Lecture 4 Glycolysis - Bioenergetics | BIS 103, Study notes of Biology

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Lecture 4Lecture 4

Glycolysis^ Glycolysis

(EmbdenEmbden-(

-Meyerhof Pathway)Meyerhof Pathway)

Cleavage of glucose andCleavage of glucose

Substrate-Substrate

-levellevel phosphorylation

phosphorylation

of ADP to ATPof ADP to ATP

Background materialBackground material

Gibbs Free EnergyGibbs Free Energy • Δ G =

Δ H - T

Δ S

• Δ G = RTlnQ – RTlnK

eq^

Q = [P

real

]/[R

real

]

• Δ G

o’ = – RTlnK

eq^

T = 298K (

o C)

• Δ G =

Δ G

o’ + RTlnQ

Table 4

Reduction potentialReduction potential • Δ E = E

oxidant

– E

reductant

Table 3

• Δ E = –

Δ G/nF

EnzymesEnzymes • Amino acids and their reactions • Classification • Regulation

CARBOHYDRATES

p. 21

Glucose

Lactate

Ribose-5-P

Oxaloacetate

Amino acids

Ketonebodies

Fatty acids Cholesterol

ATP

NADH

Pyruvate

Glucose-6-P

Glycogen

Acetyl-CoA

NADPH

NADH

LIPIDS

PROTEINS

GlycolysisGlycolysis

The “^ The

“PowertrainPowertrain”

” of Human Metabolism (Overview)of Human Metabolism (Overview)

