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Offline orgo814

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Cosubstrate
« on: November 19, 2014, 11:42:46 AM »
How does NAD+/NADP+ act as a cosubstrate? Does it simply assist in helping to oxidize or reduce a bound substrate? Thanks

Offline Babcock_Hall

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Re: Cosubstrate
« Reply #1 on: November 19, 2014, 01:18:23 PM »
Can NAD or NADP act as a reducing agent?

With respect to the terminology of "cosubstrate," I suspect that people use it to emphasize that this role is chemically distinct from the role of other organic molecules that are "coenzymes," non-protein molecules that help an enzyme catalyze a reaction (aintaining a bright line between the two is not always easy).  The term cosubstrate also helps emphasize that in the study of pathways, we are sometimes more interested in the flow of metabolites and than we are focused on molecules such as NAD.  For example in glycolysis glyceraldehyde 3-phosphate (a substrate) is converted to 1,3-bisphosphoglycerate (a product), and NAD and NADH are also involved.
« Last Edit: November 19, 2014, 04:11:51 PM by Babcock_Hall »

Offline orgo814

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Re: Cosubstrate
« Reply #2 on: November 22, 2014, 11:20:57 AM »
How does it act as a cosubstrate though? What is it's role in assisting the catalysis? That is my question

Offline Yggdrasil

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Re: Cosubstrate
« Reply #3 on: November 22, 2014, 11:38:46 AM »
A good starting point may be to look up a reaction that NAD+ or NADP+ are involved in (such as the reaction catalyzed by malate dehydrogenase during the TCA cycle).  In that reaction, is NAD+ changed after the reaction (indicating that it is acting as reactant) or does it remain unchanged (indicating that it is acting as a catalyst)?

Offline orgo814

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Re: Cosubstrate
« Reply #4 on: November 22, 2014, 11:43:43 AM »
It usually is changed to NADH if I am correct

Offline Yggdrasil

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Re: Cosubstrate
« Reply #5 on: November 22, 2014, 11:59:59 AM »
Yes, that is correct. 

Offline orgo814

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Re: Cosubstrate
« Reply #6 on: November 22, 2014, 12:19:28 PM »
So given that a cosubstrate is a coenzyme... As my professor says... How does that help the enzyme?

Offline Yggdrasil

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Re: Cosubstrate
« Reply #7 on: November 22, 2014, 12:49:22 PM »
Well, can the reaction occur without NAD+ present?

The term cofactor/coenzyme is a very broad term in biochemistry that basically means anything that's not part of the enzyme itself, that it requires to catalyze a reaction with its substrate.

Offline Babcock_Hall

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Re: Cosubstrate
« Reply #8 on: November 22, 2014, 12:55:04 PM »
So given that a cosubstrate is a coenzyme... As my professor says... How does that help the enzyme?
butlerw2,

I do not agree with your statement that a cosubstrate is a coenzyme.  A coenzyme is unchanged after one complete catalytic turnover, but a cosubstrate is converted into a coproduct.  I think we should nail this down with respect to the example of malate dehydrogenase.

Offline Yggdrasil

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Re: Cosubstrate
« Reply #9 on: November 22, 2014, 01:05:26 PM »
I do not agree with your statement that a cosubstrate is a coenzyme.  A coenzyme is unchanged after one complete catalytic turnover, but a cosubstrate is converted into a coproduct.  I think we should nail this down with respect to the example of malate dehydrogenase.

While I think I would like to agree with you, the really confusing part is that many sources do consider NAD+/NADH and NADP+/NADPH to be coenzymes (for example, http://en.wikipedia.org/wiki/Cofactor_%28biochemistry%29 and my copy of Voet & Voet also lists them as coenzymes.  In fact, Voet & Voet write, "Coenzyems are chemically changed by the enzymatic reactions in which they participate.").

Although it would be nice if biochemists had a nice definition of coenzyme/cofactor that made sense, I think we have to take into account that biochemists use the term very loosely, such that it has very little meaning other than, a small non-protein compound that is required for enzyme activity (whether or not it changes in the reaction).

