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Glycolysis Tutorial. This tutorial is intended to help you see the chemical reactions that make up the glycolysis pathway. Read the lessons and with your mouse click one ( click 1 ) or two times ( click 2 ) when instructed. CH 2 OH. CHO. C=O. H-C-OH. HO-C-H. H-C-OH. H-C-OH. CH 2 OH. O.

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glycolysis tutorial

Glycolysis Tutorial

This tutorial is intended to help you see the chemical reactions that make up the glycolysis pathway. Read the lessons and with your mouse click one (click 1) or two times (click 2) when instructed.

slide2

CH2OH

CHO

C=O

H-C-OH

HO-C-H

H-C-OH

H-C-OH

CH2 OH

O

O

-P-O

-P-O

OH

OH

Biochemistry 411 is a course that sneaks up on the unwary. The lessons ring a familiar tune. You may think you heard it in your other courses, but metabolism in this course is much more demanding in detail. To get off to a good start, pick up a pencil and draw the structures. Don’t worry about being geometrically perfect, a quick sketch is better than no sketch and you wont be graded on artistic talent. Drawing structures lets you see what is happening. For example, glucose in glycolysis. Draw the straight chain structure of glucose (click 1). Now, convert glucose into fructose by changing the top two carbons on the molecule (click 1). Note an –OH groups on C-6 where the first phosphate group attached to glucose (click 1). C-1 in fructose receives a second phosphate later in the pathway (click 1). The phosphates come from ATP and require kinase enzymes hexokinase and phosphofructokinase I [PFK-1]. Glucose-6-PO4 is converted into fructose 6-PO4 by an isomerase enzyme phosphoglucoisomerase [PGI]. See how structures show you what is happening.

slide3

CH2OPO3=

C=O

CH2O

CH2OH

CHO

CH2OH

C=O

C=O

H-C-OH

HO-C-H

HO-C-H

H-C-OH

H-C-OH

DHAP

H

H-C-OH

H-C-OH

CH2 OH

HC=O

+

O

O

O

O

CH2O

H-C-OH

-P-O

-P-O

-P-O

-P-O

CH2OPO3=

OH

OH

OH

OH

Glyceraldehyde 3-PO4

The second phase of glycolysis is called the triose or payoff phase. In this phase the fructose 1,6-bisphosphate

molecule (click 1) is cut in half (click 1). The top half, i.e., the first 3 carbons with the keto group become

dihydroxyacetone phosphate (DHAP) (click 1). C4-C6, become glyceraldehyde-3-phosphate (click 1). Note that when

the split occurs, the two bonding electron go to the top (click 2) and what was C-4 becomes a carbonium ion with a

positive charge (click 1). The carbonium ion causes a rearrangement of electrons to form a carbonyl group (click 1).

A proton is displaced in the final step (click 1). The glyceraldehyde-3-phosphate goes on to the next step (click 1).

slide4

O

COO

PO4

~OPO3

H-C-OH

CHO

C

ADP

ATP

NAD+

CH2OPO3

H-C-OH

H-C-OH

NADH

CH2OPO3

CH2OPO3

+H+

In the triose or second phase the glyceraldehyde 3-PO4 is converted into pyruvate. Glyceralaldehyde-3-PO4 is in equilibrium with DHAP via the enzyme triose phosphate isomerase (TPI). This assures that all of the carbons of glucose will be converted into pyruvate, the final product of the pathway. The first step in the triose pathway is to oxidize C-1 of glyceraldehyde-3-PO4. The glyceraldehyde-3-PO4 then becomes 3-phosphoglyceric acid (3PGA) (click 2). The slanted arrows show C-1 before and after oxidation. There is concern, however. The cell must somehow devise a way to conserve the oxidation energy. Click 1 to see how the energy is conserved. Note that to preserve free energy the cell adds phosphate to C-1 simultaneously with the oxidation by NAD+ (click 1). This creates a high energy phosphate bond (click 1) in the intermediate 1,3-bisphosphoglycerate (1,3-BPG) that is used to synthesize ATP from ADP (click 1). The enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH) catalyzes the first reaction (click 1) and phosphoglycerate kinase(PGK) catalyzes the second (click 1). Both of these reactions are freely reversible. Click 1 to go on.

Phosphoglycerate

kinase

Glyceraldehyde-3-PO4

dehydrogenase

slide5

COO

C~

OPO3

-H2O

CH2

COO

COO

COO

C=O

H-C-OPO3

H-C-OH

ADP

3-PGA

2-PGA

PEP

ATP

Pyruvate

CH2OPO3

CH2OH

CH3

To end the triose phase, 3-phosphoglycerate is converted into pyruvate (click 1). By now you should be able to predict that the phosphate on C-3 of 3PGA will used to make ATP. This is not obvious at first because the phosphate ester in 3PGA is not high energy (click 1). Therefore, to make ATP this phosphate must be converted into one that is high energy. That high energy molecule is phosphoenolpyruvate (PEP) (click 1). Your chore now is figure how to make PEP from 3PGA. A clue comes when you see that the phosphate in PEP in on C-2. Therefore, you must first shift the phosphate on 3PGA to make 2PGA (click 1). This is done by a mutase enzyme, phosphoglycerate mutase (PGM). To make the phosphate in 2PGA high energy, a H2O must be removed from 2PGA to form an enol-phosphate bond (click 1). Enol-phosphate is a high energy phosphate, in fact one of the highest in terms of release of free energy (click 1). From PEP it is simply a matter to transfer the phosphate to ADP (click 1),which brings us to the end of the pathway with the formation of ATP and pyruvate.

High energy

Low energy

slide6

What did you learn? Answer the following questions regarding glycolysis and energy.

1. What is the overall energy yield in ATP production when one molecule of glucose is

converted to pyruvate? (click for answer).

There is a net of 2 ATPs synthesized for each glucose molecule. Two ATPs are required to

bring the glucose to the fructose 1,6-bisphosphate stage (-2). One ATP each is synthesized

when glyceraldehyde-3-PO4 goes to 3PGA and PEP to pyruvate (+2). Since the latter reaction

occurs with each triose, the total is +4 for all the carbons of glucose. -2 + (+4) = +2

2. Based on free energy yield, predict the reactions that are irreversible or poorly reversible in

the glycolysis pathway. (click for answer)

There are 3. Glucose to glucose 6-PO4 catalyzed by hexokinase; fructose 6-PO4 to

fructose 1,6 bisPO4 catalyzed by phosphofructokinase-I, and PEP to pyruvate catalyzed

by pyruvate kinase. All 3 are catalyzed by kinase enzymes and all three have very large

negative delta G values (check your textbook for delta G values).

3. Why is the phosphoglycerate kinase reaction reversible? What about the other kinase reactions?

(click for answer)

The product, glycerate 1,3-bisPO4 is high energy. Thus, it can yield ATP by transferring

the phosphate group to ADP. The other kinase reactions all yield low energy phosphate esters

as products and hence cannot be reversed. Reversing would mean forming a high energy ATP

phosphoanhydride bond in ATP from a low energy phosphate ester compound and this is not

energetically feasible.