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Bioenergetics

• Bioenergetics is the quantitative study of energy transductionschanges of one form of energy into another-that occur in living
cells
• Thermodynamics is a branch of science concerned with heat and
temperature and their relation to energy and work, relationship
among various forms of energy
• The first law is the principle of the conservation of energy: 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
...
Gibbs free energy, G, expresses the amount of energy capable of doing work
during a reaction at constant temperature and pressure
I
...
Endergonic reaction: The system gains free energy and ΔGis positive
2
...
It reflects the number
and kinds of chemical bonds in the reactants and products
III
...
Reacting systems that take up heat from their surroundings are
endothermic and have positive values of ΔH

3
...
When the products of a reaction are less complex
and more disordered than the reactants, the reaction is said to proceed
with a gain in entropy
• E
...
The solid wood burns and becomes ash, smoke and gases, all of
which are more disordered than the solid fuel
• The units of ΔGand ΔH are joules/ mole or calories/ mole (recall that 1
cal : 4
...
Kelvin (J/ mol
...
we maintain this steady
state by a sophisticated set of metabolic regulatory system
• Metabolic Pathways
• A series of consecutive enzymatic reactions that produce specific
products, their reactants, intermediates and products are referred to
asmetabolites
• The reaction pathways that comprise metabolism often divided into
two categories

• Catabolism: nutrient and cell constituents are broken down
exergonically to salvage their components and to generate free
energy
• Anabolism: biosynthesis
• The free energy released by catabolic processes is conserved through
the synthesis of ATP from ADP and phosphate or reduction of coenzyme NADP+ to NADPH
Metabolic pathways are irreversible
• A highly exergonic reaction is irreversible, if such a reaction is a part
of multistep pathway, it confer directionality on the pathway, it
makes the entire pathway irreversible
Catabolic and anabolic pathways must differ
• If two metabolites are metabolically interconvertible, the pathway
from the first to the second must differ from the pathway from the

• This is b/ c if Metabolite 1 is converted to Met 2 by an exergonic
process, the conversion of Met 2 to Met 1 require that free energy in
order to bring this
• The existence of independent interconversion route is an important
property of metabolic pathway b/ c it allows independent control of
the two processes
• If Met 2 is required by the cell, it is necessary to turn off the pathway
from 2 to 1, while turning on the pathway 1 to 2
...
First cellular constituent synthesized by
green plants during photosynthesis from carbon dioxide and water, on absorption of light
...
Glucose is utilized as a source of energy, it is synthesized
from non-carbohydrate precursors and stored as glycogen to release glucose as and when the need arises
...
Krebs cycle is the final common oxidative
pathway for carbohydrates, fats aminoacids, through acetyl CoA
...
During the sequential
reactions of glycolysis, some of the free energy released from glucose is
conserved in the form of ATP and NADH
• The glycolytic breakdown of glucose is the sole source of metabolic energy in
some mammalian tissues and cell types (erythrocytes, renal medulla, brain, and
sperm)
...

• Fermentation is a general term for the anaerobic degradation of glucose or other
organic nutrientsto obtain energy, conserved as ATP
• Glycolysis differs among species only in the details of its regulation and in the
subsequent metabolic fate of the pyruvate formed
...
In these reactions, glucose is first phosphorylated at the hydroxyl group on
C-6
2
...
Which is again phosphorylated, this time at C-1, to yield fructose 1,6bisphosphate
4
...

This is the ”lysis" step that gives the pathway its name
...
Each molecule of
glyceraldehyde 3-phosphate is oxidized and phosphorylated by
inorganic phosphate to form 1,3-bisphospho glycerate
...

• The net yield is two molecules of ATP per molecule of glucose used,
because two molecules of ATP were invested in the preparatory
phase
...
However, glucose does not enter the cells by
simple diffusion
...

• 1
...
This isoperative in hepatocytes, erythrocytes and brain
• 2
...
Glucose transporters In recent years, at least six
glucose transporters GLUT-1 to GLUT-5 and GLUT-7) in the
cell membranes have been identified
...

For instance, GLUT-1 is abundant in erythrocytes whereas GLUT4 is abundant in skeletal muscle and adipose tissue
...
youtube
...

• Hexokinase undergoesa profound change in shape, an induced fit, when it binds glucose
...

• The human genome encodes four different hexokinases,
• One of the isozymes present in hepatocytes, hexokinase IV(also called glucokinase)

• The enzyme hexokinases present in almost all the tissues
...
), has low Km for
substratesabout 0
...

