Aspartate and glutamate are commonly found in the active sites of enzymes that a

Question

Aspartate and glutamate are commonly found in the active sites of enzymes that act upon DNA because:

a) Their acidic side chains are excellent nucleophiles to mediate phosphodiester bond breaking and joining reactions.

b) They carry a positive charge at physiological pH and therefore have a high affinity for the negatively charged backbone of DNA.

c) Their tendency to donate protons enables interaction with proton acceptors in the major groove.

d) They are able to coordinate divalent metal cations, which in turn activate molecules that form nucleophiles.

e) They are highly acidic and therefore are able to break DNA bonds.

2. You are characterizing a new DNA polymerase. When the enzyme is incubated with [32P]DNA and no dNTPs, you observe the release of [32P]dNMPs. This release is prevented by adding unlabeled dNTPs. Which of the following describes the reactions that most likely underlie these observations?

a)The DNA polymerase contains 3'-5' and a 5'-3' exonucleases that degrade DNA to produce [32P]dNMPs.

b)The DNA polymerase contains a 5'-3' exonuclease that degrades DNA to produce [32P]dNMPs.

c)The DNA polymerase contains a 3'-5' exonuclease that degrades DNA to produce [32P]dNMPs.

d)Any of the above could explain these observations.

e)None of the above.

Explanation / Answer

1. Answer: c) Their tendency to donate protons enables interaction with proton acceptors in the major groove.

These are acidic in nature, and hence do not have a positive charge, but a negative charge. Also, they are proton donators, and hence cannot act as nucleophiles, as nucleophiles are electron donators. Also, molecules don’t form nucleophiles in this interaction.

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