O^2

CO

H^ O^2

CHO H

OH H

HO

OH

H

OH

H CH

OH 2

H

CHO OH

H

HO

OH

H

OH

H

CHOPO^2

2- 3

GLC-6-P

GLC

ATP^

ADP

CHOH^2

O H

HO

OH

H

OH

H

CHOPO^2

ATP 2- 3

ADP

CHOPO^2

2- 3 O H

HO

OH

H

OH

H

CHOPO^2

2- 3

CHOPO^2

2- 3 O

CHOH^2

HC H

+ OH 2-CHOPO^23 +NAD^ NADH

H

C OH CHOPO^2

O 2-^3

2-OPO 3

ATP^

ADP

H

C OH CHOPO^2

O 2-^3

H

C

2-OPO 3

O CHOH 2

C

2-OPO 3

O CH 2

C

O

O CH 3

ATP^

ADP

DHAP G-3-P

1,3 bisPGA

3-PGA

2-PGA

PEP

PYR

H^

O

OH

H OH

CHOH^2 OH H

H^

O

OH

H OH

CHOPO^2 OH H

2- 3

ATP^

1 ADP

O^ POHC^322

CHOH^2 OH

H OH

H

H^

OOH

O^ POH^3

C 2

CHOPO^2 OH

2- 3

H OH

H

H^

OOH

ATP^

3 ADP

Fischer projection-open chain Ringform

O

F-1,6-bisP

++ H

123456 3,42,5 1,

Haworthprojection

HPO^4

2-

-^ O

- O

-^ O

-^ O

F-6-P

H^ O^2

OH^

OH

2 Molecules

CHO H

OH H

HO

OH

H

OH

H CH

OH 2

H

CHO OH

H

HO

OH

H

OH

H

CHOPO^2

2- 3

GLC-6-P

GLC

ATP^

ADP

CHOH^2

O H

HO

OH

H

OH

H

CHOPO^2

ATP 2- 3

ADP

CHOPO^2

2- 3 O H

HO

OH

H

OH

H

CHOPO^2

2- 3

CHOPO^2

2- 3 O

CHOH^2

HC H

+ OH 2-CHOPO^23 +NAD^ NADH

H

C OH CHOPO^2

O 2-^3

2-OPO 3

ATP^

ADP

H

C OH CHOPO^2

O 2-^3

H

C

2-OPO 3

O CHOH 2

C

2-OPO 3

O CH 2

C

O

O CH 3

ATP^

ADP

DHAP G-3-P

1,3 bisPGA

3-PGA

2-PGA

PEP

PYR

H^

O

OH

H OH

CHOH^2 OH H

H^

O

OH

H OH

CHOPO^2 OH H

2- 3

ATP^

1 ADP

O^ POHC^322

CHOH^2 OH

H OH

H

H^

OOH

O^ POH^3

C 2

CHOPO^2 OH

2- 3

H OH

H

H^

OOH

ATP^

3 ADP

Fischer projection-open chain Ringform

O

F-1,6-bisP

++ H

123456 3,42,5 1,

Haworthprojection

HPO^4

2-

-^ O

- O

-^ O

-^ O

F-6-P

H^ O^2

OH^

OH

2 Molecules

p. 25

Aerobic Glycolysis^ Aerobic

Glycolysis (Overview)

(Overview)

Cellular LogicCellular LogicWhy add a phosphate? Blood glucose level ~ 5 mM

Cell glucose level ~ 4 - 5 mM

CHO H OH H HO

OH H

OH CHOH H CHOH^2 OH H HO

OH H

OH H CHOH^2

CHOH OH H HO

OH H

OH CHOH H CHOH^2 OH H HO

OH H

OH H CHOH^2

Why add a phosphate?

1. Prevents reverse diffusion through GluT.2. Prevents diffusion through plasma membrane.3. Maintains the Glucose concentration gradient.4. Binds to enzymes better (recognition tag).

Cellular LogicCellular Logic

H

CHO

OH H

HO

OH

H

OH

H

CH^2

O

O^

O OHOH O H O P -O^ O P -O O O P -O

• O

H N N

N N NH^2

Nucleophile(-OH)

Electrophile

(P)

H

Glucose (Glc)

ATP

H+

Enzyme

The 1. Reaction of Glycolysis^ The 1. Reaction of

Glycolysis

p. 24,

Enzyme Class: TransferaseSpecifically, phosphotransferase or “kinase”

O^

O OHOH

O H

O P -O

O P -O

O OP

-OO

-

H

N N

N N

NH^2

O^

O OHOH

O H

O P -O

H

N N

N N

NH^2

• O P -O^

O

H

CHO

OH H

HO

OH

H

OH

H

CHO^2

-

H

CHO

OH H

HO

OH

H

OH

H

CHO^2

O P

• O-O

Glc-6-P

ADP

p. 26

Energy coupling…

Δ G Calculations on 1. Reaction in Glycolysis Δ G Calculations on 1. Reaction in

Glycolysis (

(PhosphorylationPhosphorylation of Glucose)

of Glucose)

Summary of Chalk Board CalculationsSummary of Chalk Board Calculations

Glc

+

Pi

Î

Glc-6-P

+

H

O^2

+13.

3.7x

-

5 mM

1 mM

0.083 mM

+21.

2.8x

-

(intracellular concentrations)

Δ G

o’ or

Δ G (kJmol

-1)^

Keq

Δ G =

Δ G

o’^ + RTln[P]/[S]

Δ G = +13.9 kJmol

-1^ + (8.315 Jmol

-1 K

-1^ x 310 K) x ln[83 x

-6 ]/[5 x 10

-3 ][1 x 10

-3 ]

Δ G = +13.9 kJmol

-1^ + (2.578 kJmol

-1 ) x 2.

Δ G = +13.9 + 7.2 = +21.1 kJmol

-

Δ G (intracellular conditions are even more unfavorable than standard conditionsfor the reaction to proceed as desired)

o’^ = –RTlnKeq Keq = e^(-

Δ G

o’^ /RT) = e^(-13,900 Jmol

-1/8.315 Jmol

-1-1K^

x 298 K) = 0.

Q: How to drive glucose phosphorylationQ: How to drive glucose

phosphorylation forward

forward despite large positive

despite large positive

Δ G? Δ G?