• Due to high affinity (low Km), glucose is utilized by hexokinase even at low
concentration, whereas glucokinase acts only at higher levels of glucose i
...
, after
a meal when blood glucose concentrations above 100mg/dl
...
It is a central
molecule with a variety of metabolic fates-glycolysis, glycogenesis, gluconeogenesisand pentose phosphate pathway

• This isomerization has a critical role in the overall chemistry of the glycolytic pathway,
as the rearrangement of the carbonyl and hydroxyl groups at C-1 and C-2 is a
necessary prelude to the next two steps
...


• The enzyme that forms fructose 1,6-bisphosphate is called PFK-1
• It is the first "committed step" (the molecules are "committed" to the pathway and will ultimately end up
in the pathway's final product) in the glycolytic pathway; glucose 6-phosphate and fructose 6-phosphate
have other possible fates, but fructose 1,6-bisphosphate is targeted for glycolysis
...
The enzyme is inhibited whenever the cell has ample ATP and is well supplied by other fuels
such as fatty acids

• Fructose 1 ,6-bisphosphate is cleaved to yield two different triose phosphates, glyceraldehyde 3phosphate, an aldose, and dihydroxyacetone phosphate, a ketos

• Interconversion of the Triose Phosphates: Only one of the two triose

phosphates formed by aldolase, glyceraldehyde 3-phosphate, can be directly
degraded in the subsequent steps of glycolysis
...

• The conversion of two molecules of glyceraldehyde 3-phosphate to
two molecules of pyruvate is accompanied by the formation of four
moleculesof ATPfrom ADP
...


• This is the first of the two energy-conserving reactions of glycolysis that eventually lead to the
formation of ATP
...


Phosptroryl Transfer from 1,3-Bisphosphoglycerate
to ADP
...
Phosphoglycerate kinase reaction is
reversible, a rare example among the kinase reactions
•

•

Conversion of 3-Phosphoglycerate to 2-Phosphoglycerate: The enzyme
phosphoglycerate mutase catalyzes a reversible shift of the phosphoryl group
between C-2 and C-3 of glycerate; Mg+2 is essential for this reaction

• Enolase promotes reversible removal of a molecule of water from 2phosphoglycerate to yield phosphoenol pyruvate (PEP)
• This enzyme requires Mg+2 or Mn+2 and is inhibited by fluoride
...
This step also is
a substrate level phosphorylation
...
) This reactions
irreversible

Fatesof Pyruvate
1
...
Pyruvate is oxidized, with lossof its carboxyl group asCO2,
to yield the acetyl group of acetyl-coenzyme A ; the acetyl group is then oxidized
completely to CO2 by the citric acid cycle
...
The energy
from the electron-transfer reactionsdrives the synthesis of ATPin mitochondria
2
...
When vigorously contracting skeletal muscle must function under
low oxygen conditions (hypoxia), NADHcannot be reoxidized to NAD+, but NAD+ is
required as an electron acceptor for the further oxidation of pyruvate
...
The third major route of pyruvate catabolism leads to ethanol
...
During the breakdown of pyruvate, electrons are transferred to NAD+
to produce NADH, which will be used by the cell to produce ATP

Yeast and other anaerobic microorganisms convert glucose to ethanol and CO2rather than pyruvate
...
Carbon-dioxide is released during this reaction
...
NADH is oxidized to NAD+ during this reaction
...
The major substrates/ precursors for gluconeogenesis are
lactate, pyruvate, glucogenic amino acids, propionate and glycerol
• Gluconeogenesis occurs mainly in the cytosol, although some precursors are
produced in the mitochondria
...
Essentially, (3 out of 10) reactions of
glycolysis are irreversible
...
These three stages by passed by alternate enzymesspecific
to gluconeogenesis

• Pyruvate is first transported from the cytosol into mitochondria or is
generated from alanine within mitochondria by transamination
• The first of the by pass reactions in gluconeogenesis is the conversion
of pyruvate to phosphoenol pyruvate (PEP)
...
pyruvate carboxylase, a mitochondrial enzyme (Require Biotin)
that converts pyruvate to oxaloacetate
...
it has to be
transported to the cytosol to be used in gluconeogenesis, here
the rest of the pathway occurs
...
It is converted
to malate and then transported to the cytosol
...
The reversible conversion of
oxaloacetate and malate is catalyzed by malate dehydrogenase, an
enzyme present in both mitochondria and cytosol
• In
the
cytosol,
phosphoenol
pyruvate
carboxy-kinase
converts oxaloacetate to phosphoenol-pyruvate
...
For the conversion of pyruvate to phosphoenol pyruvate,
2 ATPequivalents are utilized
...
The enzyme fructose 1-6bisphosphatase converts fructose1,6-bisphosphate to fructose 6phosphate
...

