Reactivity in Chemistry

Mechanisms of Glycolysis

 

GL5.  Catalysis in Phase One

Reactions in biochemistry are usually catalysed by enzymes.  In a catalysed reaction, an alternative pathway is available that makes it easier to get from reactants to products.  That doesn't mean that there are fewer steps.  In fact, normally there are more steps in a catalysed reaction than there are in an uncatalysed one. It does mean that the overall energy needed to traverse the catalysed barrier is lower than the energy needed to surpass the uncatalysed barrier.  It's like taking the stairs up to the second floor rather than taking a running leap at the window: more steps, but overall it will save time.

So far, the reactions we have seen in glycolysis are just the overall reactions.  By looking at the overall reactions, we get a pretty good sense about what is happening at each stage of the pathway.  We even get some sense of how those reactions might happen, because we can identify familar nucleophiles and electrophiles that appear to be involved.  Here, we will take a more detailed look at the catalytic pathways taken during the first phase of glycolysis.

Essentially every step of glycolysis involves catalysis, and so the reactions entail cofactors and detailed steps that we have glossed over until now.  The first step, phosphorylation of glucose to afford glucose-6-phosphate, requires the consumption of ATP. During that step, the terminal hydroxy group of glucose takes up phosphate from ATP, leaving ADP. 

It seems like that first step should be pretty straightforward, because we thinkof ATP as this high-energy power source for the cell, so it must be really reactive.  ATP is not quite as reactive as you might think, though.  That's a good thing.  If it reacted too readily, it couldn't travel around the cell at all; it would get hydrolysed the first time it encountered a water molecule, and there really are an awful lot of those in a typical cell.  In order to react, the ATP needs to be activated.

Part of the catalysis of the phosphorylation of glucose simply involves binding ATP to a magnesium ion.  Once bound to the magnesium ion, the ATP becomes more electrophilic, because of that positive charge on the magnesium ion. 

Although a nucleophile, such as water, is unlikely to donate to ATP -- partly because of the negative charge on the ATP -- it is likely to donate to ATP once coordination takes place, because the magnesium ion has leveled out that negative charge.

Another aspect of catalysis in the phosphorylation of glucose involves the removal of a proton.  A hydroxyl group is converted to a phosphate, and a proton is lost.  Acid-base catalysis is quite common in biochemistry.  There are only a handful of amino acids that commonly participate in deprotonation steps: aspartate, glutamate, lysine, and histidine.  All of these residues have two structures in equilibrium: a protonated one and a non-protonated one.  The non-protonated form is ready to remove a proton when needed.

Similarly, acid-base catalysis is carried out by nearby amino acid residues in the active site of the enzyme that carries out the isomerisation of glucose-6-phosphate to fructose-6-phosphate.  Phosphoglucoisomerase accomplishes this task by removing a proton from an alpha position, and also from an O-H group, as well as donation of protons to a different alpha position and a different oxygen.

Of course, the same sort of catalytic requirements arise again during the conversion of F6P to FBP.  ATP must be activated by magnesium, and proton transfers must be carried out by acidic and basic amino acid residues.

A completely different kind of catalysis occurs during the scission step of phase one, when the six-carbon sugar is cleaved into a pair of three-carbon sugars. You may recall that this cleavage is accomplished via a retro-aldol reaction: an aldol reaction goes into reverse, spitting out an enolate or enol and a carbonyl. 

That retro-aldol step is accomplished via iminium ion catalysis.  Very often in biochemical reactions, a lysine residue binds with a carbonyl to form either an iminium ion, containing an electrophilic C=N bond, or an enamine, with a nucleophilic N-C=C unit.

The imine unit isn't an inherently better electrophile than a carbonyl; after all, it contains a less polar C=N bond instead of a C=O bond.  However, the nitrogen in an imine is much more basic than the oxygen in a carbonyl.  It can be protonated quite easily under biological conditions.  The resulting iminium ion, containing the C=N-H+ unit, is an activated electrophile.  Of course it reacts much more quickly than a regular carbonyl.

In the context of a retro-aldol reaction, however, we need to thnk about this catalysis backwards.  Instead of an iminium ion acting as an activated intermediate to receive a nucleophile, it is accepting electrons to form a leaving group.  Instead of having an enolate leaving group in the retro-aldol reaction, we have an enamine leaving group.

There is one last reaction in phase one, the fifth overall in glycolysis.  It's the conversion of DHAP to G3P; but that's just another keto-enol tautomerism.  The catalytic mechanisms will be very much like those seen in the conversion of G6P to F6P.

 

This site is written and maintained by Chris P. Schaller, Ph.D., College of Saint Benedict / Saint John's University.  These materials are available for educational use.

Send corrections to cschaller@csbsju.edu

This material is based upon work supported by the National Science Foundation under Grant No. 1043566.

Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

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