BIBC 102

Metabolic Biochemistry

Fall 2010

Lecture 6,
October 6, 2010
If we don’t change direction,
we’ll end up where we
are going.

(Chinese Proverb)
 Physics IgNobel
Dr. Geim

http://en.wikipedia.org/wiki/List_of_Ig_Nobel_Prize_winners#2000
 Part III

Bioenergetics and Metabolism

Chapter 13 in LNC
H2O + CO2  C(H2O)n + O2

C(H2O)n + O2  H2O + CO2

urea
Types of Organic Reactions
1) Group transfer

Glucose + ATP Glu-6-P + ADP

H2O + ATP Pi + ADP

Pi in all future discussions will stand for inorganic phosphate:

the mixture, at pH 7, of H3PO4, H2PO4-1, HPO4-2, and PO4-3
 Types of Organic Reactions
2) Oxidation-reduction reactions

Ethanol + NAD+ acetaldehyde + NADH + H+

In most biochemical reactions an oxidation involves the removal of

hydrogen (H2) from an organic molecule; however, the mechanism proceeds
by the removal of
a hydride ion (H:-)
and the release of a proton (H+)
- the proton can be dumped into the highly buffered cytosol

- the hydride ion MUST be picked up by NAD+, NADP+, and other specific factors
 Types of Organic Reactions

3) Isomerizations, rearrangements

aldose ketose

glyceraldehyde 3-P dihydroxyacetone phosphate

citrate isocitrate
 Types of Organic Reactions

4) Reactions involving making/breaking of C-C

bonds
Fru-1,6, bisphosphate dihydroxyacetone-phosphate
+ glyceraldehyde-3phosphate
 Types of Organic Reactions

5) Decarboxylation/carboxylation (reactions
involving making/breaking of C-C bonds)
Pyruvate Acetaldehyde + CO2
 Types of Organic Reactions

6) Dehydrations/hydrations
Malate Fumarate
 Biochemical reactions
are subject to the laws of thermodynamics
A + B C + D

G = 0 at equilibrium
 [C] [D]
e - G’ /RT
o
K’eq = ------------ =
[A] [B]

o
G’ o
For standard conditions: 25 C, 1 atm, pH = 7
Gas constant

R = 8.313 J/mol.K
= 1.987 cal/mol.K

1 cal = 4.184 J

at 25oC RT = 2.497 kJ/mol

= 0.592 kcal/mol
Many reactions in biological systems are by themselves
not energetically favored (G > 0)

they have to be “pushed”

1. By changing concentrations of reactants

2. By coupling them to energy releasing reactions

- enzymatic mechanisms are designed to accomplish this

coupling of exergonic and endergonic reactions
coupling of exergonic and endergonic reactions:

1) A P1 G1o > 0

2) B P2 G2o < 0

3) A + B P1 + P2 G3o = G1o + G2o

The third reaction will be spontaneous if G3o is negative

We need an enzyme for two purposes:

1. To make reaction 3 possible

mechanistically
and with the required specificity

2. To speed up the reaction

example of coupling an endergonic reaction with an exergonic reaction

1. Glutamate + Ammonia  glutamine G1 > 0

2. ATP + H2O  ADP + Pi  G2 < 0

3. ATP + glutamate + ammonia  glutamine + ADP + Pi

G3 = G1 + G2 < 0

LNC Fig. 13.8
 amide

group transfer reaction

mixed
anhydride
End of Lecture 6

October 5, 2010