Conversion of glucose 6-phosphate to glucose
• Glucose 6-phosphatase catalyses the conversion of glucose 6phosphate to glucose
...
It is mostly present in liver and kidney
but absent in muscle brain and adipose tissues

• Gluconeogenesisbegins in the mitochondria with the formation of oxaloacetate through carboxylation of pyruvate
...
This enzyme is
stimulated by high levels of acetyl-CoA (produced in β-oxidation in the liver) and inhibited by high levels of ADP
...

• Malate is oxidized to oxaloacetate using NAD+ in the cytoplasm, where the remaining steps of gluconeogenesis
occur
...
One molecule of GTP is hydrolyzed to GDP during this reaction
...
However, fructose-1,6-bisphosphatase converts fructose-1,6-bisphosphate to
fructose6-phosphate, requiring one water molecule and releasing one phosphate
...

• Glucose-6-phosphate is formed from fructose 6-phosphate by phosphogluco isomerase
...
Whereas free glucose can easily diffuse
in and out of the cell, the phosphorylated form (glucose-6-phosphate) is locked in the cell, a mechanism by which
intracellular glucose levels are controlled by cells
...
Glucose is shuttled into
thecytosol by glucose transporters located in the membrane of theendoplasmic reticulum
...
Hexokinase/ glucokinase,
phosphofructokinase, and pyruvatekinase enzymes of glycolysis are replaced with glucose-6-phosphatase, fructose
-1,6-bisphosphatase, and PEPcarboxykinase
...


• Phosphofructokinase and fructose 1,6-bisphosphatase are also
reciprocally controlled by fructose 2,6-bisphosphate in the liver
...
Fructose 2,6bisphosphate strongly stimulates phosphofructokinase and inhibits
fructose 1,6-bisphosphatase
...
During starvation,
gluconeogenesis predominates because the level of F-2,6-BP is very
low
...
In addition
...
Clearly, this
Equation is not simply the reverse of the equation for conversion of glucose to
pyruvate by glycolysis, which would require only two molecules of ATP:
Glucose + 2ADP+ 2Pi + NAD+---> 2 pyruvate + 2ATP+ 2NADH+ 2H+ + 2H2O
The synthesis of glucose from pyruvate is a relatively expensive process
...
Under
intracellular conditions, the overall free-energy change of glycolysis is at least -63
kJ/ mol
...
Thus both glycolysis and gluconeogenesis are essentially irreversible
processes in cells

Kreb’ sCycle
• The overall reaction catalyzed by the pyruvate dehydrogenase
complex is an oxidative decarboxylation, an irreversible oxidation
process in which the carboxyl group is removed from pyruvate as a
molecule of CO2 and the two remaining carbons become the acetyl
group of acetyl-CoA

• The PDH complex is composed of multiple copies of three enzymes:
pyruvate dehydrogenase, E1 (with its bound cofactor TPP);
dihydrolipoyl transacetylase, E2 (with its covalently bound lipoyl
group); and dihydrolipoyl dehydrogenase, E3 (with its cofactors FAD
and NAD
• The combined dehydrogenation and decarboxylation of pyruvate to
the acetyl group of acetyl-CoA, requires the sequential action of three
different enzymes and five different coenzymes or prosthetic groupsthiamine pyrophosphate (TPP), flavin adenine dinucleotide (FAD),
coenzyme A (CoA, sometimes denoted CoA-SH, to emphasize the role
of the -SH group), nicotinamide adenine dinucleotide (NAD), and
lipoate
...


• The citric acid cycle was proposed by Hans Adolf Krebs in 1937, based
on the studies of oxygen consumption in pigeon breast muscle
...
He
published it in an other journal Enzymoligia
...
This enables the
synthesisof ATPby oxidative phosphorylation without any hindrance

• To begin the cycle, acetyl-CoA donates its acetyl group to the fourcarbon compound oxaloacetate to form the six-carbon citrate
• Citrate is isomerized to iso-citrate by the enzyme aconitase
...
the
formation of NADH and the liberation of CO2 occur at this stag
• Conversion of α-Ketoglutarate
to succinyl
CoA occurs through
oxidative
decarboxylation,
catalyzed
by α-Ketoglutarate
dehydrogenase complex
...
The mechanism of the reaction is
analogous to the conversion of pyruvate to acetyl CoA
...
This reaction is coupled with the phosphorylation
of GDP to GTP
...
GTP is
converted to ATPby the enzyme nucleoside diphosphate kinase
...
This
reaction results in the production of FADH2
...

