Biochemistry (Metabolism) by Moses K

1ST EDITION BY: MOSES KAZEVU JR
2 PROPERTY OF MOSES KAZEVU
BIOCHEMISTRY
TO THE STUDENT
This revision guide book is set out in a systematic manner to facilitate easy
understanding and interactive learning. This revision guide can be used as a
great tool for examination preparations as it contains a variety of illustrations
and simplified text to help understand each concept at a greater depth. By
combining information from different authors and sources this revision guide
provides a great simplified overview of the entire topic.
The question may be: “so, how do I use this book?” Well this revision guide
is set out in a way that each topic builds on another; it is therefore advisable
to understand each section prior to the next. This high yield revision set
touches on the important aspects of general basic metabolism. Although this
revision set contains numerous high yield facts that help students in
examinations it should not limit the width and depth of the students’ reading.
After studying through this material it is advisable also to pass through

questions to help consolidate the facts and knowledge you have acquired. If
you still do not get the desired results, NEVER GIVE UP THE SKY IS
THE LIMIT!
TO THE INSTRUCTOR
This book provides a variety of useful information including simplified

illustrations and tables that may be helpful in the teaching process.
MAKING UNAUTHORIZED COPIES OF THIS BOOK IS

PROHIBITED!
LUSAKA APEX MEDICAL UNIVERSITY

BIOCHEMISTRY DEPARTMENT 2016
CONTENTS
OVERVIEW OF METABOLISM ............................................................ 4
BIOENERGETICS .................................................................................. 24
GLYCOLYSIS ........................................................................................ 39
TRICARBOXYLIC ACID CYCLE ....................................................... 75
THE ELECTRON TRANSPORT CHAIN AND OXIDATIVE

PHOSPHORYLATION ........................................................................ 105
GLYCOGEN METABOLISM ............................................................. 123
GLUCONEOGENESIS......................................................................... 146
HEXOSE MONOPHOSPHATE SHUNT ............................................ 165
URONIC ACID PATHWAY ................................................................ 187
AMINO ACID METABOLISM ........................................................... 193
LIPID METABOLISM ......................................................................... 238
NUCLEOTIDE METABOLISM .......................................................... 281
NUCLEIC ACID METABOLISM ....................................................... 322
ACKNOWLEDGMENTS ..................................................................... 404

OVERVIEW OF METABOLISM
OBJECTIVES
1. Metabolic diversity.
2. Anabolic and catabolic processes.
METABOLISM
 Fate of dietary components after digestion and absorption constitute
metabolism- which involves the metabolic pathway taken by
individual molecules, their interrelationships and the mechanism that
regulate the pathway
 In the cell, reactions take place in an organized multistep sequence
called “pathways” such as glycolysis.
 One product of one reaction is the substrate of the subsequent
reaction.
 Different pathways interact to form an integrated and purposeful
network of chemical reactions [Note: Pathways that regenerate a
component are called cycles].
 Metabolism is the entire process of synthesis or breakdown of
compounds in the cell.
 Each metabolic pathway can be either:
1. Anabolic pathway (synthetic): Involved in the synthesis of
compounds [endergonic process i.e. ΔG>0, energy is invested to
make new bonds in reactants] e.g. protein synthesis, synthesis of
fuel reserves of triacylglycerol and glycogen.
2. Catabolic pathways (degradative): breakdown large molecules and
commonly involves oxidation reactions producing reducing
equivalents and mainly via the respiratory chain, ATP. [They are

exergonic i.e. ΔG<0 and energy is released as bonds between

reactants break].
3. Amphibolic pathways: occur at “crossroads” of metabolism linking
anabolic and catabolic pathways e.g. the citric acid cycle.
NORMAL VS ABNORMAL METABOLISM
 Knowing normal metabolism enables understanding of

abnormalities of underlying diseases.
 Normal metabolism adapts to periods of starvation, pregnancy,
lactation and exercise.
 Causes of abnormal metabolism include:
1. Enzyme deficiency
2. Abnormal secretion of hormones
3. Actions of drugs and toxins
 An important example of a metabolic disease is diabetes mellitus
OUTLINE OF CATABOLIC PATHWAYS

 The nature of diet sets the patterns of metabolism.

 The products of digestion need to be broken down.

 Dietary carbohydrates are broken down to simple sugars mainly

glucose.
 Dietary lipids are broken down to fatty acids and glycerol
 Dietary proteins are broken down to amino acids
 All products of digestion are metabolized to a common product
acetyl-CoA which is then oxidized by the citric acid cycle an
amphibolic pathway.
OVERVIEW OF CARBOHYDRATE METABOLISM
 Glucose is the chief in the metabolism of plants, animals and many

micro-organisms
 Glucose is rich in potential energy and therefore it is a good source
of fuel.
 It is the major fuel in tissues
 When glucose is completely oxidized to carbon dioxide and water
the standard free energy=-2840kj/mol
 The cells can store glucose as glycogen to maintain low cytosolic
osmolarity [The concentration of an osmotic solution especially
when measured in osmols or milliosmols per liter of solution]
 Glucose can be released from the intracellular storage polymers
and used to produce ATP either aerobically or anaerobically when
energy demand increases.
 Glucose is also a versatile precursor providing metabolic
intermediates for biosynthetic reactions
 The 3 major fates of glucose in animals are either:
a. Storage as a polysaccharide (glycogen) in skeletal muscle and in
the liver
b. Oxidation to Pyruvate via glycolysis providing ATP and
metabolic intermediates

c. Oxidation via the pentose phosphate (phosphogluconate)

pathway to yield ribose 5-Phosphate for nucleic acid synthesis
and NADPH for reductive biosynthesis processes.
 Triose phosphates give rise to glycerol moiety of triacylglcerols
 Pyruvate and intermediates of the citric acid cycle provide the
carbon skeletons for the synthesis of amino acids and acetyl-CoA
the precursor of fatty acids and cholesterol (and hence of all
steroids synthesized in the body)
 The enzyme reactions that form the metabolic pathways for
monosaccharide carbohydrates include glycolysis, the citric acid
cycle, and oxidative phosphorylation as the main means to produce
the energy molecule ATP.
 Gluconeogenesis and the pentose pathway represent 2 main
anabolic pathways to produce new carbohydrate molecules.
 Gluconeogensis is the process of forming glucose from non-
carbohydrate precursors e.g. lactate, amino acids and glycerol.
OVERVIEW OF CARBOHYDRATE METABOLISM

LIPID METABOLISM
 Lipids are a heterogeneous group

 They are water insoluble (hydrophobic) organic molecules and
because of this they are found compartmentalized i.e. in
membrane-associated lipids or as droplets of triacylglcerol in

adipocytes, or transported in plasma in association with proteins,

as in lipoprotein particles or in albumin.
 Since they are water insoluble they do not affect cytosol osmolarity
and they are unsolvated unlike polysaccharide which are.
 They are a major source of energy.
 Lipids provide a hydrophobic barrier that permits portioning of the
aqueous contents of cells and sub-cellular structures.
 Lipids also have other functions which aid in control of body
homeostasis (prostaglandins and steroid hormones)
 Deficiencies or imbalances of lipid metabolism can lead to
diseases such as atherosclerosis, diabetes and obesity.
 Lipid metabolism includes both synthesis and degradation of fatty
acids and/or more complex lipid molecules.
 The body may choose between synthesis or degradation depending
on the level of food and energy stores available.
 The oxidation of long chain fatty acids to acetyl-CoA is a central
energy yielding pathway in many organisms and tissues such as the
mammalian heart and liver were it produces 80% of the energetic
needs under all physiological circumstances.
 Electrons removed from fatty acids during oxidation pass through
the respiratory chain to drive ATP synthesis.
 Acetyl CoA produced from fatty acids may be completely oxidized
to carbon dioxide in the citric acid cycle providing more energy.
 In the liver acetyl CoA may be converted to ketone bodies-water
soluble fuels exported to the brain and other tissues when glucose
is unavailable.
 Fatty acids are converted into acetyl-CoA through beta-oxidation

 Because of the insolubility of lipids in water ingested

triacylglycerols must be emulsified before they are digested by
water-soluble enzymes in the intestine.
OVERVIEW OF FATTY ACID METABOLISM
 The source of long chain fatty acids is either dietary lipids or de

novo synthesis from acetyl-CoA
 Fatty acids can be oxidized to acetyl-CoA (beta-oxidation) or
esterified with glycerol forming triacylglycerol (fat) as the body’s
main fuel reserve.
 Triacylglycerols (fats) can undergo lipolysis to form fatty acids

 Fatty acids can also be formed by lipogenesis which converts

acetyl-CoA to fatty acids
 Acetyl-CoA from beta-oxidation has different fates which include:
1. Oxidation in the citric acid cycle
2. Synthesis of cholesterol and other steroids
3. In the liver it forms ketone bodies (acetone, acetoacetate and 3-
hydroxybutarate) that are important fuels in prolonged
starvation.
METABOLISM OF PROTEINS
 Unlike fats and carbohydrates, amino acids are not stored by the
body.
 That is, no protein exists whose sole function is to maintain a
supply of amino acids for future use.
 Amino acids are obtained from diet, synthesized de novo or
produced from normal degradation.
 Any amino acid in excess of the biosynthetic needs of the cell are
rapidly degraded
 The first phase of catabolism involves the removal of the ɑ-amino
groups (usually by transamination and subsequent oxidative
deamination), forming ammonia and the corresponding ɑ-keto
acids, the “carbon skeletons” of the amino acids.
 A portion of the free ammonia is excreted in the urine, but most is
used in the synthesis of urea which is quantitatively the most
important route of disposing of nitrogen from the body.
 In the second phase of amino acid catabolism the carbon skeletons
of the ɑ-keto acids are converted to common intermediates of
energy-producing metabolic pathways
 These compounds can be metabolized to carbon dioxide and water,

glucose, fatty acids, or ketone bodies by central pathways of
metabolism.

LEVELS OF METABOLISM
 Metabolism can be studied either at a tissue/organ level or at a
subcellular level
 At tissue and organ level, the nature of substrates entering and
metabolites leaving tissues and organs is defined.
 At subcellular level each cell organelle (e.g. mitochondrion) or
compartment (e.g. cytosol) has specific roles that form part of a
subcellular pattern of metabolic pathways.
CARBOHYDRATE AND PROTEIN METABOLIC PATHWAYS

AT TISSUE/ORGAN LEVEL

 Amino acids and glucose formed from digestion of proteins and

carbohydrates are absorbed and directed to the liver via the hepatic
portal vein.
 The liver regulates blood concentrations of most water-soluble
metabolites e.g. glucose
 Glucose is taken up and the excess is converted to glycogen
(glycogenesis) or to fat (lipogenesis).
 Between meals blood glucose concentrations are maintained in
blood by breakdown of glycogen (glycogenolysis) and non-
carbohydrate metabolites such as lactate (produced in
erythrocytes) and amino acids can be used to synthesize glucose in
a process called gluconeogenesis.
 It is important to maintain adequate blood glucose concentrations
because glucose is the major source of energy in some tissues e.g.
brain and the sole source of energy in some cells e.g. erythrocytes.
 The liver also synthesizes the major plasma proteins e.g. albumin
and deaminates amino acids that are in excess of requirements
forming urea which is transported and excreted by the kidney.
 In skeletal muscle glucose is used as a fuel in muscle contraction
 Under anaerobic conditions lactate and carbon dioxide are
produced.
 Skeletal muscle can synthesize and store glycogen, they can also
synthesize muscle protein from plasma amino acids.
 Proteins in muscles can be used in gluconeogenesis during
starvation.

LIPID METABOLIC PATHWAYS AT TISSUE/ORGAN LEVEL
 Lipids in the diet are mainly triacylglycerol and are hydrolyzed to

monoacylglycerol in the gut, then reesterified in the intestinal
mucosa.
 Here they are packaged with protein and secreted into the
lymphatic system and into the blood stream as chylomicrons.
 Chylomicrons also contain other lipid soluble nutrients e.g.
vitamins.
 Triacylglycerols are not taken up directly into the liver
 They are first metabolized by tissues that have lipoprotein lipases
e.g. adipose tissue and muscle which hydrolyze the triacylglcerols,
releasing fatty acids that are incorporated into tissue lipids or
oxidized as fuel.

 The other major source of long fatty acid is synthesis (lipogenesis)

from acetyl-CoA mainly in adipose tissue and the liver.
 On hydrolysis (lipolysis) free fatty acids are released into the
circulation and are taken up by most tissues except brain and
erythrocytes. They are esterified to acylglycerols or oxidized to
fuels.
 In the liver, triacylglycerl arising from lipogenesis, free fatty acids
and chylomicron remnants are secreted into the circulation as very
low density lipoproteins (VLDL)
 This triacylglycerol undergoes a fate similar to that of
chylomicrons
 Partial oxidation of fatty acids in the liver produces ketone bodies
(ketogenesis)
 Ketone bodies are transported to extra-hepatic tissues where they
act as a fuel source during starvation

METABOLIC PATHWAYS AT SUBCELLULAR LEVEL
 Compartmentation of pathways in separate subcellular

compartments permits integration and regulation of metabolism.
 Not all pathways are of equal importance.
 The mitochondrion acts in the metabolism of carbohydrates, lipids
and amino acids.
 It contains enzymes of the citric acid cycle, beta-oxidation of fatty
acids, ketogensis as well as the respiratory chain and ATP
synthase.
 In the cytosol glycolysis, the pentose pathway and fatty acid
synthesis take place

 In gluconeogenesis substrates such as lactate and Pyruvate which

are formed in the cytosol enter the mitochondrion to yield
oxaloacetate before formation of glucose.
 The members of the endoplasmic reticulum contain the enzyme
system for acylglycerol synthesis and the ribosomes for protein
synthesis.


REGULATION OF METABOLIC REACTIONS

 Regulation is important in controlling the synthesis and
degradation of certain metabolites
 Regulation is achieved by control of one or more key reactions
catalyzed by “regulatory enzymes”
 Substrate concentration and availability of substrate is the primary
regulator of the overall rate of the metabolic pathway.

 Non-reversible reactions are potential sites for regulation
MECHANISM FOR REGULATION (AS SEEN ON DIAGRAM

ABOVE)

1. Alteration of membrane permeability: affects substrate

concentration and availability.
2. Conversion of an inactive to an active enzyme, usually by
phosphorylation and dephosphorylation reactions
 An enzyme that catalyzes the addition of a phosphate group is
called a kinase.
 An enzyme that catalyzes the removal of a phosphate group is
called a phophatase.
 Allosteric activation of upstream enzymes: positive allosteric
feed-forward activation increasing the flow of the reaction
 Allosteric inhibition by product or inhibition of downstream
enzymes (negative allosteric inhibition) stops the subsequent
reactions
3. Alteration of the rate of translation of mRNA at ribosomal level
4. Induction of new mRNA formation
5. Repression of mRNA formation
 Note: (1) and (2) are RAPID while (3) to (5) are SLOWER ways
of regulation
SUMMARY
 The products of digestion provide the tissues with the building
blocks for the biosynthesis of complex molecules and also with the
fuel power for living processes.
 Nearly all products of digestion of carbohydrates, fats and proteins
are metabolized to a common metabolite acetyl-CoA before final
oxidation to CO2 in the citric acid cycle.
 Acetyl-CoA is also used as the precursor for biosynthesis of long-
chain fatty acids: steroids, including cholesterol and ketone bodies.
 Glucose provides carbon skeletons for the glycerol moiety of fats
and several nutritionally non-essential amino acids.
 Water soluble products of digestion are transported directly to the

liver via the hepatic portal vein. The liver regulates the blood
concentrations of glucose and amino acids.
 Pathways are compartmentalized with the cell.
 Glycolysis, glycogenesis, glycogenolysis, the pentose phosphate
pathway and lipogenesis occur in the cytosol.
 The mitochondrion contains the enzymes of the citric acid cycle,
beta-oxidation of fatty acids and oxidative phosphorylation.
 The endoplasmic reticulum also contains the enzymes for many
other processes including protein synthesis, glycerolipid formation
and drug metabolism
 Metabolic pathways are regulated by rapid mechanisms affecting
the activity of existing enzymes e.g. allosteric and covalent
modification (often in response to hormone action) and slow
mechanisms affecting the synthesis of enzymes.
BIOENERGETICS
OBJECTIVES
1. Biochemical importance
2. Gibb’s free energy
3. Laws of thermodynamics
4. Reaction coupling and high energy intermediate compounds
5. Oxidoreductase enzymes
BIOMEDICAL IMPORTANCE
 Bioenergetics is the study of energy changes accompanying
biochemical reactions.

 Biological systems are essentially isothermic and use chemical

energy to power living processes
 How an animal obtains suitable fuel from its food to provide
this energy is basic to the understanding of normal nutrition and
metabolism.
 Death from starvation occurs when available energy reserves
are depleted and certain forms of malnutrition are associated
with energy imbalance (marasmus)
 Thyroid hormones control the rate of energy release (metabolic
rate) and disease results when they malfunction.
 Obesity is caused by excess storage of surplus energy.
FREE ENERGY
 Gibbs change in free energy (ΔG) is that portion of the total energy
change in a system that is available for doing work i.e. the useful
energy also known as chemical potential energy.
LAWS OF THERMODYNAMICS
1ST LAW: The total energy of a system, including its surroundings
remains constant. Energy is neither created nor destroyed but
converted from one form to another.
 This implies that within the total system, energy is neither lost nor
gained during any change.
 Energy can be transferred from one system to another or may be
transformed into another form of energy e.g. heat
2nd LAW: The total entropy must increase if a process is to occur

spontaneously

 Entropy is the measure of disorder or randomness of the system

and it becomes maximum as equilibrium is approached.
 Under conditions of constant temperature and pressure, the

relationship between free energy changes (ΔG) of a reacting
system and the change in entropy (ΔS) is expressed by the
following equation, which combines the 2 laws of thermodynamics
ΔG=ΔH-TΔS
 Where ΔH= enthalpy (heat) change, T= absolute temperature.

 In biochemical reactions, because ΔH is approximately equal to
ΔE, the total change in internal energy of a reaction can be written
as:
ΔG= ΔE-TΔS
 If ΔG is negative the reaction proceeds spontaneously with loss of

energy and thus termed exergonic
 If ΔG is of great magnitude the reaction goes virtually to
completion and is essentially irreversible
 If ΔG is positive, the reaction proceeds only if free energy is
gained, the reactions are non-spontaneous and thus termed
endergonic.
 If the ΔG is great, the system is stable with little to no tendency for
a reaction to occur.
 If ΔG=0 the system is at equilibrium and no net change takes
place.
 When reactants are present in concentrations of 1.0mol/L
 ΔG0 is the standard free energy change
 For biochemical reactions a standard state is defined as having a
pH of 7.0
 The standard free energy change at this standard state is denoted

ΔGo’
 The standard free energy change can be calculated from the
equilibrium constant Keq
ΔGO’= -RT ln(K’eq)
Where R= the gas constant and T is the absolute temperature.

 ΔG may be larger or smaller than ΔGo’ depending on the
concentrations of various reactants including the solvent, various
ions and proteins.
 In a biochemical system, an enzyme only speeds up the attainment
of equilibrium, it never alters the final concentrations of the
reactant at equilibrium
ENDERGONIC PROCESSES PROCEED BY COUPLING
TO EXERGONIC PROCESS
 Vital processes e.g. synthetic reactions, muscular contraction,

nerve impulse conduction and active transport-obtain energy by
chemical linkage, or coupling to oxidative reactions

 The conversion of metabolite A to metabolite B occurs with

release of free energy. It is coupled with another reaction, in which
free energy is required to convert metabolite C to D.
 The terms exergonic and endergonic rather than the normal
chemical terms “exothermic” and “endothermic” are used to
indicate that the process is accompanied by loss or gain,
respectively of free energy in any form, not necessarily as heat.
 In practice an endergonic process cannot exist independently but
must be a component of a coupled exergonic-endergonic system
where the overall net change is exergonic.
 Exergonic reactions are catabolic and endergonic reactions are
anabolic.
 If the reaction above is to go from left to right, then the overall
process must be accompanied by loss of energy as heat.
 One possible mechanism of coupling could be envisaged if a
common obligatory intermediate (I) took part in both reactions i.e.
an enzyme that transfers energy between reactants.
 Some exergonic and endergonic reactions in biologic systems are
coupled in this way.

 This type of system has a built-in mechanism for biologic control

of the rate of oxidative processes since the common obligatory
intermediate allows the rate of utilization of the product or the
synthetic path way (D) to determine by mass action the rate at
which A is oxidized.
 These relationships supply a basis for the concept of respiratory
control, the process that prevents an organism from burning out of
control.
 An alternative method of coupling an exergonic to an endergonic
process is to synthesize a compound of high energy potential in the
exergonic reaction and to incorporate this new compound into the
endergonic reaction, thus affecting transference of free energy
from the exergonic to the endergonic pathway.
 The biological advantage of this medium mechanism is that the
compound of high potential energy, ~ , unlike in the previous
system, need not to be structurally related to A,B,C or D allowing
 In the cell, the principal high-energy intermediate or carrier

compound is adenosine triphosphates (ATP)
 Transfer of free energy from an exergonic to an endergonic
reaction via a high energy intermediate compound

THE INTERMEDIATE VALUE FOR THE FREE

ENERGY OF HYDROLYSIS OF ATP HAS IMPORTANT
BIOENERGETICS
STANDARD FREE ENERGY OF HYDROLYSIS OF SOME

ORGANOPHOSPHATES
COMPOUND ΔGo’
Kj/mol Kcal/mol
Phosphoenolpyruvate -61.9 -14.8
Carbamoyl phosphate -51.4 -12.3

1,3- -49.3 -11.8

Bisphosphoglycerate
(to 3-phospoglycerate)
Creatinine phosphate -43.1 -10.3
ATP--> ADP + Pi -30.5 -7.3
ADP--> AMP + Pi -27.6 -6.6
Pyrophosphate -27.6 -6.6
Glucose 1-phosphate -20.9 -5.0
Fructose 6-phosphate -15.9 -3.8
AMP -14.2 -3.4
Glucose 6-phosphate -13.8 -3.3
Glycerol 3-phosphate -9.2 -2.2
 The value for hydrolysis of the terminal phosphates of ATP divides

the list into 2 groups.
a. Low energy phosphates, exemplified by the ester phosphates
found in the intermediates of glycolysis, have ΔGo’ values
smaller than that of ATP.
b. High energy phosphates: the value is higher than that of ATP.

