Anyone good with enzyme kinetics? (Long)

[Necr0sis713]

This is in regards to the Khan Academy bio passage "The genetic basis of phenylketonuria". I'm a little confused by the method here because I haven't really taken a biochem class. I'm gonna basically post every question, and the answer, then state why i'm confused. Please note that i'm not gonna list the passage here, so i'm assuming you already know what phenylketonuria is:

1. How would you expect the mutation associated with PKU to affect the catalytic efficiency of phenylalanine transaminase? Answer: Neither Kcat nor Km will change, leading to an unchanged catalytic efficiency.

I'm assuming that since this is a deactivating mutation, the kcat and Km are inherent properties of the enzyme, so these will be unchanged?

3. How would you expect the mutation associated with PKU to affect the rate of the reaction catalyzed by phenylalanine transaminase? Answer: The reaction rate will increase, due to an increase in the concentration of phenylalanine.

Ok so for this one, I understand that they're basically using the Michaelis-Mentin equation straight plug n chug style. So more on top means higher rate? I don't really get why this would happen though because wouldn't a defective enzyme mean that there is less turnover happening? Or since [E] isn't in the equation then that wouldn't matter.

4. Individuals heterozygous for the PKU mutation have very slightly increased levels of phenylalanine. How would you expect the phenylalanine hydroxylase reaction rate of an individual heterozygous for the PKU mutation to be different in than an individual with no mutated genes? Answer: The reaction rate would decrease due to a decrease in the reaction’s Vmax

I'm thrown off here now. I thought extra substrate means faster rate, according to the previous questions? I get that the heterozygous individual has a defective, and not inactive enzyme, but why would it be different in this case?

5. Which of the following would best represent the outcome of an individual with the PKU mutation consuming a meal with a high phenylalanine content? Answer: The phenylalanine transaminase catalyzed reaction rate would increase, and the concentration of phenylalanine would increase significantly.

Now we're back to the reaction increasing from excess substrate, with a defective enzyme. I'm thrown off because in the last question it was decreased rate.

I know this is long, so if anyone is willing to help, I will highly appreciate it. It would really be helpful.

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[Necr0sis713]

umm..i'm not sure why some words got crossed out?

 

[betterfuture]

Is it possible for you to edit your post to remove the cross-out feature? Makes it a little harder to read.

 

[betterfuture]

3. How would you expect the mutation associated with PKU to affect the rate of the reaction catalyzed by phenylalanine transaminase? Answer: The reaction rate will increase, due to an increase in the concentration of phenylalanine.

Ok so for this one, I understand that they're basically using the Michaelis-Mentin equation straight plug n chug style. So more on top means higher rate? I don't really get why this would happen though because wouldn't a defective enzyme mean that there is less turnover happening? Or since [E] isn't in the equation then that wouldn't matter.

Well from what I know, if you have a known concentration of enzyme and you add, let's say, 1 molecule of substrate, you would get 1 product. However, other active sites of the enzymes are unbound or "free", so when you add more substrate the reaction rate of enzyme-substrate complex to product increases until you can no longer add anymore. This is because the enzymes' active sites are saturated, so adding any more substrate does nothing; it has reached its Vmax. So yes, adding more substrate can increase the reaction rate. If the enzyme becomes saturated, you can also increase the concentration of the enzyme to achieve a higher Vmax.

4. Individuals heterozygous for the PKU mutation have very slightly increased levels of phenylalanine. How would you expect the phenylalanine hydroxylase reaction rate of an individual heterozygous for the PKU mutation to be different in than an individual with no mutated genes? Answer: The reaction rate would decrease due to a decrease in the reaction’s Vmax

I'm thrown off here now. I thought extra substrate means faster rate, according to the previous questions? I get that the heterozygous individual has a defective, and not inactive enzyme, but why would it be different in this case?

When you have a mutation to the enzyme, PAH (phenylalanine hydroxylase), there is less of the enzyme for the substrate to bind. This means, even though substrate concentration is unchanged (phenylalanine), there is not enough or a lack of the normal functional enzyme to make product (tyrosine). Thus, the reaction rate is effected; it decreases its Vmax.

5. Which of the following would best represent the outcome of an individual with the PKU mutation consuming a meal with a high phenylalanine content? Answer: The phenylalanine transaminase catalyzed reaction rate would increase, and the concentration of phenylalanine would increase significantly.

Now we're back to the reaction increasing from excess substrate, with a defective enzyme. I'm thrown off because in the last question it was decreased rate.

I know this is long, so if anyone is willing to help, I will highly appreciate it. It would really be helpful.

Again, when you increase the concentration of substrates, more of the enzyme's active site will be bound allowing a faster rate of product formation until no more unbound active sites of the enzyme are available. This is of course for the PTA enzyme (phenylalanine transaminase) because the phenylalanine in the body is metabolized to something else. Also, the meal is rich in phenylalanine, therefore, there is an increase concentration of the molecule.

 

[Necr0sis713]

Great help. I'll look over this info in depth during my next study session.