Bioenergetics 2

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unit-1
Bioenergetics and Biochemical
Reaction Types

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MERIT LIFE SCIENCESMERIT LIFE SCIENCES
e-TUTORIALe-TUTORIAL
NEET/NET JRF CSIR EXAM /JAM/DBT
DR SHEELENDRA Ph.D. FROM BHU
FACULTY: DR SHEELENDRA BHATT

UNIT-1
BIOENERGETICS-2
TIME 8:00-10:00PM

• Heat energy can be used to do work
only through a change of temperature.
Bioenergetics & ATPBioenergetics & ATP

Standard free energy change (∆G°) of a
chemical reaction:

• When a reaction results in release of energy

The free-energy change of a reaction (ΔG) divided
into 3 types:

Standard free energy change (∆G°) of a
chemical reaction:
For every reaction ∆G can be calculated using:-
∆G° = - 2.303 RT log Keq
While:
R = Gas constant
T = AbsoluteTemp.
Keq = Equilibrium constant
Note:
∆G° indicates constant temperature & pressure and physiological pH 7.2
for cells.
Unites of free energy = calorie (cal) or kilocalorie (kcal) /mole

Units of energy

• ΔG° is the free energy change for this reaction under
standard conditions that is, when each of the
reactants A, B, C, and D is present at a concentration
of 1.0 M (for a gas, the standard state is usually chosen
to be 1 atmosphere).
• Thus, the ΔG of a reaction depends on the nature of
the reactants (expressed in the ΔG° term of equation
1) and on their concentrations (expressed in the
logarithmic term of equation 1).

•The ΔG of a reaction depends only on the free energy
of the products (the final state) minus the free energy
of the reactants (the initial state).
•The ΔG of a reaction is independent of the path (or
molecular mechanism) of the transformation. The
mechanism of a reaction has no effect on ΔG.
•The ΔG provides no information about the rate of a
reaction.

∆G values of pathways can be
calculated
The ∆G value of an overall pathway can be calculated as
the algebraic sum of the ∆G values of the individual
reactions making the pathway:-
∆Gpathway= ∆G1 + ∆G2 + ∆G3 + ∆G4 + ∆G5

Free energy of a reaction
The free energy change (∆G) of a reaction determines
its spontaneity. A reaction is spontaneous if ∆G is
negative (if the free energy of products is less than
that of reactants).
∆Go
' = standard free energy change (at pH 7, 1M
reactants & products); R = gas constant; T = temp.
For a reaction A + B  C + D
∆G = ∆Go
' + RT ln
[C] [D]
[A] [B]

∆Go
' of a reaction may be positive, & ∆G negative,
depending on cellular concentrations of reactants and
products.
Many reactions for which ∆Go
' is positive are
spontaneous because other reactions cause depletion
of products or maintenance of high substrate
concentration.
For a reaction A + B  C + D
∆G = ∆Gº' + RT ln
[A] [B]
[C] [D]

At equilibrium
∆G = 0.
K'eq, the ratio [C][D]/[A]
[B] at equilibrium, is the
equilibrium constant.
An equilibrium constant
(K'eq) greater than one
indicates a spontaneous
reaction (negative ∆G°').
∆G = ∆Gº' + RT ln
0 = ∆Gº' + RT ln
∆Gº' = - RTln
defining K'eq =
∆Gº' = - RT ln K'eq
[C] [D]
[A] [B]
[C] [D]
[A] [B]
[C] [D]
[A] [B]
[C] [D]
[A] [B]

K'eq
∆G º'
kJ/mol
Starting with 1 M reactants &
products, the reaction:
104
- 23 proceeds forward (spontaneous)
102
- 11 proceeds forward (spontaneous)
100
= 1 0 is at equilibrium
10
-2 + 11 reverses to form “reactants”
10
-4 + 23 reverses to form “reactants”
∆Go
' = − RT ln K'eq
Variation of equilibrium constant with ∆Go
‘ (25 o
C)

Energy coupling
 A spontaneous reaction may drive a non-spontaneous reaction.
 Free energy changes of coupled reactions are additive.
A. Some enzyme-catalyzed reactions are
interpretable as two coupled half-reactions, one
spontaneous and the other non-spontaneous.
 At the enzyme active site, the coupled reaction is kinetically
facilitated, while individual half-reactions are prevented.
 Free energy changes of half reactions may be summed, to yield the
free energy of the coupled reaction.