 The intermediate position of ATP allows it to play an important

role in energy transfer.
 The high energy change on hydrolysis of ATP is due to charge
repulsion of adjacent negatively charged oxygen atoms and to
stabilization of the reaction products especially phosphate as
resonance hybrids.
 ATP is most favored because it has high energy bonds.
 Repelling O- on ATP causes P-O bond to possess high energy.
HIGH ENERGY PHOSPHATES ARE DESIGNATED BY ~P
 The symbol ~P indicates that the group attached to the bond on

transfer to an appropriate acceptor, results in the transfer of the
larger quantity of free energy.
 For this reason, the term group transfer potential is preferred by
some “high-energy bond”
 Thus ATP contains 2 high energy phosphate groups and ADP
contains one, whereas the phosphate group in AMP (adenosine
monophosphate) is of low energy type, since it is a normal ester
link
 High energy bonds are designated by (~P)
 ATP can be able to act as a donor of high energy phosphate to
form other compounds.
 ADP can accept high energy phosphates to form ATP.
 In effect, an ATP/ADP cycle connects those processes that
generate ~P to those processes that utilize ~P, continuously
consuming and regenerating ATP.
 This occurs at a very rapid rate, since the total ATP/ADP pool is
extremely small and sufficient to maintain an active tissue for only
a few seconds.

THE ROLE OF ATP/ADP CYCLE IN TRANSFER OF HIGH

ENERGY PHOSPHATE

ATP ALLOWS THE COUPLING OF THERMODYNAMICALLY

UNFAVORABLE REACTIONS TO FAVORABLE ONES
 The phosphorylation of glucose to glucose 6-phosphate, the first

reaction of glycolysis is highly endergonic and cannot proceed
under physiologic conditions.
i. Glucose + Pi --> Glucose 6-phosphate + H2O (ΔGo’ =+13.8
kj/mol)
 To take place, the reaction must be coupled with another- more

exergonic reaction such as the hydrolysis of the terminal phosphate
of ATP
ii. ATP--> ADP + Pi (ΔGo’=-30.5kj/mol)

 When (i) and (ii) are coupled in a reaction catalyzed by

hexokinase, phosphorylation of glucose readily proceeds in a
highly exergonic reaction that under physiologic conditions is
irreversible. Many “activation” reactions follow this pattern.
ΔGo’= -16.7KJ (overall reaction exergonic)
FREE ENERGY CHANGES CAN BE EXPRESSED IN TERMS

OF REDOX POTENTIALS
 In reactions involving oxidation and reduction, the free energy

change is proportionate to the tendency of reactants to donate or
accept electrons.
 Thus, in addition to expressing free energy change in terms of
ΔGo’, it is possible, in an analogous manner, to express it
numerically as an oxidation-reduction or REDOX potential (Eo’)

 The redox potential of a system (Eo) is usually compared with the

potential of the hydrogen electrode (0.0 volts at pH 0.0), however
for biologic systems, the REDOX potential (E’o) is normally
expressed at pH 7.0 at which pH the electrode potential of the
hydrogen electrode is -0.42 volts.
SYSTEM Eo’
H+/H2 -0.42
NAD+/ NADH -0.32
Lipoate ox/red -0.29
Acetoacetate/3 hydroxybutyrate -0.27
Pyruvate/lactate -0.19
Oxaloacetate/malate -0.17
Fumerate/ succinate +0.03
Cytochrome b, Fe3+/ Fe2+ +0.08
Ubiquinone; Ox/red +0.10
Cytochrome C1 Fe3+/ Fe2+ +0.22
Cytochrome ɑ Fe3+/ Fe2+ +0.29

Oxygen/water +0.82
 Enzymes involved in oxidation and reduction are called

OXIDOREDUCTASE and are classified into 4 groups;
a. Oxidase
b. Dehydrogenase
c. Hydroperoxidase
d. Oxygenase
OXIDASE USE OXYGEN AS A HYDROGEN ACCEPTOR
 Oxidases catalyze the removal of hydrogen from a substrate using

oxygen as a hydrogen acceptor. They form water or hydrogen
peroxide as a reaction product. EXAMPLE: CYTOCHROME
OXIDASE
DEHYDROGENASE CANNOT USE OXYGEN AS A

HYDROGEN ACCEPTOR
 Are substrate specific

 Always carry the prefix of substrate e.g. glyceraldehyde 3-
phosphate dehydrogenase, lactate dehydrogenase
HYDROPEROXIDASES USE H2O2 OR AN ORGANIC

PEROXIDE AS SUBSTRATE.
OXYGENASE CATALYZE THE DIRECT TRANSFER AND

INCORPORATION OF OXYGEN INTO A SUBSTRATE
MOLECULE.

SUMMARY
 Biologic systems use chemical energy to power the living
processes
 These processes follow the thermodynamic laws
 Exergonic reactions take place spontaneously with loss of free
energy (G is negative)
 Endergonic reactions require the gain of free energy (G is
positive) and only occur when coupled to exergonic reactions
 When G is zero the reaction is at equilibrium. Equilibrium
position is not changed by enzymes.
 Four subclasses of enzymes are involved in oxidation reduction
reactions (oxido-reductase) these include: Oxidase, dehydrogenase,
oxygenase and hydroperoxidase.
 ATP acts as the “energy currency” of the cell, transferring free
energy derived from substances of higher energy potential to those
of lower energy potentials.
GLYCOLYSIS
OBJECTIVES

1. Reaction pathways
2. Energy generation
3. Regulation of glycolysis
4. Hormones participating in glycolysis
5. Fate of Pyruvate (aerobic and anaerobic)
CARBOHYDRATE METABOLISM
 Carbohydrates are biomolecules containing the elements carbon,

hydrogen and oxygen in a ratio (CH2O)n where n>2
 Monosaccharides are the simplest units of carbohydrates. They
contain single sugar units only e.g. mannose, glucose, fructose
 Oligosaccharides are large molecules containing 2-10 monomer
subunits.
 An oligosaccharide with 2 monomer subunits is known as a
disaccharide e.g.
 sucrose (glucose + fructose),
 Lactose (glucose + Galactose) and
 Maltose (glucose + glucose).
 Polysaccharides are classes of carbohydrates that contain more
than 10 monomer subunits, they are also known as glycans,
examples include cellulose, starch, and glycogen.
 The uses of carbohydrates include:
a. They are found in DNA/RNA as Deoxyribose/ribose
b. Cell receptors in cell communication
c. They form antigens in the immune system
d. Energy provision
 The preferred energy source for the brain cells is glucose
although in low glucose levels ketone bodies are used but the
sole source of energy in the RBC is glucose.
e. Biosynthesis of other macromolecules through Acetyl-CoA

 Carbohydrates can be classified according to the number of

carbons they have.
 They can also be classified as either ketoses or aldoses depending
on the functional group. Below is a table of examples:
Number of Carbons Aldoses Ketoses
3C (triose) Glyceraldehyde Dihydroxyacetone
4C (tetrose) Erythrose Erythrulose
5C (pentose) Xylose Xylulose
Ribose ribulose
6C (hexose) Glucose Fructose
Mannose
Galactose
 Apart from trioses the other sugar aldoses end in “-ose” and the
ketoses end in “-lose”.
 Glucose is the most abundant carbohydrate, it is not only an
excellent fuel, but is also a remarkably versatile precursor, capable
of supplying a huge array of metabolic intermediates for
biosynthetic reactions. Glucose has a high potential energy.

 Metabolism of glucose can happen:

i) At cellular level
ii) At tissue level
 At cellular level processes like glycolysis (in cytosol), ETC
(electron transport chain on the mitochondrial membrane) and
Krebs cycle (in the matrix of the mitochondria) are involved.
 At tissue and organ level the liver, muscle and red blood cells are
involved. It involves oxidation of lactate produced by R.B.Cs in
the liver to carbon dioxide, production of glycogen (in the liver and
skeletal muscle) and amino acid synthesis and breakdown in the
liver.
 Digested carbohydrates are absorbed in the small intestine and go
to the liver via the hepatic portal vein.
 In metabolism of glucose kinase enzymes (enzymes that add
phosphate groups) are used.
 One kinase enzyme is called a hexokinase. Hexokinase has a high
affinity (low Km) for its substrate, glucose under all normal

conditions and so acts at a constant rate to provide glucose 6-

phosphate to meet the cell’s need.
 Liver and pancreatic B islet cells also contain an isoenzyme of
hexokinase, glucokinase which has a km very much higher than the
normal intracellular concentration of glucose.
 Glucokinase is found mostly in the nucleus of liver cells and
pancreatic B islet cells.
 Hexokinase is inhibited allosterically by its product glucose 6-
phosphate but glucokinase is not.
 Both enzymes are non-specific, they can work on most D-hexose
sugars.
 In the tissues other than the liver and pancreatic B islet cells, the
availability of glucose for glycolysis (or glycogen synthesis in
muscles and lipogenesis in adipose tissue) is controlled by
transport into cells which in turn is regulated by insulin.
 Remember uptake of glucose in the red blood cells is not
controlled by insulin i.e. red blood cells lack the single pass
insulin receptors.
 In the metabolism of carbohydrates reducing agents are used these
include:
 NADPH: Involved in reductive biosynthetic processes such
as synthesis of fatty acids and it is the phosphorylated version
of NAD
 NADH: Participates in oxidative processes e.g. ETC

OVERVIEW OF GLYCOLYSIS
 Glucose usually arises in the blood as a breakdown of higher

polysaccharides or from its synthesis from non-carbohydrate
sources (gluconeogenesis).
 Glucose enters most cells by specific carriers that transport it from
the exterior of the cell into the cytosol
 The enzymes of glycolysis are located in the cytosol
 In glycolysis (from the Greek Glykys, “sweet” or “sugar” and
lysis, “splitting”), a molecule of glucose is degraded in a series of
enzyme-catalyzed reactions to yield 2 molecules of the 3 carbon
compound Pyruvate.
 During sequential reactions of glycolysis some of the free energy
released from glucose is conserved in the form of ATP and NADH.
 The entire process of glycolysis takes place in the cytosol.
 The chemical strategy of glycolysis is:
1. Add phosphoryl groups to the glucose
2. Chemically convert phosphorylated intermediates into

compounds with high phosphate group-transfer potentials
3. Chemically couple the subsequent hydrolysis of reactive
substances to ATP synthesis.
 Glycolysis is a catabolic process where glucose is oxidized to

Pyruvate by 10 enzymatic steps.
 The process is divided into 2 phases:
a. The first 5 steps constitute the preparatory phase in which

energy in the form of ATP is invested (at reaction 1 and reaction
3), whereby the free energy content of the intermediates is
raised and the carbon chains of all the metabolized hexoses are
converted to a common product, glyceraldehyde 3-phosphate.
 Two molecules of ATP are invested in the preparatory phase.
b. The subsequent 5 reactions constitute the payoff phase where 4

ATP molecules (at reaction 7 and 10) and 2 NADH molecules
(at reaction 6) are produced.
 Reactions 5-10 happen twice because 2 moles of
glyceraldehyde 3-phosphate are produced by the end of the
preparatory phase.
 There is a net production of 2 ATP molecules
 Glucose phosphorylation is coupled with hydrolysis of ATP

 Phosphorylation serves to:
 Make glucose ionic thus preventing it from crossing the lipid
bilayer through diffusion out of the cell
 Make the concentration of glucose in the cell low and so
glucose always diffuses down a concentration gradient
 The 10 enzymatic reactions can be controlled at the irreversible
reactions
 Reactions 1,3 and 10 are irreversible
 Reaction 3 is the rate limiting step
 Glycolysis can occur aerobically or anaerobically

 A gross synthesis of 4ATP and a net synthesis of 2 ATP, 2 water
and 2 NADH molecules are produced in glycolysis
 The overall reaction is:
FATE OF NADH
 NAD+ is the primary oxidizing agent of glycolysis
 NADH produced by glycolysis (reaction 6) must be continually re-
oxidized to keep the pathway supplied with NAD+.
 There are 3 common ways that this occurs:
a. Under anaerobic conditions in muscle NAD+ is regenerated
when NADH reduces pyruvate to lactate (homolactic
fermentation)
b. Under anaerobic conditions in yeast, pyruvate is decarboxylated
to yield carbon dioxide and acetaldehyde and the latter is
reduced by NADH to yield NAD+ and ethanol (alcoholic
fermentation)
c. Under aerobic conditions, the mitochondrial oxidation of each
NADH to NAD+ yields 2.5 ATPs.
 Thus in aerobic glycolysis NADH may be thought of as a “high-
energy” compound whereas in anaerobic glycolysis its free energy
of oxidation is dissipated as heat.


INDIVIDUAL REACTIONS OF GLYCOLYSIS

PREPARATORY PHASE
 In the preparatory stage, before glucose molecule can be split the
rather asymmetric glucose molecule is converted to almost
symmetrical fructose 1,6-bisphosphate by donation of 2 PO4
(Phosphate) groups from ATP.
STEP 1
 Glucose is phosphorylated to glucose 6-phosphate (G 6-P)

NOTE:
 This reaction is irreversible
 ATP acts as PO4 donor and it reacts as Mg-ATP complex.
 G 6-P is important for certain pathways e.g. glycolysis,
glycogenesis, glycogenolysis, gluconeogenesis, HMP-shunt,
uronic pathway. Thus it is a committed step in metabolic
pathways.
 The hexokinase enzyme is a relatively non-specific enzyme
contained in all cells that catalyze the phosphorylation of hexoses
such as D-glucose, D-mannose and D-fructose.
 G 6-P is an allosteric inhibitor of hexokinase.
 The liver and pancreatic B islet cells contain glucokinase which
catalyzes the same reaction but which is involved in the
maintenance of blood glucose levels
 Glucokinase is induced by insulin when glucose levels are high
(after a meal)
 Hexokinase is not induced by insulin at physiological state.
 At physiological state glucokinase is not allosterically inhibited by
glucose 6-phosphate
STEP 2
 G 6-P after formation is converted to fructose 6-phosphate by

phosphohexose isomerase (phosphoglucose isomerase or glucose-
6-phosphate isomerase), which involves aldose-ketose
isomerization.
 The enzyme can only act on -anomers
 Step 2 exposes the hydroxyl group at carbon 1; in hexose glucose
the –OH at 1 is sterically hindered.
STEP 3
 Fructose 6-phosphate is phosphorylated to fructose 1,6-

bisphosphate (a symmetrical molecule)
 The phosphorylation is done at carbon 1 by the enzyme
phosphofructokinase-1 (PFK-1)
NOTE:
 The reaction is irreversible
 One ATP is utilized for phosphorylation

 PFK-1 is the key enzyme in glycolysis which regulates breakdown
of glucose. The enzyme is inducible as well as allosteric modified.
 PFK-2 an isoenzyme catalyzes the reaction to form fructose 2,6-
Bisphosphate (F 2,6-BP)
 F 2,6-BP is an allosteric activator of PFK-1; other activators of
PFK-1 include AMP.
 Inhibitors of PFK-1 include ATP and citrate
 At this stage 2 ATP molecules have been used in phosphorylation
STEP 4
 Fructose 1,6-bisphosphate is split into 2 triose-phosphate

molecules i.e. glyceraldehyde 3-phosphate and dihydroxyacetone
phosphate by an aldolase enzyme.
 The reaction is reversible and does not use energy or form ATP.
 Aldolases are tetramers containing 4 subunits
 They have 2 isoenzymes
a. Aldolase A occurs in most tissue
b. Aldolase B occurs in liver and kidney

 The carbons 1, 2, and 3 form Dihydroxyacetone phosphate and the

carbons 4, 5, and 6 form glyceraldehyde 3-phosphate
STEP 5
 Glyceraldehyde 3-phosphate and dihydroxyacetone are

interconverted by the enzyme triose phosphate isomerase.

 At this stage two molecules of glyceraldehyde 3-phosphate have

been formed these molecules then enter the pay-off phase.
PAY OFF PHASE
STEP 6
 The oxidation of glyceraldehyde 3-phosphate to 1,3-

Bisphophoglycerate
 The enzyme glyceraldehyde 3-phosphate dehydrogenase is NAD+
dependent.
 NAD+ is the primary oxidizing agent of glycolysis.
 NADH produced here must be continually be re-oxidized to keep
this pathway supplied with NAD+
 Note: Arsenate can substitute for phosphate forming high unstable
1-As-3-PG which readily hydrolyses thus producing no ATP-one
mechanism of Arsenate toxicity.

STEP 7
 The reaction is a phosphoryl transfer from 1,3-bisphosphoglycerate

to ADP.
 The reaction is catalyzed by phosphoglycerate kinase.
 Since 2 molecules of triose phosphate are formed per molecule of
glucose, 2 molecules of ATP are generated
 This unique example where ATP can be produced at substrate level
without participating in electron transport chain. This type of
reaction where ATP is formed at substrate level is called as
substrate level phosphorylation.

THE RAPOPPORT-LUEBERING SHUNT (1925)
 Maintains a high steady state concentration of 2,3

bisphosphoglycerate (2,3 –BPG) produced by a diversion in
glycolytic pathway.
 In erythrocytes the reaction catalyzed by phosphoglycerate kinase
is bypassed by a process that effectively dissipates as heat, the free
energy associated with the high-energy phosphate of 1,3-BPG
 Bisphosphoglycerate mutase catalyzes the conversion of 1,3-BPG
to 2,3-BPG which is converted to 3-phosphoglycerate by 2,3
Bisphosphoglycerate phosphatase.
 The react yields no ATP, however it does serve to provide 2,3
Bisphosphoglycerate (2,3- BPG). It binds and cross-links the beta
chains of hemoglobin this causes a decrease in hemoglobin affinity
for oxygen and so making oxygen more readily available to
tissues.

 Mutase: an enzyme that shifts a group of a substrate from one

carbon to another. E.g. Bisphosphoglycerate mutase
STEP 8
 Conversion of 3-phosphoglycerate to 2-phosphoglycerate

 The reaction is catalyzed by phosphoglycerate mutase.
STEP 9
 Dehydration of 2-Phosphoglycerate to phosphoenolpyruvate (PEP)

 2 molecules of water are produced

 Fluoride ions inhibit enolase enzyme
STEP 10
 Transfer of a phosphoryl group from PEP to ADP
 Pyruvate kinase is more active in a fed state than a fasting state.
KETO-ENOL FORMS OF PYRUVATE

 Keto form is the predominant form as opposed to the enol form.


 A <---> B -->C
 If the rate of conversion from B to C is faster than rate of
conversion of A to B then A<--->B will mimic a forward reaction
thus reaction 7 appears irreversible.
REGULATION OF GLYCOLYSIS
 The reactions catalyzed by hexokinase (and glucokinase),
phosphofructokinase and Pyruvate kinase are the major sites of
regulation of glycolysis.
 The rate limiting reaction is reaction number 3.

ENERGETICS OF GLYCOLYSIS
THE ELEGENT EVIDENCE OF REGULATION
 Standard state values are scattered: + and –

 ΔG in cells is revealing
 Most values near zero
 3 out of 10 reactions have large, negative ΔG
 Large negative ΔG reactions are sites of regulation
 Glucose-6 phosphate allosterically inhibits hexokinase. (this is
seen when energy reserves and sources are depleted and the body
cannot sustain any further carbohydrate degradation)
REGULATION OF HEXOKINASE
 Hexokinase is found in most tissue and is geared to provide

glucose-6-phosphate for ATP production even when blood glucose
is low
 Hexokinase has a low Km (michaelis constant) for glucose(Vmax)
even at fasting blood glucose levels (about 5mM)
 Hexokinase is inhibited by its product glucose 6-phosphate
 Therefore, it is most active when glucose 6-phosphate is being
rapidly used.
 Hexokinase is not induced by insulin at physiological
concentrations
REGULATION OF GLUCOKINASE
 Glucokinase is found in the liver and pancreatic B islet cells.

