Biochemistry usmle review

Danil hammoudi.MD

Sinoe Medical Association

 

Part 1

Carbohydrate Metabolism

 

Pathways

 

Glycolysis

 

 

Overall Reaction for the Pathway

 

Glucose + 2 ADP + 2 Pi + 2 NAD+

--->

2 Pyruvate + 2 ATP + 2 NADH + 2 H+ + 2 H2O

 

 

a-D-Glucose

 

ATP



ADP

Mg++

Hexokinase

 

a-D-Glucose-6-phosphate

 

 

Phosphoglucoisomerase

 

b-D-Fructose-6-phosphate

 

ATP



ADP

Mg++

Phosphofructokinase

 

b-D-Fructose-1,6-bisphosphate

 

 

Aldolase

 

Glyceraldehyde-3-phosphate

+

Dihydroxyacetone phosphate

 

 

Triose phosphate isomerase

 

 

Glyceraldehyde-3-phosphate

 

NAD+ + Pi


NADH

Glyceraldehyde-3-phosphate dehydrogenase

 

1,3-Bisphosphoglycerate

 

ADP


ATP

Mg++

Phosphoglycerate kinase

 

3-Phosphoglycerate

 

 

Phosphoglycerate mutase

 

2-Phosphoglycerate

 

 

Mg++

Enolase

 

Phosphoenolpyruvate

 

ADP


ATP

Mg++

Pyruvate kinase

 

Pyruvate

 

 

 

Gibbs Free Energy Changes

Rxn#

Enzyme

DG°'
(kJ/mol)

DG
(kJ/mol)

1

Hexokinase

-16.7

-33.5

2

Phosphoglucoisomerase

+1.7

-2.5

3

Phosphofructokinase

-14.2

-22.2

4

Aldolase

+23.9

-1.3

5

Triose phosphate isomerase

+7.6

+2.5

6

Glyceraldehyde-3-phosphate
dehydrogenase

+12.6

-3.4

7

Phosphoglycerate kinase

-37.6

+2.6

8

Phosphoglycerate mutase

+8.8

+1.6

9

Enolase

+3.4

-6.6

10

Pyruvate kinase

-62.8

-33.4

 

The DG values are estimated from intracellular concentrations of glycolytic intermediates in rabbit skeletalmuscle. N.B., the DG values after reaction number 5 are doubled since two G-3-P molecules exist after reaction number 5. (Mathews p.459)

Glycolysis & Gluconeogenesis

 

 

Overall Reaction for the Pathway

 

Glucose + 2 ADP + 2 Pi + 2 NAD+

--->

2 Pyruvate + 2 ATP + 2 NADH + 2 H+ + 2 H2O

 

 

 

 

a-D-Glucose

 

 

 

a-D-Glucose-6-phosphate

 

 

 

D-Fructose-6-phosphate

 

 

 

D-Fructose-1,6-bisphosphate

 

 

 

Glyceraldehyde-3-phosphate + Dihydroxyacetone phosphate

 

 

 

Glyceraldehyde-3-phosphate

 

 

 

1,3-Bisphosphoglycerate

 

 

 

3-Phosphoglycerate

 

 

 

2-Phosphoglycerate

 

 

 

Phosphoenolpyruvate

 

 

 

Pyruvate

 

 

Gibbs Free Energy Changes

Rxn#

Enzyme

DG°'
(kJ/mol)

DG
(kJ/mol)

1

Hexokinase

-16.7

-33.5

2

Phosphoglucoisomerase

+1.7

-2.5

3

Phosphofructokinase

-14.2

-22.2

4

Aldolase

+23.9

-1.3

5

Triose phosphate isomerase

+7.6

+2.5

6

Glyceraldehyde-3-phosphate
dehydrogenase

+12.6

-3.4

7

Phosphoglycerate kinase

-37.6

+2.6

8

Phosphoglycerate mutase

+8.8

+1.6

9

Enolase

+3.4

-6.6

10

Pyruvate kinase

-62.8

-33.4

 

The DG values are estimated from intracellular concentrations of glycolytic intermediates in rabbit skeletalmuscle. N.B., the DG values after reaction number 5 are doubled since two G-3-P molecules exist after reaction number 5. (Mathews p.459)

 

 

 

 

 

Kreb's Citric Acid Cycle

 

 

One Turn of the Cycle

Acetyl-CoA + 3 NAD+ + FAD + GDP + Pi + 3 H2O

--->

3 NADH + FADH2 + CoA-SH + GTP + 3 CO2

 

 

 


Acetyl-CoA

 


Oxaloacetate


Citrate


Malate

 

 

 


Isocitrate

 

 

 


Fumarate

 

 

 


a-Ketoglutarate


Succinate


Succinyl-CoA

 

 

Gibbs Free Energy Changes

Rxn#

Enzyme

DG°'
(kJ/mol)

DG
(kJ/mol)

1

Citrate synthase

-32.2

 

2

Aconitase

+6.3

 

3

Isocitrate dehydrogenase

-20.9

 

4

a-Ketoglutarate dehydrogenase
complex

-33.5

 

5

Succinyl-CoA synthetase

-2.9

 

6

Succinate dehydrogenase

0.0

 

7

Fumerase

-3.8

 

8

Malate dehydrogenase

+29.7

 

 

 

 

 

 

Pentose Phosphate Pathway

 

 

 

Overall Reaction for the Pathway

 

3 Glucose-6-Phosphate + 6 NADP+ + 3 H2O

--->

2 Fructose-6-Phosphate + Glyceraldehyde-3-Phosphate + 6 NADPH + 6 H+ + 3 CO2

 

 

 

 

Glucose-6-phosphate

 

 

 

6-Phosphogluconolactone

 

 

 

6-Phosphogluconate

 

 

 

Ribulose-5-phosphate

 

 

 

Xylulose-5-phosphate      +      Ribose-5-phosphate

 

 

 

Glyceraldehyde-3-phosphate      +      Sedoheptulose-7-phosphate

 

 

 

Erythrose-4-phosphate      +          Fructose-6-phosphate

 

 

 

Glyceraldehyde-3-phosphate      +       Fructose-6-phosphate

 

 

 

Glycogen Biosynthesis & Galactose Pathway

 

 

View the 3-D version of this pathway.

 

 

 

 

 

Glucose-6-phosphate

 

Galactose

 

 

 

 

 

Glucose-1-phosphate

 

Galactose-1-phosphate

 

 

 

Uridine diphosphate glucose

 

Uridine diphosphate galactose

 

 

 

 

 

Glycogen