Download [edit]Making Endergonic reactions happen

Bio Chemistry
1.
Discuss the difference between the exergonic and endergonic reactions with
suitable examples?
In chemical thermodynamics, an endergonic reaction (also called an unfavorable reaction or
a nonspontaneous reaction) is a chemical reaction in which the standard change in free
energy is positive, and energy is absorbed. In layman's terms the total amount of energy is a loss
(it takes more energy to start the reaction than what you get out of it) so the total energy is a
negative net result. For an overall gain in the net result see Exergonic Reaction.
Under constant temperature and constant pressure conditions, this means that the change in the
standard Gibbs free energy would be positive
for the reaction at standard state (ie at standard pressure (1 bar), and standard
concentrations (1 molar) of all the reagents).

[edit]Equilibrium
constant
The equilibrium constant for the reaction is related to ΔG° by the relation:
where T is the absolute temperature and R is the gas constant. A positive value of ΔG°
therefore implies
so that starting from molar stoichiometric quantities such a reaction would move
backwards toward equilibrium, not forwards.
Nevertheless, endergonic reactions are quite common in nature, especially
in biochemistry and physiology. Examples of endergonic reactions in cells
include protein synthesis, and the Na+/K+ pumpwhich drives nerve
conduction and muscle contraction.
[edit]Making
Endergonic reactions happen
Endergonic reactions can be achieved if they are either pulled or pushed by
an exergonic (stability increasing, negative change in Free Energy) process.
[edit]Pull
Reagents can be pulled through an endergonic reaction, if the reaction products are
cleared rapidly by a subsequent exergonic reaction. The concentration of the
products of the endergonic reaction thus always remains low, so the reaction can
proceed.
A classic example of this might be the first stage of a reaction which proceeds via
a transition state. The process of getting to the top of the activation energy barrier to
the transition state is endergonic. However, the reaction can proceed because
having reached the transition state, it rapidly evolves via an exergonic process to the
more stable final products.
[edit]Push
Endergonic reactions can be pushed by coupling them to another reaction which is
strongly exergonic, through a shared intermediate.
This is often how biological reactions proceed. For example, on its own the reaction
may be too endergonic to occur. However it may be possible to make it occur by
coupling it to a strongly exergonic reaction – such as, very often, the
decomposition of ATP into ADP and inorganic phosphate ions, ATP → ADP +
Pi, so that
This kind of reaction, with the ATP decomposition supplying the free
energy needed to make an endergonic reaction occur, is so common in
cell biochemistry that ATP is often called the "universal energy
currency" of all living organisms.
2.
What is redox potential? Write standard reduction potential of biochemically
important half reactions.
Measurement and Interpretation
In aqueous solutions, the reduction potential is a measure of the tendency of the solution to either
gain or lose electrons when it is subject to change by introduction of a new species. A solution
with a higher (more positive) reduction potential than the new species will have a tendency to
gain electrons from the new species (i.e. to be reduced by oxidizing the new species) and a
solution with a lower (more negative) reduction potential will have a tendency to lose electrons to
the new species (i.e. to be oxidized by reducing the new species). Just as the transfer
of hydrogen ions between chemical species determines the pH of an aqueous solution, the
transfer of electrons between chemical species determines the reduction potential of an aqueous
solution. Like pH, the reduction potential represents an intensity factor. It does not characterize
the capacity of the system for oxidation or reduction, in much the same way that pH does not
characterize the acidity.[clarification needed]
Because the absolute potentials are difficult to accurately measure, reduction potentials are
defined relative to a reference electrode. Reduction potentials of aqueous solutions are
determined by measuring the potential difference between an inert sensing electrode in contact
with the solution and a stable reference electrode connected to the solution by a salt bridge. The
sensing electrode acts as a platform for electron transfer to or from the reference half cell. It is
typically platinum, although gold and graphite can be used. The reference half cell consists of a
redox standard of known potential. The standard hydrogen electrode (SHE) is the reference from
which all standard redox potentials are determined and has been assigned an arbitrary half cell
potential of 0.0 mV. However, it is fragile and impractical for routine laboratory use. Therefore,
other more stable reference electrodes such as silver chloride and saturated calomel (SCE) are
commonly used because of their more reliable performance.
Although measurement of the reduction potential in aqueous solutions is relatively
straightforward, many factors limit its interpretation, such as effects of solution temperature and
pH, irreversible reactions, slow electrode kinetics, non-equilibrium, presence of multiple redox
couples, electrode poisoning, small exchange currents and inert redox couples. Consequently,
practical measurements seldom correlate with calculated values. Nevertheless, reduction
potential measurement has proven useful as an analytical tool in monitoring changes in a system
rather than determining their absolute value (e.g. process control and titrations).