 It is found in the nucleus of these cells.
 It functions at a significant rate only after a meal (when blood
glucose is high)
 When blood glucose levels are high the enzyme is transported to

the cytosol for the breakdown of glucose and as levels return back
to normal it is translocated back to the nucleus.
 Glucokinase has a high Km for glucose (about 6mM). Therefore, it
is very active after a meal, when glucose levels in the hepatic
portal vein are high and it is inactive during the post-absorptive
state or fasting when glucose levels are low.
 Glucokinase is induced when insulin levels are high.
 Glucokinase is not inhibited by its product glucose-6-phosphate at
physiological concentrations.
COMPARING GLUCOKINASE AND HEXOKINASE
GLUCOKINASE HEXOKINASE
Found in nucleus but is Found in cytosol

translocated to cytosol when
glucose levels are high
High Km (low affinity) Low Km (high affinity)
Is not allosterically inhibited by Is allosterically inhibited by

glucose-6-phosphate glucose-6-phosphate
Insulin induced Not insulin induced
 NOTE: both enzymes work on the same hexoses and glucokinase

is not just limited to glucose. They both work only on D-isomers
and not L.
REGULATION OF PFK-1

 Phosphofructokinase 1 is an allosteric enzyme regulated by several

factors
 Its function is at rapid in the liver when blood glucose is high or in
cells such as muscle when there is need for ATP
 PFK-1 is activated by fructose 2,6- bisphosphate an important
regulatory mechanism in the liver
 After a meal fructose-2,6-bisphosphate is formed from fructose
6-phosphate by PFK-2
 Fructose-2,6-bisphosphate activates PFK-1 and glycolysis is
stimulated. The liver using glycolysis to produce fatty acids for
triacylglycerol synthesis (via Acetyl-CoA)
 In fasting state (when glucagon is elevated) PFK-2 is
phosphorylated by protein kinase A which is activated by the
cAMP cascade.
 Phosphorylated PFK-2 converts fructose-2,6-bisphosphate to
fructose-6-phosphate, fructose-2,6-bisphosphate levels fall and
PFK-1 is less active
 In the fed state insulin causes phosphatases to be stimulated. A
phosphatase dephosphorylates PFK-2 causing it to become more
active in forming fructose-2,6-bisphosphate from fructose 6-
phosphate. Fructose-2,6-bisphosphate levels rise and PFK-1 is
more active.
 Thus PFK-2 is a bi-functional enzyme it acts as a kinase (in the
fed state when it is dephosphorylated) and as a phosphatase (in
the fasting state when it is phosphorylated)
 PFK-1 is activated by AMP in the muscle

 In muscle during exercise, AMP levels are high and ATP levels
are low
 Glycolysis is promoted by more active PFK-1 and ATP is
generated
 PFK-1 is inhibited by ATP and citrate
 In the muscle when ATP is high the cell does not need ATP and
glycolysis is inhibited.
 High levels of citrate indicate that adequate amounts of
substrates are entering the tricarboxylic acid cycle (TCA),
therefore glycolysis slows down

CLINICAL APPLICATION: Phosphofructokinase deficiency (a form of

glycogen storage disease [type 7] in which glycogen accumulates in
muscles) results in inefficient use of glucose stores by RBCs and
muscle. Patients experience hemolytic anemia as well as muscle
cramping
REGULATION OF PYRUVATE KINASE
 Pyruvate kinase is activated by fructose-1,6-bisphosphate and

inhibited by alanine, ATP and by phosphorylation in the liver
during fasting when glucagon levels are high
 Glucagon via cAMP activates protein kinase A which
phosphorylates and inactivates pyruvate kinase in the liver (but not
muscle)
 The inhibition of pyruvate kinase promotes gluconeogenesis in the
liver.
 Pyruvate kinase is activated in the fed state. Insulin stimulates
phosphatases that dephosphorylate and active pyruvate kinase in
the liver.
CLINICAL APPLICATION: Deficiency of pyruvate kinase causes

decreased production of ATP from glycolysis. RBCs have insufficient
ATP for their membrane pumps and a hemolytic anemia results.


SOME EFFECTORS OF THE REGULATORY ENZYMES OF

GLYCOLYSIS
ENZYME INIHBITORS ACTIVATORS
Hexokinase Glucose 6-phosphate
Phosphofructokinase- ATP, citrate ADP, AMP, fructose

1 2,6 bisphosphate,
fructose 6-phosphate
Pyruvate kinase ATP Fructose 1,6

bisphosphate
HORMONES INFLUENCING GLYCOLYSIS
 Insulin and glucagon are two important enzymes that influence

glycolysis.
 These enzymes modulate glycolysis during the state in which the
body can be found i.e. fed state and fasting state.
 Normal blood glucose is about 100mg/dl
 After a meal (fed state) rich in carbohydrates the blood glucose
levels are higher than normal
 In between meals (during fasting) the blood glucose levels are
lower than normal
INSULIN

 Insulin is released from the pancreatic B islet cells; it functions to

lower the blood glucose level after a meal rich in carbohydrates
 Cells of the body (except red blood cells) contain insulin receptors.
These receptors are single pass transmembrane protein.
 When insulin binds to its receptor, 3 genes in the nucleus are
stimulated to produce mRNA (through transcription) which is
translated into the enzymes and membrane protein which include:
a. Glucokinase and hexokinase
b. Pyruvate kinase
c. Glucose transporter
 Furthermore, insulin activates protein phosphatases which
dephosphorylates cytosolic enzyme:
 Dephosphorylating PFK-2 activates its kinase activity
leading to production of fructose 2,6- bisphosphate from
fructose 6-phosphate. F-2,6-BP is a powerful activator of
PFK-1 thus stimulating glycolysis
 Dephosphorylating pyruvate kinase activates the enzyme and
this promotes glycolysis
 This counteracts the effects of glucagon, cAMP cascade and
protein kinase A.
GLUCAGON
 Glucagon is released from pancreatic alpha islet cells; it functions

to raise the blood glucose level during fasting state. (remember
GLUCAGON= OH NO “GLUCOSE” IS “GONE”)
 Cells of the body contain glucagon receptors which are 7 pass
transmembrane proteins associated with G-stimulatory proteins.
 When glucagon binds to its receptor, G-stimulatory proteins are
activated.

 Activate G-stimulatory proteins activate the enzyme adenylyl

cyclase (adenylate cyclase) which converts ATP to cAMP
 cAMP activates protein kinase A which phosphorylates cytosolic
enzymes
 Phosphorylation of PFK-2 activates its (phosphatase
activity), this leads to the breakdown of F-2,6BP to F-6-P. the
concentration of F-2,6BP drops and its effect on PFK-1 is
inhibited thus stopping glycolysis (remember reaction 3 is the
rate limiting step)
 Phosphorylation of pyruvate kinase inactivates the enzyme
and this further slows the breakdown of glucose to pyruvate
 Glucagon and insulin are antagonist hormone because their

activities bring about opposite effect.
ENERGETICS OF GLYCOLYSIS
 2 ATP molecules are used up in the preparatory phase (reaction 1
and 3) to prime glucose and raise its energy level.
 In the payoff phase 4 ATP molecules are produces (reaction 7 and
reaction 10) through substrate level phosphorylation. This implies
that a net of 2ATP is gained from one cycle of glycolysis with one
mole of glucose.
 The 2 reducing equivalents (2NADH + 2H+) produced at reaction 6
are also considered as high energy compounds during aerobic
glycolysis because through the electron transport chain 2.5ATP
molecules are produced from 1 reduced equivalent

 5 ATP molecules are thus produced from the 2 reducing

equivalents in the electron transport chain
 A total of 7 ATP molecules is therefore produced during aerobic
respiration from glycolysis
NOTE: 1NADH= 2.5 ATP, 1QH2 (FADH2) = 1.5
FATES OF PYRUVATE
1. Conversion to lactate (lactic acid fermentation)
 Pyruvate can be reduced in the cytosol by NADH, forming
lactate and regenerating NAD+
 NADH which is produced by glycolysis must be reconverted

to NAD+ so that carbons of glucose can continue to flow
through glycolysis
 Lactate dehydrogenase converts pyruvate to lactate
 This happens in anaerobic conditions in the RBC and the
muscle during exercise.
 Lactate is used by the liver for gluconeogenesis or by tissues
such as the heart and kidney where it is converted to pyruvate
and oxidized for energy.
 The lactate dehydrogenase reaction is reversible
2. Conversion to acetyl CoA

 Pyruvate can enter mitochondria

 There it can be converted by pyruvate dehydrogenase
complex to acetyl CoA which can enter the TCA cycle
3. Conversion to alanine
 Pyruvate can be transaminated to form the amino acid alanine
 The enzyme involved is alanine aminotransferase which
requires pyridoxal phosphate as a co-factor

4. Conversion to Ethanol in yeast and other micro-organisms (ethanol

fermentation)
 Pyruvate decarboxylase catalyzes the decarboxylation of
pyruvate to acetaldehyde. This reaction requires Thiamine
pyrophosphate (TPP) as a co-factors as well as magnesium
 Acetaldehyde is converted to ethanol by the enzyme alcohol
dehydrogenase which is NADH dependent
 This regenerate NAD+ to return to glycolysis.
 This reaction does not take place in humans but in yeast and
other micro-organisms

SUMMARY
 Glycolysis is the cytosolic pathway of all mammalian cells for the
metabolism of glucose to pyruvate.
 It is a catabolic pathway involving 10 enzyme catalyzed reactions:
the first 5 being preparatory reactions requiring 2 ATP molecules
while producing 2 molecules of glyceraldehyde-3-phosphate and
the subsequent 5 pay-off reactions producing 2 ATP molecules and
2 molecules of pyruvate.
 In erythrocytes the first site in glycolysis for ATP production may
be bypassed producing 2, 3-bisphosphoglycerate which is
important in decreasing the affinity of hemoglobin for oxygen.
 The pyruvate produced has various fate which include conversion

to lactate (in RBC and muscle) under anaerobic conditions,
alanine, Acetyl-CoA (that enters the TCA cycle), and ethanol (in
yeast and some micro-organisms).
 Glycolysis is regulated by 3 enzymes catalyzing non-equilibrium
reactions: hexokinase/glucokinase, phosphofructokinase-1 and
pyruvate kinase
 Conditions that involve an inability to metabolized pyruvate
frequently lead to lactic acidosis.
TRICARBOXYLIC ACID CYCLE

OBJECTIVES
1. Significance
2. Link reaction
3. Tricarboxylic acid cycle reactions
4. Catabolic role
5. Anabolic role
6. Regulation of the tricarboxylic
SIGNIFICANCE AND COMPARTMENTALIZATION

 For organism that are eukaryotic and some bacteria which live
under aerobic conditions and oxidize their organic fuel to carbon
dioxide and water, glycolysis is but the first stage in the complete
oxidation of glucose.
 Rather than being reduced to lactate, ethanol or some other
fermentation product, the Pyruvate produced by glycolysis is
further oxidized to water and carbon dioxide.
 The aerobic phase of catabolism is called respiration.
 The process is more specifically termed cellular respiration

 It is divided into 3 major stages:
a. Organic fuel molecules- glucose, fatty acids and some amino
acids- are oxidized to yield two-carbon fragments in the form of
the acetyl-coenzyme A (acetyl-CoA)
b. The acetyl groups are fed into the citric acid which
enzymatically oxidizes them to carbon dioxide, the energy
released is conserved in the reduced carriers NADH and FADH2
c. The reduced co-enzymes are themselves oxidized giving up
proton (H+) and electrons. The electrons are transferred to
oxygen- the final electron acceptor via a chain of electron-
carrying molecules known as respiratory chain. In course of
electron transfer, the large amount of energy released in the
form of ATP, by a process called oxidative phosphorylation.
 The carriers (FADH2 and NADH) produce 28 ATP molecules
from the electron transport chain and oxidative
phosphorylation.
STAGES OF CELLULAR RESPIRATION


MITOCHONDRION: THE POWER HOUSE OF THE CELL
 The mitochondrion is the site of aerobic respiration in cells. The

krebs cycle and the ETC take place in the mitochondrion.
 The mitochondrion is a double membrane bound organelle.
 The outer membrane is selectively permeably whereas the inner
mitochondrial membrane is impermeably to metabolites without
transporters i.e. NADH and FADH2 are impermeable but Pyruvate
is permeable
 The invaginations in the inner mitochondrial membrane are called

cristae these increase surface area.
 It also possess an intermembrane space rich in hydrogen ions
 All the enzymes required for the TCA cycle are found in the
mitochondrial matrix.
COMPARTMENTALIZATION
 Kreb’s cycle and beta oxidation- matrix

 ETC- inner membrane
BIOMEDICAL IMPORTANCE
 Final common pathway for carbohydrates, proteins, fats through

formation of 2-carbon unit acetyl-CoA
 Acetyl-CoA is oxidized to carbon dioxide and water giving out
energy-catabolic role
 Intermediates of TCA cycle plays a major role in synthesis also
like heme formation (succinyl-CoA), formation of non-essential
amino acids, FA synthesis, cholesterol and steroid synthesis-
Anabolic role.
LINK REACTION: CONVERSION OF PYRUVATE TO

ACETYL-CoA

 In the presence of oxygen, Pyruvate undergoes oxidative

decarboxylation to from a 2C “acetyl-CoA”. Pyruvate formed in
cytosol is transported to mitochondrion by a ‘transport’ protein
 Since the overall reaction involves both oxidation and loss of
carbon dioxide (decarboxylation), it is termed oxidative
decarboxylation.
 The mechanism of the reaction is one of the most complex
involved in metabolism of carbohydrates.
 The reaction is catalysed by a multi-enzyme complex called
Pyruvate dehydrogenase complex which can exist both as
“inactive” or “active form”
 The enzyme consists of:
 E1- Pyruvate dehydrogenase
 E2- Dihydrolipoyl transacetylase
 E3- Dihydrolipoyl dehydrogenase
 Pyruvate dehydrogenase uses Thiamine pyrophosphate (TPP) as a
co-factor
 Dihydrolipoyl transacetylase: lipoic acid bound, CoA as substarte

 Dihydrolipoyl dehydrogenase: uses FAD a co-factor bound, NAD+

as substrate.
ADVANTAGES OF A MULTICOMPLEX ENZYME
1. Minimum side reactions

2. Coordinated control
3. Higher rate of reaction: Because product of one enzyme acts as a
substrate of the other, and is available for the active site of the next
enzyme without much diffusion.
MOLECULAR STRUCTURE OF CO-ENZYME A (CoA)
REGULATION OF PDC ACTIVITY BY PHOSPHORYLATION
 Pyruvate dehydrogenase complex exists in two forms

1. Phosphorylated (inactive) form
2. Dephosphorylated (active) form

 A kinase associated with the multienzyme complex phosphorylates

the pyruvate decarboxylase subunit inactivating the pyruvate
dehydrogenase complex.
 Products of the pyruvate dehydrogenase reaction acetyl-CoA
and NADH activate the kinase
 Substrates CoA and NAD+ inactivate the kinase
 The kinase is also inactivated by adenosine diphosphate (ADP)
 A phosphatase dephosphorylates and activates the pyruvate
dehydrogenase
 When the concentration of substrates is high the dehydrogenase is
active and the pyruvate is converted to acetyl-CoA
 When the concentration of products is high the dehydrogenase is
relatively inactive

 NADH and ATP also directly regulate the pyruvate dehydrogenase

complex
 ATP and NADH inhibit the enzyme complex
SUMMARY OF CONVERSION OF PYRUVATE TO ACETYL-

CoA
 The overall reaction can be represented as follows:

1. ‘Acetyl’ moiety of Pyruvate is transferred to CoA-SH
2. Carbon of COO- group is liberated as carbon dioxide
(decarboxylation)
3. Remaining 2H atoms. One from –COOH group of pyruvic acid

and another from CoA-SH (-SH group) are transferred to NAD+ by
way of a mechanism involving lipoic acid and FAD
 E1 catalyzes first the decarboxylation of Pyruvate, producing
hydroxyethyl-TPP and then the oxidation of hydroxyethyl group to
an acetyl group. The electrons from this oxidation reduce disulfide
of lipoate bound to E2 and the acetyl group is transferred into the
thioester linkage with one –SH group of reducing lipoate
 E2 catalyzes the transfer of the acetyl group to Co-Enzyme A
forming acetyl-CoA
o Arsenate has the ability to inhibit this enzyme subunit to a
certain extent
 E3 catalyzes the generation of the disulfide (oxidized) form of
lipoate, electrons pass first to FAD and then to NAD+

DETAILS OF REACTIONS
 Pyruvate is decarboxylated to a hydroxyethyl derivative of thiazole

ring of enzyme bound thiamine pyrophosphate (TPP)
 Which in turn, reacts with oxidized lipoamide to form acetyl
lipoamide
 In the presence of dihydrolipoyl transacetylase, acetyl lipoamide
reacts with CoA-SH to form “acetyl-CoA” and reduced lipoamide
 The latter is reoxidized by a flavoprotein (FP) in the presence of
dihydrolipoyl dehydrogenase forming FADH2
 Finally, the reduced FADH2 is oxidized by NAD+ which in turn
transfers reducing equivalents to the electron transport chain.
 Since the link reaction happens twice for 2 molecules of pyruvate,
2(NADH+ H+ ) are produced and this results in the production of

5ATP molecules from the respiratory chain and oxidative

phosphorylation (since 1NADH+= 2.5ATP)
 Clinical Application: Congenital Lactic Acidosis
 In this X-linked dominant pyruvate dehydrogenase
deficiency disease, the pyruvate dehydrogenase complex is
not functioning and so pyruvate is converted to lactate
 The implications of this is that
o Not a lot of energy is produced from TCA and
oxidative phosphorylation
o Lactic acid accumulates leading to lactic acidosis
 Tissues that uses a lot of energy e.g. central nervous system
are most affected while tissues that use little energy from
aerobic respiration e.g. cells in the cornea are least affected
 This disease can be moderate, mild, very severe
o Very severe cases there is intrauterine death
o In mild cases the person has CNS defects and dies in
infancy
o In milder cases when the person ingests high
carbohydrates CNS problems manifest and a person
cannot co-ordinate their movement (Episodic Ataxia), this
can be managed by a ketogenic diet (rich in fats and poor
in carbohydrates) as an alternative source of fuel
THE TRICARBOXYLIC ACID CYCLE REACTIONS

 All the reactions take place in the mitochondrial matrix where all
the enzymes are found
 There are a total of 8 reactions in the cycle.
 This pathway is termed a cycle because the reactant (oxaloacetate)
is regenerate as citrate breaks down through the series of reactions.

 Five reactions of the citric acid cycle are reversible (reactions

2,5,6,7 and 8)
 Three reactions of the citric acid cycle are irreversible (reactions 1,
3 and 4)
REACTION 1: FORMATION OF CITRATE
 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.
 Citroyl-CoA is a transient intermediate formed on the active site of
the enzyme (citrate synthase), which undergoes hydrolysis to free
CoA and citrate, which are released from the active site
 The hydrolysis of this high-energy thioester intermediate makes the
forward reaction highly exergonic
 The CoA liberated in this reaction is recycled to participate in the
oxidative decarboxylation of another molecule of Pyruvate by the
PDH complex.
 Citrate (the product) is an inhibitor of this reaction.

REACTION 2: FORMATION OF ISOCITRATE VIA CIS-

ACONITATE
 Citrate is isomerize to isocitrate via an enzyme bound intermediate

called cis-aconitate
 The enzyme called aconitase catalyses 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.
 Aconitase (aconitate hydratase) can promote the reversible addition
of water to the double bond of enzyme-bound cis-aconitate in 2
diferent ways, one leading to citrate and the other leading to
isocitrate

 Although the equilibrium mixture at pH 7.4 and 25oC contains less

than 10% isocitrate, in the cell the reaction is pulled to the right
because isocitrate is rapidly consumed in the next step of the cycle,
lowering its steady-state concentration.
 Aconitase contains an iron-sulfur center which acts both in the
binding of the substrate at the active site and the catalytic
additional or removal of water
 In iron-depleted cells, aconitase loses its iron-sulfur center and
acquires a new role in the regulation of iron homeostasis.
 Aconitase is one of the many enzymes known to “moonlight” in a
second role.
REACTION 3: OXIDATION OF ISOCITRATE TO ɑ-

KETOGLUTARATE AND CARBON DIOXIDE

 In the next step, isocitrate dehydrogenase catalyzes oxidative

decarboxylation of isocitrate to form ɑ-ketoglutarate.
 There are 2 forms of isocitrate dehydrogenase in the cells, one
requiring NAD+ as electron acceptors and the other requiring
NADP+
 The overall reactions are otherwise identical
 In eukaryotic cells, the NAD+-dependent enzyme occurs in the
mitochondrial matrix and serves to catalyze the TCA cycle
reaction 3
 In the cytosol it catalyses the generation of NADPH, which is
essential for reductive anabolic reactions
REACTION 4: OXIDATION OF ɑ-ketoglutarate to succinyl-CoA

and carbon dioxide
 The next step is another oxidative decarboxylation in which ɑ-

ketoglutarate is converted to succinyl-CoA and carbon dioxide by
the action of the ɑ-ketoglutarate dehydrogenase complex, NAD+
serves as electron acceptors and CoA as the carrier of the succinyl
group.

 The energy of oxidation of ɑ-ketoglutarate is conserved in the

formation of the thioester bond of succinyl-CoA
 The ɑ-ketoglutarate dehydrogenase complex enzyme is a complex
of different enzymatic activities similar to Pyruvate dehydrogenase
complex with E1, E2 and E3
o Although the E1 components of the 2 complexes are
structurally similar, their amino acid sequences differ and
they bind to different substances i.e. E1 of PDC binds to
pyruvate while E1 of alpha ketoglutarate dehydrogenase
binds to alpha-ketoglutarate.
o The E2 complexes are also very similar both having
covalently bound lipoic acid
o The E3 subunits are identical in the two enzyme complexes
 The enzyme requires the same five co-factors as the pyruvate
dehydrogenase complex: uncombined enzyme CoA (CoA-SH),
thiamine pyrophosphate (TPP), lipoic acid, FAD and NAD+
REACTION 5: SUBSTRATE LEVEL PHOSPHORYLATION

 Conversion of succinyl-CoA to succinate

 Succinyl-CoA, like acetyl-CoA, has a thioester bond with a
strongly negative standard free energy of hydrolysis.
 In the next step of the citric acid cycle, energy released in the
breakage of this bond is used to drive the synthesis of a
phosphandhydride bond either GTP or ATP with a net ΔGo’ of only
-2.9kj/mol
 Succinate is formed in the process
 The enzyme that catalyzes this reversible reaction is called
succinyl-CoA synthetase or succinic thiokinase
 Because this does not involve the electron transport chain it is not
termed oxidative phosphorylation.
REACTION 6: OXIDATION OF SUCCINATE TO FUMARATE
 The succinate formed from succinyl-CoA is oxidized to fumerate

by the flavoprotein succinate dehydrogenase
 It requires an FAD+ cofactor

REACTION 7: HYDRATION OF FUMARATE TO MALATE
 The reversible hydration of fumerate to L-malate is catalyzed by

fumerase (formally, fumarate hydratase)

REACTION 8: OXIDATION MALATE TO OXALOACETATE
 In the last reaction of the citric acid cycle, NAD-linked L-malate

dehydrogenase catalyzes the oxidation of L-malate to oxaloacetate
 The equilibrium of this reaction lies far to the left under standard
thermodynamic conditions, but in intact cells oxaloacetate is
continually removed by the highly exergonic citrate synthase
reaction (step 1), this keeps the concentration of oxaloacetate in the
cell extremely low, pulling the malate dehydrogenase reaction
toward the formation of oxaloacetate.

