Glycolysis

1

Biochemistry of Metabolism

Glycolysis

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

H O

OH

HOH

CH2OPO32

H

OH

H

1

6

5

4

Glycolysis takes place in the cytosol of cells.

OH

OHH

3 2

glucose-6-phosphate

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.

2

H O

OH

HOH

CH2OH

H

OH

H H O

OH

HOH

CH2OPO32

H

OH

H

23

4

5

6

1 1

6

5

4

3 2

ATP ADP

Mg2+

OHH OHH

23 3

glucose glucose-6-phosphate

Hexokinase

1. Hexokinase catalyzes:

Glucose + ATP glucose-6-P + ADP

The reaction involves nucleophilic attack of the C6 hydroxyl O of glucose on P of the terminal phosphate of ATP.

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

N

NN

N

NH2

O O O

d i

ATP adenosine triphosphate

O

OHOH

HH

H

CH2

H

OPOPOPO

O O O

adenine

ribose

Mg++ interacts with negatively charged phosphate oxygen atoms, providing charge compensation & promoting a favorable conformation of ATP at the active site of the Hexokinase enzyme.

3

H O

OH

HOH

CH2OH

H

OH

H H O

OH

HOH

CH2OPO32

H

OH

H

4

5

6

1 1

6

5

4

ATP ADP

Mg2+

The reaction catalyzed by Hexokinase is highlyspontaneous

OH

OHH

OH OH

OHH

OH23 3 2


Hexokinase

spontaneous.

A phosphoanhydride bond of ATP (~P) is cleaved.

The phosphate ester formed in glucose-6-phosphate has a lower G of hydrolysis.

H O

OH

H

OHH

OH

CH2OH

H

OH

H H O

OH

H

OHH

OH

CH2OPO32

H

OH

H

23

4

5

6

1 1

6

5

4

3 2

ATP ADP

Mg2+

Hexokinase

Induced fit:

Glucose bindingto Hexokinase stabilizes a

the C6 hydroxyl of the bound glucose is close tothe terminal phosphate of

glucose

H ki

glucose glucose-6-phosphate stabilizes a conformationin which:

p pATP, promoting catalysis.

water is excluded from the active site. This prevents the enzyme from catalyzing ATP hydrolysis, rather than transfer of phosphate to glucose.

Hexokinase

4

glucose

Hexokinase

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.

Hexokinase

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.

H O

OH

H

OHH

OH

CH2OPO32

H

OH

H

1

6

5

4

3 2

CH2OPO32

OH

CH2OH

H

OH H

H HO

O6

5

4 3

2

1

2. Phosphoglucose Isomerase catalyzes:

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

OHH

glucose-6-phosphate fructose-6-phosphate Phosphoglucose Isomerase

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

The mechanism involves acid/base catalysis, with ring opening, isomerization via an enediolate intermediate, and then ring closure. A similar reaction catalyzed by Triosephosphate Isomerase will be presented in detail.

5

CH2OPO32

OH

CH2OH

HH

H HO

O6

5

4 3

2

1 CH2OPO32

OH

CH2OPO32

HH

H HO

O6

5

4 3

2

1

ATP ADP

Mg2+

Phosphofructokinase

3. Phosphofructokinase catalyzes:

fructose-6-P + ATP fructose-1,6-bisP + ADP

This highly spontaneous reaction has a mechanism similar

OH H OH H

fructose-6-phosphate fructose-1,6-bisphosphate

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

The Phosphofructokinase reaction is the rate-limiting stepof Glycolysis.

The enzyme is highly regulated, as will be discussed later.

5

4

3

2

1CH2OPO32

C

C

C

C

O

HO H

H OH

H OH

3

2

1

CH2OPO32

C

CH2OH

O

C

C

CH2OPO32

H O

H OH+

1

2

3

Aldolase

4. Aldolase catalyzes: fructose-1,6-bisphosphate

6

5

CH2OPO32

1 2 2 33

fructose-1,6- bisphosphate

dihydroxyacetone glyceraldehyde-3- phosphate phosphate

Triosephosphate Isomerase

y , p pdihydroxyacetone-P + glyceraldehyde-3-P

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

Note that C atoms are renumbered in products of Aldolase.

