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BC2-Week 2-Principle of Bioenergetics

The document covers principles of bioenergetics, including thermodynamics, glycolysis, gluconeogenesis, and pentose phosphate pathways. It discusses the roles of ATP in energy transfer, the significance of oxidation-reduction reactions, and the function of electron carriers such as NAD, NADP, FAD, and FMN. Key concepts include energy conservation, Gibbs free energy, and the mechanisms of energy transduction in living cells.

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thuy36030
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8 views50 pages

BC2-Week 2-Principle of Bioenergetics

The document covers principles of bioenergetics, including thermodynamics, glycolysis, gluconeogenesis, and pentose phosphate pathways. It discusses the roles of ATP in energy transfer, the significance of oxidation-reduction reactions, and the function of electron carriers such as NAD, NADP, FAD, and FMN. Key concepts include energy conservation, Gibbs free energy, and the mechanisms of energy transduction in living cells.

Uploaded by

thuy36030
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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TOPIC 2:

PRINCIPLES OF BIOENERGETICS,
GLYCOLYSIS, GLUCONEOGENESIS,
PENTOSE PHOSPHATE PATHWAYS
Vũ Thanh Ngọc, PhD
Department of Applied Chemistry
School of Biotechnology
HCMC International University
[email protected]
Topic 2 Week
1. Principles of bioenergetics 2

2. Glycolysis 3

3. Gluconeogenesis 3

4. Pentose phosphate pathways 3


1. Bioenergetics and thermodynamics
Laws of thermodynamics
Quantitative relationships among free energy, enthalpy, and entropy
2. Phosphoryl group transfers and ATP
Roles of ATP in biological energy exchange
3. Biological oxidation-reduction reactions
Energetics of electron-transfer reactions
Electron carriers: NAD and NADP, FAD and FMN
Bioenergetics is the quantitative study of:
 The energy transductions that occur in living cells of the nature

 Function of the chemical processes underlying these transductions


How does the cells tap into this process?
Potential energy:
 Stationary
 Exist as chemical bonds, concentration gradients, and electrical
charges in the cells

Kinetic energy:
 Energy in motion
 Result in the movement of molecules
First law – energy conservation:
“For any physical or chemical change, the total amount of energy in
the universe remains constant; energy may change form or it may be
transported from one region to another, but it cannot be created or
destroyed.”
In thermodynamics, a system can be classified based on the exchange
of energy and materials with another system:
Isolated system: NO energy or material can be exchanged
with the surrounding
Closed system: energy but NO material can be exchanged
with the surroundings
Open system: BOTH material and energy can be exchanged
with the surroundings

 Living cells or organisms are open systems


Second law – entropy expansion:
“In all natural processes, the entropy of the universe increases.”

 Reactions occur spontaneously only when they increase disorder


in the system and its surroundings. Otherwise, the system will
REQUIRE energy (Gibbs free energy) for non-spontaneous reactions.
Gibbs free energy, G: amount of energy capable of doing work during
a reaction at constant temperature and pressure
 ΔG > 0, endergonic reactions (non-spontaneous)
ΔG < 0, exergonic reactions (spontaneous)
Enthalpy, H: heat content of the reacting system
 ΔH > 0, endothermic reactions
ΔH < 0, exothermic reactions
Entropy, S: the randomness or disorder in a system
Under constant temperature and pressure:

ΔG = ΔH – TΔS

J/mol or cal/mol K J/mol.K or cal/mol.K


1 cal = 4.184 J
K: Kelvin, 25 oC = 298 K
equilibrium constant Keq:

[A], [B], [C], and [D]: molar concentrations of the reaction


components at the point of equilibrium.
ΔG’º = -RT ln K’eq

Gas constant, R = 8.315 J/mol.K = 1.987 cal/mol.K)