For example, in the reaction catalyzed by the Glycolysis
enzyme Hexokinase, the half-reactions are:
ATP + H2O ↔ ADP + Pi ∆Go
' = −31 kJ/mol
Pi + glucose ↔ glucose-6-P + H2O ∆Go
' = +14 kJ/mol
Coupled reaction:
ATP + glucose ↔ ADP + glucose-6-P ∆Go
' = −17 kJ/mol
The structure of the enzyme active site, from which H2O
is excluded, prevents the individual hydrolytic reactions,
while favoring the coupled reaction.

B.Two separate reactions, occurring in the same cellular compartment, one
spontaneous and the other not, may be coupled by a common intermediate
(reactant or product).
A hypothetical, but typical, example involving PPi:
Enzyme 1:
A + ATP ↔ B + AMP + PPi ∆Go
' = + 15 kJ/mol
Enzyme 2:
PPi + H2O ↔ 2Pi ∆Go
' = – 33 kJ/mol
Overall spontaneous reaction:
A + ATP + H2O ↔ B + AMP + 2Pi ∆Go
' = – 18 kJ/mol
Pyrophosphate (PPi) is often the product of a reaction that needs a driving
force.
Its spontaneous hydrolysis, catalyzed by Pyrophosphatase enzyme, drives
the reaction for which PPi is a product.

Ion Transport may be coupled
to a chemical reaction, e.g.,
hydrolysis or synthesis of ATP.
In this diagram & below,
water is not shown. It should
be recalled that the ATP
hydrolysis/synthesis reaction
is: ATP + H2O ↔ ADP + Pi.
S1 S2
ATP
ADP + Pi
Side 1 Side 2

The free energy change (electrochemical potential
difference) associated with transport of an ion S
across a membrane from side 1 to side 2 is:
R = gas constant, T = temperature, Z = charge on the ion,
F = Faraday constant, ∆Ψ = voltage.
∆G = R T ln + Z F ∆Ψ
[S]1
[S]2
S1 S2
Side 1 Side 2

∆G for ion flux - varies with ion gradient & voltage.
∆G for chemical reaction - negative ∆Go
' for ATP
hydrolysis; ∆G depends also on [ATP], [ADP], [Pi].
Since free energy changes
are additive, the
spontaneous direction
for the coupled reaction
will depend on relative
magnitudes of:
S1 S2
ATP
ADP + Pi
Side 1 Side 2

Two examples:
ActiveTransport: Spontaneous ATP hydrolysis
(negative ∆G) is coupled to (drives) ion flux against a
gradient (positive ∆G).
ATP synthesis: Spontaneous H+
flux (negative ∆G) is
coupled to (drives) ATP synthesis (positive ∆G).

“High energy” bonds
Phosphoanhydride bonds (formed by splitting out H2O
between 2 phosphoric acids or between carboxylic &
phosphoric acids) have a large negative ∆G of hydrolysis.
N
NN
N
NH2
O
OHOH
HH
H
CH2
H
OPOPOP-O
O
O- O-
O O
O-
adenine
ribose
ATP
adenosine triphosphate
phosphoanhydride
bonds (~)

N
NN
N
NH2
O
OHOH
HH
H
CH2
H
OPOPOP-O
O
O- O-
O O
O-
adenine
ribose
ATP
adenosine triphosphate
phosphoanhydride
bonds (~)
Phosphoanhydride linkages are said to be "high energy"
bonds. Bond energy is not high, just ∆G of hydrolysis.
"High energy" bonds are represented by the "~" symbol.
~P represents a phosphate group with a large negative
∆G of hydrolysis.

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).
“High energy” bonds

Example: AMPPNP.
Such analogs have been used to study the dependence of
coupled reactions onATP hydrolysis.
In addition, they have made it possible to crystallize an
enzyme that catalyzes ATP hydrolysis with an ATP analog
at the active site.
AMPPNP (ADPNP) ATP analog
N
NN
N
NH2
O
OHOH
HH
H
CH2
H
OPOPNP-O
O
O- O-
O O
O-
H
Artificial ATP
analogs have
been designed
that are resistant
to cleavage of
the terminal
phosphate by
hydrolysis.