6

CH2OPO3

2

C

CH

C

C

NH

HO

H OH

H OH

(CH2)4 Enzyme

4

3

2

1

+H3N+ C COO

CH2

CH2

H

lysine

A lysine residue at the active site functions in catalysis.

C

CH2OPO32

H OH

6

5

Schiff base intermediate of Aldolase reaction

CH2

CH2

NH3

y y

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

Cleavage of the bond between C3 & C4 follows.

5

4

3

2

1CH2OPO32

C

C

C

C

O

HO H

H OH

H OH

3

2

1

CH2OPO32

C

CH2OH

O

C

C

CH2OPO32

H O

H OH+

1

2

3

Aldolase

5. Triose Phosphate Isomerase (TIM) catalyzes:

6

5

CH2OPO32

1 2 2 33

fructose-1,6- bisphosphate

dihydroxyacetone glyceraldehyde-3- phosphate phosphate


p ( ) y

dihydroxyacetone-P glyceraldehyde-3-P

Glycolysis continues from glyceraldehyde-3-P. TIM's Keqfavors dihydroxyacetone-P. Removal of glyceraldehyde-3-P by a subsequent spontaneous reaction allows throughput.

7

C

C O

C

C

H O

H OH

C

C

H OH

OH

H

H OH H+ H+ H+H+


The ketose/aldose conversion involves acid/base catalysis,

CH2OPO32 CH2OPO3

2CH2OPO32

dihydroxyacetone enediol glyceraldehyde- phosphate intermediate 3-phosphate

The ketose/aldose conversion 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.

C

CH2OPO32

O O

C

CH2OPO32

HC O

OH

proposed phosphoglycolatep penediolate

intermediate

phosphoglycolate transition state

analog

2-Phosphoglycolate is a transition state analog that binds tightly at the active site of Triose Phosphate Isomerase (TIM).( )

This inhibitor of catalysis by TIM is similar in structure to the proposed enediolate intermediate.

TIM is judged a "perfect enzyme." Reaction rate is limited only by the rate that substrate collides with the enzyme.

8

Triosephosphate Isomerase p pstructure is an barrel, or TIM barrel.

In an barrel there are 8 parallel -strands surrounded by 8 -helices.

TIM Short loops connect alternating -strands & -helices.

TIM barrels serve as scaffolds for active site residues in a diverse array of enzymes.

Residues of the active site are

TIM

Residues of the active site are always at the same end of the barrel, on C-terminal ends of -strands & loops connecting these to -helices.

There is debate whether the many different enzymes withThere is debate whether the many different enzymes with TIM barrel structures are evolutionarily related.

In spite of the structural similarities there is tremendous diversity in catalytic functions of these enzymes and little sequence homology.

9

C

CH2OPO32

O O

C

CH2OPO32

HC O

OH

TIM

Explore the structure of the Triosephosphate Isomerase (TIM) homodimer with the transition state inhibitor

2 32 3

proposed enediolate

intermediate

phosphoglycolate transition state

analog

(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.

C

H O

C

O OPO32 + H+

NAD+ NADH 11

Glyceraldehyde-3-phosphate Dehydrogenase

C

CH2OPO32

H OH C

CH2OPO32

H OH+ Pi

2

3

2

3

glyceraldehyde- 1,3-bisphospho- 3-phosphate glycerate

6. Glyceraldehyde-3-phosphate Dehydrogenasecatalyzes:

glyceraldehyde-3-P + NAD+ + Pi

1,3-bisphosphoglycerate + NADH + H+

10

C

C

H O

H OH

C

C

O OPO32

H OH+ Pi

+ H+

NAD+ NADH 1

2 2

1


CH2OPO32 CH2OPO3

23 3


Exergonic oxidation of the aldehyde in glyceraldehyde-g y g y y3-phosphate, to a carboxylic acid, drives formation of an acyl phosphate, a "high energy" bond (~P).

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

H3N+ C COO

CH2

H C

C

CH2OPO32

H O

H OH

1

2

3

A cysteine thiol at the active site of Glyceraldehyde-

SH

cysteine

2 33

glyceraldehyde-3- phosphate

y y y3-phosphate Dehydrogenase has a role in catalysis.

