Question

In regards to protein function:

A) For specific DNA binding proteins,

1. what is the structure of a typically DNA binding protein and how does it interact with DNA?

2. why is there a difference between the major and amino groove in terms of protein binding?

B) describe how the Lac repressor interacts with DNA to find its binding site

C) describe how a catalyst lowers the activation energy of a reaction

D) how is the structure of enzymes used to design drugs for diseases like HIV?

E) what are the three steps of motor protein action?

Answer 1

1. DNA-binding proteins are proteins that have DNA-binding domains and thus have a specific or general affinity for single- or double-stranded DNA.

2. Sequence-specific DNA-binding proteins generally interact with the major groove of B-DNA, because it exposes more functional groups that identify a base pair.

b. The lac repressor operates by a helix-turn-helix motif in its DNA-binding domain, binding base-specifically to the major groove of the operator region of the lac operon, with base contacts also made by residues of symmetry-related alpha helices, the "hinge" helices, which bind deeply in the minor groove.

c. Catalysts provide a new reaction pathway in which lower activation energy is offered or it can be said that the enzyme offers a new path of lower energy for the reaction to occur. This occurs in the active site of the enzyme. A catalyst increases the rate of a reaction by lowering the activation energy so that more reactant molecules collide with enough energy to surmount the smaller energy barrier.

d. Those enzymes whose active site is in compliance with the important enzymes of HIV can be used as the drug to target HIV. These novel enzymes act as permanent inhibitors and when they bind the crucial enzymes of HIV the drug or enzyme inactivates them.