Molecular Biochemistry I

Glycolysis and Fermentation

Contents of this page:
Glycolysis pathway reactions
Summary of pathway
Regulation of glycolysis

Glycolysis Pathway
The Glycolysis pathway  is described below and summarized in Fig. 17.3 p. 584 of Biochemistry, by Voet & Voet, 3rd Edition.

The reactions of Glycolysis take place in the cytosol of cells.

Glucose enters the Glycolysis pathway by conversion to glucose-6-phosphate. Initially, there is energy input corresponding to cleavage of two ~P bonds of ATP.

1. Hexokinase catalyzes:  glucose + ATP glucose-6-phosphate + ADP

The Hexokinase reaction involves nucleophilic attack of the C6 hydroxyl oxygen of glucose on the phosphorous of the terminal phosphate of ATP.

ATP binds to the enzyme as a complex with Mg++.

The positively charged Mg++ interacts with negatively charged phosphate oxygen atoms of ATP, providing charge compensation and promoting a favorable conformation of ATP at the active site.  (See also diagram p. 585.)

The reaction catalyzed by Hexokinase is highly spontaneous. A phosphoanhydride bond of ATP (~P) is cleaved. The phosphate ester formed in glucose-6-phosphate has a lower DG of hydrolysis.

Induced fit:  Glucose binding to Hexokinase stabilizes a conformation in which
  • The C6 hydroxyl of the bound glucose is close to the terminal phosphate of ATP, promoting catalysis.
  • Water is excluded from the active site. This prevents the enzyme from catalyzing ATP hydrolysis, rather than transfer of phosphate to glucose. 

It is a common motif for an enzyme active site to be located at an interface between protein domains that are connected by a flexible hinge region. The structural flexibility allows access to the active site, while permitting precise positioning of active site residues, and in some cases exclusion of water, as substrate binding promotes a particular conformation.

2. Phosphoglucose Isomerase catalyzes: 

glucose-6-phosphate (aldose) fructose-6-phosphate (ketose)

The Phosphoglucose Isomerase mechanism involves acid/base catalysis, with ring opening, isomerization via an enediolate intermediate, and then ring closure (diagram p. 587). A similar reaction catalyzed by Triose Phosphate Isomerase is presented in more detail below.

3. Phosphofructokinase catalyzes: 

fructose-6-phosphate + ATP fructose-1,6-bisphosphate + ADP

This highly spontaneous reaction has a mechanism similar to that of Hexokinase.

The Phosphofructokinase reaction is the rate-limiting step of Glycolysis. The enzyme is highly regulated, as will be discussed later.

4. Aldolase catalyzes: 

fructose-1,6-bisphosphate dihydroxyacetone phosphate + glyceraldehyde-3-phosphate.

The Aldolase reaction is an aldol cleavage, the reverse of an aldol condensation. 

Note that carbon atoms are renumbered in reaction products. 

A lysine residue at the active site of the Aldolase enzyme functions in catalysis.

The keto group of fructose-1,6-bisP reacts with the e-amino group of the active site lysine, to form a protonated Schiff base intermediate.

Cleavage of the bond between C3 and C4 follows. (See p. 590).

5. Triose Phosphate Isomerase (TIM) catalyzes (diagrams p. 591-594):

dihydroxyacetone phosphate (ketose) glyceraldehyde-3-phosphate (aldose)

Glycolysis continues from glyceraldehyde-3-phosphate. The equilibrium constant (Keq) for the TIM reaction favors dihydroxyacetone phosphate, but removal of glyceraldehyde-3-phosphate by a subsequent spontaneous reaction allows throughput. 

The ketose/aldose conversion of TIM involves acid/base catalysis, and is thought to proceed via an enediol intermediate, as with Phosphoglucose Isomerase,

Active site Glu and His residues are thought to extract and donate protons during catalysis.

2-Phosphoglycolate is an example of a transition state analog that binds tightly at the active site of Triose Phosphate Isomerase. This inhibitor of catalysis by TIM is similar in structure to the proposed enediolate intermediate.

TIM is considered a "perfect enzyme", because the reaction rate is limited only by the rate at which substrate collides with the enzyme.

The structure of Triose Phosphate Isomerase is an ab barrel, or TIM barrel.

In an ab barrel there are 8 parallel b-strands surrounded by 8 a-helices. Short loops connect alternating b-strands and a-helices. 

TIM barrels serve as scaffolds for active site residues in a diverse array of enzymes. Residues that form the active site are always located at the same end of the barrel, associated with the C-terminal ends of b-strands and the loops connecting these to a-helices.

There is debate over whether the many different TIM barrel enzymes are evolutionarily related, since in spite of the structural similarities there is tremendous diversity in catalytic functions of these enzymes and little sequence homology.