A reaction important for equilibrating ~P among
adenine nucleotides within a cell is that catalyzed by
Adenylate Kinase:
ATP + AMP ↔ 2 ADP
The Adenylate Kinase reaction is also important because
the substrate for ATP synthesis, e.g., by mitochondrial
ATP Synthase, is ADP, while some cellular reactions
dephosphorylate ATP all the way to AMP.
The enzyme Nucleoside Diphosphate Kinase (NuDiKi)
equilibrates ~P among the various nucleotides that are
needed, e.g., for synthesis of DNA & RNA.
NuDiKi catalyzes reversible reactions such as:
ATP + GDP ↔ ADP + GTP,
ATP + UDP ↔ ADP + UTP, etc.

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.

Why do phosphoanhydride linkages have a high ∆G
of hydrolysis? Contributing factors for ATP & PPi
include:
 Resonance stabilization of products of hydrolysis exceeds resonance
stabilization of the compound itself.
 Electrostatic repulsion between negatively charged phosphate
oxygen atoms favors separation of the phosphates.

Creatine Kinase catalyzes:
Phosphocreatine + ADP ↔ ATP + creatine
This is a reversible reaction, though the equilibrium
constant slightly favors phosphocreatine formation.
 Phosphocreatine is produced when ATP levels are high.
 When ATP is depleted during exercise in muscle, phosphate is transferred
from phosphocreatine to ADP, to replenish ATP.
−
O P
H
N C
O
O−
N
NH2
+
CH2
CH3
C
O
O−
phosphocreatine
Phosphocreatine (creatine
phosphate), another
compound with a "high
energy" phosphate linkage,
is used in nerve & muscle
for storage of ~P bonds.

Phosphoenolpyruvate (PEP), involved in ATP synthesis
in Glycolysis, has a very high ∆G of Pi hydrolysis.
Removal of Pi from ester linkage in PEP is spontaneous
because the enol spontaneously converts to a ketone.
The ester linkage in PEP is an exception.
C
C
O O−
OPO3
2−
CH2
C
C
O O−
O
CH3
C
C
O O−
OH
CH2
ADP ATP
H+
PEP enolpyruvate pyruvate

Generally phosphate esters, formed by splitting out
water between a phosphoric acid and an OH group,
have a low but negative ∆G of hydrolysis. Examples:
 the linkage between the first phosphate and the ribose hydroxyl of ATP.
N
NN
N
NH2
O
OHOH
HH
H
CH2
H
OPOPOP-O
O
O- O-
O O
O-
adenine
ribose
ATP (adenosine triphosphate)
ester linkage

Other examples of phosphate esters with low but
negative ∆G of hydrolysis:
 the linkage between phosphate & a hydroxyl group in glucose-6-
phosphate or glycerol-3-phosphate.
glycerol-3-phosphate
CH2
CH
CH2
OH
HO
O P
O
O−
O−
H O
OH
H
OHH
OH
CH2
H
OH
H
1
6
5
4
3 2
O P
O
OH
OH
glucose-6-phosphate

 the linkage between phosphate and the hydroxyl group of an amino
acid residue in a protein (serine, threonine or tyrosine).
Regulation of proteins by phosphorylation and dephosphorylation will
be discussed later.
Protein OH + ATP Protein O P
O
O−
O−
+ ADP
Pi H2O
Protein Kinase
Protein Phosphatase

ATP has special roles in energy coupling & Pi transfer.
∆G 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.
Compound
∆Go
' of phosphate
hydrolysis, kJ/mol
Phosphoenolpyruvate (PEP) −61.9
Phosphocreatine −43.1
Pyrophosphate −33.5
ATP (to ADP) −30.5
Glucose-6-phosphate −13.8
Glycerol-3-phosphate −9.2

Coenzyme A-SH + HO C
O
R
Coenzyme A-S C
O
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 ∆G of hydrolysis.
Some other
“high energy”
bonds:

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.
Coenzyme A-SH + HO C
O
CH3
Coenzyme A-S C
O
CH3 + H2O
acetic acid
acetyl-CoA

Coenzyme A includes
β-mercaptoethylamine,
in amide linkage to the
carboxyl group of the B
vitamin pantothenate.
The hydroxyl of
pantothenate is in ester
linkage to a phosphate
of ADP-3'-phosphate.
The functional group is
the thiol (SH) of
β-mercaptoethylamine.
N
N N
N
NH2
O
OHO
HH
H
CH2
H
OPOPOH2C
O−
O O
O−
P
O
O−−
O
C
C
C
NH
CH2
CH2
C
NH
CH3H3C
HHO
O
CH2
CH2
SH
O
β-mercaptoethylamine
pantothenate
ADP-3'-phosphate
Coenzyme A

3',5'-Cyclic AMP (cAMP), is used by
cells as a transient signal.
Adenylate Cyclase catalyzes cAMP
synthesis: ATP → cAMP + PPi.
The reaction is highly spontaneous
due to the production of PPi, which
spontaneously hydrolyzes.
Phosphodiesterase catalyzes
hydrolytic cleavage of one Pi ester
(red), converting cAMP → 5'-AMP.
N
N N
N
NH2
O
OHO
HH
H
H2
C
H
O
P
O
O-
1'
3'
5' 4'
2'
cAMP
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 vsThermodynamics:
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.