SUMMARY OF THE TCA CYCLE

REACTIONS OF TCA CYCLE
1. Citrate synthase (irreversible)

2. Aconitase
3. Iso-citrate dehydrogenase (irreversible)
4. ɑ-ketoglutarate dehydrogenase (irreversible)
5. Succinyl-Coenyme A synthetase
6. Succinate dehydrogenase
7. Fumerase
8. Malate dehydrogenase
TOTAL ENERGY PER GLUCOSE

CYTOSOL
 Glycolysis: 2NADH + 2 ATP

 This results in a total of 7ATP molecule
MITOCHONDRION
 Pyruvate dehydrogenase: 2NADH

 Krebs cycle: 6NADH, 2 FADH2, 2 GTP
IN MITOCHONDRION
 Each NADH makes 2.5ATP

 Each FADH2 makes 1.5 ATP
 GTP makes ATP
So…
 From TCA cycle and Pyruvate dehydronase

 8 NADH X 2.5 ATP/NADH= 20 ATP
 2 FADH2 X 1.5 ATP/FADH2= 3 ATP
 2 GTP X 1 ATP/ GTP= 2 ATP
 TOTAL IN MITOCHONDRION= 25 ATP
 Complete oxidation of glucose= 25ATP + 7ATP = 32ATP
THE AMPHIBILIC NATURE OF THE CITRIC ACID

CYCLE
 In aerobic organisms, the citric acid cycle is an amphibolic
pathway, one that serves in both catabolic and anabolic processes.

 Besides its role in the oxidative catabolism of carbohydrates, fatty

acids and amino acids, the cycle provides precursors for many
biosynthetic reactions through reactions that served the same
purpose in anaerobic ancestors.
SYNTHESIS OF TCA INTERMEDIATES (ANAPLEROTIC

REACTIONS)
 Anaplerotic reactions replenish intermediates of the TCA cycle as

they are removed for the synthesis of glucose, fatty acids, amino
acids or other compounds.
A. Oxaloacetate
 A key anaplerotic reaction is catalyzed by pyruvate
carboxylase which carboxylates pyruvate forming
oxaloacetate.
 Pyruvate carboxylase requires biotin a cofactor that is
commonly involved in carbon dioxide fixation
 Pyruvate carboxylase found in the brain, liver and adipose
tissue (but not muscle) is activated by acetyl-CoA
B. Amino acids anaplerotic reactions
 Glutamate is converted to -ketoglutarate. Amino acids that
form glutamate include glutamine, proline, arginine and
histidine.
 Aspartate is transaminated to form oxaloacetate. Asparagine
can produce aspartate.
 Valine, isoleucine, methionine and threonine produce
propionyl-CoA which is converted to methylmalonyl-CoA,
which is converted to succinyl-CoA an intermediate of the
TCA.
 Phenylalanine, tyrosine and aspartate form fumerate.

SYNTHESIS OF GLUCOSE
 Synthesis of glucose occurs through the pathway known as

gluconeogenesis and involves TCA intermediates
 As glucose is synthesized, malate or oxaloacetate is removed from
the TCA cycle and replenished by anaplerotic reactions
 Pyruvate, produced from lactate or alanine is converted by
pyruvate carboxylase to oxaloacetate which forms malate.
 Various amino acids that supply carbon for gluconeogenesis
are converted to intermediates of the TCA cycle which forms
malate and thus glucose.
SYNTHESIS OF AMINO ACIDS
 Synthesis of amino acids from glucose involves TCA intermediates

 Glucose is converted into pyruvate which forms oxaloacetate,
which by transamination forms aspartate and subsequently
asparagine
 Glucose is converted to pyruvate which forms both oxaloacetate
and acetyl-CoA which condense forming citrate. Citrate forms
isocitrate and then -ketoglutarate, producing glutamate,
glutamine, proline and arginine.
SYNTHESIS OF OTHER COMPOUNDS
 Through aspartate and glutamate, the carbons of oxaloacetate and

ɑ-ketoglutarate are then used to build other amino acids, as well as
purines and pyrimidine nucleotides.
 Succinyl-CoA is a central intermediate in the synthesis of the
porphyrine ring of heme groups, which serve as oxygen carriers (in
haemoglobin and myoglobin) and electron carriers (in
cytochromes)
PARTICIPATION OF TCA CYCLE IN FATTY ACID

SYNTHESIS FROM GLUCOSE
 From glucose, pyruvate is produced and converted to oxaloacetate

(by pyruvate carboxylase) and to acetyl-CoA (by PDH)
 Oxaloacetate and acetyl-CoA condense forming citrate which is
used for fatty acid synthesis

REGULATION OF TCA CYCLE

 Regulation of the Krebs’ cycle is not under hormonal control
(directly) but it is controlled by the energy needs of the cell.
 Intracellular increase of calcium signifies that the cell is under
metabolic activity e.g. in myocytes and so Krebs’ cycle enzymes
are sensitive to (allosterically activated by) calcium
 Regulation of enzymes also depends on the energy needs of the
cell
 The regulatory enzymes of the TCA cycle are also sensitive
to ADP + AMP and ATP
o High levels ADP and AMP have stimulatory effects on
the enzymes of the TCA cycle (they signify that the cell
needs energy)
o High levels of ATP have inhibitory effects on the

enzymes (this signifies that the cell is rich in energy)
o A high ATP/ADP ratio inhibits the TCA cycle, a low
ATP/ADP ratio stimulates the TCA
 The reducing equivalents also participate in regulation

 FAD and NAD+ are stimulatory substances for Krebs’
cycle regulatory enzymes
 FADH2 and NADH are inhibitory substance for Krebs
cycle regulatory enzymes
 A high ratio of NADH/NAD+ inhibits the TCA cycle
and a low ratio of NADH/NAD+ stimulates the TCA
cycle
REACTION CONTROLLING ENZYMES
1. Citrate synthase-reaction 1
2. Isocitrate dehydrogenase- reaction 3
3. ɑ-ketoglutarate dehydrogenase- reaction 4
REGULATION OF ACTIVITY BY:
1. Substrate availability
2. Product inhibition
3. Allosteric inhibition or activation by other intermediates

 The overall rate of the citric acid cycle is controlled by the rate of
conversion of pyruvate to acetyl-CoA and by the flux through
citrate synthase, isocitrate dehydrogenase, and ɑ-ketoglutarate
dehydrogenase. These fluxes are largely determined by the
concentrations of substrates and products: the end products ATP
and NADH are inhibitory, and the substrates NAD+ and ADP are
stimulatory.
 The production of Acetyl-CoA for the citric acid cycle by the PDH
complex is inhibited allosterically by metabolites that signal a
sufficiency of metabolic energy (ATP, acetyl-CoA, NADH, and
fatty acids) and stimulated by metabolites that indicate a reduced
energy supply (AMP, NAD+, CoA). Complexes of consecutive
enzymes in a pathway allow substrate channeling between them.

SUMMARY
 The citric acid cycle is the final pathway for the oxidation of
carbohydrate, lipid and protein whose common end-metabolite,
acetyl-CoA reacts with oxaloacetate to form citrate.
 Pyruvate from glycolysis must first go through the pyruvate
dehydrogenase complex to form acetyl-CoA, the complex requires
five co-factors (CoA, TPP, FAD, NAD+ and lipoic acid) a similar
complex is since in the TCA cycle (succinate dehydrogenase
complex)
 By series of 8 reactions involving dehydrogenations and
decarboxylations, citrate is degraded releasing coenzymes and
2carbon dioxide molecules and regenerating oxaloacetate
 The reduced Co-enzymes are oxidized by the respiratory chain
linked to formation of ATP. Thus the cycle is the major route for
the generation of ATP and is located in the mitochondrial matrix
adjacent to the enzymes of the respiratory chain and oxidative
phosphorylation.
 The total energy produced from the complete oxidation of
carbohydrates in the form of glucose is 32ATP molecules.
 The citric acid cycle is amphibolic, since in addition to oxidation it
is important in the provision of carbon skeletons for
gluconeogenesis, fatty acid synthesis and interconversion of amino
acids.
 The 3 irreversible reactions (reactions 1,3 and 4) are the site of
regulation of the TCA cycle

THE ELECTRON TRANSPORT CHAIN AND

OXIDATIVE PHOSPHORYLATION
 Aerobic organisms are able to capture a far greater portion of the
available free energy of respiration and respiratory substrates than
anerobic organisms.
 Most of this takes place inside the mitochondria which have been
termed the “power-house” of the cell.
 Respiration is coupled to the generation of high-energy
intermediate, ATP by oxidative phosphorylation and the
chemiosmotic theory.
 The outer membrane of the mitochondria is relatively permeable to
most metabolites, the inner mitochondrial membrane is selectively
permeable and only metabolites with specific transporters can pass
through.
 Impermeable to NADH and FADH2
 Permeable to Pyruvate, succinate, malate, ATP, ADP
COMPARTMENTALIZATION
 Krebs’ cycle and beta-oxidation happens in the matrix

 ETC on inner membrane
 Glycolysis in cytosol

 Hydrogen and electron flow through the respiratory chain through

redox span of 1.1v from NAD+/NADH to O2/H2O
 The respiratory chain consists of a number of REDOX carriers that
proceed from the NAD-linked dehydrogenase systems through
flavoproteins and cytochromes to molecular oxygen.
 Not all substances are however linked directly to flavoprotein
dehydrogenases which in turn are linked to the cytochromes of the
respiratory chain.
 These are 4 complexes involved in the electron transport chain.
 These complexes may be found embedded in the inner membrane
linking the intermembrane space and the mitochondria matrix.
 Complex I- NADH dehydrogenase complex
 Complex II- succinate dehydrogenase
 Complex III- cytochrome bc1

 Complex IV- cytochrome C oxidase

 Apart from ubiquinone these carriers are arranged in order of
increasing redox potentials
 Ubiquinone or Q (co-enzyme Q) links the flavoproteins to
cytochrome b, the membrane of the cytochrome chain of lowest
redox
 Q acts as a mobile component of the respiratory chain that collects
reducing equivalents from the more fixed flavoprotein complexes
and passes them to cytochromes i.e. from complex I/II to complex
III
 Cytochrome C a soluble cytochrome which transfer electrons from
complex III to complex IV
 During electron transport, energy released is used to transport H+
across the inner mitochondrial membrane to create an electro-
chemical gradient

PATHWAY I (ELECTRONS FROM NADH + H+)

 Complex I (NADH dehydrogenase) is found on the inner

membrane and it extends into the matrix from the inter membrane
space.
 Complex I catalyzes the transfer of a hydride ion from NADH and
a proton from the matrix to ubiquinone (Q)
 NADH + H+ + Q --> NAD+ + QH2
 NADH is reoxidised to NAD+ and this transfer of electrons
provides energy that pumps 4 protons (H+) from the matrix to the
intermembrane space.
 Complex I is therefore a proton pump driven by the energy of
electron transfer and the reaction it catalyzes is vectorial: It moves
protons in a specific direction from one location (the matrix, which

becomes negatively charged with the departure of protons) to

another (the intermembrane space which becomes positively
charged)
 In complex I flavin mononucleotide (FMN) receives eletrons from
NADH and transfers them through iron-sulfur (Fe-S) centers to
coenzyme Q. FMN is derived from riboflavin
 Ubiquinol (QH2) the reduced form of uniquinone diffuses in the
inner mitochondrial membrane from complex I to complex III
where it is oxidized to Q in a process that also involves the
outward movement of H+
 Complex III also pumps 4 protons into the intermembrane space.
 Complex III cytochrome bc1 complex couples the transfer of
electrons from ubiquinol (QH2) to cytochrome C with the vertical
transport of 4 protons from the matrix to the intermembrane space.
 QH2 is oxidized to Q and 2 molecules of cytochrome C are reduced
 Cytochrome C is a soluble protein of the intermembrane space
 Cytochrome C moves to complex IV and donates its electrons to
complex IV (cytochrome oxidase)
 Complex IV also called cytochrome oxidase carries electron from
cytochrome C to molecular oxygen, reducing it to water
 Complex IV in the process pumps 2H+ into the intermembrane
space (keep in mind the other 2 electrons combine with 2H+ and ½
O2 to form water)

PATHWAY II (ELECTRONS FROM FADH2)

 Some electrons enter this chain of carriers through alternative

paths
 Succinate dehydrogenase (complex II) oxidizes succinate to
fumerate. The flavoprotein that passes through several Fe-S centers
to ubiquinone is present.
 Electron derived from the oxidation of fatty acids pass to
ubiquinone via the electron-transporting flavoprotein i.e. FAD
 Ubiquinol passes electrons to complex III that passes the electrons
to cytochrome C while pumping 4 protons into the intermembrane
space
 Cytochrome C passes electrons from complex III to complex IV
which pumps 2 protons into the intermembrane space (recall that 2
protons combine with oxygen the final electron carrier to form
water at this stage)
PATHWAY 1 PATHWAY 2
 Starts with complex II

 Starts with complex I
(succinate dehydrogenase)
(NADH dehydrogenase
complex)
 Pumps a total of 6 H+ into the
 Pumps a total of 10 H into
+
intermembrane space
the intermembrane space
 Uses FADH2
 Uses NADH 1 𝐴𝑇𝑃
1 𝐴𝑇𝑃  6𝐻 + × = 1.5𝐴𝑇𝑃
 10𝐻 + × = 2.5 𝐴𝑇𝑃 4𝐻 +
4𝐻 +

 NOTE: 4 PROTONS pumped into the intermembrane space

generate 1 ATP molecule
OXIDATIVE PHOSPHORYLATION
 Electron transport chain is coupled to oxidative phosphorylation
 It is done on the inner mitochondrial membrane catalyzed by
ATPase/ ATP synthase
 Oxidative because synthesis of ATP involves oxidation of NADH
and FADH2 respectively at the expense of oxygen (reduced to
water) which leads to the phosphorylation of ADP to ATP
A. Oxidation step: electron transport chain
 NADH + H+ + ½ O2--> NAD+ + H2O
 FADH2 + ½ O2 --> FAD + H2O

B. Phosphorylation step
 ADP + Pi --> ATP
 The chemiosmotic model explains how ATP is really synthesized
 According to the model the electro-chemical energy inherent in the
difference in proton concentration and the separation of charge
across the inner membrane- the proton-motive force drives the
synthesis of ATP as protons flow passively back into the matrix
through a protein pore (hydrophilic) associated with the F0 Subunit
of ATP synthase located in the membrane.
 The enzyme ATP synthase has 2 distinct components:
 F1 a peripheral membrane protein and F0 which is integral to the
membrane.
 The first factor F1 is essential for oxidative phosphorylation, it is
activated as hydrogen ions flow through the F0 subunit.
 The ATP synthase molecules are the only place that will allow
hydrogen ions to diffuse back into the matrix (exergonic flow of
hydrogen)
 As protons flow through the F0 subunit, the subunit rotates
activating the F1 subunit to phosphorylate ADP to ATP.
 The flow of 4 protons through the F0 subunit results in the
phosphorylation of one ADP molecule
 Certain anti-porters are present on the inner membrane of the
mitochondrion these include:

1. Phosphate transporters
 Transport OH- out of the matrix
 Transports inorganic phosphates into the matrix
 The inorganic phosphates are used in the phosphorylation of
ADP
2. ATP/ADP anti-porter
 Transports ADP in and ATP out
 ADP provides the substrate from the cytosol to be
phosphorylated to ATP
 ATP has to be removed, a bulk up of ATP would
allosterically inhibit ATPase and ATP production would stop
INHIBITORS OF ETC
1. Atractyloside: ATP/ADP antiporter

 Blocks the transport of ATP out/ADP in matrix
 ATP concentrations in matrix increases and this inhibits its
production

 ADP concentrations in matrix decreases and this means

ATPase has no substrate to phosphorylate.
2. Oligomycin: ATP synthase
 Inhibits ATPase and this prevents the phosphorylation of
ADP to ATP
UNCOUPLERS
 Uncouplers separate the process of oxidation from the process of

phosphorylation
 This results in the release of energy as heat and other forms rather
than ATP.
 DNP (2,4 Dinitrophenol) shuttles H+ into the mitochondrial matrix
thus disrupting the concentration gradient of H+ and therefore
disrupting electrochemical gradient and ultimately ATP synthesis
 Thermogenin is an uncoupling protein that acts as a proton
conductance pathway dissipating the electro-chemical potential
across the mitochondrial membrane. This is seen in brown adipose
tissue.

WHAT ABOUT NADH FROM GLYCOLYSIS?
 NADH made in the cytosol can’t get into the matrix of

mitochondrion because it has no transporter protein on the
mitochondrial membrane.
 Therefore there are 2 mechanisms that transfer electrons from the
cytosolic NADH:
1. In muscle and brain: Glycerol phosphate shuttle
2. In liver, kidneys and heart: Malate/Aspartate shuttle
GLYCEROL PHOSPHATE SHUTTLE

 In the cytosol, dihydroxyacetone phosphate in skeletal muscle and

brain accepts 2 reducing equivalents from NADH in a reaction
catalyzed by cytosolic glycerol 3-phosphate dehydrogenase
 An isoenzyme of glycerol 3-phosphate dehydrogenase is bound to
the outer face of the inner membrane then transfers 2 reducing
equivalents from glycerol 3-phosphate in the intermembrane space
to ubiquinone via a reduction of FAD to FADH2
 Glycerol 3-phosphate is oxidized to dihydroxyacetone phosphate
 Note that this shuttle does not involve membrane transport
systems. Electrons are transferred from NADH + H+ to FAD and
eventually ubiquinone which enters the ETC later. Complex I and
II are bypassed.
 Note FADH2 produces 1.5 ATP therefore FADH2 being used
produces a total of 30.0 ATP molecules.

MALATE-ASPARTATE SHUTTLE
 This shuttle is for transporting reducing equivalents from cytosolic
NADH into the mitochondrial matrix and it is used in the liver,
kidneys and heart.
1. NADH in the cytosol (intermembrane space) passes 2 reducing
equivalents to oxaloacetate producing malate

2. Malate crosses the inner membrane via the malate-ɑ

ketoglutarate antiporter.
3. In the matrix, malate passes 2 reducing equivalents to NAD+
and the resulting NADH is oxidized by the respiratory chain, the
oxaloacetate formed from the malate cannot pass directly into
the cytosol.
4. Oxaloacetate is first transaminated to aspartate
5. Aspartate can leave via glutamate-aspartate antiporter
6. Oxaloacetate is regenerated in the cytosol completing the cycle.

 Note NADH via electron transport yields 2.5 ATP thus a total of
32 ATP molecules is produced
 The NADH produced donates its electron to Complex I carrying on
with the ETC
REGULATION
 It is generally limited by the availability of ADP as substrate of
phosphorylation
 It also depends on oxygen availability as well as Pi (inorganic
phosphate)
 Some inhibitors regulate the process of ETC and oxidative
phosphorylation

SUMMARY
 Electrons are passed on from reducing equivalents to the electron
carriers found on the inner mitochondrial membrane.
 The transfer of electron releases energy which allows protons to be
pumped across the mitochondrial membrane thus creating an
electro-chemical gradient which result in the flow of protons down
an electro-chemical gradient as ADP is phosphorylated to ATP
(this is known as oxidative phosphorylation)
 Oxygen is the last electron carrier that is reduced to water
 Reducing carriers cannot pass through the inner membrane which
is highly selective and so electrons from the cytosolic reducing
carrier enter either through the glycerol-3-phosphate shuttle
(results in production of 30.0 ATP) or the malate-aspartate shuttle
(results in the production of 32.0 ATP)

 Both the electron transport chain and oxidative phosphorylation are

regulated processes
 Uncoupling of the two process by chemicals e.g. 2,4-Dinitrophenol
or proteins e.g. thermoginin disrupts the proton gradient across the
inner membrane and the energy is lost as heat (this is seen in
brown adipose tissue)
GLYCOGEN METABOLISM
OBJECTIVES
1. Glycogen synthesis (glycogenesis)
2. Glycogen breakdown (glycogenolysis)
3. Roles of hormones in glycogen metabolism
4. Regulation of glycogen metabolism
WHAT IS GLYCOGEN?
 Glycogen is the major storage carbohydrate in animals
corresponding to starch.
 It is a branched polymer of ɑ-D-glucose
 It is mainly found in the liver and skeletal muscle
 In the liver glycogen consists 6-10% of the weight of the liver and
1-2% the of weight muscle.
 However, because of a greater mass in muscle than liver (weighing
about 1.5kg in an average adult male) collectively muscle (400mg)
contains about 3 to 4 times as much glycogen as does the liver
(100mg).
 The general mechanisms for storing and mobilizing glycogen are
the same in the muscle and liver.