A: Couple to much more favorable reaction (larger negativeA: Couple to much more favorable reaction (

larger negative

Δ G) such as to Δ G) such as to

the hydrolysis of ATP!!the hydrolysis of ATP!!ATP

+

H

O^2

Î^

ADP

+

Pi

-30.

2.2x

-46.

6.8x

Δ G

o’ or

Δ G (kJmol

-1)^

Keq

Intracellular [ATP]/[ADP][Pi] = 500 or higher (“phosphorylation potential”

)

Δ G =

Δ G

o’^ + RTln[P]/[S]

Δ G = - 30.5 + RTln 1/500 Δ G = - 30.5 + (- 15.4) = - 46.5 kJmol

-

Combination (coupling) of both reactions via an enzyme (hexokinaseCombination (coupling) of both reactions via an enzyme (

hexokinase):

):

Glc

+

Pi

Î

Glc-6-P

+

H

O^2

+13.

3.7x

-

Intracellular conditions

+21.

2.8x

-

Δ G

o’ or

Δ G (kJmol

-1)^

Keq

ATP

+

H

O^2

Î^

ADP

+

Pi

-30.

2.2x

Intracellular conditions

-46.

6.8x

Glc

+

ATP

Î

Glc-6-P

+

ADP

-16.

8.1x

Intracellular conditions

-25.

1.9x

Note:Coupling of a reaction to ATP hydrolysis can shift its Keq up to 10

8 –fold !!

(2.8x

-4^ Î

1.9x

4 )

Hexokinase (induced fit)

(Liver)

