Difference between Kd and Km re: biochem

[Doctor_Strange]

Hey,

I know Km is the substrate affinity constant and that a lower Km means stronger affinity/binding between E and S, but I am confused about Kd.

As I understand it: A + B -> AB and Kd = A + B/ AB (basically the reverse constant). What I do not get is how a lower Kd corresponds to higher affinty?

THanks

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[salemstein]

I think Kd is AB -> A + B. No matter what the "K" is, its always products over reactants. Kd = [A] x (B] / [AB]. Low Kd means bigger denominator, so more of the AB (substrate attached to enzyme) form. It also means less have dissociated into individual [A] and units.

 

[Doctor_Strange]

I think Kd is AB -> A + B. No matter what the "K" is, its always products over reactants. Kd = [A] x (B] / [AB]. Low Kd means bigger denominator, so more of the AB (substrate attached to enzyme) form. It also means less have dissociated into individual [A] and units.

Sorry I meant to say that K is for A + B -> AB but the reverse that is AB -> A + B would be defined not by "K" but by "Kd"

 

[aldol16]

Sorry I meant to say that K is for A + B -> AB but the reverse that is AB -> A + B would be defined not by "K" but by "Kd"

Kd is just a special name for a special K. The concept is the same - it's still an equilibrium constant. Certain equilibria are just important and so biochemists give them special names. The dissociation constant is one of them.

Actually, the A + B ---> AB reaction does have a special name for its K - it's Ka, or the association constant. It's rarely used because people often confuse it with another Ka, the acid dissociation constant, which actually takes the form of Kd, not Ka.

 

[Doctor_Strange]

Kd is just a special name for a special K. The concept is the same - it's still an equilibrium constant. Certain equilibria are just important and so biochemists give them special names. The dissociation constant is one of them.

Actually, the A + B ---> AB reaction does have a special name for its K - it's Ka, or the association constant. It's rarely used because people often confuse it with another Ka, the acid dissociation constant, which actually takes the form of Kd, not Ka.

OK, that makes sense, but the Bio SB says that a a substrate and enzyme with a low Kd suggests higher affinity. I cant but help think that Kd = Km in regards to biochemistry, but im sure they are not the same...

 

[theonlytycrane]

E + S <- k-1 / k1 -> ES - k2 -> E + P

For the michaelis-menten model, Km = rate of dissociation of ES / rate of formation of ES = k-1 + k2 / k1. (Km is a dissociation constant as you stated above).

If the enzyme / substrate have greater binding affinity, k1 gets bigger which decreases Km.

If the enzyme / substrate have weaker binding affinity, k-1 and/or k2 get bigger which increases Km.

Km is inversely proportional to enzyme / substrate binding affinity and is also the substrate concentration when v = vmax / 2.

 

[Doctor_Strange]

E + S <- k-1 / k1 -> ES - k2 -> E + P

For the michaelis-menten model, Km = rate of dissociation of ES / rate of formation of ES = k-1 + k2 / k1. (Km is a dissociation constant as you stated above).

If the enzyme / substrate have greater binding affinity, k1 gets bigger which decreases Km.

If the enzyme / substrate have weaker binding affinity, k-1 and/or k2 get bigger which increases Km.

Km is inversely proportional to enzyme / substrate binding affinity and is also the substrate concentration when v = vmax / 2.

Sorry, so where does Kd fit into this? I understand though the components of k1 and k2 involved, but was not aware of the nuances associated with how it impacts Km! (maybe beyond the scope of the mcat?)

 

[theonlytycrane]

Km is a dissociation constant by definition. It's a "Kd". I was just providing information to better explain how Km is inversely proportional to enzyme / substrate binding affinity.

If you prefer, just MCAT memorize: Km is inversely proportional to enzyme / substrate binding affinity and is also the substrate concentration when v = vmax / 2.

 

[aldol16]

OK, that makes sense, but the Bio SB says that a a substrate and enzyme with a low Kd suggests higher affinity. I cant but help think that Kd = Km in regards to biochemistry, but im sure they are not the same...

Low Kd does have higher affinity. You're talking about ES ---> E + S. If you have a low Kd, that means the left is favored and so the substrate (or inhibitor) binds with greater affinity. Another, simpler way to think about it is this: It's a dissociation constant. Dissociation of what? Well, when you're talking about proteins or inhibitors, it's dissociation of the small molecule from the protein. And you want that dissociation to be small for high affinity.

 

[Doctor_Strange]

Low Kd does have higher affinity. You're talking about ES ---> E + S. If you have a low Kd, that means the left is favored and so the substrate (or inhibitor) binds with greater affinity. Another, simpler way to think about it is this: It's a dissociation constant. Dissociation of what? Well, when you're talking about proteins or inhibitors, it's dissociation of the small molecule from the protein. And you want that dissociation to be small for high affinity.

So now I understand. Last question, and this is more conceptual if anything, could we than technically refer to Km as an "association constant" (I would not do so, but just another way to think about it for me...) between E and S?

 

[aldol16]

So now I understand. Last question, and this is more conceptual if anything, could we than technically refer to Km as an "association constant" (I would not do so, but just another way to think about it for me...) between E and S?

But a low Km means high affinity/association...