Biochemical Energetics

PERANAN ATP= BIOENERGETIKA

• Merupakan ilmu pengetahuan tentang perubahan energi
yang menyertai reaksi biokimia.

• Energi dapat berupa energi panas atau energi kimia.

Kepentingan Biomedis :

• Energi diperoleh dari metabolisme yang normal oleh

karena pemahaman terhadap dasar nutrisi yang kuat.
• Kelaparan /stavasi---> kematian cadangan energi habis.
Marasmus---> gangguan keseimbangan energi.Obesitas---
> surplus energi berlebihan.
 Free energy of a reaction
The free energy change (DG) of a reaction determines
its spontaneity.

For a reaction A + B  C + D
[C] [D]
DG = DG ' + RT ln
o
[A] [B]

DGo' = standard free energy change (at pH 7, 1M

reactants & products); R = gas constant; T = temp.
 For a reaction A + B  C + D
[C] [D]
DG = DGº' + RT ln
[A] [B]

DGo' of a reaction may be positive, & DG negative,

depending on cellular concentrations of reactants
(A&B) and products. (C&D)
.
For example, in the reaction catalyzed by the Glycolysis
enzyme Hexokinase, the half-reactions are:

ATP + H2O  ADP + Pi DGo' = -31 kJ/mol

Pi + glucose  glucose-6-P + H2O DGo' = +14 kJ/mol

Coupled reaction:
ATP + glucose  ADP + glucose-6-P DGo' = -17 kJ/mol
 “High energy” bonds
NH 2
ATP
adenosine triphosphate N
N

O O O N N

-O P O P O P O CH2 adenine
O
O- O- O- H H
H H
phosphoanhydride OH OH
bonds (~) ribose

Phosphoanhydride bonds (formed by splitting out H2O

between 2 phosphoric acids or between carboxylic &
phosphoric acids) have a large negative DG of hydrolysis.
 NH 2
ATP adenine
adenosine triphosphate N
N

O O O N N

-O P O P O P O CH 2
O
O- O- O- H H ribose
phosphoanhydride H H
bonds (~) OH OH

Phosphoanhydride linkages are said to be "high energy"

bonds. Bond energy is not high, just DG of hydrolysis.
"High energy" bonds are represented by the "~" symbol.
~P.
 “High energy” bonds

Compounds with “high energy bonds” are said to

have high group transfer potential.

For example, Pi may be spontaneously cleaved from

ATP for transfer to another compound (e.g., to a
hydroxyl group on glucose).
Potentially, 2 ~P bonds can be cleaved, as 2 phosphates are
released by hydrolysis from ATP.

AMP~P~P  AMP~P + Pi (ATP  ADP + Pi)

AMP~P  AMP + Pi (ADP  AMP + Pi)

Alternatively:
AMP~P~P  AMP + P~P (ATP  AMP + PPi)
P~P  2 Pi (PPi  2Pi)
 Inorganic polyphosphate

Many organisms store energy as inorganic

polyphosphate, a chain of many phosphate residues
linked by phosphoanhydride bonds:
P~P~P~P~P...
Hydrolysis of Pi residues from polyphosphate may be
coupled to energy-dependent reactions.
Depending on the organism or cell type, inorganic
polyphosphate may have additional functions.
E.g., it may serve as a reservoir for Pi, a chelator of
metal ions, a buffer, or a regulator.
Phosphocreatine (creatine phosphate), another compound
with a "high energy" phosphate linkage, is used in nerve &
muscle for storage of ~P bonds.

O CH3
O
-
H
O P N C N CH2 C
O-
O- NH2+

phosphocreatine

Creatine Kinase catalyzes:

Phosphocreatine + ADP  ATP + creatine
O O- O O- O O-
C C C
ADP ATP
C OPO32- C OH C O

CH2 H+ CH2 CH3

PEP enolpyruvate pyruvate

Phosphoenolpyruvate (PEP), involved in ATP synthesis

in Glycolysis, has a very high DG of Pi hydrolysis.
 NH2

N
N

ester linkage
O O O N N
adenine
-O P O P O P O CH2
O
O- O- O- H H
ribose
H H
ATP (adenosine triphosphate) OH OH
 O
6 CH O P OH
2
CH2 OH
OH
5 O
H H HO CH O
H
4 H 1
OH
CH2 O P O-
OH OH
3 2
O-
H OH
glucose-6-phosphate glycerol-3-phosphate