Isoenzymes: catalyze the same reaction but differ in propertiesIsoenzymes

: catalyze the same reaction but differ in properties

CHO H

OH H

HO

OH

H

OH

H CH

OH 2

H

CHO OH

H

HO

OH

H

OH

H

CHOPO^2

2- 3

GLC-6-P

GLC

ATP^

ADP

CHOH^2

O H

HO

OH

H

OH

H

CHOPO^2

ATP 2- 3

ADP

CHOPO^2

2- 3 O H

HO

OH

H

OH

H

CHOPO^2

2- 3

CHOPO^2

2- 3 O

CHOH^2

HC H

+ OH 2-CHOPO^23 +NAD^ NADH

H

C OH CHOPO^2

O 2-^3

2-OPO 3

ATP^

ADP

H

C OH CHOPO^2

O 2-^3

H

C

2-OPO 3

O CHOH 2

C

2-OPO 3

O CH 2

C

O

O CH 3

ATP^

ADP

DHAP G-3-P

1,3 bisPGA

3-PGA

2-PGA

PEP

PYR

H^

O

OH

H OH

CHOH^2 OH H

H^

O

OH

H OH

CHOPO^2 OH H

2- 3

ATP^

1 ADP

O^ POHC^322

CHOH^2 OH

H OH

H

H^

OOH

O^ POH^3

C 2

CHOPO^2 OH

2- 3

H OH

H

H^

OOH

ATP^

3 ADP

Fischer projection-open chain Ringform

O

F-1,6-bisP

++ H

123456 3,42,5 1,

Haworthprojection

HPO^4

2-

-^ O

- O

-^ O

-^ O

F-6-P

H^ O^2

OH^

OH

2 Molecules

CHO H

OH H

HO

OH

H

OH

H CH

OH 2

H

CHO OH

H

HO

OH

H

OH

H

CHOPO^2

2- 3

GLC-6-P

GLC

ATP^

ADP

CHOH^2

O H

HO

OH

H

OH

H

CHOPO^2

ATP 2- 3

ADP

CHOPO^2

2- 3 O H

HO

OH

H

OH

H

CHOPO^2

2- 3

CHOPO^2

2- 3 O

CHOH^2

HC H

+ OH 2-CHOPO^23 +NAD^ NADH

H

C OH CHOPO^2

O 2-^3

2-OPO 3

ATP^

ADP

H

C OH CHOPO^2

O 2-^3

H

C

2-OPO 3

O CHOH 2

C

2-OPO 3

O CH 2

C

O

O CH 3

ATP^

ADP

DHAP G-3-P

1,3 bisPGA

3-PGA

2-PGA

PEP

PYR

H^

O

OH

H OH

CHOH^2 OH H

H^

O

OH

H OH

CHOPO^2 OH H

2- 3

ATP^

1 ADP

O^ POHC^322

CHOH^2 OH

H OH

H

H^

OOH

O^ POH^3

C 2

CHOPO^2 OH

2- 3

H OH

H

H^

OOH

ATP^

3 ADP

Fischer projection-open chain Ringform

O

F-1,6-bisP

++ H

123456 3,42,5 1,

Haworthprojection

HPO^4

2-

-^ O

- O

-^ O

-^ O

F-6-P

H^ O^2

OH^

OH

2 Molecules

p. 25

Aerobic Glycolysis^ Aerobic

Glycolysis (Overview)

(Overview)

H

CHO

OH H

HO

OH

H

OH

H

CH^2

OH

H

CHO

OH H

HO

OH

H

OH

H

CH^2

OPO

2- 3

GLC-6-P

GLC

ATP

ADP

CH^2

OH O H

HO

OH

H

OH

H

CH^2

OPO

2- 3

1

2

Fischer projection-open chain HaworthprojectionRingform

F-6-P

H

CHO

OH H

HO

OH

H

OH

H

CH^2

OH

H

CHO

OH H

HO

OH

H

OH

H

CH^2

OPO

2- 3

GLC-6-P

GLC

ATP

ADP

CH^2

OH O H

HO

OH

H

OH

H

CH^2

OPO

2- 3

1

2

Fischer projection-open chain HaworthprojectionRingform

F-6-P

p. 25

Isomerization^ Isomerization

Reaction 2:Reaction 2:Phosphogluco isomerasePhosphogluco

isomerase or Glucose-6-P ketolisomerase (see p 24) Δ G^ Δ G

o^ o ’ = 1.67 kJ/mol= 1.67 kJ/mol’

Δ G = - Δ G =

- 2.92 kJ/mol2.92 kJ/mol

CH^2

OH O H

HO

OH

H

OH

H

CH^2

OPO

2- 3

ATP

ADP

CH^2

OPO

2- (^3) O H

HO

OH

H

OH

H

CH^2

OPO

2- 3

CH^2

OPO

2- (^3) O

CH^2

OH H

HC

OH CH^2

OPO

2- 3

DHAP G-3-P

3

4

5

O

(^123456) F-1,6-bisP

(^123456)

CH^2 F-6-P

OH O H

HO

OH

H

OH

H

CH^2

OPO

2- 3

ATP

ADP

CH^2

OPO

2- (^3) O H

HO

OH

H

OH

H

CH^2

OPO

2- 3

CH^2

OPO

2- (^3) O

CH^2

OH H

HC

OH CH^2

OPO

2- 3

DHAP G-3-P

3

4

5

O

(^123456) F-1,6-bisP

(^123456)

F-6-P

p. 25

Phosphorylation^ Phosphorylation

Reaction 3: PhosphofructokinaseReaction 3:

Phosphofructokinase-

-1 (PFK1 (PFK-

-1)1) or

ATP:Fructose-6-P 1-phosphotransferase ΔΔ GG

oo^ ’’ == -

-14.2 kJ/mol14.2 kJ/mol

ΔΔ GG

erythrocyteerythrocyte

== --18.8 kJ/mol 18.8 kJ/mol

CH^2

OH O H

HO

OH

H

OH

H

CH^2

OPO

2- 3

ATP

ADP

CH^2

OPO

2- (^3) O H

HO

OH

H

OH

H

CH^2

OPO

2- 3

CH^2

OPO

2- (^3) O

CH^2

OH H

HC

OH CH^2

OPO

2- 3

DHAP G-3-P

3

4

5

O

(^123456) F-1,6-bisP

(^123456)