• Malate is then oxidized to oxaloacetate by malate dehydrogenase
...
The
oxaloacetate is regenerated which can combine with
another molecule of acetyl CoA, and continue the cycle

• There is no direct participation of oxygen in Krebs cycle
...
This is
due to the fact that NAD+ and FAD (NADH and FADH2,respectively)
required for the operation of the cycle can be regenerated in the
respiratory chain only in the presence of 02
...

Oxidation of 3 NADH by electron transport chain coupled with
oxidative phosphorylation results in the synthesis of 9ATP, whereas
FADH2 leads to the formation of 2 ATP
...
thus, a total of twelve ATP are produced from
one acetyl CoA

(1)
• The first reaction of the cycle is the condensation of
acetyl-CoA with oxaloacetate to form citrate,
catalyzed by citrate synthase
• In this reaction the methyl carbon of the acetyl group
is joined to the carbonyl group (C-2) of oxaloacetate
...
It rapidly undergoes
hydrolysis to free CoA and citrate, which are released
from the active site
...
The large, negative standard freeenergy change of the citrate synthase reaction is
essential to the operation of the cycle because, as
noted earlier, the concentration of oxaloacetate is
normally very low, the CoA liberated in this reaction is
recycled
to
participate in
the oxidative
decarboxylation of another molecule of pyruvate by
the PDH complex
...
Formation of Isocitrate via cis-Aconitate

The enzyme aconitase (more formally,
aconitate hydratase) catalyzes the reversible
transformation of citrate to isocitrate, through
the intermediary formation of the tricarboxylic
acid cis-aconitate, which normally does not
dissociate from the active site
...
Mn2+ in the active site interacts with the carbonyl group of the
intermediate oxalosuccinate, which is formed transiently but does not Ieave the
binding site until decarboxylation converts it to a-ketoglutarate

(4)
• The next step is another oxidative decarboxyIation, in which α-ketoglutarate is converted to
succinyl CoA and CO2 by the action of the α-ketoglutarate dehydrogenase complex; NAD+
serves as electron acceptor and CoA as the carrier of the succinyl group
...
Conversion of Succinyl-CoA to Succinate

(6)
In eukaryotes, succinate dehydrogenase is tightly bound to the mitochondrial inner membrane; in
bacteria, to the plasma membrane
...
Electrons pass from succinate through the FAD and iron-sulfur
centers before entering the chain of electron carriers in the mitochondrial inner membrane (the
plasma membrane in bacteria)
...
5 ATPmolecules per pair of electrons
...
The reversible hydration of fumarate to L-malate is catalyzed by fumarase (formally, fumarate

hydratase)

(8)
...


Hexose Monophosphate Shunt
• Hexose monophosphate pathway or HMPshunt is also called pentose
phosphate pathway or phospho gluconate pathway
...
As such, no ATP is
directly utilized or produced in HMP pathway
...
The
tissues such as
liver,
adipose
tissue,
adrenal
gland,
erythrocytes, testes and lactating mammary gland, are highly active
in HMP shunt
...


Oxidative phase
• Glucose 6-phosphate dehydrogenase (G6PD) is an NADP-dependent
enzyme
that
converts
glucose
6-phosphate
to
6phosphogluconolactone
• The latter is then hydrolysed by the gluconolactone hydrolase to 6phosphogluconate
...

This enzyme catalyzes an irreversible reaction
...
lt is the ratio of NADPH/ NAD+ that ultimately
determines the flux of this cycle

Non oxidative phase
• The non-oxidative reactions are concerned with the interconversion of three,
four, five and seven carbon monosaccharides
...

Fructose 6-phosphate and glyceraldehyde 3-phosphate can be further
catabolized through glycolysis and citric acid cycle
...

• In the HMPshunt, hexoses are converted into
pentoses, the most important being ribose 5-phosphate
...