[edit]Standard
reduction potential,
See also: Standard hydrogen electrode
The standard reduction potential (
) is measured under standard conditions: 25°C, a
1 M concentration for each ion participating in the reaction, a partial pressure of 1 atm for
each gas that is part of the reaction, and metals in their pure state. The standard reduction
potential is defined relative to a standard hydrogen electrode (SHE) reference electrode, which is
arbitrarily given a potential of 0.00 volts. Historically, many countries, including the United States
and Canada[1], used standard oxidation potentials rather than reduction potentials in their
calculations. These are simply the negative of standard reduction potentials, so it is not a major
problem in practice. However, because these can also be referred to as "redox potentials", the
terms "reduction potentials" and "oxidation potentials" are preferred by the IUPAC. The two may
be explicitly distinguished in symbols as
3.
and
.
Explain the different carriers and mechanism involved in oxidative
phosphorylation.
Adenosine-5'-triphosphate (ATP) is a multifunctional nucleoside triphosphate used in cells as
a coenzyme. It is often called the "molecular unit ofcurrency" of
intracellular energy transfer.[1] ATP transports chemical energy within cells for metabolism. It is
produced by photophosphorylation andcellular respiration and used by enzymes and structural
proteins in many cellular processes, including biosynthetic reactions, motility, and cell
division.[2] One molecule of ATP contains three phosphate groups, and it is produced by ATP
synthase from inorganic phosphate and adenosine diphosphate (ADP) or adenosine
monophosphate (AMP).
Metabolic processes that use ATP as an energy source convert it back into its precursors. ATP is
therefore continuously recycled in organisms: the human body, which on average contains only
250 grams (8.8 oz) of ATP,[3] turns over its own body weight in ATP each day.[4]
ATP is used as a substrate in signal transduction pathways
by kinases that phosphorylate proteins and lipids, as well as by adenylate cyclase, which uses
ATP to produce the second messenger molecule cyclic AMP. The ratio between ATP and AMP is
used as a way for a cell to sense how much energy is available and control the metabolic
pathways that produce and consume ATP.[5] Apart from its roles in energy metabolism and
signaling, ATP is also incorporated into nucleic acids by polymerases in the processes of DNA
replication and transcription.
The structure of this molecule consists of a purine base (adenine) attached to the 1' carbon atom
of a pentose sugar (ribose). Three phosphate groups are attached at the 5' carbon atom of the
pentose sugar. It is the addition and removal of these phosphate groups that inter-convert
ATP, ADP and AMP. When ATP is used in DNA synthesis, the ribose sugar is first converted
to deoxyribose by ribonucleotide reductase.
ATP was discovered in 1929 by Karl Lohmann,[6] but its correct structure was not determined until
some years later. It was proposed to be the main energy-transfer molecule in the cell by Fritz
Albert Lipmann in 1941.[7] It was first artificially synthesized by Alexander Todd in 1948.[8]
4.
Explain the enzymatic reactions of TCA cycle and give its metabolic
significance?
The citric acid cycle — also known as the tricarboxylic acid cycle (TCA cycle), the Krebs
cycle, or theSzent-Györgyi–Krebs cycle[1][2] — is a series of chemical reactions used by
all aerobic organisms to generate energy through the oxidization of acetate derived
from carbohydrates, fats and proteins into carbon dioxide and water. In addition, the cycle
provides precursors[which?] for the biosynthesis of compounds including certain amino acids as well
as the reducing agent NADH that is used in numerous biochemical reactions. Its central
importance to many biochemical pathways suggests that it was one of the earliest established
components of cellular metabolism and may have originated abiogenically.[3]
The name of this metabolic pathway is derived from citric acid (a type of tricarboxylic acid) that is
first consumed and then regenerated by this sequence of reactions to complete the cycle. In
addition, the cycle consumes acetate in the form of acetyl-CoA, reduces NAD+ to NADH, and
produces carbon dioxide. The NADH generated by the TCA cycle is fed into the oxidative
phosphorylation pathway. The net result of these two closely linked pathways is the oxidation of
nutrients to produce energy in the form of ATP.
In eukaryotic cells, the citric acid cycle occurs in the matrix of the mitochondrion. Bacteria also
use the TCA cycle to generate energy, but since they lack mitochondria, the reaction sequence is
performed in thecytosol with the proton gradient for ATP production being across the plasma
membrane rather than the inner membrane of the mitochondria.
The components and reactions of the citric acid cycle were established in the 1930s by seminal
work from the Nobel laureates Albert Szent-Györgyi[4] and Hans Adolf Krebs.[5]
Components of the TCA cycle were derived from anaerobic bacteria and the TCA cycle
itself may have evolved more than once.[6] Theoretically there are several alternatives to
the TCA cycle, however the TCA cycle appears to be the most efficient.[7] If several
alternatives independently evolved, they all undoubtedly rapidly converged to the TCA
cycle.
5.
Explain the biosynthesis and significance of cholesterol metabolism?