 Storing glucose as glycogen does not affect the cells’ osmotic

properties i.e. a concentration of glycogen exerts a lesser osmotic
effect than an equal concentration of glucose would in a cell.
 Glycogen is stored in large cytosolic granules
 Glycogen granules are complex aggregates that synthesize and
degrade glycogen.
 Muscle glycogen is a readily available source of glucose-1
phosphate for glycolysis within the muscle itself.
 Muscle glycogen can exhaust in less than an hour during vigorous
activity.
 Muscle glycogen does not yield free glucose directly as muscle
lacks glucose-6 phosphatase
 Glucose -6 phosphatase is found in smooth endoplasmic reticulum
of hepatocytes (liver) and so the liver can synthesize free glucose.
 Liver glycogen acts as storage and exports glucose to maintain
blood concentration during fasting states (and in between meals)
 After 12-18 hours of fasting the liver glycogen is almost totally
depleted.
 Liver glycogen supplies neurons of the brain which cannot use
fatty acids as fuels.
 In humans the total amount of energy stored as glycogen is far less
than the amounts stored as fat (triacylglycerol) but fats cannot be
converted to glucose in mammals (the reaction that forms Acetyl-
CoA cannot be reversed back to glucose) and fats cannot be
catabolized anaerobically.
STRUCTURE OF GLYCOGEN
 Glycogen has a complex structure of highly branched chains

 The linkages between glucose residues are 1-4 except at branch

point where it is 1-6
 Branching is more frequent in the interior of the molecule than the
periphery
 On an average branching is seen after 8 to 10 residues.
 Each chain has 12 to 14 glucose residues.
 The structure of glycogen starts at a central glycogenin molecule;
glycogen chains extend in tiers.
 There are 12 tiers in a mature glycogen molecule consisting of 55,

000 glucose residues.

 The glycogen molecule branches and has many non-reducing ends

at which addition and release of glucose residues occurs during
synthesis and degradation respectively.
 NOTE: The reducing end in glucose has the ability to reduce blue
Cu2+ ions to brick-red Cu+ ions while it is oxidized to a carboxylic
acid.
GLYCOGEN SYNTHSIS (GLYCOGENESIS)

 Takes place in the liver cell and muscle.
 Glucose enters the cells (via GLUT-2) and is phosphorylated to
glucose-6 phosphate by the enzymes hexokinase (in muscle) and
glucokinase (in the liver)
 ATP provides the phosphate group
 Glucose-6 phosphate is isomerized to glucose 1-phosphate by
phosphoglucomutase.

 The enzyme itself is phosphorylated and the phosho-group takes

part in a reversible reaction in which glucose 1,6- Bisphosphate is
an intermediate.
 Glucose 1-phosphate reacts with Uridine triphosphates (UTP)
forming UDP-glucose in a reaction catalyzed by UDP-
glucosepyrophosphorylase.
 UDP is the carrier of glucose it is a sugar nucleotide
 Inorganic pyrophosphate is released in this reaction (PPi)

 PPi is cleaved by pyrophosphatase to 2 inorganic phosphates (Pi)
 This removal of product helps to drive the process in the direction
of glycogen synthesis.
𝑝𝑦𝑟𝑜𝑝ℎ𝑜𝑠𝑝ℎ𝑎𝑡𝑎𝑠𝑒
𝑃𝑃𝑖 → 2𝑃𝑖
 UDP-glucose pyrophosphorylase is present in large amount

 UDP-glucose pyrophosphorylase has a low Km for glucose-1

Phosphate
 Km is Michaelis-Menten kinetic constant.
 It is the substrate concentration required for an enzyme to function
at half its maximum rate. (low Km =high affinity for substrate and
High Km =low affinity for substrate)
STRUCTURE OF THE SUGAR NUCLEOTIDE UDP-

GLUCOSE

 UDP-glucose is the intermediate donor of glucose residues in the

reaction catalyzed by glycogen synthase which promotes the
transfer of glucose from UDP-glucose to a non-reducing end of a
branched glycogen molecule.
GLYCOGENIN IS BOTH THE PRIMER AND ENZYME

DURING GLYCOGEN SYNTHESIS
 A primer is a molecule that serves as the starting material for a

polymerization process
 Glycogen synthase cannot initiate a new glycogen chain de novo
(starting from the beginning/ a new)
 It requires a primer, usually a pre-formed (1-4) polyglucose chain
or branch having at least 8 glucose residues.
 Glycogenin is both the primer on which new chains are assembled
and the enzyme that catalyzes their assembly.

 The first step in the synthesis of a new glycogen molecule is the

transfer of a glucose residue from UDP-glucose to the hydroxyl
group of tyrosine at position 194 of glycogenin, catalyzed by the
protein’s intrinsic glycosyl transferase activity.
 Glycogenin adds about 8 residues of glucose. (auto-glycosylation)
 After this glycogen synthase takes over further extending of the
glycogen chain.
GLYCOGEN SYNTHASE
 Glycogen synthase is the key regulatory enzyme for glycogen
synthesis.
 It transfers glucose residues from UDP-Glucose to the non-

reducing ends of a glycogen primer.
 UDP is released and reconverted to UTP by reacting with ATP.
 At this point 2 ATP molecules are invested (1st ATP in the
phosphorylation of glucose to glucose 6-phosphate and 2nd used to
convert UDP to UTP)
 The primers which are attached to glycogenin are glycogen
molecules that were partially degraded in the liver during fasting or
in muscle and liver during exercise.
 Glycogen synthase is the rate limiting enzyme
 It adds about 5-6 residues.
BRANCH SYNTHESIS IN GLYCOGEN

 Addition of glucose residues to a pre-existing glycogen chain, or

“primer” occurs at the non-reducing ends, outer end of the
molecules so that the branches of the glycogen “tree” become
elongated as successive 1-4 linkages are formed.
 When the chain has been lengthened to at least 11 glucose
residues, branching enzyme transfers a part of the 1-4 chain (at
least 6 glucose residues) to a neighboring chain to form a 1-6
linkage, establishing a branch point
 The branches grow by further additions of 1-4 glucosyl units (by
glycogen synthase) and further branching

GLYCOGENOLYSIS
 Glycogenolysis is not the reverse of glycogenesis.
 Glycogen phosphorylase catalyzes the rate-limiting step in
glycogenolysis. It removes glucose residues one at a time from the
non-reducing ends of glycogen molecules.
 Glycogen phosphorylase is pyridoxal dependent enzyme (vitamin
B6)
 Phosphorylase use Pi to cleave -1,4 bonds, producing glucose 1-
phosphate.
 The phosphorylase can continue to hydrolyze -1,4 linkages until
it reaches a point four glucose units from an  1,6 branch.

 The four units remaining at a branch are removed by the

debranching enzyme which has both glucosyl 4:4 transferase ([1-
4]:  [1-4] glucan transferase) which transfers a trisaccharide unit
from one branch to the other exposing the 1-6 branch point, and an
1,6 glucosidase activity.
 The enzyme cleaves an  1-4 bond and forms a new  1-4 bond.
 The last glucose unit at the branch point, which is linked 1-6 is
hydrolyzed by ɑ 1-6 glucosidase (debranching enzyme) forming
free glucose.
 Further phosphorylase action can then proceed.
 Combined action of phosphorylase and these other enzymes leads
to the complete breakdown of glycogen.
RATE OF GLUCOSYL UNITS RELEASED FROM GLYCOGEN
LIVER
 In the liver, glycogen is degraded to maintain blood glucose.

 Glucose 1-phosphate is converted by phosphoglucomutase to
glucose 6-phosphate.
 Inorganic phosphates are released from glucose 6-phosphate by
glucose 6-phosphatases (found in the SER membrane) and free
glucose enters the blood (via GLUT 2). This enzyme also acts in
gluconeogenesis.
MUSCLE
 In muscle glycogen is degraded to provide energy for contraction

 Phosphoglucomutase converts glucose 1-phosphate to glucose 6-
phosphate which enters the glycolytic pathway.
 The end product can either be lactate or CO2 + H2O depending on
the availability of oxygen.
 Muscle does not contain glucose 6-phosphatase and so does not

contribute to maintenance of blood glucose. (but note that there are
a few free glucose molecules that are released i.e. those molecules
of the branching points these however are also NOT used to
contributed to blood glucose levels.)
CATABOLIC PATHWAY OF GLYCOGEN
REGULATION OF GLYCOGEN METABOLISM

 It is important to maintain blood glucose levels because the red
blood cell uses glucose as the sole source of energy and the brain
prefers glucose as its primary source of energy.

 It is for this reason that the synthesis and degradation of glycogen

has to be tightly regulated
 The body can be found in 2 physiological states:
a. Fasting state: in between meals
b. Fed state: after meals
 After a meal blood glucose levels increase
 During fasting states i.e. in between meals blood glucose may fall
very low.
 Blood glucose level has to be maintained at 70-120mg/dl
 The principle organ involved in the maintenance of blood glucose
levels is the liver.
 Skeletal muscle does not have glucose-6- phosphatase and so it
does not contribute to maintaining the blood glucose level.
 In the liver glycogenesis accelerates during periods when the body
is fed, whereas glycogenolysis accelerates during periods of
fasting.
 In skeletal muscle, glycogenolysis occurs during active exercise
and glycogenesis begins as soon as the muscle is again at rest.
 Regulation of the entire process of glycogen metabolism is done by
regulating the key regulatory enzymes
 In glycogen breakdown glycogen phosphorylase is the key
enzyme.
 In glycogen synthesis glycogen synthase is the key enzyme.
 Both enzymes can be regulated by:
a. Covalent modification by reversible
phosphorylation/dephosphorylation reaction
b. Allosterically

 The hormones that play a role in metabolism of glycogen are

insulin, glucagon, epinephrine and other thyroid and steroid
hormones.
 Insulin lowers the blood glucose levels during the fed state.
 Glucagon and epinephrine raise glucose levels during fasting state.
(remember glucagon= OH NO “GLUCOSE” IS “GONE)
 Epinephrine binds to beta-adrenergic receptors in the liver and
muscle
 Glucagon binds has receptors in the liver, so does insulin.
REGULATION OF GLYCOGEN BREAKDOWN

(GLYCOGENOLYSIS)
 Activation of glycogen degradation is by cAMP (cyclic adenosine

monophosphate)-directed pathway.
 Glucagon (in liver) or epinephrine (in liver and muscle) are the
hormones that regulate glycogen breakdown, they stimulate
glycogenolysis and inhibit glycogenesis thus preventing a futile
cycle.
 Glycogen phosphorylase is the key enzyme in glycogen
breakdown.
GLYCOGEN PHOSPHORYLASE
 Plays a role in glycogen degradation.

 It is both allosterically regulated and covalently modified
 Glycogen phosphorylase has isoenzymes that play roles in tissue
specific areas.
 Glycogen phosphorylase is often referred to as phosphorylase
(because it was the first phosphorylase to be discovered)

 Glycogen phosphorylase of skeletal muscle exists as 2

interconvertible forms: Glycogen phosphorylase “a” which is
catalytically active and glycogen phosphorylase “b” which is
catalytically inactive. In skeletal muscle it is a dimer.
 In the liver one of the serine hydroxyl groups of the active
phosphorylase “a” is phosphorylated. It is inactivated by hydrolytic
removal of the phosphate by protein phosphatase- 1 to form
phosphorylase “b”. Reactivation requires phosphorylation
catalyzed by phosphorylase kinase.
 Glycogen phosphorylase “b” predominates in resting muscle but
during vigorous activity epinephrine triggers phosphorylation of a
specific serine residue in phosphorylase “b” converting it to its
more active form, phosphorylase “a”
 The enzyme (phosphorylase b kinase) responsible for activating
phosphorylase by transferring a phosphoryl group to its serine
residue is itself activated by epinephrine, glucagon, thyroid
hormone through the cAMP cascade including the enzyme adenlyl
cyclase.
ACTIVATION OF DEGRADATION VIA c-AMP PATHWAY
 As the hormones e.g. glucagon and epinephrine bind to plasma

membrane G-protein coupled receptors (GPCRs) this signals the
need for glycogen breakdown either to elevate blood glucose levels
or to provide energy for exercising muscle.
 G-proteins activate adenlyl cylase that catalyze the synthesis of
cAMP from ATP. The reaction releases inorganic pyrophosphate.
 cAMP activates cAMP-dependant protein kinase A
 cAMP activates protein kinase A by binding to its 2 regulatory
subunits causing the release of 2 active catalytic subunits.

 Protein kinase A has 2 regulatory subunits and 2 catalytic subunits

(R2C2)
 These active catalytic subunits catalyze the phosphoryl transfer of
a phosphate group from ATP to specific serine or threonine
residues on protein substrates.
 Protein kinase A then phosphorylates several enzymes of glycogen
metabolism.
 Phosphorylase kinase is phosphorylated and this converts it from
its inactive “b” form to the active “a” form.
 Active phosphorylase kinase phosphorylates glycogen
phosphorylase b to its active “a” form which then begins glycogen
breakdown

 Note that through amplification a small concentration of hormones

bound to receptors can activate a number of protein kinase A
molecules that in turn activates more phosphorylase kinase
molecules. This cause production of many active glycogen
phosphorylase “a” molecules that can degrade glucose

REGULATION OF GLYCOGEN SYNTHESIS
 Activation of glycogen synthesis is done by inhibition of the

cAMP-directed pathway.

 Insulin mediates glycogen synthesis and inhibits glycogen

degradation.
 Glycogen synthase is the key enzyme in glycogen synthesis.
GLYCOGEN SYNTHASE
 Exists either in a phosphorylated inactive form or a non-

phosphorylated active form.
 The active form is dephosphorylated (glycogen synthase a) and
may be inactivated by phosphorylation to form glycogen synthase
“b” (on the serine residues).
REGULATION OF GLYCOGEN SYNTHESIS
 Insulin, a pancreatic peptide hormone is released after a meal and

stimulates the synthesis of glycogen in liver and muscle.
 In fed state, glycogen degradation decreases because glucagon is
low and the cAMP cascade is not activated.
 cAMP is converted to AMP by a cell membrane
phosphodiesterase.
 As cAMP decreass the regulatory subunits rejoin the catalytic
subunits of protein kinase A (R2C2) and the enzyme is inactivated.
 Insulin causes the activation of the phosphatase that
dephosphorylates the enzymes of glycogen metabolism.
 Protein phospatase-1 dephosphorylates glycogen synthase b
(inactive) to glycogen synthase a (active)
 Glycogen kinase-3 an important kinase enzyme of the 11 kinase
enzymes affecting glycogen synthase is inactivated preventing
phosphorylation of glycogen synthase.
 In addition, insulin stimulates the transport of glucose into muscle
cells, producing increased substrate for glycogen synthesis.

ALLOSTERIC REGULATION OF GLYCOGEN METABOLISM
 Glycogen synthase in liver and muscle is allosterically activated by

glucose-6-phosphate and high levels of ATP. It is inhibited by low
levels of AMP.
 Glycogen phosphorylase is allosterically inhibited by glucose-6-
phosphate and low levels of ATP. It is allosterically activated by
high levels of AMP.
 Calcium-Calmodulin complex activates glycogen degradation and
inhibits glycogen synthesis.
 Calcium-calmodulin complex activates muscle phosphorylase
kinase b.

 NOTE: VON GIERKE’S DISEASE (Type Ia) is a deficiency in

the enzyme glucose-6-phosphatase.
SUMMARY
 The main stores of glycogen in the body are found in skeletal
muscle, where they serve as a fuel reserve for the synthesis of
ATP during muscle contraction, and in the liver, where they are
used to maintain the blood glucose concentration, particularly
during the early stages of a fast.
 Glycogen is a highly branched polymer of -D-glucose.
 The primary glycosidic bond is an ( 1-4) linkage. After about
eight to ten glucosyl residues, there is a branch containing an (
1-6) linkage.
 UDP-glucose, the building block of glycogen, is synthesized from
glucose 1-phosphate and UTP by UDP-glucose
pyrophosphorylase

 Glucose from UDP-glucose is transferred to the non-reducing ends

of glycogen chains by primer-requiring glycogen synthase, which
makes ( 1-4) linkages.
 The primer is made by glycogenin.
 Branches are formed by amylo- ( 1-4) ( 1-6)-transglucosidase,
which transfers a chain of six to eight glucosyl residues from the
nonreducing end of the glycogen chain (breaking an ( 1-4)
linkage).
 Glycogen phosphorylase cleaves the ( 1-4) bonds between
glucosyl residues at the non-reducing ends of the glycogen
chains, producing glucose 1-phosphate. This sequential
degradation continues until four glucosyl units remain on each
chain before a branch point.
 The resulting structure is called a limit dextrin that is degraded by
the bifunctional debranching enzyme. Oligo- ( 1-4) ( 1 -4)-
glucan transferase (common name, glucosyl 4:4 transferase)
removes the outer three of the four glucosyl residues attached at a
branch, and transfers them to the non-reducing end of another
chain where they can be converted to glucose 1-phosphate by
glycogen phosphorylase. Next, the remaining single glucose
residue attached in an ( 1-4) linkage is removed hydrolytically by
the amylo-(  1-6) glucosidase activity of debranching enzyme,
releasing free glucose.
 Glucose 1-phosphate is converted to glucose 6-phosphate by
phosphoglucomutase.
 In the muscle, glucose 6-phosphate enters glycolysis. In the liver,
the phosphate is removed by glucose 6-phosphatase, releasing
free glucose that can be used to maintain blood glucose levels at
the beginning of a fast.
 A deficiency of the phosphatase causes glycogen storage disease
Type 1a (Von Gierke disease).
 This disease results in an inability of the liver to provide free
glucose to the body during a fast. It affects both glycogen
degradation and gluconeogenesis.
 Glycogen synthesis and degradation are reciprocally regulated to

meet whole-body needs by the same hormonal signals, namely, an
elevated insulin level results in overall increased glycogenesis
and decreased glycogenolysis, whereas an elevated glucagon (or
epinephrine) level causes increased glycogenolysis and
decreased glycogenesis.
 Key enzymes are phosphorylated by a family of protein kinases,
some of which are cAMP-dependent (a compound increased by
glucagon and epinephrine). Phosphate groups are removed by
protein phosphatase-1 (activated when insulin levels are elevated).
 Glycogen synthase, phosphorylase kinase and phosphorylase
are also allosterically regulated to meet tissues needs. In the well-
fed state, glycogen synthase is activated by glucose 6-phosphate,
but glycogen phosphorylase is inhibited by glucose 6-phosphate,
as well as by ATP. In the liver, glucose also serves an allosteric
inhibitor of glycogen phosphorylase.
 The Ca2+ released from the endoplasmic reticulum in muscle
during exercise and in liver in response to epinephrine activates
phosphorylase kinase by binding to the enzyme’s calmodulin
subunit.
 This allows the enzyme to activate glycogen phosphorylase,
thereby causing glycogen degradation.
GLUCONEOGENESIS
OBJECTIVES
1. Significance
2. Gluconeogenesis reactions
3. Hormonal control
4. Blood sugar control

 Gluconeogenesis is the term used to include all pathways

responsible for converting non-carbohydrate precursors to glucose
or glycogen.
 Liver and kidney are the major glucogenic tissues (but the
Gluconeogenesis pathway occurs mostly in the liver and to a small
extent in the kidneys at the proximal convoluted tubule)
 The epithelium of the GIT also function in gluconeogenesis
although to a small extent.
 Gluconeogenesis meets the needs of the body for glucose when
carbohydrate is not available in sufficient amounts from the diet or
from glycogen reserves.
 A supply of glucose is necessary especially for nervous system and

erythrocytes. Failure of Gluconeogenesis is fatal.
 Hypoglycemia causes brain dysfunction which can lead to coma or

death.
 Other tissues that require a constant supply of glucose
include: the renal medulla (kidney), lens and cornea (eye)
and testis
 The major precursor for Gluconeogenesis are lactate, glucogenic
amino acids (alanine) which form Pyruvate or tricarboxylic acid
cycle intermediates and glycerol which form dihydroxyacetone
phosphate.
 In the muscle lactate is formed from pyruvate by the action of
lactate dehydrogenase (regenerating NAD+). The lactate
produced is taken to the liver were it is converted to pyruvate
by lactate dehydrogenase (regenerating NADH +H+). (This
is part of the Corri cycle)
 NOTE: muscle lacks glucose-6 phosphatase and so does not
contribute maintaining to blood glucose level.
 RBCs also produce lactate from their anaerobic respiration
and this lactate is taken to the liver to be reconverted to
pyruvate
 TCA intermediates and glycolytic intermediates can be
replenished from glucogenic amino acids which are
ultimately used in the gluconeogenesis pathway these
include:
o Glutamate which forms alpha-ketoglutarate
o Isoleucine, methionine, valine which form succinyl-CoA
o Tyrosine and phenylalanine which form fumarate
o Alanine which forms pyruvate
o Aspartate which forms oxaloacetate
 In adipocytes triglycerides are broken down to glycerol and
free fatty acids that are released into the blood, the glycerol
can enter the liver and be converted to dihydroxyacetone

phosphate
 Beta-oxidation of odd chained fatty acids form proprionyl-
CoA which can be converted to succinyl-CoA however, this
is negligible in humans.

 Gluconeogenesis involves several enzymatic steps that do not

occur in glycolysis thus glucose is not generated by a simple
reversal of glycolysis.
 Synthesis of glucose from Pyruvate utilizes many of the same
enzymes of glycolysis.
 The synthesis of 1 mole of glucose from 2 moles of Pyruvate
requires the energy equivalent of about 6 moles of ATP (4 ATP
and 2GTP)
 Although Gluconeogenesis is an energetically expensive process it
is essential
GLYCOLYSIS
GLUCONEOGENESIS
 Blood glucose levels are maintained within a very narrow range,

even though the nature of a person’s diet may vary widely and the
normal person eats periodically and fasts between meals and at
night. Even under circumstances when a person does not eat for
extended periods of time blood glucose levels decrease only
slowly.
 The major hormones that regulate blood glucose are insulin and
glucagon.