Standard condition: T = 298 K (25oC), 1 atm, [H+] = 1 M or pH = 0
Biochemical standard condition: pH = 7, concentration of water = 55.5 M
 ΔG’º and K’eq: standard transformed constants
characteristic for each reaction
Small free energy change leads to
exponential change in equilibrium constant
Standard conditions,
NOT conditions existing in cells
 Actual free-energy change?
 When ΔG < 0, the reaction is thermodynamically feasible, but may not
happen by itself.
 Ex: combustion of firewood to CO2 and H2O is very favorable
thermodynamically, but firewood remains stable for years. Why?
 the activation energy for the combustion reaction is higher than
the energy available at room temperature
To occur, the reaction needs help to overcome the activation barrier
of the transition state.
2 sequential chemical reactions:
ATP is the chemical link between catabolism and
anabolism.
Heterotrophic cells obtain free energy (chemical energy)
via catabolism of nutrient molecules.
 Use that energy to make ATP from ADP and Pi
 Exergonic conversion of ATP to ADP and Pi, or to AMP
and PPi, is coupled to endergonic processes:
 Synthesis of macromolecules

 Membrane transport against concentration gradient

 Mechanical motion
Chemical basis:
1. ATP is unstable due to charge repulsion
2. The leaving inorganic Pi undergoes
resonance stabilization
3. ADP is immediately ionized to ADP3- + H+
Since ΔG = ΔG’º + RT ln ([B]/[A]), we should be able to get the actual free
energy change in the cell if the concentration of adenine nucleotides and
inorganic phosphate are given.

The phosphorylation potential, ΔGP:

ΔGP = ΔG’º + RT ln ([ADP][Pi]/[ATP])


OTHER PHOSPHORYLATED COMPOUNDS AND THIOESTERS
ALSO HAVE LARGE FREE ENERGIES OF HYDROLYSIS
Phosphoenolpyruvate (PEP)
OTHER PHOSPHORYLATED COMPOUNDS AND THIOESTERS
ALSO HAVE LARGE FREE ENERGIES OF HYDROLYSIS
1,3-bisphosphoglycerate
OTHER PHOSPHORYLATED COMPOUNDS AND THIOESTERS
ALSO HAVE LARGE FREE ENERGIES OF HYDROLYSIS

Phosphocreatine
OTHER PHOSPHORYLATED COMPOUNDS AND THIOESTERS
ALSO HAVE LARGE FREE ENERGIES OF HYDROLYSIS

Thioesters such as acetyl-CoA


OTHER PHOSPHORYLATED COMPOUNDS AND THIOESTERS
ALSO HAVE LARGE FREE ENERGIES OF HYDROLYSIS
OTHER PHOSPHORYLATED COMPOUNDS AND THIOESTERS
ALSO HAVE LARGE FREE ENERGIES OF HYDROLYSIS

To summarize, for hydrolysis reactions with large, negative ΔG’º,


the products are more stable than the reactants because:
(1) the bond strain in reactants due to electrostatic repulsion is relieved
by charge separation
(2) the products are stabilized by ionization

(3) the products are stabilized by isomerization (tautomerization)

(4) the products are stabilized by resonance


ATP PROVIDES ENERGY BY GROUP TRANSFERS,
NOT BY SIMPLE HYDROLYSIS

Besides direct hydrolysis, energy of ATP


breakdown is coupled to endergonic
transformations of substrates by transferring a
phosphoryl, pyrophosphoryl, or adenylyl group
from ATP to a substrate or enzyme molecule

ATP hydrolysis in two steps


THE ENERGY RANK OF SOME BIOLOGICAL
PHOSPHORYLATED COMPOUNDS
THE ROLE OF INORGANIC POLYPHOSPHATE

 Inorganic polyphosphate (polyP) is a linear polymer composed of many Pi


residues linked through phosphoanhydride bonds.
 Present in all organisms

 May serve as a reservoir of phosphoryl groups with high group transfer


potential.
The transfer of phosphoryl group is not the only way of channeling
energy inside the cell. Another way is electron transfer in oxidation-
reduction reactions.
BIOLOGICAL OXIDATION-REDUCTION REACTIONS

 The free energy can be conserved and transformed as electrons are


transferred in oxidation-reduction reactions
 The flow of electrons can be coupled to do biological work

 Oxidation-reductions can be described as half-reactions:


BIOLOGICAL OXIDATION-REDUCTION REACTIONS
Some terms:
 Reductant (Reducing agent): donate election