Explore at right the structure of the Triosephosphate Isomerase (TIM) homodimer, with the transition state inhibitor 2-phosphoglycolate bound to one of the TIM monomers.

Note the structure of the TIM barrel, and the loop that forms a lid that closes over the active site after binding of the substrate.

Triose Phosphate Isomerase

6. Glyceraldehyde-3-phosphate Dehydrogenase catalyzes:

glyceraldehyde-3-phosphate + NAD+ + Pi 1,3,bisphosphoglycerate + NADH + H+

Exergonic oxidation of the aldehyde in glyceraldehyde-3-phosphate, to a carboxylic acid, drives formation of an acyl phosphate, a "high energy" bond (~P), in 1,3-bisphosphoglycerate

This is the only step in Glycolysis in which NAD+ is reduced to NADH.

A cysteine thiol at the active site of Glyceraldehyde-3-phosphate Dehydrogenase has a role in catalysis (p. 596). 

The aldehyde of glyceraldehyde-3-phosphate reacts with the active site cysteine thiol to form a thiohemiacetal intermediate. Oxidation to a carboxylic acid (in a "high energy" thioester) occurs, as NAD+ is reduced to NADH.  

The "high energy" acyl thioester is attacked by Pi to yield the acyl phosphate (~P) product.

Recall that NAD+ accepts 2 e- plus one H+ (a hydride) in going to its reduced form. 

7. Phosphoglycerate Kinase catalyzes:

1,3-bisphosphoglycerate + ADP 3-phosphoglycerate + ATP

This transfer of phosphate to ADP, from the carboxyl group on 1,3-bisphosphoglycerate, is reversible (low DG), since one ~P bond is cleaved and another is synthesized. The enzyme undergoes a substrate-induced conformational change similar to that of Hexokinase.

8. Phosphoglycerate Mutase catalyzes:  3-phosphoglycerate 2-phosphoglycerate

Phosphate is shifted from the hydroxyl on C3 of 3-phosphoglycerate to the hydroxyl on C2. 

An active site histidine side-chain participates in phosphate transfer, by donating and accepting the phosphate. The process involves a 2,3-bisphosphate intermediate.

The Phosphoglycerate Mutase reaction is illustrated in the animation at right.

of Phosphoglycerate Mutase

9. Enolase catalyzes:  2-phosphoglycerate phosphoenolpyruvate + H2O

This dehydration reaction is Mg++-dependent.

2 Mg++ ions interact with oxygen atoms of the substrate carboxyl group at the active site. The Mg++ ions help to stabilize the enolate anion intermediate that forms when a lysine side-chain amino group extracts a proton from carbon #2.

10. Pyruvate Kinase catalyzes:  phosphoenolpyruvate + ADP pyruvate + ATP

This transfer of phosphate from PEP to ADP is spontaneous. PEP has a larger DG of phosphate hydrolysis than ATP, because removal of phosphate from PEP yields an unstable enol, that spontaneously converts to the keto form of pyruvate (p. 602). Required inorganic cations K+ and Mg++ bind to anionic residues at the active site of Pyruvate Kinase.

Summary of Glycolysis:

The pathway continues from glyceraldehyde-3-phosphate. Recall that there are two glyceraldehyde-3-phosphate per glucose metabolized.


Balance sheet for high energy bonds of ATP: 

  • 2 ATP expended
  • 4 ATP produced (2 from each of two 3C fragments from glucose) 
  • Net production of 2 ~P bonds of ATP per glucose.

Glycolysis Pathway (omitting H+):

   glucose + 2 NAD+ + 2 ADP + 2 Pi 2 pyruvate + 2 NADH + 2 ATP

In aerobic organisms, pyruvate produced in Glycolysis is oxidized to CO2 via Krebs Cycle, and the NADH produced in Glycolysis and Krebs Cycle is reoxidized via the respiratory chain, with production of much additional ATP. 


Anaerobic organisms lack a respiratory chain. They must reoxidize NADH produced in Glycolysis through some other reaction, because NAD+ is needed for the Glyceraldehyde-3-phosphate Dehydrogenase reaction (see above). Usually NADH is reoxidized as pyruvate is converted to a more reduced compound.

The complete pathway, including Glycolysis and the re-oxidation of NADH, is called fermentation.

For example, Lactate Dehydrogenase catalyzes reduction of the keto group in pyruvate to a hydroxyl, yielding lactate, as NADH is oxidized to NAD+.

Lactate, in addition to being an end-product of fermentation, serves as a mobile form of nutrient energy, and possibly as a signal molecule in mammalian organisms. Cell membranes contain carrier proteins that facilitate transport of lactate.