 After a meal blood glucose is supplied by dietary carbohydrates,

however during fasting the liver maintains blood glucose levels by
the process of glycogenolysis and Gluconeogenesis.
 All cells use glucose for energy; however, the production of
glucose during fasting is particularly important for tissues such as
the brain and red blood cells.
 During exercise, blood glucose is also maintained by liver
glycogenolysis and Gluconeogenesis.
REACTIONS
a. Conversion of Pyruvate to phosphoenol Pyruvate (PEP)
 In the liver, Pyruvate is converted to PEP in 2 steps
 Pyruvate (produced from lactate, alanine and other amino
acids) is first converted to oxaloacetate by Pyruvate
carboxylase a mitochondrial enzyme that requires,
magnesium, manganese, biotin and ATP.
 Biotin is required to transfer carbon dioxide. In deficiency of
biotin the enzyme does not function and gluconeogenesis is
inhibited.
 Pyruvate carboxylase is activated by acetyl-CoA
o During fasting epinephrine (from adrenal medulla) and
glucagon (from alpha cell of pancreas) are released
when blood glucose level falls. In adipocytes they
stimulate breakdown of triglycerides to glycerol (used
as a substrate in gluconeogenesis) and free fatty acids
o Beta oxidation of fatty acid in hepatocytes produces a
lot of acetyl-CoA and acetyl-CoA stimulates
gluconeogenesis by activating pyruvate carboxylase
 At this point 2 ATP molecules have been used.

 Oxaloacetate cannot directly cross the inner mitochondrial

membrane.
 Therefore, it is converted to malate (by mitochondrial) malate
dehydrogenase) which can cross the mitochondrial
membrane (through the malate-alpha ketoglutarate antiporter)
and be reconverted to oxaloacetate in the cytosol by cytosolic
malate dehydrogenase.
 Oxaloacetate is decarboxylated by PEP carboxykinase
(PEPCK) to form Phosphoenol Pyruvate (PEP). This reaction
requires guanosine triphosphates (GTP)
 2 GTP are used
 PEP is converted to fructose 1,6 bisphosphate by reversal of
the glycolytic reaction
b. Conversion of fructose 1,6 bisphosphate to fructose 6-phosphate
 Fructose 1,6-bisphosphate is converted to fructose 6-
phosphate in a reaction that releases inorganic phosphate
catalyzed by fructose 1,6 bisphosphatase
 Fructose 6-phosphate is converted to glucose 6-phospate by
the same isomerase (phosphohexose isomerase) used in
glycolysis
 Fructose 2,6-Bisphosphate stimulate PFK-1 and inhibits
fructose 1,6-Bisphosphatase.
c. Conversion of glucose -6 phosphate to glucose
 Glucose 6- phosphate releases inorganic phosphates (Pi)
which produces free glucose that enters the blood.
 The enzyme is glucose 6-phosphatase
 Glucose 6-phospatase is involved in both Gluconeogenesis
and glycogenolysis

THE BYPASS OF REACTIONS OF GLUCONEOGENESIS
 3 glycolysis reactions have such a large negative ΔG that they are

essentially irreversible and are catalyzed by:
a. Hexokinase (or glucokinase)
b. Phosphofructokinase
c. Pyruvate kinase
 The first 2 enzymes are bypassed by simple hydrolysis reactions.


SYNTHESIS OF BLOOD GLUCOSE FROM GLUCOSE 6

PHOSPHATE
 Glucose 6-phosphatase is found embedded in the membrane of the

smooth endoplasmic reticulum in the liver
 GLUT-2 transporter can transport blood glucose in either direction.

BYPASS OF PYRUVATE KINASE
 Pyruvate kinase (last step of glycolysis) catalyzes:

Phosphoenolpyruvate + ADP--> Pyruvate + ATP
 For bypass of the Pyruvate kinase reaction, cleavage of 2 ~P bonds
are required (one from ATP and the other from GTP)
 ΔG for cleavage of one ~P of ATP (-30.5KJ) is sufficient to drive
synthesis of phosphoenolpyruvate (PEP)
 PEP has a higher negative ΔG of phosphate hydrolysis than ATP
 Pyruvate is therefore converted to oxaloacetate then PEP.


REGULATION OF PYRUVATE CARBOXYLASE
 Pyruvate carboxylase is allosterically activated by acetyl-CoA

 The concentration of oxaloacetate tends to be limiting for krebs
cycle.
 When Gluconeogenesis is active in the liver, oxaloacetate is
diverted to form glucose. Oxaloacetate depletion hinders acetyl-
CoA entry into krebs cycle. The increase in the concentration of
acetyl-CoA activates Pyruvate carboxylase to make oxaloacetate.

REGULATION OF GLUCONEOGENESIS
 Glycolysis and gluconeogenesis should be regulated reciprocally
preventing a futile cycle in which glucose produced is quickly
broken down
 If they are not regulated reciprocally the following would happen:

 A cycle in which ATP is broken down and not formed

 Hormone secretions have a direct or indirect effect on the
availability of substrates
 3 mechanisms are responsible for regulating the activity of
enzymes
a. Changes in the rate of enzyme synthesis (requires several hours)
 The secretion of insulin in response to increased blood
glucose enhances the synthesis of key enzymes in glycolysis.
 Glucocorticoids and glucagon-stimulated cAMP induces the
synthesis of key enzymes responsible for gluconeogenesis.
b. Covalent modification by reversible phosphorylation (rapid)
 Glucagon and to a lesser extent epinephrine are responsible
for increasing blood glucose levels. They inhibit glycolysis
and stimulate gluconeogenesis in the liver by increasing the
concentration of cAMP
 cAMP activates cAMP-dependent protein kinase, leading to
the phosphorylation and inactivation or pyruvate kinase

 CREB (cAMP response element binding protein) which

activates, through other factors, transcription of the gene for
PEP carboxykinase, leading to increased gluconeogenesis is
also phosphorylated
 Additionally, a bi-functional enzyme (PFK-2) that makes and
degrades (F-2,6-BPase) an allosteric regulator fructose-2,6-
bisphosphate is also phosphorylated
RECIPROCAL REGULATION BY FRUCTOSE-2,6-

BISPHOSPHATASE
 Fructose-2,6-Bisphosphate stimulates glycolysis

 Fructose-2,6-Bisphosphate allosterically activates the glycolysis
enzyme phosphofructokinase-1 (PFK-1)
 Fructose-2,6-bisphosphate also activates transcription of the gene
for glucokinase the liver variant of hexokinase, that phosphorylates
glucose to glucose-6-phosphate for entry into glycolysis
 Fructose-2,6-bisphosphate is formed by phosphorylation of
fructose-6-phosphate by PFK-2
 The break-down of fructose-2,6-bisphosphate is also by the same
enzyme (this time called fructose-2,6-bisphosphatase)
 This bifunctional enzyme is under the allosteric control of
fructose-6-phosphate which stimulates the kinase and inhibits the
phosphatase
 When glucose is abundant the concentration of fructose-2,6-
bisphosphate increases stimulating glycolysis by activating PFK-1
and inhibiting gluconeogenesis by inhibiting F-2,6-BPase
 When glucose is short, glucagon stimulates the production of
cAMP (by the enzyme adenylate cyclase), activating cAMP-
dependent protein kinase which in turn phosphorylates PFK-2 and
activates fructose-2,6-bisphosphatase
 Gluconeogenesis is stimulated by a decrease in the concentration

of fructose-2,6-bisphosphate which deactivates PFK-1 and
deinhibits fructose-1,6-bisphosphatase
 This mechanism ensures that glucagon stimulation of
glycogenolysis in the liver results in glucose release rather than
glycolysis.
c. Allosteric modification (instantaneous) by AMP and ATP and

other intermediates e.g. citrate
THE CORRI CYCLE

 The corri cycle operates during exercise

 For a brief burst of ATP utilization, muscle cells utilize ~P stored

as phosphocreatine
 Once phosphocreatine is exhausted ATP is provided mainly by
glycolysis with the input coming from glycogen breakdown and
from glucose uptake from blood
 Note: Aerobic fat metabolism is more significant during a lengthy
period of exercise such as a marathon run.
 In the corri cycle lactate produced from pyruvate passes via the
blood to the liver where it may be converted to glucose
 The glucose may travel back to the muscle to fuel glycolysis
 The corri cycle costs 6(~P) in the liver for every 2 (~P) made
available in the muscle. The net cost is 4 (~P)

 Although costly in ~P bonds, the corri cycle allows the organism to

accommodate to large fluctuations in energy needs of skeletal
muscle between rest and exercise.
SUMMARY
 Gluconeogenesis is a ubiquitous multistep process in which
glucose is produced from lactate, pyruvate, or oxaloacetate, or any
compound (including citric acid cycle intermediates) that can be
converted to one of these intermediates. Seven of the steps in
gluconeogenesis are catalyzed by the same enzymes used in
glycolysis; these are the reversible reactions.
 Three irreversible steps in glycolysis are bypassed by reactions
catalyzed by gluconeogenic enzymes:
1. conversion of pyruvate to PEP via oxaloacetate, catalyzed by
pyruvate carboxylase and PEP carboxykinase;
2. Dephosphorylation of fructose 1,6-bisphosphate by FBPase-1;
and
3. Dephosphorylation of glucose 6-phosphate by glucose 6-
phosphatase.
 Formation of one molecule of glucose from pyruvate requires 4

ATP, 2 GTP, and 2 NADH; it is energetically expensive.
 In mammals, gluconeogenesis in the liver, kidney, and small
intestine provides glucose for use by the brain, muscles, and
erythrocytes.
 Pyruvate carboxylase is stimulated by acetyl-CoA, increasing the
rate of gluconeogenesis when the cell has adequate supplies of
other substrates (fatty acids) for energy production.
 Glycolysis and gluconeogenesis are reciprocally regulated to
prevent wasteful operation of both pathways at the same time.
 The corri cycle involves gluconeogenesis as the liver provides
glucose to muscle during exercise.

HEXOSE MONOPHOSPHATE SHUNT

OBJECTIVES
1. Significance
2. HMS reactions
3. Changes of the HMS under different cellular conditions
4. Tissue specific activity of the HMS
 An alternative pathway for glucose 6-phosphate catabolism is to

the pentose phosphate pathway (also called the phosphogluconate
pathway or the hexose monophosphate shunt).

 The pentose pathway does not generate or use ATP but has 2
functions:
1. To produce NADPH for synthesis of fatty acids and steroids.
2. Synthesis of ribose 5-phosphate used in nuclei acid synthesis
 Glucose, fructose and Galactose are the main hexoses absorbed
from the G.I.T derived from dietary starch, sucrose and lactose
respectively.
 The pentose phosphate pathway takes place in the cytosol.
 In this oxidative pathway NADP+ is the electron acceptor yielding
NADPH

 Rapidly dividing cells e.g. bone marrow, skin and intestinal

mucosa and those of tumors use the pentose ribose 5-phosphate to
make RNA, DNA and coenzymes such as ATP, NADH, FADH2
and coenzyme A
 In other tissues, the essential product of the pentose pathway is not
the pentose’s but the electron donor NADPH, needed for reductive
biosynthesis or to counter the damaging effects of oxygen radicals.
 Tissues that carry out extensive fatty acid synthesis (liver, adipose,
lactating mammary gland) or very active synthesis of cholesterol
and steroid hormones (liver, adrenal gland, gonads) require the
NADPH provided by this pathway.
 Red blood cells and the cells of the lens and cornea are directly
exposed to oxygen and thus to the damaging free radicals
generated by oxygen.
 By maintaining reducing atmosphere (a high ratio of NADPH to
NADP+ and a high ratio of reduced to oxidized glutathione)
 In erythrocytes, the NADPH produced by the pentose phosphate
pathway is so important in preventing oxidative damage that a
genetic defect in glucose 6-phosphate dehydrogenase, the first
enzyme of the pathway, can have serious medical consequences.
TISSUE FUNCTION
Adrenal gland Steroid synthesis
Liver Fatty acid and cholesterol

synthesis
Testes Steroid synthesis

Adipose tissue Fatty acid synthesis
Ovary Steroid synthesis
Mammary gland Fatty acid synthesis
Red blood cell Maintenance of reduced

glutathione (that acts as an
antioxidant)
PATHWAYS REQUIRING NADPH
SYNTHESIS
 Fatty acid biosynthesis

 Cholesterol biosynthesis
 Neurotransmitter biosynthesis
 Nucleotide biosynthesis
DETOXIFICATION
 Reduction of oxidized glutathione

 Cytochrome P450 monoxygenase (liver)
 Superoxides are also produced in neutrophils during
oxidative/respiratory burst.
THE PENTOSE PHOSPHATE PATHWAY IS A SHUNT
 The pentose phosphate pathway begins with the glycolytic

intermediate glucose 6-phosphate.

 It reconnects with glycolysis because 2 of the end products of the

pentose pathway are glyceraldehyde 3-phosphate and fructose 6-
phosphate, 2 intermediates further down the glycolytic pathway.
 It is for this reason that the pentose pathway is often referred to as
a shunt.
 NADPH is a phosphorylated form of NADH.

 In general, with some exceptions, NADH is used to drive the
phosphorylation of ADP to ATP.
 NADPH is used where reducing potential is required for synthetic
reactions

ROLE OF NADPH IN THE RBC

 In erythrocytes oxyhaemoglobin can spontaneously dissociate
forming superoxides.
𝑠𝑝𝑜𝑛𝑡𝑎𝑛𝑒𝑜𝑢𝑠 𝑑𝑖𝑠𝑠𝑜𝑐𝑖𝑎𝑡𝑖𝑜𝑛 (1%)
𝐻𝑏 − 𝐹𝑒 2+ − 𝑂2 → 𝐻𝑏 − 𝐹𝑒 3+ + 𝑂2− (𝑠𝑢𝑝𝑒𝑟𝑜𝑥𝑖𝑑𝑒)
 Superoxides can participate in a chain of oxidative reactions

producing radicals and H2O2, these products damage cell
membranes and cause hemolysis, shortening the life span of an
R.B.C
𝑠𝑢𝑝𝑒𝑟𝑜𝑥𝑖𝑑𝑒 𝑑𝑖𝑠𝑚𝑢𝑡𝑎𝑠𝑒
𝑂2− + 2𝐻 + → 𝐻2 𝑂2
 These radicals have to be removed to detoxify the R.B.C

 Detoxification of Superoxides requires NADPH.
2𝐺𝑆𝐻 (𝑟𝑒𝑑𝑢𝑐𝑒𝑑 𝑔𝑙𝑢𝑡𝑎𝑡ℎ𝑖𝑜𝑛𝑒) + 𝐻2 𝑂2

𝑔𝑙𝑢𝑡𝑎𝑡ℎ𝑖𝑜𝑛𝑒
𝑝𝑒𝑟𝑜𝑥𝑖𝑑𝑎𝑎𝑠𝑒
→ 𝐺𝑆 − 𝑆𝐺 (𝑜𝑥𝑖𝑑𝑖𝑧𝑒𝑑 𝑓𝑜𝑟𝑚) + 2𝐻2 𝑂
 Oxidized glutathione has to be reduced by NADPH to glutathione
and this reaction is catalyzed by glutathione reductase
𝑔𝑙𝑢𝑡𝑎𝑡ℎ𝑖𝑜𝑛𝑒 𝑟𝑒𝑑𝑢𝑐𝑡𝑎𝑠𝑒
𝐺𝑆 − 𝑆𝐺 + 2𝑁𝐴𝐷𝑃𝐻 → 2 𝐺𝑆𝐻 + 2𝑁𝐴𝐷𝑃+
DETOXIFICATION OF SUPEROXIDE ANION AND

HYDROGEN PEROXIDE
1. Superoxide dismutase
2. Glutathione peroxidase
3. Glutathione reductase

REACTIONS OF THE PENTOSE PHOSPHATE

PATHWAY
 The pentose phosphate pathway has 2 phases:
a. Oxidative phase
b. Non-oxidative phase
OXIDATIVE PHASE
 Produces NADPH
 Glucose 6-phosphate (G6P) is converted to 6
phosphogluconolactone and then 6-phosphogluconate.
 The reaction which is catalyzed by glucose 6-phosphate

dehydrogenase (G6PDH) is the rate limiting step
 It is activated by NADP+, insulin
 It is inhibited by NADPH
 Reactions are irreversible
 Cells have a greater need for NADPH than ribose 5-phosphate.
NON-OXIDATIVE
 Exchanging intermediate substrates between glycolysis and HMP

shunt
 Catalyzed by transketolase (which require thiamine
pyrophosphate) and transaldolase.
 Reactions are reversible

REACTIONS OF THE OXIDATIVE PHASE
 Glucose 6-phosphate is converted via the enzyme glucose-6-

phosphate dehydrogenase to 6-phosphogluconolactone and NADP+
is reduced to NADPH + H+.
 Glucose 6-phosphate dehydrogensase is the regulatory enzyme.
 The enzyme is highly specific for NADP+, the Km for NAD+ is
1000 greater than the Km for NADP+
 Note NADPH + H+ is formed twice in two separate reactions

STEP 1
STEP 2
 6-Phosphogluconolactone is hydrolyzed to 6-phosphogluconate

with the help of the enzyme gluconolactonase. (lactonase)

STEP 3
 6-phosphogluconate is oxidatively decarboxylated.

 The enzyme involved is 6-phosphogluconate dehydrogenase.
 Carbon dioxide is released and a second NADPH + H+ is generated
from NADP+
 The remaining carbons form ribulose-5 phosphate (a ketose)


REACTIONS OF THE NON-OXIDATIVE PHASE
 One cycle of the non-oxidative phase requires 3 ribose-5-

phosphates
 Ribulose 5-phosphate (a ketose) is isomerized to ribose 5-
phosphate or epimerized to xylulose 5-phosphate.
 Ribose 5-phosphate and xylulose 5-phosphat undergo reactions
catalyzed by transketolase and transaldolase that transfer carbon
units ultimately forming 2 moles of fructose 6-phosphate and
glyceraldehyde 3-phosphate
 Transketolase require thiamine pyrophosphate and transfers 2
carbon units
 Phosphopentose isomerase converts ribulose 5-phosphate to its
aldose isomer ribose 5-phosphate
 Ribulose 5-phosphate can also be epimerized to xylulose 5-
phosphate by ribose 5-phosphate epimerase.
DETAILS OF NON-OXIDATIVE PHASE OF THE HEXOSE

MONOPHOSPHATE PATHWAY
 In tissue primarily requiring NADPH, the pentose phosphates

produced in the oxidative phase are recycled into glucose 6-
phosphate
 In the non-oxidative phase ribulose 5-phosphate is first epimerized
to xylulose 5-phosphate.
 In a series of rearrangements of the carbon skeleton 6 five carbon
sugar phosphates are converted to 5 six carbon sugar phosphates,
completing the cycle and allowing continued oxidation of glucose
6-phosphate with the production of NADPH.
 Continued recycling leads ultimately to the conversion of glucose
6-phosphate to six carbon dioxide molecules.
 Transketolase catalyzes the transfer of 2-carbon fragments from a
ketose donor to an aldose acceptor.
 In the first appearance in the pentose phosphate pathway,
transketolase transfers C1 and C2 of xylulose-5 phosphate (a
ketose) to ribose-5phosphate forming a seven carbon product
sedoheptulose-7 Phosphate
 The remaining 3 carbon fragment from xylulose is glyceraldehyde-
3 phosphate
 Transaldolase catalyzes a reaction similar to the aldolase reaction

of glycolysis: a 3 carbon fragment is removed from sedoheptulose
7-phosphate and condensed with glyceraldehyde-3 phosphate
forming fructose -6 phosphate and the tetrose erythrose-4
phosphate.
 Transketolase acts again forming fructose 6-phosphate and
glyceraldehyde-3-phosphate from erythrose 4-phosphate and
xyluose-4 phosphate
 Two molecules of glyceraldehyde-3 phosphate formed by 2
iterations of these reactions can be converted to a molecule of
fructose 1,6-Bisphosphate as in gluconeogenesis and finally
FBPase-1 and phosphohexose isomerase converts fructose 1,6-
bisphosphate to glucose 6-phosphate.
 Generally, six pentose phosphates have been converted to five
hexose phosphates, the cycle is now completed. (note that these 6
pentose phosphates can come from ingestion through diet)


REGULATION OF PENTOSE PHOSPHATE PATHWAY

 Glucose 6-phosphate dehydrogenase is the regulatory enzyme
 NADPH is a potent competitive inhibitor of the enzyme.
 Usually the ratio NADPH/NADP+ is high so the enzyme is
inhibited.
 But with increased demand for NADPH activity it is stimulated.
 The reactions of the non-oxidative portion of the pentose pathway
are readily reversible.
 The concentrations of the products and reactants can shift
depending on the metabolic needs of a particular cell or tissue:

1. Mode1: Rapidly dividing cells require more ribose-5 phosphate

than NADPH
2. Mode 2: The need for NADPH and ribose 5-phosphate is balanced
3. Mode 3: More NADPH is needed than ribose 5-phosphate: fatty

acid synthesis in adipose cell

4. Mode 4:The cell needs both NADPH and ATP

GLUTATHIONE AND NADPH

 Glutathione is a tripeptide composed of glutamate, Cysteine and
glycine.
 Reduced glutathione (GSH) maintains the normal reduced state of
the cell.
FUNTCIONS
1. Serves as a reductant
 Conjugates to drugs making them water soluble.
 Involved in amino acid transport across cell membranes.
 Co-factor in some enzymatic reactions: rearrangement of
protein disulfide bonds.