The aldehyde of glyceraldehyde-3-phosphate reacts with the cysteine thiol to form a thiohemiacetalintermediate.

11

CH CH2OPO32

OHEnz-Cys SH

Enz-Cys S CH CH CH2OPO32

OHOH

HC

+

O

glyceraldehyde-3-phosphate

thiohemiacetalOxidation to a

b li id

Enz-Cys S C CH CH2OPO32

OHO

NAD+

NADH

Pi

OHO

thiohemiacetal intermediate

acyl-thioester intermediate

carboxylic acid (in a ~ thioester) occurs, as NAD+

is reduced to NADH.

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

Enz-Cys SH C CH CH2OPO32O3PO

2

1,3-bisphosphoglycerate

H

CNH2

O

CNH2

OH H

Recall that NAD+ accepts 2 e plus one H+ (a hydride)

N

R

N

R

+

2e + H+

NAD+ NADH

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

12

C

C

CH2OPO32

O OPO32

H OH

C

C

CH2OPO32

O O

H OH

ADP ATP

1

22

3 3

1

Mg2+

Phosphoglycerate Kinase

1,3-bisphospho- 3-phosphoglycerate glycerate

7. Phosphoglycerate Kinase catalyzes:1,3-bisphosphoglycerate + ADP

3-phosphoglycerate + ATP3 phosphoglycerate + ATP

This phosphate transfer is reversible (low G), since one ~P bond is cleaved & another synthesized.

The enzyme undergoes substrate-induced conformational change similar to that of Hexokinase.

C

C

O O

H OPO 21C

C

O O

H OH

1

Phosphoglycerate Mutase

C

CH2OH

H OPO32

2

3

C

CH2OPO32

H OH2

3

3-phosphoglycerate 2-phosphoglycerate

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

Phosphate is shifted from the OH on C3 to the OH on C2.

13

C

C

CH2OH

O O

H OPO32

2

3

1C

C

CH2OPO32

O O

H OH2

3

1


H3N+ C COO

CH2

H

histidine

3-phosphoglycerate 2-phosphoglycerate

CO O

1

An active site histidine side-chain participates in Pi transfer, by donating & accepting phosphate.

CHN

HC NH

CH

C

CH2OPO32

H OPO32

2

3

1


The process involves a 2,3-bisphosphate intermediate.

View an animation of the Phosphoglycerate Mutase reaction.

C

C

CH2OH

O O

H OPO32

C

C

CH2OH

O O

OPO32

C

C

CH2

O O

OPO32

OH

2

3

1

2

3

1

HEnolase

9. Enolase catalyzes:

2-phosphoglycerate phosphoenolpyruvate + H2O

This dehydration reaction is Mg++-dependent.

2-phosphoglycerate enolate intermediate phosphoenolpyruvate

y g p

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 Lys extracts H+ from C #2.

14

CO O

ADP ATPCO O

Pyruvate Kinase

C

C

CH3

O2

3

1ADP ATPC

C

CH2

OPO32

2

3

1

phosphoenolpyruvate pyruvate

10. Pyruvate Kinase catalyzes:

phosphoenolpyruvate + ADP pyruvate + ATP

C

C

O O

O2

1ADP ATPC

C

O O

OPO32

2

1 C

C

O O

OH2

1

Pyruvate Kinase

This phosphate transfer from PEP to ADP is spontaneous.

PEP has a larger G of phosphate hydrolysis than ATP.

CH33CH23 CH23

phosphoenolpyruvate enolpyruvate pyruvate

Removal of Pi from PEP yields an unstable enol, which spontaneously converts to the keto form of pyruvate.

Required inorganic cations K+ and Mg++ bind to anionic residues at the active site of Pyruvate Kinase.

15

Hexokinase

glucose Glycolysis

ATP

ADP glucose-6-phosphate

Phosphoglucose Isomerase

Phosphofructokinase

Phosphoglucose Isomerase

fructose-6-phosphate

ATP

ADP fructose-1,6-bisphosphate

Aldolase

glyceraldehyde-3-phosphate + dihydroxyacetone-phosphate

Triosephosphate Isomerase Glycolysis continued


glyceraldehyde-3-phosphate

NAD+ + Pi

NADH + H+


ADPGlycolysis Phosphoglycerate Kinase

E l

ATP

3-phosphoglycerate


2-phosphoglycerate

continued.