Other examples of phosphate esters with low but

negative DG of hydrolysis:
 the linkage between phosphate & a hydroxyl group
in glucose-6-phosphate or glycerol-3-phosphate.
 Protein Kinase O

Protein OH + ATP Protein O P O- + ADP

O-
Pi H2O
Protein Phosphatase

 the linkage between phosphate and the hydroxyl

group of an amino acid residue in a protein (serine,
threonine or tyrosine).
ATP has special roles in energy coupling & Pi transfer.
DG of phosphate hydrolysis from ATP is intermediate
among examples below.
ATP can thus act as a Pi donor, & ATP can be synthesized
by Pi transfer, e.g., from PEP.
DGo' of phosphate
Compound hydrolysis, kJ/mol
Phosphoenolpyruvate (PEP) -
Phosphocreatine -
Pyrophosphate -
ATP (to ADP) -
Glucose-6-phosphate -
Glycerol-3-phosphate -
 O
Some other
“high energy” Coenzyme A-SH + HO C R
bonds:

Coenzyme A-S C R + H2O

A thioester forms between a carboxylic acid & a thiol

(SH), e.g., the thiol of coenzyme A (abbreviated CoA-SH).
Thioesters are ~ linkages. In contrast to phosphate esters,
thioesters have a large negative DG of hydrolysis.
 O

Coenzyme A-SH + HO C CH3

acetic acid

Coenzyme A-S C CH3 + H2O

acetyl-CoA

The thiol of coenzyme A can react with a carboxyl group

of acetic acid (yielding acetyl-CoA) or a fatty acid
(yielding fatty acyl-CoA).
The spontaneity of thioester cleavage is essential to the
role of coenzyme A as an acyl group carrier.
Like ATP, CoA has a high group transfer potential.
 SH

CH2

Coenzyme A includes b-mercaptoethylamine

CH2

b-mercaptoethylamine, NH

in amide linkage to the C O

carboxyl group of the B CH2

vitamin pantothenate. CH2

pantothenate

The hydroxyl of NH
NH2

pantothenate is in ester C O
N
N
linkage to a phosphate HO C H

of ADP-3'-phosphate. H3C C CH3 O O N N

H2C O P O P O CH2
The functional group is O
O- O- H H
the thiol (SH) of H H
b-mercaptoethylamine. ADP-3'-phosphate O OH

-
O P O-

Coenzyme A O
 cAMP NH2
3',5'-Cyclic AMP (cAMP), is used
by cells as a transient signal. N
N
Adenylate Cyclase catalyzes cAMP
synthesis: ATP  cAMP + PPi. N N
The reaction is highly spontaneous H2 O
due to the production of PPi, which 5' C 4'
H H 1'
spontaneously hydrolyzes. O
H 3' 2' H
Phosphodiesterase catalyzes P O OH
O
hydrolytic cleavage of one Pi ester O-
(red), converting cAMP  5'-AMP.
This is a highly spontaneous reaction, because cAMP is
sterically constrained by having a phosphate with ester
links to 2 hydroxyls of the same ribose. The lability of
cAMP to hydrolysis makes it an excellent transient signal.
List compounds exemplifying the following roles
of "high energy" bonds:

 Energy transfer or storage

ATP, PPi, polyphosphate, phosphocreatine

 Group transfer
ATP, Coenzyme A

 Transient signal
cyclic AMP
Kinetics vs Thermodynamics:
A high activation energy barrier usually causes
hydrolysis of a “high energy” bond to be very slow in
the absence of an enzyme catalyst.
This kinetic stability is essential to the role of ATP and
other compounds with ~ bonds.
If ATP would rapidly hydrolyze in the absence of a
catalyst, it could not serve its important roles in energy
metabolism and phosphate transfer.
Phosphate is removed from ATP only when the reaction
is coupled via enzyme catalysis to some other reaction
useful to the cell, such as transport of an ion,
phosphorylation of glucose, or regulation of an enzyme
by phosphorylation of a serine residue.
 NAD+ is a coenzyme, that reversibly binds to
enzymes.

 FAD is a prosthetic group, that remains tightly

bound at the active site of an enzyme.