Oxidation & reduction
Oxidation & reduction will be covered in more detail later.
The evolution of photosynthesis, and the generation of
the oxygen that is now plentiful in our environment,
allowed development of metabolic pathways that derive
energy from transfer of electrons from various
reductants ultimately to molecular oxygen.

Oxidation of an iron atom involves loss of an electron
(to an acceptor): Fe++
(reduced)  Fe+++
(oxidized) + e-
Since electrons in a C-O bond are associated more with
O, increased oxidation of a C atom means increased
number of C-O bonds.
Oxidation of carbon is spontaneous (energy-yielding).
Two important e−
carriers in metabolism: NAD+
& FAD.
Increasing oxidation of carbon
H
CH H
H
H
CH OH
H
H
C
H
O
O
C
O
OH
C
H
O

NAD+
, Nicotinamide
Adenine Dinucleotide,
is an electronacceptor
in catabolic pathways.
The nicotinamide ring,
derived from the vitamin
niacin, accepts 2 e-
& 1 H+
(a hydride) in going to
the reduced state,
NADH.
NADP+
/NADPH is
similar except for Pi.
NADPH is e−
donor in
synthetic pathways.
H
C
NH2
O
CH2
H
N
H
OH OH
H H
O
OP
O
HH
OH OH
H H
O
CH2
N
N
N
NH2
OP
O
O
−
O
+
N−
O
nicotinamide
adenine
esterified to
Pi in NADP+
Nicotinamide
Adenine
Dinucleotide

NAD+
/NADH
The electron transfer reaction may be summarized
as :
NAD+
+ 2e−
+ H+
↔ NADH.
It may also be written as:
NAD+
+ 2e−
+ 2H+
↔ NADH + H+
N
R
H
C
NH2
O
N
R
C
NH2
O
H H
+
+ 2 e−
+ H+
NAD+
NADH

FAD (Flavin Adenine Dinucleotide), derived from the
vitamin riboflavin, functions as an e−
acceptor.
The dimethylisoalloxazine ring undergoes
reduction/oxidation.
FAD accepts 2e−
+ 2H+
in going to its reduced state:
FAD + 2e−
+ 2H+
↔ FADH2
C
C
C
H
C
C
H
C
N
C
C
N
N
C
NH
C
H3C
H3C
O
O
CH2
HC
HC
HC
H2C
OH
O P O P O
O
O-
O
O-
Ribose
OH
OH
Adenine
C
C
C
H
C
C
H
C
N
C
C
H
N
N
H
C
NH
C
H3C
H3C
O
O
CH2
HC
HC
HC
H2C
OH
O P O P O
O
O-
O
O-
Ribose
OH
OH
Adenine
FAD FADH2
2 e−
+ 2 H+
dimethylisoalloxazine

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.

Chemistry of ATP (Adenosine – tri –
phosphate):ATP is a nucleotide type molecule made of the following
components:-
1.The nitrogenous base adenine
2.The pentose sugar ribose
3.Three phosphate groups

phosphate)
Thus:-Thus:-
ATP ADP + Pi ∆G = -7.3 kcal/mole
ADP AMP + Pi ∆G = -7.2 kcal/mole
AMP Adenosine + Pi ∆G = -3.2 kcal/mole
ATP, ADP and AMP are present in all forms of life. They
occur not only in the cytosol of cells but also in the
mitochondria & nucleus. In normal respiring cells ATP
makes up 80% of the three ribonucleotides. ADP & AMP
account for 20%.

phosphate):
At pH 7, ATP occurs as the multiply charged anion ATP4-
whereas ADP
occurs as ADP3-
. This is because their phosphate groups are completely
ionized at the intracellular PH. ATP and ADP occur inside cells as
magnesium complexes:-
ATP4-
+ Mg2+
(ATP-Mg)2-
ADP3-
+ Mg2+
(ADP-Mg)

phosphate):
Inside cells the concentration of ATP remains normally relatively
constantly high. It’s rate of formation equals it’s rate of
hydrolysis. Thus the terminal phosphate group of ATP
undergoes continuous removal & replacement from the pool of
inorganic phosphate during cell metabolism.