 Oxidant (Oxidizing agent): accept electron

 Redox pair (conjugate reductant-oxidant pair): electron donor and


acceptor in a half-reaction

Fe2+ and Fe3+ constitute a conjugate redox pair


BIOLOGICAL OXIDATION-REDUCTION REACTIONS

Reduction potentials measure affinity of the electron acceptor of


each redox pair for electrons, referenced to the half reaction:

Standard reduction potential, E°

 Reactions with higher E° has greater ability to gain electrons


REDUCTION POTENTIAL OF A REDOX PAIR

 Nernst equation:
E = Eº + RT/nF ln ([e- acceptor]/[e- donor])

 At room temperature (298 K or 25 oC):


E = Eº + (0.026V/n) ln ([e- acceptor]/[e- donor])

Where n is the number of electrons transferred


F is the Faraday constant (96480 J·V-1mol-1, or 23509 cal·V-1mol-1)
STANDARD REDUCTION POTENTIALS CAN BE USED
TO CALCULATE THE FREE-ENERGY CHANGE

Relationship between free energy and reduction potential


ΔG = -nF ΔE or ΔG’º = -nF ΔE’º
 provides a convenient way to measure ΔG of any biological oxidation
reactions
BIOLOGICAL OXIDATIONS OFTEN INVOLVE
DEHYDROGENATION
The oxidation state of carbon in the biosphere
 In some cases, oxidation (loss of
electrons) is coincident with the
loss of hydrogen.
 Many biological oxidation
reactions are dehydrogenations
in which 1 or 2 hydrogen atoms
are transferred from a substrate
to a hydrogen acceptor.
 Many enzymes that catalyze
oxidation reactions are
dehydrogenases.
CELLULAR OXIDATION OF GLUCOSE TO CO2
REQUIRES SPECIALIZED ELECTRON CARRIERS

 Series of controlled reactions, some of which are oxidations.


 Electrons removed in these oxidation steps are transferred to coenzymes
specialized for carrying electrons, such as NAD+ and FAD
ELECTRON CARRIERS

 NAD+ and NADP+

 FAD and FMN


NAD+ AND NADP+
NADH and NADPH act with dehydrogenases as electron carriers.
Both of them are soluble, can be used by many different dehydrogenases.
NAD+ AND NADP+
When NAD+ or NADP+ is reduced, the hydride ion could in principle be transferred
to either side of the nicotinamide ring: the front (A side) or the back (B side)
NAD+ AND NADP+

 The (+) sign does not indicate the net charge of the molecules.
 Cellular concentration of NAD+ & NADH is ~10 μM.
 Cellular concentration of NADP+ & NDAPH is ~ 1 μM.
 The ratio of NAD+/NADH is high  used mostly in catabolic oxidation
 The ratio of NADP+/NADPH is low  used mostly in anabolic reduction
 The hydride ion (·H) on NADH or NADPH can be incorporated at either A or B
form. There’s no enzyme out there that can promiscuously catalyze both.
NAD+ AND NADP+
The structure motif that binds NAD+ or NADP+ in dehydrogenases is called the
“Rossmann fold”.

The nucleotide binding domain of the enzyme


lactate dehydrogenase.
NAD+ AND NADP+
FAD AND FMN
 FAD and FMN are electron carriers that are tightly bound in flavoproteins.

Structures of oxidized and


reduced FAD and FMN
FAD AND FMN
 Flavoproteins are enzymes that catalyze oxidation-reduction reactions using
either FMN or FAD as coenzyme

 Flavoproteins also serve as light receptors in cryptochromes and photolyases.


OTHER ELECTRON CARRIERS

 Quinones
 Iron-sulfur proteins
 Cytochromes
 …
SUMMARY
1. Bioenergetics and thermodynamics
Laws of thermodynamics
Quantitative relationships among free energy, enthalpy, and entropy
2. Phosphoryl group transfers and ATP
Roles of ATP in biological energy exchange
3. Biological oxidation-reduction reactions
Energetics of electron-transfer reactions
Electron carriers: NAD and NADP, FAD and FMN

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