecule have a higher (more positive) reduction potential?

• A more positive reduction potential means the molecule has a stronger tendency to accept electrons and be reduced.

• Higher reduction potentials for the acceptor make electron transfer from donor and acceptor more favorable