∆G values for some characteristic
reactions
Super high energy compounds are compounds generated during
catabolism. They are phosphorylated compounds. Once formed along a
catabolic pathway, they undergo immediate hydrolysis
(dephosphorylation). As a result a large amount of energy is released
this is used by the cell to synthesize ATP from ADP and the hydrolyzed
inorganic phosphate.

∆G values for some characteristic
reactions

The Bioenergetics of Muscle Contraction
The contraction of muscle requires a large amount of energy that
cannot be fulfilled by the ATP stored inside muscle tissue. In
addition to ATP there is a super-high energy compound stored in
muscle cells that plays a major role in the energetics of muscle. This
super-high energy compound is also present in large concentrations
in other contractile tissues such as brain & nerve tissue.

The Bioenergetics of Muscle Contraction
This compound is PHOSPHOCREATINE. It serves as a storage
form of high energy phosphate groups. The ∆G value for the
hydrolytic reaction of phosphocreatine is highly negative (-10.3
kcal/mole). This is greater than that of ATP. The energy released is
sufficient to allow coupled synthesis of ATP from ADP:-

The Bioenergetics of Muscle
Contraction
Phosphocreatine thus functions to keep the ATP
concentration in muscle cells at constantly high level
whenever some of the ATP of muscle cells is used for
contraction, ADP is formed. Through the action of
creatine kinase phosphocreatine is quickly hydrolyzed
and donates its phosphate group to ADP to form ATP.

The phosphocreatine level inside muscle is 3-4 times greater
than that of ATP and thus stores enough high energy phosphate
groups to keep the ATP level constantly high during short
periods of intense muscular contraction.
Contraction

Contraction:

Bioenergetics
• Bioenergetics
• The quantitative study of…
• Cellular energy transduction
• Nature and function of the chemical processes for energy
transductions
• Fundamental laws in thermodynamics governing
bioenergetics
• First law : Energy conservation
• Second law: Increase in entropy
Living Orgamism
1. Metabolism
2. Reproduction
Energy: work to survive and reproduce
Energy transduction in biological system

Free Energy Change for Biological Reactions
• Thermodynamic quantities describing the energy changes in chemical
reaction
• Gibbs free energy, G
• The amount of energy capable of doing work during a reaction at constant
T and P
• Positive ∆G : endergonic
• Negative ∆G : exergonic, spontaneous reaction
• Enthalpy, H
• The heat content of the reacting system
• Number & kinds of chemical bonds in the reactants and products
• Positive ∆H : endothermic
• Negative ∆H : exothermic
• Entropy, S
• Quantitative expression for the randomness or disorder in a system
• ∆G = ∆H –T∆S
• Cells use free energy for reactions
• Energy source
• Heterotrope :Nutrient
• Autotrope: Solar energy

Standard Free Energy Change vs. Equilibrium Constant
• aA + bB  cC + dD
• Equilibrium constant [Ceq]c
[Deq]d
[Aeq]a
[Beq]b
• ∆Go
: standard free energy change (J/mol)
• 298K=25o
C, 1M of initial reactants and products,1 atm (101.3 kPa)
• Standard transformed constants
• pH 7, 55.5M water, 1mM Mg2+
(ATP as reactant)
• ∆G’o
,K’eq
• ∆G’o
= -RT ln K’eq
• Spontaneous reaction
• K’’
eq >1
• ∆Go
: negative
Keq =

∆G’o
for some representative chemical reactions

∆G’o
are additive
• Sequential chemical reactions
• (1) A  B : ∆G’1
o
,K’eq1
glucose + Pi  G-6P + H2O ; ∆G’o
= 13.8 kJ/mol
• (2) B  C : ∆G’2
o
,K’eq2
ATP + H2O  ADP + Pi ;∆G’o
= -30.5 kJ/mol
• (1) + (2) : A  C : ∆G’1
o
+ ∆G’1
o
,K’eq1 X K’eq2
ATP + glucose  ADP + Pi ; ∆G’o
= -16.7 kJ/mol
• Coupling of endergonic and exergonic reaction to make exergonic
reaction

