TBR: Enzyme Active Site Question

[justadream]

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TBR presents a graph that shows that a particular enzyme's max rate is achieved at a pH = 9.0

TBR asks which amino acids would best represent the catalytic group of this enzyme.

The answer is: Amino acids with side-chain pKa values close to 9.0.

Can someone explain why rate is maximized when you have amino acids with side chain pKa close to the pH of the max rate?

This is TBR Bio II page 147 #49.

 

[Sammy1024]

I believe this is a passage based question? It's giving you a fact that pH 9 is max rate and then an animo acid's pH is determined by its side chains so a side chain close to 9 would lead to highest rate.

 

[justadream]

@Sammy1024

"then an animo acid's pH is determined by its side chains so a side chain close to 9 would lead to highest rate."

Can you elaborate more on what that means?

 

[Sammy1024]

Okay so I looked up the question. You're given 4 pairs of amino acids and asks which pair would have the highest rate.

pH of an animo acid is roughly the side chain pka's/# of pka's.

So when you calculate the pHs of the pairs given,

A. 6.0 + 3.9/2 = 4.95
B. 8.3 + 10.01/2 = 9.2
C. 12.5 + 10.8/2 = 11.65
D. 10.8 + 8.3/2 = 9.55

Since the graph shows an optimal date at a pH close to 9, you would choose B as the answer.

 

[justadream]

@Sammy1024

Right, I understand the calculations but my question is:

WHY do you want the pH to be near the pKas of the side-chain of the amino acids?

Like what is special about amino acids being placed at a pH that is equal to their side-chain pKas? From my chemistry knowledge, I know that at pH = pKa, the amino acid has a positive charge and a negative charge (and is thus electrically neutral).

Is that property somewhat important for making the amino acid more "acitve"?

 

[Sammy1024]

You want the pair closest to pH=9 because the question is asking which of the pairs is closest to the graph shown in the question. The graph in a sense is saying that most of theses unknown amino acids average out to a pH of 9. And then the question wants you to figure out what is the unknown.

So you're looking for a pair of amino acids that have the highest reaction at 9.

I believe that somewhere in the TBR books (maybe Gchem) it says that optimal activity occurs wherever the initial velocity is the greatest, slowest at pI value. (That's the fact you should know).

Did it make sense or should I explain more?

 

[justadream]

@Sammy1024

Could you clarify:

"I believe that somewhere in the TBR books (maybe Gchem) it says that optimal activity occurs wherever the initial velocity is the greatest, slowest at pI value. (That's the fact you should know)."

 

[Sammy1024]

In most scenarios the speed is being called into question during electrophoresis type passages where they put some amino acids in a gel, at some pH and shoot electricity through the gel. The amino acids that move the fastest are furthest from their pI values and when they reach their pI values, they stop moving.

 

[justadream]

@Sammy1024

Oh yes, I remember that but what's the relation of pI to this problem?

Is it that pI of these amino acids is 9?

 

[Sammy1024]

There's no actual relation in the passage, but you can apply the same concept to answer the question. If they hadn't given you the graph, then you would have to go the pI route.

 

[justadream]

@Sammy1024

You say amino acid activity is slowest at the pI. Why is that?

 

[The Brown Knight]

TBR presents a graph that shows that a particular enzyme's max rate is achieved at a pH = 9.0

TBR asks which amino acids would best represent the catalytic group of this enzyme.

The answer is: Amino acids with side-chain pKa values close to 9.0.

Can someone explain why rate is maximized when you have amino acids with side chain pKa close to the pH of the max rate?

This is TBR Bio II page 147 #49.

I'm guessing you are aware that you only need to know that the pH and pKa need to be similar from the passage to correctly answer the question.
However, the specifics as to WHY that happens depends on the mechanism of the enzyme's catalysis. It could be just the ideal pH to cause deprotonation of the cysteine to activate it as a nucleophile to attack the reactant. Other enzymes can work by acid-base catalysis where one side chain would donate a proton to activate the substrate for a subsequent nucleophilic attack by another residue.
If the pH were say too low, the aforementioned cysteine would be too weak to be nucleophilic and enzyme activity declines; if pH were too high, other side chains could become deprotonated and somehow not support the catalytic residue well.
Another explanation that comes to mind is that at too high/low pH's, the enzyme's net charge on side chains changes and causes drastic conformational changes (tertiary structure of the enzyme changes) that can alter the active site as well.
Of course at extreme pH ranges, you can denature or hydrolyze the enzyme.

 

[justadream]

I'm guessing you are aware that you only need to know that the pH and pKa need to be similar from the passage to correctly answer the question.
However, the specifics as to WHY that happens depends on the mechanism of the enzyme's catalysis. It could be just the ideal pH to cause deprotonation of the cysteine to activate it as a nucleophile to attack the reactant. Other enzymes can work by acid-base catalysis where one side chain would donate a proton to activate the substrate for a subsequent nucleophilic attack by another residue.
If the pH were say too low, the aforementioned cysteine would be too weak to be nucleophilic and enzyme activity declines; if pH were too high, other side chains could become deprotonated and somehow not support the catalytic residue well.
Another explanation that comes to mind is that at too high/low pH's, the enzyme's net charge on side chains changes and causes drastic conformational changes (tertiary structure of the enzyme changes) that can alter the active site as well.
Of course at extreme pH ranges, you can denature or hydrolyze the enzyme.

Okay so you are saying it depends on the enzyme. There is not some universal property that all amino acids are "most active" at their pKa of the side chain.

I'm not really even sure how you could infer that you wanted to find amino acids with side chain pKas near 9.0 (other than perhaps just looking at what was given to you and finding no other option).

 

[The Brown Knight]

Okay so you are saying it depends on the enzyme. There is not some universal property that all amino acids are "most active" at their pKa of the side chain.

I'm not really even sure how you could infer that you wanted to find amino acids with side chain pKas near 9.0 (other than perhaps just looking at what was given to you and finding no other option).

This was said in the passage, regardless of what you know about it. And, for the purposes of MCAT, passage = Bible.