2. The sulfhydryl of GSH is used to reduce peroxides (ROS) formed

during oxygen transport
 Reactive oxygen species (ROS) damage macromolecules
(DNA, RNA and protein) and ultimately lead to cell death.
 The resulting oxidized form of GSH is 2 molecules linked by
a disulfide bridge (GS-SG)
 The enzyme glutathione reductase uses NADPH as a cofactor
to reduce GS-SG back to 2 moles of GSH. Thus the pentose
pathway is linked to supply of adequate amounts of GSH.
 Defective glucose 6-phosphate dehydrogenase leads to insufficient

production of NADPH, which causes insufficient glutathione
GLUTATHIONE AND ERYTHROCYTES
 GSH is extremely important particularly in the highly oxidizing

environment of the R.B.C cell
 Mature R.B.Cs have no mitochondria and are totally dependent on
NADPH from the pentose phosphate pathway to regenerate GSH
from GSSG via glutathione reductase
 In fact as much as 10% of glucose consumption by erythrocytes is
mediated by the pentose pathway.
 The reduced form of glutathione serves as a sulfhydroxyl buffer
 It maintains Cysteine residues in hemoglobin and other proteins in
a reduced state.
 GSH is essential for normal RBC structure and keeping
haemoglobin in Fe2+ state
 Reduced glutathione also detoxifies peroxides
2GSH + ROOH--> GSSG + H2O + R-OH

 Cells with low levels of GSH are susceptible to hemolysis

 Individuals with reduced GSH are subject to hemolysis.
 This is often clinically seen as black urine under certain conditions
CONDTIONS FOR HEMOLYTIC ANAEMIA RELATED G6PD

DEFICIENCY
 The ingestion of oxidative agents that generate peroxides or

reactive oxygen species (ROS)
 Antimalarials-pamaquine
 Purine glycoside from fava beans
 Individuals with G6PD deficiency cannot produce sufficient GSH
to cope with the ROS.
 Proteins become cross-linked leading to Heinz body formation and
cell lysis.
SUMMARY
 The Pentose phosphate pathway present in the cytosol can account
for the complete oxidation of glucose producing NADPH and
carbon dioxide but not ATP
 The pathway has an oxidative phase, which is irreversible and
generates NADPH (from 2 reactions) and a non-oxidative phase
which is reversible and provides ribose precursors for nucleotide
synthesis. The complete pathway is only present in those tissue
having a requirement for NADPH for reductive synthesis e.g.
lipogenesis or steroidogenesis whereas the non-oxidative phase is
present in all cells requiring ribose
 In erythrocytes the pathway has a major function in preventing
hemolysis by providing NADPH to maintain glutathione by

providing NADPH to maintain glutathione in the reduced state as

the substrate for glutathione peroxidase
URONIC ACID PATHWAY

OBJECTIVES
1. Biomedical significance
2. Pathway reactions
3. Pentosuria
BIOMEDICAL SIGNIFICANCE OF URONIC ACID

PATHWAY.
 The uronic acid pathway is an alternative pathway for the
oxidation of glucose that does not provide a means of producing
ATP, but is utilized in the oxidation of glucose to:
1. D-Glucoronic acid: which is used in detoxification of foreign
chemicals (xenobiotics) and enters in the formation of
mucopolysaccharides
2. Xylulose-5 phosphate used in the hexose monophosphate
pathway
3. Ascorbic acid in certain animals except guinea pigs and humans
 Inherited deficiency of one an enzyme in this pathway produces
“essential Pentosuria”
IMPORTANCE OF UDP-GLUCORONIC ACID

 UDP-glucoronate which is mainly used for detoxification of
foreign chemicals and for synthesis of mucopolysaccharides.

 It conjugates to less polar compounds as bilirubin, steroids and

some drugs making them more water soluble (detoxification)
 It is used in the synthesis of Glycosaminoglycans (GAGS)
 UDP-glucoronic acid (Active form) is needed in
(mucopolysaccharides) heparin, hyaluronic acid…
 In plants and some animals (not humans) glucoronic acid serves as
a precursor of L-ascorbic acid (vitamin C)
 The uronic acid pathway also provides a mechanism by which
dietary D-xylulose enters the central pathway
 The unutilized glucoronic produced in this pathway is converted to
xylulose 5-phosphate which is further metabolized through the
non-oxidative phase of the HMP pathway.
FORMATION OF UDP-GLUCORONIC ACID

 Glucose 6 phosphate is isomerized to glucose 1-phosphate by a
phosphoglucomutase.
 Glucose 6 phosphate then reacts with uridine triphosphates (UTP)
to form uridine diphosphate glucose (UDP Glc) in a reaction
catalyzed by UDPGlc pyrophosphorylase
 All the above reactions above are similar to those already
described under glycogenesis (glycogen synthesis)

 UDPGlc is oxidized at carbon 6 by NAD-dependent UDP Glc

dehydrogenase in a two-step reaction to yield UDP-glucoronate
o UDP-Glc is oxidized by an enzyme UDP-Glc dehydrogenase
to UDP-glucoronate
o UDP-glucoronate is then hydrolyzed to form D-glucoronate
FORMATION OF L-GULONIC ACID
 D-glucoronate is first reduced by the NADPH dependent enzyme

glucoronate reductase to L-gulonate.
 L-gulonate has different fates in different organisms

 It can be used to synthesize ascorbic acid in some animals and
plants.
 It can be also used to synthesize xylulose
 L-gulonate is oxidized to 3-keto-L-gulonate which is then
decarboxylated to L-xylulose.
 L-xylulose is converted to the D isomer by NADPH-dependent

reduction to xylitol, followed by oxidation in an NAD-dependent
reaction to D-xylulose
 D-xylulose is converted to D-xylulose 5 phosphate at the expense
of ATP which is metabolized via the pentose pathway.
 In another instance D-xylulose is converted to D-xylulose-1
phosphate and then glyceraldehyde


THE URONIC ACID PATHWAY
PENTOSURIA
 Pentosuria is the condition in which an unusual reducing

substance, one of the pentose sugars, is constantly excreted in the
urine and gives a positive reaction on testing with benedicts
solution
 Biochemical defect: the enzyme (L-xylitol dehydrogenase) that
causes the conversion of L-xylulose to xylitol is deficient. As a
result excess L-xylulose is excreted in urine.
SUMMARY
 The uronic acid pathway is the source of glucoronic acid for
conjugation of many endogenous and exogenous substances before
excretion as glucoronides in urine and bile
 In humans, ascorbic acid is not produced by this pathway
 A defect in the conversion of L-xylulose to xylitol leads to
pentosuria in which excess L-xylulose is excreted in urine
AMINO ACID METABOLISM

OBJECTIVES
1. Amino acid synthesis
2. Amino acid catabolism: carbon chain, amino group and urea
formation.
3. Disorders of amino acid metabolism
AMINO ACIDS
 Amino acids are the building blocks of proteins.
 They structurally consist of:
 A carboxyl group (-COO-)
 An amino group (-NH3+)
 A hydrogen (H)
 A side chain (R-group)
 Almost all amino acids are chiral in nature (i.e. consist of 4
different groups surrounding the alpha carbon) except GLYCINE
which has 2 H atoms attached to the -carbon.
 It is for this reason that all the other amino acids are optically
active and show D- and L- configurations while glycine does not.
 All the other amino acids have an L-configuration (designated
Lamino acid)
 The 20 amino acids include:
 Glycine, lysine, leucine, isoleucine, tryptophan, proline,
serine, glutamine, glutamate, aspartate, valine, alanine,
phenylalanine, histidine, threonine, methionine, tyrosine,
aspartic acid, Cysteine, and arginine.
 Concerning amino acids in a protein, they contain an amino
terminus which is on the left and a carboxyl terminus which is on
the right.

 These amino acids form proteins used to synthesis hormones,

enzymes, transport molecules, antibodies and form part of the
structural component of membranes. Furthermore amino acids can
be used in metabolism to provide energy when all the other energy
reserves are depleted.
 Amino acids that form proteins are specified by the genetic code: a
set of codons that code for the synthesis of protein in addition
some stop codons stop the synthesis of proteins.
 Amino acids can be classified according to the chemistry of their
side chain:
A. Hydrophobic side chains contain
1. Aliphatic groups: Glycine, Alanine, Valine, Leucine and
Isoleucine
2. Aromatic rings: Phenylalanine, proline (which is an imino
group)
 Some ringed side chains are however hydrophilic these
include: tyrosine
B. Amino acids with hydroxyl groups include: Serine, threonine
and tyrosine
 These are all hydrophilic
C. Amino acids with sulfur: Cysteine (hydrophilic) and methionine
(hydrophobic)
D. Amino acids with basic side chains: Histidine, Arginine and
lysine
 To remember these amino acids use the pneumonic
“BASICally the HIStory of ARGentina is a Lie” to help you
remember these basic side chained amino acids.
E. Amino acids with acid and amine side chains:
1. Acid groups: Aspartic acid, glutamic acid

2. Amide groups: glutamine, and asparagine (both are

hydrophilic)
 The 20 amino acids have been designated by 1 letter to represent
an amino acid e.g. the letter “Y” represents the amino acid
TYROSINE. Below are the other one letter designations for the 20
amino acids:
 Amino acid residues as a group end in the letters “yl” e.g. arginyl
for an arginine residue.
 Note that amino acids can also be given a 3 letter designation e.g.
“Trp” represents tryptophanyl; an amino acid residue of
tryptophan.
 Below are the 20 amino acids with their 3 letter designations:

 It is also important to note that at physiological pH the alpha-

amino group (pKa is about 9) is protonated and becomes positively
charged and the carboxyl group (pKa is about 2) is dissociated and
carries a negative charge.
TABLE OF SUMMARY OF ALL 20 AMINO ACIDS

NAME DESIGNATIONS CARBON R-GROUP HYDRO-

NUMBER CLASS PHOBIC/PHILIC
1 3
LETTER
LETTER
GLYCINE G Gly 2 ALIPHATIC HYDORPHOBIC
ALANINE A Ala 3 ALIPHATIC HYDORPHOBIC
VALINE V Val 5 ALIPHATIC HYDORPHOBIC
LEUCINE L Leu 6 ALIPHATIC HYDORPHOBIC
ISOLEUCINE I Ile 6 ALIPHATIC HYDORPHOBIC
CYSTEINE C Cys 3 SULFUR HYDROPHILIC
METHIONINE M Met 5 SULFUR HYDROPHOBIC
ARGININE R Arg 6 BASIC HYDOPHIILIC
LYSINE K Lys 6 BASIC HYDROPHILIC
GLUTAMIC E Alu 5 ACID HYDROPHILIC

ACID
ASPARTIC D Asp 4 ACID HYDROPHILIC

ACID
GLUTAMINE Q Gln 5 AMINE HYDROPHILIC

ASPARAGINE N Asn 4 AMINE HYDROPHILIC
SERINE S Ser 3 -OH HYDROPHILIC
TYROSINE Y Tyr 9 -OH, RING HYDROPHILIC
THREONINE T Thr 4 -OH HYDROPHILIC
TRYPTOPHAN W Trp 10 RING HYDROPHOBIC
PROLINE P Pro 5 IMINO, HYDROPHOBIC

RING
PHENYL- F Phe 9 RING HYDROPHOBIC

ALANINE
HISTIDINE H His 5 RING, HYDROPHILIC

BASIC,
 The 20 amino acids present in the proteins are all biologically

essential for health however humans can synthesize 12 of the 20
common amino acids from the amphibolic intermediates of
glycolysis and the Krebs cycle.
 Since these amino acids are synthesized in the body even if they
are lacking from diet the individual’s nutrition is not affect, it is for
this reason that these amino acids are termed NUTRITIONALLY

non-essential amino acids.
 The nutritionally non- essential amino acids include:
 Alanine, asparagine, Cysteine, glutamate, glycine, proline,
serine, tyrosine and glutamate
 The nutritionally essential amino acids include:

 Methionine, valine, leucine, isoleucine, histidine
phenylalanine, tryptophan, Arginine, threonine and lysine
 To remember these amino acids just use this pneumonic:
“ESSENTIALLY My Very Lazy Infant Has Produced Ten
Thousand Lives”
 Note: you do not need to know both nutritionally essential
and non-essential amino acids classification; all you have to
do is to know one class and you can work out the other class
provided you already know all the 20 amino acids.
 Nutritionally Semi-essential amino acids are growth promoting
factors. They are not synthesized in adequate amounts in children
during growth but are produced sufficiently in adults these include:
Histidine and Arginine.

AMINO ACID ANABOLISM

 All amino acids are derived from intermediates in glycolysis, the
citric acid cycle or the pentose phosphate pathway.
 Nitrogen enters these pathways by way of glutamate and
glutamine.
 Some pathways are simple others are not.
 10 amino acids are just one or several steps removed from the
common metabolite from which they are derived.
 Biosynthesis of aromatic amino acids are more complex
 The enzymes glutamate dehydrogenase, glutamine synthetase and
aminotransferases occupy central position in the amino acid
biosynthesis.
 The combined effect of these 3 enzymes is to transform
ammonium ion into the alpha-amino nitrogen of various amino
acids.
 Most bacteria and plants can synthesize all 20 common amino

acids, mammals can synthesize about half of them, these are the
nutritionally non-essential amino acids, not needed in the diet.
 The remainder, the nutritionally essential amino acids must be
obtained from food
 A useful way to organize these biosynthetic pathways is to group
into 6 families corresponding to their metabolic precursors as
shown below:
GLUTAMATE AND GLUTAMINE

 Reductive amination of -ketoglutarate is catalyzed by glutamate
dehydrogenase

 Amination of glutamate to glutamine is catalyzed by glutamine

synthetase.
ALANINE
 Transamination of pyruvate forms alanine.
ASPARTATE AND ASPARAGINE

 Transamination of oxaloacetate forms aspartate
 The conversion of aspartate to asparagine is catalyzed by
asparagine synthetase, it resembles glutamine synthase except that
glutamine not ammonium ion provides the nitrogen.
SERINE
 Oxidation of the -hydroxyl group of the glycolytic intermediate
3-phosphoglycerate converts it to an oxo acid whose subsequent
transamination and dephosphorylation leads to serine
GLYCINE
 Is formed from choline and from serine
PROLINE
 Proline is formed from glutamate by reversal of the reactions of
proline catabolism.
CYSTEINE
 While not nutritionally essential, it is formed from methionine
which is nutritionally essential. Following conversion of

methionine to homocysteine, homocysteine and serine form

cysteine and homoserine.
TYROSINE
 Phenylalanine hydroxylase converts phenylalanine to tyrosine.
 Phenylalanine is formed from the reaction of phosphoenol
pyruvate and erythrose 4-phosphate (from glycolysis and HMP
intermediates)
 Tyrosine can also be formed directly from phenylalanine
VALINE, LEUCINE AND ISOLEUCINE

 While leucine, valine and isoleucine are all nutritionally essential
amino acids, tissue aminotransferases reversibly interconvert all 3
amino acids and their corresponding -keto acids
 These keto acids thus can replace their amino acids in diet.


THE NITROGEN CYCLE

 The biosynthetic pathways leading to amino acids and nucleotides
share a requirement for nitrogen.
 Because soluble, biologically useful nitrogen compounds are
generally scarce in natural environments, most organisms maintain
strict economy in their use of ammonia, amino acids and
nucleotides.
 Free amino acids, purines and Pyrimidines formed during
metabolic turnover of proteins and nucleic acids are often salvaged
and reused.
 The most important source of nitrogen is air, which is four-fifths
molecular nitrogen (N2)
 A few species can convert atmospheric nitrogen into forms useful
to living organisms.
 The first step in the cycle is fixation (reduction) of atmospheric
nitrogen by nitrogen-fixing bacteria to yield ammonia (NH3 or
NH4+)
 This is done by nitrogen fixing bacteria that live as Symbionts in
the root nodules of leguminous plants e.g. Rhizobium
 Although ammonia can be used by most living organisms, soil
bacteria that derive their energy by oxidizing ammonia to nitrite
(NO2-) (nitrifying bacteria and archea) and ultimately Nitrate (NO3-
) (nitrifying bacteria) are so abundant and active that nearly all the
ammonia reaching the soil is oxidized to nitrate.
 This process is known as nitrification.
 Plants and many bacteria can take up and readily reduce nitrate and
nitrile through the action of nitrate and nitrite reductase.
 The ammonia so formed is incorporated into amino acid by plants.

 Animals then use plants as a source of amino acids, both

nutritionally non-essential and essential to build their proteins.
 When organisms die, microbial degradation of their proteins
returns ammonia to the soil where nitrifying bacteria can again
convert it to nitrite and nitrate.
 A balance is maintained between fixed nitrogen and atmospheric
nitrogen by bacteria that convert nitrate to N2 under anaerobic
conditions, a process called Denitrification.
 These soil bacteria use NO3- rather than O2 as the ultimate electron
acceptor in a series of reactions that ( like oxidative
phosphorylation) generates a transmembrane proton gradient
which is used to synthesize ATP.
 The nitrogen cycle is short-circuited by a recently discovered
group of bacteria (denitrifying bacteria) that promote anaerobic
ammonia oxidation or anammox a process that converts ammonia
and nitrate to N2.
NITROGENASE COMPLEX

 Only certain bacteria and archea can fix atmospheric nitrogen e.g.
cyanobacteria of fresh and salt waters, methanogenic archea (strict
anaerobes that obtain energy and carbon by converting H2 and CO2
to methane), other kinds of free-living soil bacteria such as
Azotobacter species and the nitrogen fixing bacteria that live as
Symbionts in the root nodules of leguminous plants.
 The first important product of nitrogen fixation is ammonia, which
can be used by all organisms either directly or after its conversion
to other soluble compounds such as nitrate, nitrites or amino acids.
 The reduction of nitrogen to ammonia is an exergonic reaction
𝑁2 + 3𝐻2 → 2𝑁𝐻3 ∆𝐺 ′𝑜 = −33.5𝑘𝑗/𝑚𝑜𝑙
 The 𝑁 ≡ 𝑁 triple bond however is very stable, with a bond energy

of 930kj/mol
 Nitrogen fixation therefore has extremely high activation energy
and atmospheric nitrogen is almost chemically inert under normal
condition.
 This reaction is used in the industrial preparation of ammonia by
the Haber process.
 The Haber process requires temperatures of 400 to 500OC and
nitrogen and hydrogen at pressure of tens of thousands of
kilopascals (700 atms) together with a finely divided iron catalyst
to provide the necessary activation energy.
 Biological nitrogen fixation however must occur at biological
temperatures and at 0.8 atms of nitrogen and the high activation
barrier is overcome by other means.
 This is accomplished at least in part by the binding and hydrolysis
of ATP.
 Overall reaction

𝑁2 + 10𝐻 + + 8 𝑒 − + 16𝐴𝑇𝑃 → 2𝑁𝐻4+ + 16𝐴𝐷𝑃 + 16𝑃𝑖 + 𝐻2

 Biological nitrogen fixation is carried out by a highly conserved
complex of proteins called the nitrogenase complex, the crucial
components of which are dinitrogenase reductase and
dinitrogenase
 Dinitrogenase reductase is a dimer of 2 identical subunits.
 It contains a single 4Fe- 4S redox centers, bound between the
subunits and can be oxidized and reduced by one electron.
 It also has 2 binding sites for ATP/ADP (one site on each subunit)
 Dinitrogenase, a tetramer with 2 copies of 2 different subunits
contains both iron and molybdenum its redox centers have a total
of 2 Mo, 32 Fe and 30S per tetramer
 About half of the iron and sulfur is present as two bridged pairs of
4Fe-4S centers called P-clusters, the remainder is present as a part
of a novel iron-molybdenum cofactor.

 Nitrogen fixation is carried out by a highly reduced form of

dinitrogenase and requires 8 electrons:
 Six for the reduction of N2
 Two for production of one molecule of H2 as an obligatory
part of the reduction mechanism.
 Dinitrogenase is reduced by transfer of electrons from
dinitrogenase reductase.
 The required 8 electrons are transferred from reductase to
dinitrogenase one at a time, a reduced reductase molecule binds to
the dinitrogenase and transfers a single electron, then oxidized
reductase dissociates from dinitrogenase in a repeating cycle.
 Each turn of the cycle requires the hydrolysis of 2 ATP molecules
by the dimeric reductase.

 The immediate source of electrons to reductase varies with reduced

ferredoxin, reduced flavodoxin and perhaps other sources playing a
role. In at least one species the ultimate source of electrons to
reduce ferredoxin is pyruvate.
 The role of ATP in this process is somewhat unusual.
 ATP can contribute not only chemical energy, through hydrolysis
of one or more of its phosphoanhydride bonds but also binding
energy through non-covalent interactions that lower the activation
energy.
 In the reaction carried out by dinitrogenase reductase both ATP
binding and ATP hydrolysis bring about protein conformational
changes that help overcome the high activation energy of nitrogen
fixation.
 The binding of 2 ATP molecules to the reductase shifts the
reduction potential (E’O) of this protein from -300 to -420 mV an
enhancement of its reducing power that is required to transfer
electron to dinitrogenase.
 The ATP molecules are then hydrolyzed just before the actual
transfer of one electron to dinitrogenase.
ONE CARBON UNIT CARRIERS IN AMINO ACID

METABOLISM
 Some synthetic pathways require the addition of single carbon
groups that exist in a variety of oxidation states including formyl,
methenyl, methylene and methyl.
 These single carbon groups can be transferred from carrier
compounds such as tetrahydrofolate- FH4 (an activated form of
folic acid) and S-adenosylmethionine (SAM) to specific structures
that are being synthesized or modified.

FOLIC ACID: A CARRIER OF ONE-CARBON UNITS

 The active form of folic acid tetrahydrofolic acid (THF) cannot be
synthesized in the body, it is produced from folate by dihydrofolate
reductase in a 2-step reaction requiring 2 NADPH.
 The carbon unit carried by THF is bound to nitrogen N5 or N10, or
to both N5 and N10.
 THF allows one carbon compounds to be recognized and
manipulated by biosynthetic enzymes.
 Folate deficiency presents as a megaloblastic anaemia due to
decreased availability of the purines and thymidine
monophosphate (TMP) needed for DNA synthesis.
 Serine, glycine and formaldehyde produce N5,N10-methylene-THF
 Serine transfers a carbon group to THF and is converted to
glycine reversibly.

 When glycine transfers a one-carbon unit to THF,, NH4+ and

CO2 are produced.
 Formaldehyde is produced from -N-CH3 of epinephrine.
 Histidine is degraded to forminoglutamate (FLGLU) and the
formino group is transferred to THF.
 Formate derived from tryptophan produces N10-formyl-THF.