Importance of NADPH
• NADPH is required for the biosynthesis of fatty acids and
steroids hence HMP shunt is more active in the tissues
concerned with lipogenesis e
...
adipose tissue, liver etc
• NADPH is used in the synthesis of certain amino acids involving
the enzyme glutamate dehydrogenase
• There is a continuous production of H2O2 in the living cells
which can chemically damage unsaturated lipids, proteins and
DNA
...
NADPH is responsible for the regeneration of
reduced glutathione from the oxidized one
...

• Phagocytosis is the engulfment of foreign Particles, including
microorganisms carried out by white blood cells
...


Fatty Acid Metabolism
• Lipids are indispensable for cell structure and function
...
Triacylglycerol's are highly concentrated form of energy,
yielding 9 Cal/g, in contrast to carbohydrates and proteins that
produce only 4 Cal/g
...
The triacylglycerol's are non-polar and hydrophobic in nature,
hence is stored in pure form without any association with
water
...

One gram of glycogen combines with 2g of water for storage

• Fats can support the body's energy needs for long periods of
food deprivation
...

Cholesterols also a precursor for bile acids and steroid
hormones
...

Besides, hey are
also utilized by muscle,
liver, heart etc
...
The enzyme/namely hormonesensitive triacylglycerol lipase, removes the fatty acid either from carbon 1 or 3 of
the triacylglycerol to form diacylglycerol
...
The
complete degradation of triacylglycerol to glycerol and free acids is known as
lipolysis

Regulation of hormone-sensitiveTG-lipase
• Hormone sensitive TG-lipase is so named because its activity ismostly
controlled by hormones
...
enhance the
activity of adenylate cyclase and, thus, increase lipolysis
...
The control of cAMP
mediated lipolysiss illustrated in fig

• Increased levels of cAMP promote lipolysis
...
it should be therefore kept in
mind that lipolysis and lipogenesis are not simultaneously
operative
• Fate of glycerol: The adipose tissue lacks the enzyme glycerol
kinase, hence glycerol produced in lipolysis cannot be
phosphorylated here
...
the latter may be used for
the synthesisof triacylglycerols and phospholipids
...
The free fatty acids
enter various tissues and are utilized for the energy
...
Certain tissues, however, cannot
oxidize fatty acids, e
...
brain, erythrocytes

Fatty acid oxidation
The β-oxidation of fatty acids involves
1
...
Transport of fatty acids into mitochondria
3
...
There action occurs in two steps and requires ATP,
coenzyme A and Mg2+
...

• In the activation, two high energy phosphates are utilized, since ATP is
converted to pyrophosphate(PPi)
• The enzyme inorganic pyrophosphatase hydrolyses PPi to phosphate(Pi)
...
A specialized carnitine carrier system (carnitine shuttle) operates
to transport activated fatty acids from cytosol to the mitochondria
...
Acyl group of acyl CoA is transferred to carnitine, catalyzed by
carnitine acyltransferase (present on the outer surface of inner
mitochondrial membrane
2
...
Carnitine acyltransferase ii (found on the inner surface of inner
mitochondrial membrane) converts acyl-carnitine to acyl CoA
4
...
A double bond is formed
between two and three carbons
Hydration: Enoyl CoA hydratase brings about the hydration of the
double bond to form β-hydroxyacyl Co
Oxidation : β –Hydroxy acyl CoA dehydrogenase catalyses the
second oxidation and generates NADH
...
This occurs by a thiolytic
cleavage catalysed by β –ketoacyl CoA thiolase

Oxidation of Palmitoyl CoA
• The summary of β-oxidation of palmitoyl CoA is shown below
Palmitoyl CoA+ 7CoASH + 7FAD + 7NAD+ 7H2O- --> 8Acetyl
CoA+ 7 FADH2 +7NADH+ 7H+
• PalmitoylCoAundergoes7 cycles o f β-oxidation to yield 8
acetyl CoA
...

The β-oxidation occurs in a modified form in peroxisomes
...

• The reducing equivalents from FADH2 are not transferred to
the electron transport chain, but handed over directly to
02
...
The
real cause of SIDS is not known
...
The enzyme defect has a frequency of 1 in
10,000 birth
...

lt is caused by eating unripe ackee fruit which contains an un
usual toxic amino acid, hypoglycin A
...
The only difference is that in the last and final β
–oxidation cycle, a three-carbon fragment is left behind (in
place of 2 carbon unit for saturated fatty acids)
...

• Methyl malonyl CoA racemase converts the methyl
malonyl CoA to L-form
...

• The next enzyme, methyl malonylCoA mutase, is
dependent on vitamin B12 (deoxy adenosyl cobalamin)

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