The ΔG of a Reaction Depends on
Changes in Enthalpy (Bond Energy) and
Entropy
At any constant temperature and pressure, two factors determine
the ΔG of a reaction and thus whether the reaction will tend to
occur:
the change in bond energy between reactants and products and
the change in the randomness of the system. Gibbs showed that
free energy can be defined as
where H is the bond energy, or enthalpy, of the system; T is its
temperature in degrees Kelvin (K); and S is a measure of
randomness, called entropy.
If temperature remains
constant, a reaction proceeds
spontaneously only if the
free energy change ΔG in the
following equation is
negative:

In an exothermic reaction, the products contain less bond energy than the
reactants, the liberated energy is usually converted to heat (the energy of
molecular motion), and ΔH is negative.
In an endothermic reaction, the products contain more bond energy than the
reactants, heat is absorbed, and ΔH is positive.
Reactions tend to proceed if they liberate energy (if ΔH < 0), but this is only
one of two important parameters of free energy to consider; the other is
entropy.

Entropy S is a measure of the degree of
randomness or disorder of a system.
Entropy increases as a system becomes more
disordered and decreases as it becomes more
structured.
Consider, for example, the diffusion of solutes from one
solution into another one in which their concentration is
lower.
This important biological reaction is driven only by an
increase in entropy; in such a process ΔH is near zero.

suppose that a 0.1 M solution of glucose is
separated from a large volume of water by a
membrane through which glucose can diffuse.
Diffusion of glucose molecules across the
membrane will give them more room in which
to move, with the result that the randomness, or
entropy, of the system is increased.

Common Biochemical Reaction

Common Biochemical Reaction
Two basic chemical principle
1. A covalent bond can be broken in two general way: homolytic cleavage
and heterolytic cleavge

2. Biochemical reactions involve interactions between nucleophiles and
electrophiles

Most of the reactions in living cells fall into one of five general
categories
1.Reaction that make or break carbon-carbon bond
2.Internal rearrangements, isomerization, and elimination
3.Free-radical reaction
4.Group transfer: acyl, glycosyl, phosphoryl
5.Oxidation-reduction

Reaction that make or break carbon-carbon bond

Internal rearrangements, isomerization, and
elimination

Free-radical-mediated decarboxylation

Acyl group transfer

Phosphoryl group transfer

The oxidation states of carbon in biomolecules

Oxidation-Reduction

Phosphoryl group transfers and ATP
The free energy change for ATP hydrolysis is large negative

Other phosphorylated compounds also have large free
energies of hydrolysis

For hydrolysis reactions with large negative free-energy changes, the
products are more stable than the reactants for one or more of the
following reasons
1.The bond strain is relieved by charge separation (ATP).
2.The products are stabilized by ionization (ATP, 3-phosphoglycerate,
thioester) .
3.The products are stabilized by isomerization (PEP)
4.The products are stabilized by resonance (creatin, inorganic phosphate,
thioester)

ATP provides energy by group transfer

ATP serve as the universal energy currency in
all living cells Because of its intermediate
position on the scale of group transfer
potential.

ATP donates phosphoryl, pyrophosphoryl,
and adenyl group

Transphosphorylation between nucleotide by
nucleotide diphosphate kinase

Inorganic phosphate may serve as a reservoir
of phosphoryl group with high energy
transfer potential
Polyphosphate kinase-1 (in bacterial)
Polyphosphate kinase-2

Biological oxidation-reduction reaction
1.The transfer of phosphoryl groups is a central feature of metabolism
2.Electron transfer in oxidation-reduction reaction is another important
transfer in living cells.
3.The flow of electrons is responsible for all work done by living organism
4.In heterotroph, the source of electron are reduced compounds (food)
5.In autotroph, the source of electron is a chemical species excited by the
absorption of light (e.g. H2O).
6.Cells contain a variety of molecular energy transducers, which convert
the every of electron flow into useful work
7.Biological oxidation often involve dehydrogenation
- alkane (-CH2-CH2-) convert to alkene (-CH=CH-)
- oxidation is coincident with the loss of hydrogen

Oxidation states of carbon in the biosphere

A Few Types of Coenzymes and Proteins Serve as Universal Electron
1.Electrons from hundreds of different substrates into a few types of
universal electron carriers
2.NAD, NADP, FMN, and FAD are water soluble coenzymes that undergo
reversible oxidation and reduction in many of the electron-transfer
reactions of metabolism
3.Lipid-soluble quinones, such as ubiquinone, act as electorn carriers and
proton donors in membrane
4.Iron-sulfur proteins and cytochromes that undergo reversible oxidation-
reduction reaction

Bioenergetics 2

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