Recall that there are 2 GAP per glucose.

Enolase

Pyruvate Kinase

H2O

phosphoenolpyruvate

ADP

ATP pyruvate

16

Glycolysis

Balance sheet for ~P bonds of ATP:Balance sheet for P bonds of ATP:

How many ATP ~P bonds expended? ________

How many ~P bonds of ATP produced? (Remember there are two 3C fragments from glucose.) ________

2

4

Net production of ~P bonds of ATP per glucose: ________ 2

Balance sheet for ~P 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 Net production of 2 P bonds of ATP per glucose.

Glycolysis - total pathway, omitting H+: glucose + 2 NAD+ + 2 ADP + 2 Pi

2 pyruvate + 2 NADH + 2 ATP

In aerobic organisms:t d d i Gl l i i idi d t CO pyruvate produced in Glycolysis is oxidized to CO2

via Krebs Cycle NADH produced in Glycolysis & Krebs Cycle is

reoxidized via the respiratory chain, with production of much additional ATP.

17

C

C

CH2OPO32

H O

H OH

C

C

CH2OPO32

O OPO32

H OH+ Pi

+ H+

NAD+ NADH 1

2

3

2

3

1


Fermentation:

Anaerobic

They must reoxidize NADH produced in Glycolysis through some other reaction, because NAD+ is needed for the Glyceraldehyde-3-phosphate Dehydrogenase reaction

CH2OPO3 CH2OPO33 3


Anaerobic organisms lack a respiratory chain.

the Glyceraldehyde 3 phosphate Dehydrogenase reaction.

Usually NADH is reoxidized as pyruvate is converted to a more reduced compound.

The complete pathway, including Glycolysis and the reoxidation of NADH, is called fermentation.

C

C

CH3

O

O

O

C

HC

CH3

O

OH

ONADH + H+ NAD+

Lactate Dehydrogenase

3 3

pyruvate lactate

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

Lactate in addition to being an end product ofLactate, in addition to being an end-product of fermentation, serves as a mobile form of nutrient energy, & possibly as a signal molecule in mammalian organisms.

Cell membranes contain carrier proteins that facilitate transport of lactate.

18

C

C

CH3

O

O

O

C

HC

CH3

O

OH

ONADH + H+ NAD+


pyruvate 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 otherLactate 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

C

C

O

O

O

C

HC

O

OH

ONADH + H+ NAD+


CH3 CH3

pyruvate lactate

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.

19

C

OO

OH HNADH + H+ NAD+CO2

Pyruvate Alcohol Decarboxylase Dehydrogenase

C

C

CH3

O C

CH3

OHC

CH3

OH

H

CO2

pyruvate acetaldehyde ethanol

Some anaerobic organisms metabolize pyruvate toSome 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.

Glycolysis, omitting H+:

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

Fermentation, from glucose to lactate:

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

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

20

Glycolysis Enzyme/ReactionGo'

kJ/molG

kJ/mol

Hexokinase -20.9 -27.2

Phosphoglucose Isomerase +2.2 -1.4

Phosphofructokinase 17 2 25 9Phosphofructokinase -17.2 -25.9

Aldolase +22.8 -5.9

Triosephosphate Isomerase +7.9 negative

Glyceraldehyde-3-P Dehydrogenase& Phosphoglycerate Kinase

-16.7 -1.1

Phosphoglycerate Mutase +4.7 -0.6

Enolase -3.2 -2.4

Pyruvate Kinase -23.0 -13.9*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 3 enzymes that catalyze spontaneous reactions: Hexokinase, Phosphofructokinase & Pyruvate Kinase.

Local control of metabolism involves regulatory effects g yof varied concentrations of pathway substrates or intermediates, to benefit the cell.

Global control is for the benefit of the whole organism, & often involves hormone-activated signal cascades.

Liver cells have major roles in metabolism includingLiver cells have major roles in metabolism, including maintaining blood levels various of nutrients such as glucose. Thus global control especially involves liver.

Some aspects of global control by hormone-activated signal cascades will be discussed later.

