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My biochemistry textbook, "Harper's Illustrated Biochemistry", states:

Coenzymes serve as recyclable shuttles that transport many substrates from one point within the cell to another. The function of these shuttles is twofold. First, they stabilize species such as hydrogen atoms (FADH2) or hydride ions (NADH) that are too reactive to persist for any significant time in the presence of the water, oxygen, or the organic molecules that permeate cells.

Second, they increase the number of points of contact between substrate and enzyme, which increases the affinity and specificity with which small chemical groups such as acetate (coenzyme A), glucose (UDP), or hydride (NAD+) are bound by their target enzymes."

To be specific I don't understand the meaning of the words in bold, above:

  • what are these so-called small chemical groups?
  • are they already bound to the enzyme or are they substrates?
  • what does increasing the specificity mean?
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Summary

Co-enzyme is a general term employed early in the development of biochemistry and applied to non-protein components required for enzyme activity. Thus the term is not a chemical or mechanistic description and is of limited contemporary importance. Nevertheless a group of molecules designated as coenzymes, though differing in chemical structure, share the function of being activated carriers for particular chemical groups (not substrates).

The term “shuttle” neither describes, nor is generally applied to, this function: indeed it is reserved for the process of moving molecules back and forward between cellular compartments. This is quite distinct from whether or not the reactivation of the coenzyme occurs within the protein or after dissociation into the surrounding milieu. (Incidentally, the fact that both situations are found illustrates the limitation of defining cofactors tightly bound to proteins as prosthetic groups, and those that are not as coenzymes.)

The basic reason for the other molecular portion of a coenzyme of the activated carrier class is to provide a thermodynamically activated structure — a chemical bond to the group being carried that ensures its reactivity. Other features differ quite widely and may relate to the specific type of interaction of different coenzymes with proteins.

Cofactors, coenzymes, cosubstrates and prosthetic groups

For historical reasons the terminology in this area is generally descriptive rather than chemically systematic, but is best considered first as it has tended to influence perceptions of function (specifically the term “shuttle” in the quotation in the question). The all-embracing term ‘cofactor’ was coined for non-protein components of proteins that were necessary for their activity. There was then a fairly clear-cut distinction made between cofactors that were metal ions and those that were organic molecules. Here the terminology becomes somewhat less clear. Organic cofactors were designated ‘coenzymes’, but then a distinction was made betweeen those which are loosely bound to the protein and those which are tightly bound, the latter being termed ‘prosthetic groups’. Initially prosthetic groups were regarded as a sub-class of coenzymes, but some authors now consider coenzymes and prosthetic groups as a subdivision of organic co-factor, perhaps influenced by the haem prosthetic group in the non-enzymatic protein, haemoglobin. Furthermore, coenzymes such as NAD can be regarded as co-substrates in an enzymic reaction, and it is difficult to argue that they are distinct from co-substrates such as ATP and SAM, which are not generally termed coenzymes. This state of affairs is illustrated in the table below.

Name Co-enzyme? Prosth. Gp? Co-sub.? Act. Carr.? Group
NAD, NADP Y N Y Y electron
Coenzyme A Y N ? Y acyl
FAD Y Y N Y electron
Lipoic Acid N Y N Y electron
Tetrahydrofolate Y N ? Y 1-C unit
Pyridoxal phosphate Y Y N N
Thiamine pyrophosphate Y Y N N
Haem N N N N
ATP N N Y Y phosphoryl
S-adenosyl methionine N N Y Y methyl
UDPG N N Y Y glucose

[Source of designations: Coenzymes — Berg et al., Prosthetic Group — Wikipedia, Cosubstrate — own judgement, activated carrier — general literature]

‘Activated carriers’

It is possible to find a functional chemical communality among many — although not all — of the cofactors and cosubstrates in the table above by considering that they function as ‘activated carriers’ of chemical groups that are transferred to a substrate during the enzymic catalysis. Such groups range from single carbon units to larger acyl and phosphatide groups. It is usual also to include cofactors involved in redox reactions in this category. For species such as NAD and FAD one can argue that the activated group is a hydride ion, although it is necessary to consider electrons as the activated species if one wishes to encompass all redox reactions.

For repeated use of a cofactor it is necessary to reactivate it, which in different cases occurs within the enzyme (e.g. FAD-containing enzymes) or after release in solution (e.g. NAD-containing enzymes). Activated carriers of the former type illustrate that Harper’s statement of the function of coenzymes as “shuttles that transport many substrates from one point within the cell to another” is quite incorrect.