It seems like butlerw2 understands how NAD+ helps reactions, but is just getting confused by what exactly the term coenzyme means.

Offline Arkcon

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Re: Cosubstrate
« Reply #10 on: November 22, 2014, 03:03:00 PM »
Well, its already been said that NAD+ accepts a proton.  An old simplistic definition of oxidizer is a proton acceptor -- a reducing agent give a hydrogen, oxidizer accepts it, that sort of thing.  If the substrate is one molecule, and the enzyme is a catalyst and not changed, and the substrate needs to be oxidized or reduced, then NAD+/NADH are needed.

Of course, if the enzyme works on two substances, oxidizing one and reducing another, it wouldn't need NAD+/NADH.  Hmmm ... I guess that just makes NAD+/NADH just another substrate. 

Ha.  When I started typing, I thought I was going to help clear this up.  Now it seems I just said what everyone else said.  butlerw2:, give all that's been posted, is there still a question?  Or has this all dissolved into semantics?
Hey, I'm not judging.  I just like to shoot straight.  I'm a man of science.

Offline Yggdrasil

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Re: Cosubstrate
« Reply #11 on: November 22, 2014, 10:39:15 PM »
The important thing to know about cofactors and coenzymes is that they are substances that extend the ability of proteins to perform chemistry.  Proteins have a limited repertoire of side chains that allow them to catalyze some simple reactions (e.g. acid/base reactions, nucleophilic substitutions), but they need help performing other types of reactions (e.g. redox chemistry).  In the case of malate dehydrogenase and other oxidoreductases that use NAD+, the NAD+ provides a hydride acceptor to facilitate the oxidation of their substrates.

On the issue of coenzymes vs cosubstrates, there are two classes of coenzymes.  Coenzymes that are tightly associated with the enzymes and do not dissociate between enzyme turnover events are called prosthetic groups.  The heme group in many oxidoreductases such as catalase is an example of a prosthetic group.  Cosubstrates, the other class of coenzyme, are not tightly bound by the enzyme and cycle off and on enzyme between turnover events.  NAD+ is an example of a cosubstrate.

Well, its already been said that NAD+ accepts a proton.  An old simplistic definition of oxidizer is a proton acceptor -- a reducing agent give a hydrogen, oxidizer accepts it, that sort of thing.

Most biological oxidizing agents are hydride acceptors (not proton acceptors).  The difference is that two electrons are transferred with the hydrogen nucleus during hydride transfer.  Because no electron transfer occurs when a proton moves from one molecule to another, proton transfers are not redox reactions.

Offline Babcock_Hall

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Re: Cosubstrate
« Reply #12 on: November 23, 2014, 03:29:39 PM »
Chapter 11 of Zubay's Biochemistry states, "Tightly bound coenzymes are often referred to as prosthetic groups."  I have several points that I hope will clarify things in the end.  One, there are enzymes for which NAD is a coenzyme in the most restrictive sense of the word, such as UDP-galatose 4-epimerase.  It is reduced in the first half-reaction and oxidized in the second, and UDP-Gal is converted into UDP-Glc but does not dissociate as part of the catalytic cycle.  Pyridoxal phosphate is another coenzyme that does not dissociate as part of the catalytic cycle.  Two, IIRC there are some pathways in which a substance such as Coenzyme A is a substrate in the first step and a product in the second.  For this reason among others, drawing a bright line between coenzymes and cosubstrates is at best difficult.  Perhaps saying that there are two classes of coenzymes is the best alternative, and we can leave it at that and focus on NAD itself.

NAD is a hydride-ion (a hydride ion is one proton plus two electrons) acceptor, and NADH is a hydride-ion donor.  FAD requires two electrons and two protons to be converted into FADH2.  When one studies the electron transport chain in detail, it helps to keep track of the number of protons, as well as the number of electrons.   

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