Biochemical Reaction Mechanisms

Biochemical Reaction Mechanisms

1. Mechanism of action of 1. Mechanism of action of -chymotrypsin-chymotrypsin

2. Glycolysis: metabolism of glucose2. Glycolysis: metabolism of glucose

3. Biosynthesis of steroids from squalene3. Biosynthesis of steroids from squalene

Mechanism of action of-chymotrypsin

Mechanism of action of-chymotrypsin

(An enzyme that hydrolyzes peptides (An enzyme that hydrolyzes peptides in the digestive system)in the digestive system)

Catalytic triad: Asp102, His 57, Ser 195Catalytic triad: Asp102, His 57, Ser 195

N

NH

CH2

His57

H OCH2

Ser 195

N CR'

O

R

H

N

NH

CH2

His57

H

Ser 195

H

12

O

CH2

R

O

R'CN

CH2

Asp102

COO

CH2

Asp102

COO

-chymotrypsin mechanism…-chymotrypsin mechanism…

N

NH

CH2

His57

H

Ser 195

H

RN

O

CH2

O

R'

C

CH2

Asp102

COO

3 4

N

NH

CH2

His57

CH2

Asp102

COO

H

RN

H

Ser 195

O

CH2

O

R'

C

H

OH

free amine + acylated serine amine replaced by water

-chymotrypsin mechanism…-chymotrypsin mechanism…

His57

CH2

Asp102

COO Ser 195

CH2

HN

N

O

CH2

O

R'

CHO

H

His57

CH2

Asp102

COO Ser 195

CH2

HN

N

O

CH2H

O

R'

CHO

56

free acid

GlycolysisGlycolysis

Metabolism of glucose to form Metabolism of glucose to form pyruvate and ATPpyruvate and ATP

Glycolysis converts glucose into two pyruvate moleculesGlycolysis converts glucose into two pyruvate molecules

……with the production of 2 ATPs (high with the production of 2 ATPs (high energy storage in cells)energy storage in cells)

1.1. Isomerization of glucose to fructoseIsomerization of glucose to fructose2.2. Formation of iminium ion; retro aldol to form Formation of iminium ion; retro aldol to form

two 3-carbon sugars (as phosphates)two 3-carbon sugars (as phosphates)3.3. Isomerization of dihydroxyacetone to Isomerization of dihydroxyacetone to

glyceraldehyde (as phosphates)glyceraldehyde (as phosphates)4.4. Oxidation, isomerization, dehydration and Oxidation, isomerization, dehydration and

dephosphorylation to form pyruvate and ATPdephosphorylation to form pyruvate and ATP

Isomerization of glucose to fructoseIsomerization of glucose to fructose

COH

C

C

C

C

CH2OPO3-2

OH

H

OH

HO

H

H

OHH

COHH

C

C

C

C

CH2OPO3-2

OH

H

OH

HO

H

OHH

CH2OH

C

C

C

C

CH2OPO3-2

O

H

OH

HO

H

OHH

glucose-6-phosphate fructose-6-phosphateglucose-fructose enol

Iminium ion; retro aldol additionIminium ion; retro aldol addition

CH2OPO3-2

C

C

C

C

CH2OPO3-2

O

H

OH

HO

H

OHH

fructose-1,6-bisphosphate

H2N Enz

CH2OPO3-2

C

C

C

C

CH2OPO3-2

NH

H

O

HO

H

OHH

Enz

H

CH2OPO3-2

C

C

NH

HHO

Enz

C

C

CH2OPO3-2

OH

OHH

+

glyceraldehyde-3-phosphate

(enol form)

Isomerization to glyceraldehydeIsomerization to glyceraldehyde

CH2OPO3-2

C

C

NH

HHO

Enz

(enol form)

H2OCH2OPO3

-2

C

CH2OH

O

glyceraldehyde-3-phosphate

dihydroxyacetone-phosphate

H2N Enz+

CH2OPO3-2

C

CH2OH

O

CH2OPO3-2

C

C

OH

OHH

(turned upsidedown)

dihydroxyacetone-phosphate (enol form)

CH2OPO3-2

C

C

OH

OH

H

Oxidation, isomerization and dephosphorylation (ATP forming)Oxidation, isomerization and dephosphorylation (ATP forming)

glyceraldehyde-3-phosphate

CH2OPO3-2

C

C

OH

OH

H[O]

CH2OH

C

C

OPO3-2

OO

H(sev. steps)CH2

C

C

OPO3-2

OO-H2O

phosphoenolpyruvate

CH2

C

C

OPO3-2

OO

phosphoenolpyruvate

CH3

C

C

O

OOADP ATP

pyruvate

Biosynthesis of Steroids from Squalene

Biosynthesis of Steroids from Squalene

Squalene (a shark oil terpene) Squalene (a shark oil terpene)

squalene

Epoxidation of Squalene Epoxidation of Squalene

O

squalene oxidase

Acid-Catalyzed Epoxide Ring Opening; A Ring Formation Acid-Catalyzed Epoxide Ring Opening; A Ring Formation

OH+

+

OH

AA

Reaction of Alkene with Carbocation; B Ring Reaction of Alkene with Carbocation; B Ring

OH

+

+

OH

AA

BBAA

Cyclization to form C Ring Cyclization to form C Ring

OH

H

+

+

OH

BB

CC

AA

AA

BB

Cyclization to form D Ring Cyclization to form D Ring

OH

H

OH

H

+

+

DDCC

AA BB

Hydride and Methyl Shifts Hydride and Methyl Shifts

OH

H

H

+

OH

+

Eventually...Cholesterol ! Eventually...Cholesterol !

OH

+

(several steps)

CH3

OH

CH3

H H

HH

Grading / Final ExamGrading / Final Exam

You may replace any of the 5 tests by an improved grade on that section of the Exam.

Only the higher grade counts.

You need not retake a section if you are happy with your grade on that test.

Everyone must take Section 6 (Ch 25, 26, 27 & 29) plus Section 7 (comprehensive; mostly synthesis)

Hour test Exam 1 42 --2 30 383 28 424 41 --5 37 36

Ch. 25-29 -- 38compreh. -- 32

Example:Example:

Your (best) score on these seven sections plusthe sum of your gla scores determines your grade.