CH^2 F-6-P

OH O H

HO

OH

H

OH

H

CH^2

OPO

2- 3

ATP

ADP

CH^2

OPO

2- (^3) O H

HO

OH

H

OH

H

CH^2

OPO

2- 3

CH^2

OPO

2- (^3) O

CH^2

OH H

HC

OH CH^2

OPO

2- 3

DHAP G-3-P

3

4

5

O

(^123456) F-1,6-bisP

(^123456)

F-6-P p. 25

Reaction 4: Aldolase^ Reaction 4:

Aldolase or Fructose-1,6-BisP glyceraldehyde-3-P lyase

CleavageCleavage

Δ G^ Δ G

o^ o ’ = +23.9 kJ/mol= +23.9 kJ/mol’

Δ G = - Δ G =

-0.23 kJ/mol0.23 kJ/mol

Aldol Cleavage in Glycolysis

(Reaction No. 4)

CHCH CC

OPOP 2 2

OO

CC

HOHO

HH

CC RestRest

HH

OO

HH

CC RestRest

HH

OO

β α

C^ C

OO

CC

HOHO

HH

CHCH HH

OPOP 2 2

C^

O R^1 C R^2

R^3 C^

O R^4 R^5

H

C^

O R^1 C R^2

R^3

+^

C^

O

R^5

R^4

C^

O R^1 C R^2

R^3 H

Requirements for cleavage: C-OH must be

β^ to carbonyl carbon

H

H

p. 27

Aldol Cleavage in^ Aldol

Cleavage in Glycolysis

Glycolysis

α β

p. 27

Reverse Reaction (Aldol

Aldol Condensation

Condensation)

Requirements for condensation: H on C that is

α^ to carbonyl carbon on substrate 1 (C-H acidic)

and need for carbonyl group on substrate 2

C^

O R^1 C R^2

R^3 H

C^

O R^1 C R^2

R^3

C^

O R^1 C R^2

R^3

Resonance stabilized

C^

O

R^5

R^4

C^

O R^1 C R^2

R^3 C^

OH R^4 R^5

Substrate 1

Substrate 2

H

H

AldolaseAldolaseo^ o Δ G^ ’= + 23.9 kJ/mol= + 23.9 kJ/mol Δ G’

F-1,6-BP

DHAPDHAPG3PG3P

How can we forcethis reaction to go

forward?? Le Chatelier's

Principle

PFK-PFK

-1^1

AldolaseAldolase

F6PF6P

Δ G^ Δ G

o^ o ’== -’

- 14.2 kJ/mol14.2 kJ/mol Δ G = -^ Δ G = - 18.8 kJ/mol18.8 kJ/mol

Δ G^ Δ G

o^ o ’= + 23.9 kJ/mol= + 23.9 kJ/mol’

F-1,6-BP Common IntermediateCommon Intermediate

DHAPDHAPG3PG3P

PFK-PFK

-1^1

AldolaseAldolase

Δ G^ Δ G

o^ o ’== -’

- 14.2 kJ/mol14.2 kJ/mol Δ G = -^ Δ G = - 18.8 kJ/mol18.8 kJ/mol

Δ G^ Δ G

o^ o ’= + 23.9 kJ/mol= + 23.9 kJ/mol’

HexokinaseHexokinase

Δ G^ Δ G

o^ o ’== -’

- 16.6 kJ/mol16.6 kJ/mol Δ G = -^ Δ G = - 24.8 kJ/mol24.8 kJ/mol

oo ΔΔ GG ’’= + 1.7 kJ/mol= + 1.7 kJ/mol Δ G = -^ Δ G =

- 2.9 kJ/mol2.9 kJ/mol

Phosphogluco isomerasePhosphogluco

isomerase

F-1,6-BP

F6PF6P

DHAPDHAPG3PG3P