Harper’s chemical explanation of coenzyme structure in terms of stabilizing reactive species is unhelpful and, indeed, misleading as it implies such species are generated in cells. Instead, this should be considered from the opposite viewpoint: that the groups being transfered are more ‘reactive’ than in the target molecules, although the word ‘reactive’ is best avoided as it is ambiguous. The common feature of the molecular structure of cofactors is that the chemical bond between the group that is being transferred and the rest of the molecule is such that its breakage involves a decrease in Gibbs Free Energy sufficient to drive the formation of a stable bond to the target substrate. An illustration of this is the reaction of acetyl-CoA in which it is a thio-ester bond (red) that provides this activation.

Citrate Synthetase

Non-catalytic components of coenzymes

One aspect of the structure of cofactors that serve as activated carriers for different chemical groups is obviously the region of the molecule containing the group to be transferred and the ‘activate bond’. Parts of the rest of the cofactor structure will be involved interaction of the cofactor at its binding site on the enzyme, and contribute to the strength and specificity of the binding. That much is self-evident, and is the gist of the second point in the Harper extract in the question, including the emboldened text. The reference to ‘groups’, which the poster did not understand, are those listed in the table above, and encircled by red rings in the composite of co-enzyme structures, below.

Some coenzyme structures

It can also be seen how extensive the ‘rest’ of the structure of the coenzyme is in most cases, far more extensive than would seem necessary for simply enabling specific and strong binding. It is also remarkable that in many cases the ‘structural extension’ involves a nucleotide (generally adenosine) diphosphate moiety (yellow background).

Why? The student is warned that what follows is speculation (not original on my part) for which there is — and can not be — any evidence. However, it has been suggested that the nucleotide phosphate moiety is a relic of a postulated RNA world, in which the functional part of the coenzyme was covalently attached to the RNA of ribozymes. When the transition to protein enzymes occurred a nucleotide binding site evolved on proteins to attach the coenzyme, rather than an alternative molecular change, which perhaps occurred in other cases (tetrahydrofolate? lipoate?).

Coenzymes that are not activated carriers

Because of the emphasis above on cofactors/coenzymes that are activated carriers, it seems to me necessary to give an example of coenzyme that does not work in this way. I have chosen pyridoxal phosphate, which is actually covalently bound to the enzymes in which it is a coenzyme. These catalyse quite variety of different types of reaction — the racemization of L-alanine to D-alanine is illustrated — but the important point is that there is no group transfer involved, with the coenzyme being in the same state at the end of the reaction as at the beginning. In this respect it is similar to, say, the catalytic triad of serine proteases, and can be thought of being chemically more sophisticated and versatile for catalysis than a combination of amino acid residues.

pyridoxal phosphate catalysed racemization

[From the Wikipedia entry for pyridoxal phosphate]

…and shuttles?

“The original meaning of the word ‘shuttle’ was as a noun, referring to the device used in weaving to carry the weft thread. By reference to the continual to-and-fro motion associated with that, the term was then applied in transportation to both the vehicle involved, and as a verb, to the motion itself” (adapted from the Wikipedia entry).

The author of the chapter in Harper from which the quotation in the question is taken seems to be using a metaphor in which the coenzyme is equivalent to the shuttle, and the activated group to which it is temporarily covalently bound is equivalent to the weft thread. There are two problems with this. He goes on to say that such shuttles “transport many substrates from one point within the cell to another”. There is confusion about the way that the term ‘substrate’ is employed — rather unusually it appears to be equivalent to what he refers to as ‘species’ or ‘small chemical group’. However the reference to transport from one point within the cell to another is just plain wrong. Some coenzymes diffuse into the containing milieu (usually aqueous) where they are reactivated in a different enzymic reaction, but others stay bound to their holoenzyme. And transfer of groups during chemical reaction can hardly be regarded as transport between points. The second problem is that the term ‘shuttle’ is already in widespread and specific use in biochemistry in relation to surrogate transport of metabolites across membranes such as the inner mitochondrial membrane. This author‘s use of the term is particularly confusing in relation to one particular coenzyme: for NADH in aerobic cells the malate–aspartate shuttle transfers its electrons from cytoplasm to mitochondrial matrix.

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  • $\begingroup$ This is a long answer, which is why I started with a summary. I have tried both to answer the poster's question and provide a general perspective on coenzymes in the hope that it will be of wider interest. An answer this long will, no doubt, have deficiencies in fact, clarity and typography. If these are pointed out to me I will endeavour to remedy them. $\endgroup$
    – David
    Dec 10, 2023 at 21:32

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