Cholesterol, from the Greek chole- (bile) and stereos (solid) followed by the chemical suffix ol for an alcohol, is an organic chemical substance classified as a waxy steroid of fat. It is an
essential structural component of mammalian cell membranes and is required to establish
proper membrane permeabilityand fluidity. In addition, cholesterol is an important component for
the manufacture of bile acids, steroid hormones, and vitamin D. Cholesterol is the
principal sterol synthesized by animals, predominantly in the liver; however, small quantities can
be synthesized in other eukaryotes such as plants andfungi. It is almost completely absent
among prokaryotes, i.e. bacteria. Although cholesterol is important and necessary for the
aforementioned biological processes, high levels of cholesterol in the blood have been linked to
damage to arteries and cardiovascular disease.[2]
François Poulletier de la Salle first identified cholesterol in solid form in gallstones, in 1769.
However, it was only in 1815 that chemist Eugène Chevreulnamed the compound
"cholesterine".[3]
Function
Cholesterol is required to build and maintain membranes; it modulates membrane fluidity over the
range of physiological temperatures. The hydroxyl group on cholesterol interacts with
the polar head groups of the membrane phospholipids and sphingolipids, while the
bulky steroid and the hydrocarbon chain are embedded in the membrane, alongside
the nonpolar fatty acid chain of the other lipids. Through the interaction with the phospholipid fatty
acid chains, cholesterol increases membrane packing, which reduces membrane fluidity. [7] In this
structural role, cholesterol reduces the permeability of the plasma membrane to neutral
solutes,[8] protons, (positive hydrogen ions) and sodium ions.[9]
Within the cell membrane, cholesterol also functions in intracellular transport, cell signaling and
nerve conduction. Cholesterol is essential for the structure and function of
invaginated caveolae and clathrin-coated pits, including caveola-dependent and clathrindependent endocytosis. The role of cholesterol in such endocytosis can be investigated by
using methyl beta cyclodextrin (MβCD) to remove cholesterol from the plasma membrane.
Recently, cholesterol has also been implicated in cell signaling processes, assisting in the
formation of lipid rafts in the plasma membrane. Lipid raft formation brings receptor proteins in
close proximity with high concentrations of second messenger molecules. [10] In many neurons,
a myelin sheath, rich in cholesterol, since it is derived from compacted layers of Schwann
cell membrane, provides insulation for more efficient conduction of impulses. [11]
6.
Elucidate the biosynthetic pathway of phenylalanine?
Phenylalanine (abbreviated as Phe or F)[2] is an α-amino acid with
the formula C6H5CH2CH(NH2)COOH. This essential amino acid is classified asnonpolar because
of the hydrophobic nature of the benzyl side chain. L-Phenylalanine (LPA) is an electrically
neutral amino acid, one of the twenty common amino acids used to biochemically form proteins,
coded for by DNA. The codons for L-phenylalanine are UUU and UUC. Phenylalanine is a
precursor fortyrosine, the monoamine signaling
molecules dopamine, norepinephrine (noradrenaline), and epinephrine (adrenaline), and the
skin pigment melanin.
Phenylalanine is found naturally in the breast milk of mammals. It is used in the manufacture of
food and drink products and sold as a nutritional supplement for its
reputed analgesic and antidepressant effects. It is a direct precursor to the
neuromodulator phenylethylamine, a commonly used dietary supplement.
Phenylketonuria
The genetic disorder phenylketonuria (PKU) is the inability to metabolize phenylalanine.
Individuals with this disorder are known as "phenylketonurics" and must regulate their intake of
phenylalanine. A (rare) "variant form" of phenylketonuria called hyperphenylalaninemia is caused
by the inability to synthesize a coenzyme called biopterin, which can be supplemented. Pregnant
women with hyperphenylalaninemia may show similar symptoms of the disorder (high levels of
phenylalanine in blood) but these indicators will usually disappear at the end of gestation.
Individuals who cannot metabolize phenylalanine must monitor their intake of protein to control
the buildup of phenylalanine as their bodies convert protein into its component amino acids.
Phenylketonurics often use blood tests to monitor the amount of phenylalanine in their blood. Lab
results may report phenylalanine levels in different units, including mg/dL and umol/L. One mg/dL
of phenylalanine is approximately equivalent to 60 umol/L.
A non-food source of phenylalanine is the artificial sweetener aspartame. This compound, sold
under the trade names "Equal" and "NutraSweet", is metabolized by the body into several
chemical byproducts including phenylalanine. The breakdown problems phenylketonurics have
with protein and the attendant build up of phenylalanine in the body also occurs with the ingestion
of aspartame, although to a lesser degree. Accordingly, all products in Australia, the U.S. and
Canada that contain aspartame must be labeled: "Phenylketonurics: Contains phenylalanine." In
the UK, foods containing aspartame must carry ingredient panels that refer to the presence of
"aspartame or E951" [4] and they must be labeled with a warning "Contains a source of
phenylalanine." These warnings are specifically placed to aid individuals who suffer from PKU so
that they can avoid such foods.
7.
Give an account on biosynthesis of purine nucleotides?
8.
Explain the principle and applications of Ion-exchange chromatography?