21

H O

OH

H

OHH

OH

CH2OH

H

OH

H H O

OH

H

OHH

OH

CH2OPO32

H

OH

H

23

4

5

6

1 1

6

5

4

3 2

ATP ADP

Mg2+

Hexokinase

Hexokinase is inhibited by product glucose-6-phosphate: by competition at the active site by allosteric interaction at a separate enzyme site.


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.

H O

OH

H

OHH

OH

CH2OH

H

OH

H H O

OH

H

OHH

OH

CH2OPO32

H

OH

H

23

4

5

6

1 1

6

5

4

3 2

ATP ADP

Mg2+

Hexokinase

Glucokinaseis a variant of Hexokinase

Glucokinase has a high KM for glucose. It is active only at high [glucose].

One effect of insulin, a hormone produced when blood glucose is high is activation in liver of transcription of

glucose glucose-6-phosphate found in liver.

glucose is high, is activation in liver of transcription of the gene that encodes the Glucokinase enzyme.

Glucokinase is not subject to product inhibition by glucose-6-phosphate. Liver will take up & phosphorylate glucose even when liver [glucose-6-phosphate] is high.

22

Glucokinase is subject to inhibition by glucokinase Glucokinase is subject to inhibition by glucokinase regulatory protein (GKRP).

The ratio of Glucokinase to GKRP in liver changes in different metabolic states, providing a mechanism for modulating glucose phosphorylation.

Glycogen Glucose

Hexokinase or Glucokinase

Glucose-6-Pase Glucose-1-P Glucose-6-P Glucose + Pi Glycolysis

Pathway

Glucokinase, with high KMfor glucose, allows liver to

Glucose-6-phosphatase catalyzes hydrolytic release of Pifrom gl cose 6 P Th s gl cose is released from the li er

Pathway

Pyruvate Glucose metabolism in liver.

store glucose as glycogen in the fed state when blood [glucose] is high.

from glucose-6-P. Thus glucose is released from the liver to the blood as needed to maintain blood [glucose].

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

23

C

C

O O

O2

1ADP ATPC

C

O O

OPO32

2

1

Pyruvate Kinase Pyruvate Kinase, the last step Glycolysis, is controlled in liver partly b d l ti f th

High [glucose] within liver cells causes a transcription factor carbohydrate responsive element binding protein(ChREBP) to be transferred into the nucleus, where it

CH33CH23

phosphoenolpyruvate pyruvate

by modulation of the amount of enzyme.

( ) ,activates transcription of the gene for Pyruvate Kinase.

This facilitates converting excess glucose to pyruvate, which is metabolized to acetyl-CoA, the main precursor for synthesis of fatty acids, for long term energy storage.

CH2OPO32

OH

CH2OH

H

O H

H HO

O6

5

4 3

2

1 CH2OPO32

OH

CH2OPO32

H

O H

H HO

O6

5

4 3

2

1

ATP ADP

Mg2+

Phosphofructokinase

Phosphofructokinase is usually the rate-limiting step of the Glycolysis pathway.

Phosphofructokinase is allosterically inhibited by ATP.

OH H OH H

fructose-6-phosphate fructose-1,6-bisphosphate

p y y

At low concentration, the substrate ATP binds only at the active site.

At high concentration, ATP binds also at a low-affinity regulatory site, promoting the tense conformation.

24

20

30

40

50

60

FK

Act

ivit

yhigh [ATP]

low [ATP]

Th t f i f PFK hi h [ATP] h l

0

10

20

0 0.5 1 1.5 2[Fructose-6-phosphate] mM

Pg [ ]

The tense conformation of PFK, at high [ATP], has lower affinity for the other substrate, fructose-6-P. Sigmoidaldependence of reaction rate on [fructose-6-P] is seen.

AMP, present at significant levels only when there is extensive ATP hydrolysis, antagonizes effects of high ATP.

Glycogen Glucose

Hexokinase or Glucokinase

Glucose-6-Pase Glucose-1-P Glucose-6-P Glucose + Pi

Glycolysis

Inhibition of the Glycolysis enzyme Phosphofructokinase

Glycolysis Pathway

Pyruvate Glucose metabolism in liver.

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.

Documents

Glycolysis