  • Skeletal muscles ferment glucose to lactate during exercise, when the exertion is brief and intense. Lactate released to the blood may be taken up by other tissues, or by skeletal muscle after exercise, and converted via Lactate Dehydrogenase back to pyruvate, which may be oxidized in Krebs Cycle or (in liver) converted to back to glucose via gluconeogenesis.
  • Lactate serves as a fuel source for cardiac muscle as well as brain neurons.
    Astrocytes, which surround and protect neurons in the brain, ferment glucose to lactate and release it. Lactate taken up by adjacent neurons is converted to pyruvate that is oxidized via Krebs Cycle.
Some anaerobic organisms metabolize pyruvate to ethanol, which is excreted as a waste product. NADH is converted to NAD+ in the reaction catalyzed by Alcohol Dehydrogenase.  Thiamine pyrophosphate, the cofactor for Alcohol Dehydrogenase, is discussed elsewhere.

Fermentation Pathway, from glucose to lactate (omitting H+):

   glucose + 2 ADP + 2 Pi 2 lactate + 2 ATP

Anaerobic catabolism of glucose yields only 2 “high energy” bonds of ATP.

Regulation of Glycolysis

Glycolysis Enzyme *

DGo' (kJ/mol)

DG (kJ/mol)




Phosphoglucose Isomerase









Triosephosphate Isomerase



Glyceraldehyde-3-phosphate Dehydrogenase, & Phosphoglycerate Kinase



Phosphoglycerate Mutase






Pyruvate Kinase



*Values in this table from D. Voet & J. G. Voet  (2004)  Biochemistry, 3rd Edition, John Wiley & Sons, New York, p. 613.

Flux through the Glycolysis pathway is regulated by control of the 3 enzymes that catalyze highly spontaneous  reactions:  Hexokinase, Phosphofructokinase, & Pyruvate Kinase.

Hexokinase, the first step in the Glycolysis pathway, is inhibited by its product glucose-6-phosphate:

Cells trap glucose by phosphorylating it, preventing exit on glucose carriers. Product inhibition of Hexokinase ensures that cells will not continue to accumulate glucose from the blood, if [glucose-6-phosphate] within the cell is ample.

Glucokinase is a variant of Hexokinase found in liver.

Glucokinase, with its high KM for glucose, allows the liver to store glucose as glycogen in the fed state when blood [glucose] is high.

The liver enzyme Glucose-6-phosphatase catalyzes hydrolytic release of Pi from glucose-6-phosphate. Thus glucose is released from the liver to the blood as needed to maintain blood [glucose].

The enzymes Glucokinase and Glucose-6-phosphatase, both found in liver but not in most other body cells, allow the liver to control blood [glucose]. 

Pyruvate Kinase, the last step of the Glycolysis pathway, is controlled in liver partly by modulation of the amount of enzyme.

Phosphofructokinase is usually the rate-limiting step of the Glycolysis pathway.
Phosphofructokinase catalyzes:
fructose-6-phosphate + ATP fructose-1,6-bisphosphate + ADP 

Phosphofructokinase (PFK) is allosterically inhibited by ATP

At low concentration, the substrate ATP binds only at the active site. At high concentration, ATP binds also at a lower-affinity regulatory site, promoting the tense conformation. The tense conformation of Phosphofructokinase has a lower affinity  for its other substrate, fructose-6-phosphate. 

Sigmoidal dependence of reaction rate on [fructose-6-phosphate] is observed at high [ATP], as depicted at right. 

Effect of [ATP] on  Phosphofructokinase

AMP, which is present at significant levels only when there is extensive ATP hydrolysis, antagonizes the effect of high [ATP]. 

Inhibition of Phosphofructokinase, the rate-limiting step of Glycolysis, when [ATP] is high, prevents breakdown of glucose, in a pathway whose main role is to make ATP. It is more useful to the cell to store glucose as glycogen when ATP is plentiful (see diagram of interconnected pathways above).

Studio Exercises:

1. Explore in the Biochemistry Simulations tutorials at right concepts of enzyme kinetics and enzyme regulation relevant to this class:

  • In the module on Glucokinase, compare the dependence on [glucose] of catalysis by Glucokinase and Hexokinase.

  • In the module on Phosphofructokinase, explore effects of varied [ATP] at zero [fructose-2,6-bisphosphate]. (The activator fructose-2,6-bisphosphate will be discussed in the section on gluconeogenesis.) 

Note: Hold down the Control key while clicking on the above icon.

2. Website: Explore the following materials developed by Jon Maber.

Copyright 1998-2007 by Joyce J. Diwan. All rights reserved.

Additional material on Glycolysis:
Readings, Test Questions, & Tutorial

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