S-ADENOSYLMETHIONINE (SAM)
 SAM is synthesized from methionine and ATP
 Methyl groups are supplied by SAM for the following conversions
a. Guanidinoacetate to creatine
b. Phosphatidylethanolamine to phosphatidylcholine
c. Norepinephrine to epinephrine
d. Acetylserotonin to melatonin
e. Polynucleotides to methylated polynucleotides
 When SAM transfers its methyl group to an acceptor S-
adenosylhomocysteine (SAH) is produced
 SAH releases adenosine to form homocysteine, which obtains a
methyl group from vitamin B12 to form methionine, methionine
reacts with ATP to regenerate SAM.

ANABOLIC REACTIONS OF AMINO ACIDS

GLUTAMATE AND GLUTAMINE
 Reduced nitrogen in the form of ammonium ions is assimilated

into amino acids and then into other nitrogen containing
biomolecules.
 2 amino acids, glutamate and glutamine provide the critical entry
point.
 Glutamate is the source of amino groups for most other amino
acids, through transamination reactions.
 The amide nitrogen of glutamine is a source of amino groups in a
wide range of biosynthetic processes.
 One or both of these amino acids are present at higher
concentrations-sometimes an order of magnitude or more higher-
than other amino acids.
 The biosynthetic pathways to glutamate and glutamine are simple
and all or some of the steps occur in most organisms.
GLUTAMATE
 Glutamate in humans can be formed from:

a. Reactions involvingketoglutarate and NH4+
b. Reactions involving transamination catalyzed by amino
transferases where -keto acids react with other amino acids to
form other keto acid and other amino acids counterparts.
 The formation of glutamate from -ketoglutarate and NH4+ is a
one step reaction.
 It is catalyzed by L-glutamate dehydrogenase, an enzyme present
in all organisms.
 In this reaction the reducing power is furnished by NADPH:

 L-glutamate dehydrogenase is located in the mitochondrial matrix

 Glutamate dehydrogenase can use either NADH or NADPH as a
coenzyme.
 NADH is used primarily in oxidative deamination of the carbon
skeleton.
 NADPH is used in reductive amination (the simultaneous gain of
ammonia coupled with the reduction of the carbon skeleton.)
 The direction of the reaction depends on the relative concentrations

of glutamate, ketoglutarate and ammonia, and the ratio of
oxidized to reduced co-enzymes.
 E.g. after ingestion of a meal containing protein, glutamate levels

in the liver are elevated and the reaction proceeds in the direction
of amino acid degradation and formation of ammonia, however if
the concentration of ammonia in the blood increases the reaction is
driven towards the synthesis of glutamate thus lowering the
ammonia concentration due to its toxic effect.
 NOTE: GTP allosterically inhibits glutamate dehydrogenase while
ADP activates it (indicating the energy state of the cell)
GLUTAMINE
 The most important pathway for the assimilation of NH4+ into

glutamine requires 2 reactions.
 First glutamine synthetase catalyzes the reaction of glutamate and
NH4+
 This reaction takes place in 2 steps with enzyme bound glutanyl
phosphate as an intermediate.
 The reaction is catalyzed by the enzyme glutamine synthetase

 Glutamaine synthetase is found in all organisms
 In addition to producing glutamine for protein synthesis, glutamine
synthetase has a central role in amino acid metabolism in

mammals, it converts free ammonium ions which are toxic to

glutamine for transport in blood.
 The reaction is driven by hydrolysis of ATP.
PROLINE BIOSYNTHESIS FROM GLUTAMIC

SEMIALDEHYDE
 Glutamate is converted to proline by cyclization and reduction

reactions.
 Proline is a cyclic derivative of glutamate.
 In the first step of proline synthesis, ATP reacts with -carboxyl
group of glutamate to form an acyl phosphate which is replaced by
NADPH or NADH to glutamate semialdehyde
 This intermediate undergoes rapid spontaneous cyclization and is
then reduced further to yield proline



BIOSYNTHESIS OF ASPARTATE
 Aspartate is synthesized from:

a. The transamination of oxaloacetate with glutamate as the
amino group donor
 This reaction is catalyzed by aspartate amino transferase
 It produces aspartate and ketoglutarate
b. Deamination of asparagines
 The reaction is catalyzed by asparaginase
 It requires an input of water

BIOSYNTHESIS OF ASPARAGINE FROM ASPARTATE AND

GLUTAMINE
 Asparagine is synthesized by the amination of aspartate

 Glutamine is the amino donor.
 The reaction requires hydrolysis of 2 phosphate bonds and is
catalyzed by the enzyme asparagine synthetase.

SERINE BIOSYNTHESIS FROM 3-PHOSPHOGLYCERATE
 In the first step the hydroxyl group of 3 phosphoglycerate is

oxidized by a dehydrogenase (using NAD+) to yield 3-
phosphopyruvate.
 Transamination (catalyzed by aminotransferase) from glutamate
yields 3-phosphoserine which is hydrolyzed to free serine by
phosphoserine phosphatase.
GLYCINE BIOSYNTHESIS FROM SERINE
 Removal of a carbon by serine hydroxymethyl transferase forms

glycine
 THF accepts the beta-carbon (C-3) of serine which forms a
methylene bridge between N-5 and N-10 to yield N5N10-methylene
tetrahydrofolate
 The overall reaction which is reversible also requires pyridoxal
phosphate.

CYSTEINE BIOSYNTHESIS FROM METHIONINE AND

SERINE
 The amino acid is synthesized by 2 consecutive reactions in which

homocysteine combines with serine forming cystathionine
[catalyzed by cystathionine -synthase (B6)] that in turn is
hydrolyzed to ketobutyrate and Cysteine. (catalyzed by
cystathionine lyase)
 Homocysteine is derived from methionine
 In the synthesis of homocysteine, methionine adenosyl transferase
catalyzes the condensation of methionine with ATP forming S-
adenosyl methionine (SAM)

 Formation of SAM is driven by hydrolysis of 3 phosphate bonds in

ATP.
 The methyl attached to the tertiary sulfur of SAM is “activated”
and is donated to a variety of acceptors
 After donation of the methyl group S-adenosylhomocysteine
(SAH)is produced, this can then be hydrolyzed to homocysteine
and adenosine (catalyzed by homocysteinase)
 Because methionine is a nutritionally essential amino acid,
cysteine synthesis can be sustained only if the dietary intake of
methionine is adequate.
TYROSINE SYNTHESIS FROM PHENYLALANINE
 Tyrosine is formed from phenylalanine by phenylalanine

hydroxylase.
 The reaction requires molecular oxygen and the coenzyme
tetrahydrobiopterin (BH4) which can be synthesized from GTP by
the body.
 One atom of molecular oxygen becomes the hydroxyl group of
tyrosin and the other atom is reduced to water.
 Durng the reaction BH4 is oxidized by dihydrobiopterin (BH2)
 BH4 is regenerated from BH2 by NADH-requiring
dihydropteridine reductase.
 NOTE: tyrosine like Cysteine is formed from an essential amino
acid and is therefore non-essential only in the presence of adequate
dietary phenylalanine.


ALANINE
 Alanine is synthesized from pyruvate by transamination from

glutamate
 The enzyme involved is alanine transaminase.


AMINO ACID CATABOLISM

 Amino acid degradation makes a significant contribution to the
generation of metabolic energy.
 Amino acids undergo oxidative degradation in 3 different
metabolic circumstances:
1. During normal synthesis and degradation of cellular proteins
(protein turnover) some amino acids that are released from
proteins breakdown and are not needed for new protein
synthesis undergo oxidative degradation
2. When diet is rich in protein and the ingested amino acids exceed
the body’s needed requirements for protein synthesis, the
surplus is catabolized: amino acids cannot be stored.

3. During starvation or in uncontrolled diabetes mellitus, when

carbohydrates are either unavailable or not properly utilized,
cellular proteins are used as fuels.
 Amino acids lose their amino group to form keto acids, the
“carbon skeletons” of amino acids.
 The keto acids undergo oxidation to carbon dioxide and water
or provide 3 and 4-carbon units that can be converted by
gluconeogenesis into glucose, the fuel for brain, skeletal muscle
and erythrocytes.
 Amino acid catabolic pathways converge on the central catabolic
pathways with the carbon skeletons of most amino acids finding
their way to the citric acid cycle.
 Amino acid catabolism includes a key step in which the amino
group is separated from the carbon skeleton and shunted into the
pathways of amino group metabolism

METABOLIC FATES OF THE AMINO GROUP

 Amino acids derived from dietary proteins are the source of most
amino groups.
 Most amino acids are metabolized in the liver.
 Some of the ammonia generated in this process is recycled and
used in a variety of biosynthetic pathways, the excess is either
excreted directly or converted to urea or uric acid for excretion
depending on the organism.
 Excess ammonia generated in other (extrahepatic) tissue travels to
the liver (in the form of glutamine) for conversion to the excretory
form.
 Glutamate and glutamine play essential roles in nitrogen
metabolism acting as a kind of general collection point for amino
groups.
 In the cytosol of the hepatocytes, amino groups from most amino
acids are transferred to -ketoglutarate to form glutamate which
enters the mitochondria and gives up its amino group to form
ammonium ions.
 Excess ammonia generated in most other tissue is converted to the
amide nitrogen of glutamine which passes to the liver and then into
the liver mitochondria.
 Glutamine or glutamate or both are present in high concentrations
than any other amino acid in most tissues.
 In skeletal muscle, excess amino groups are generally transferred
to pyruvate to form alanine, another important molecule in the
transport of amino groups to the liver.
 The first step in the catabolism of most L-amino acids, once they
have reached the liver is removal of the -amino groups, promoted
by the enzymes called amino transferases/ transaminase.
 Amino transferase enzymes are named after the amino acid that is
donating the amino group i.e. alanine transferase, aspartate
transferase.
 In these transamination reactions, the -amino group is transferred
to the -amino groups of -ketoglutarate leaving behind the
corresponding -keto acid anlog of the amino acid.
 There is no net deamination in these reactions because -
ketoglutarate becomes aminated as the -amino acid is
deaminated.
 The effect of transamination is to collect the amino groups from
many different amino acids in the form of L-glutamate.
 The glutamate then functions as an amino group donor for
biosynthetic pathways or for excretion pathways that lead to the
elimination of nitrogenous waste products.
 These transamination reactions are freely reversible.
 The collected glutamate amino acids in the liver lose their amino
groups which are then prepared for excretion.
 In hepatocytes, glutamate is transported from the cytosol into
mitochondria where it undergoes oxidative deamination catalyzed
by L-glutamate dehydrogenase which require NAD+ or NADP+
reducing equivalents although it prefers NAD+ for this reaction.
 The combined action of an aminotransferase and glutamate
dehydrogenase is referred to as trans-deamination.
 NH4+ is produced in the process and it enters the urea cycle.
 The -ketoglurate formed from glutamate deamination can be
used in the citric acid cycle and for gluconeogenesis.
 NOTE: for transport of toxic free ammonia to kidney and lungs
glutamate is combined with ammonia to form glutamine catalyzed
by the enzyme glutamine synthetase (Click here to refer the
anabolic synthesis of glutamine)
 Some amino acids bypass the trans-deamination pathway and

undergo direct oxidative deamination forming the corresponding
-keto acid and ammonium ion.
 Serine and threonine can be directly deaminated by dehydratases
 Serine is deaminated to pyruvate.
 Threonine is deaminated to -ketobutyrate.
UREA CYCLE

 If not reused for the synthesis of new amino acids or other

nitrogenous products, amino groups are channeled into a single
excretory end product.
 Most aquatic species such as bony fish are ammonotelic excreting
amino nitrogen as ammonia.
 Most terrestrial animals are ureotelic excreting amino nitrogen in
the form of urea, bird and reptiles are uricotelic excreting amino
nitrogen as uric acid.
 In ureotelic organisms the ammonia deposited in the mitochondria
of hepatocytes is converted to urea in the urea cycle.
 Urea production occurs almost exclusively in the liver and is the
fate of most of the ammonia channeled there.
 The urea passes into the bloodstream and thus to the kidneys and is
excreted into the urine.
 Urea is produced from ammonia in five enzymatic steps.
 The urea cycle begins inside the liver mitochondria but 3 of the
subsequent steps take place in the cytosol, the cycle thus spans 2
cellular compartments.
 The first amino group to enter the urea cycle is derived from
ammonia in the mitochondrial matrix
 The liver also receives some ammonia via the portal vein from the
intestine from the bacterial oxidation of amino acids.
 The ammonium ions generated in the liver mitochondria are
immediately used together with carbon dioxide (as HCO3-)
produced by mitochondrial respiration to form cabamoyl
phosphate in the matrix.
 This ATP-dependant reaction is catalyzed by carbamoyl phosphate
synthetase 1 a regulatory enzyme.

 The mitochondrial form of the enzyme is distinct from the

cytosolic (II) form, which has a separate function in pyrimidine
biosynthesis.
 One amino group enters the urea cycle as carbamoyl phosphate
formed in the mitochondrial matrix (by the reaction of ammonium
ions, HCO3- and 2 ATP) and the other enters as aspartate formed in
the matrix by transamination of oxaloacetate and glutamate.
 The carbamoyl phosphate which functions as an activated
carbamoyl group donor now enters the urea cycle. The cycle has
four subsequent enzymatic steps.
 First, carbamoyl phosphate donates its carbamoyl group to
ornithine to form citrulin with the release of an inorganic
phosphate.
 Ornithine plays a role resembling that of oxaloacetate in the TCA
cycle, accepting material at each turn of the cycle.
 The reaction is catalyzed by ornithine transcarbamoylase and the
citruline passes from the mitochondrion to the cytosol.
 The second amino group now enters from aspartate (generated by
transamination and transported into the cytosol from
mitochondrion) by a condensation reaction between the amino
group of aspartate and the ureido (carbomyl) group of citruline
forming argininosuccinate
 This cytosolic reaction is catalyzed by argininosuccinate
synthetase requiring ATP and proceeds thrpugh citrullyl-AMP
intermediate.
 The argininosuccinate is then cleaved by argininosuccinase to form
free arginine and fumerate.
 Fumerate enters the mitochondria to join the pool of TCA
intermediates
 This is the only reversible step in the urea cycle.
 In the last reaction of the urea cycle the cytosolic enzyme arginase
cleaves arginine to yield urea and ornthine
 Ornithine is transported into the mitochondria to initiate another
round of the urea cycle.

LIPID METABOLISM
OBEJECTIVES
1. Fatty acid oxidation (beta oxidation)
2. Ketogenesis
3. Lipid biosynthesis
4. Regulation of lipid metabolism
FATTY ACIDS
 Fatty acids are carboxylic acids with a long aliphatic chain which
is either saturated or unsaturated.

 Fatty acids that are saturated only contain single C-C bonds in their
carbon skeleton while unsaturated fatty acids have double bonds in
their carbon skeleton.
 If a fatty acid has many double bonds in the carbon skeleton it is
termed a “polyunsaturated” fatty acid
 If a fatty acid has one double bond in the carbon skeleton it is
termed a “monounsaturated” fatty acid.
 Saturated chains of fatty acids pack tightly and form more rigid
organized aggregates (i.e. membranes)
 Unsaturated chains bend and are packed in a less ordered way with
greater potential for movement.
 Fatty acids are usually derived from triglycerides or phospholipids.
 Fatty acids are important sources of fuel because, when
metabolized they yield large quantities of ATP.
 According to the number of carbons fatty acids can be categorized
into:
a. Short-chain fatty acids (SCFA) are fatty acids with aliphatic
tails of fewer than 6 carbons e.g. butyric acid (4C)
b. Medium-chain fatty acids (MCFA) are fatty acids with aliphatic
tails of 6-12 carbons; these form medium-chained triglycerides.
c. Long chain fatty acids (LCFA) are fatty acids with aliphatic
tails with carbons greater than 12.
 The 16 and 18 carbon fatty acids are of importance to energy
production, it is therefore important to know them.

SYMBOL NAME SATURATED SITE OF

(CARBON #) OR UNSATURATION
UNSATURATED
16:0 Palmitic acid Saturated -
18:0 Stearic acid Saturated -
16:1 Palmitoleic Unsaturated C9

acid
18:1 Oleic acid Unsaturated C9
18:2 Linoleic acid Unsaturated C9 and C12
18:3 linoleic Unsaturated C6, C9 and C12

acid
18:3 linoleic Unsaturated C9, C12 and C15

acid
 Note that all the unsaturated carbon double bonds are in cis
configuration.
 In fatty chains carbons are named as follows:

EXAMPLES OF FATTY ACIDS

RELEASE OF FATTY ACIDS FROM ADIPOSE TISSUE

 95% of lipids are found deposited in adipose tissue.
 At room temperature if triacylglycerols (most common lipid form)
are liquid they are referred to as oils but if they are solid they are
termed fats.
 In adipose tissue lipase enzyme, a highly hormone sensitive
enzyme is present to breakdown triacylglycerol to free fatty acids
and glycerol.
 The hormones responsible for this are glucagon and epinephrine.
 The process is as follows:
1. Epinephrine binds to beta-adrenergic receptors (serpentine
receptors associated with G-proteins) in the cell wall of the
adipocytes which causes adenylyl cyclase to catalyze the
conversion of ATP to cAMP.

 The G-proteins have 3 subunits: an alpha subunit, a beta sub-

unit and a gamma subunit
 The beta-adremergic receptor interacts with the G-
stimulatory subunit which acquires GTP while releasing GDP
and in the process leaves the beta and the gamma subunits
 The activate G subunit then activate adenylate cyclase which
inturn converts ATP to cAMP
2. cAMP formed sets off a chain of cascade reactions where
cAMP activates a protein kinase which phosphorylates and thus
in turn activates a hormone-sensitive lipase (in the fat cell-
triacylglycerol lipase)
3. This lipase cleaves free fatty acids from their attachment to
glycerol in the fat stored in the fat droplet of adipocytes.
4. Free fatty acids and glycerol are released and free fatty acids
enter into the blood.
5. In the blood they attach to plasma albumin, it then diffuses
across the cell membrane using a protein transporter and it is
activated using ATP to form acyl CoA in the cytosol.
 Most fatty acids in human plasma are 16 or 18 carbon atoms
long.
6. The acyl-CoA molecule is then transported across the inner
membrane of the mitochondrion via the carnitine-carnitine
shuttle.
7. Beta-oxidation then takes place in the mitochondrial matrix



FATTY ACID OXIDATION

TYPES OF OXIDATION
1. Oxidation: oxidation at C3, shortening of the chain is by 2

carbons
2. Peroxisomal oxidation: does not involve chain shortening.
3. oxidation (Omega oxidation): no chain shortening.
4. oxidation: carbon 1 (C1) oxidation
 The enzymes of fatty acid oxidation in animal cells are located in

the mitochondrial matrix.
 Fatty acid chains with chain lengths of 12 or fewer carbons enter
mitochondria without the help of membrane transporters.
 Those with 14 or more carbons, which constitute the majority of
free fatty acids obtained from diet or released from adipose tissue
cannot pass directly through the mitochondrial membranes- they
must first undergo the 3 enzymatic reactions of the carnitine
shuttle.
STEPS IN FATTY ACID OXIDATION
1. Activation of fatty acids.

2. Transportation of fatty acids across mitochondrial membranes into
mitochondrial matrix.
3. Beta-oxidation of fatty acids.
STEP1: ACTIVATION OF FATTY ACIDS
 The first reaction is catalyzed by a family of isozymes (different

isozymes specific for fatty acids having short, intermediate or long
carbon chains) present in the outer mitochondrial membrane,
cytoplasm and ER. The acyl-CoA synthetase (thiokinase) which
promote the general reaction:
 Thus acyl-CoA synthetase catalyzes the formation of a thioester

linkage between the fatty acid carboxyl group and the thiol group

of Co-enzyme A to yield a fatty acyl-CoA, coupled to the cleavage

of ATP to AMP and PPi (inorganic pyrophosphate)
 Fatty acyl-CoAs like acetyl-CoA are high energy compounds, their
hydrolysis to free fatty acids and CoA has a large, negative
standard free-energy change.
 The formation of a fatty acyl-CoA is made more favorable by the
hydrolysis of ATP.
 ATP is converted to AMP and pyrophosphate when a fatty acid is
activated.
 The pyrophosphate produced during the reaction is cleaved by
pyrophosphorylase to 2 inorganic phosphates this pulls the
preceding activation reaction in the formation of fatty acyl-CoA
formation.
 Thus 2 high energy bonds are required for fatty acid activation.
 By activation the relative stability of –C-C- bond in a fatty acid is
overcome, which allows stepwise oxidation.

STEP 2: TRANSPORTATION OF FATTY ACIDS INTO

MITOCHONDRIA
 Mitochondrial inner membrane is impermeable to bulky polar

molecules like CoA.
 Hence acyl group from cytosol is carried into the mitochondrial
matrix by the carnitine-carnitine shuttle using carnitine as a carrier
(forming fatty acyl carnitine)
 Remember:
 Short chain fatty acids are carried directly into the
mitochondrial matrix

 Long-chain and medium chain fatty acids are converted to

acyl carnitines and are transported into the mitochondria.
 Acyl-CoA are reformed inside the mitochondria.
CARNITINE A CARRIER OF FATTY ACYL GROUPS
 It is synthesized from lysine and methionine in the liver and

kidney.
 Carnitine carries the fatty acyl groups across the inner

mitochondrial membrane

FORMATION OF FATTY ACYL CARNITINE
 Fatty acids destined for mitochondrial oxidation are transiently

attached to the hydroxyl group of carnitine to form fatty acyl-
carnitine.
 This transesterification is catalyzed by carnitine acyl transferase I
(carnitine palmitoyl transferase I) in the outer membrane.
 NOTE:
 Either the acyl-CoA passes through the outer membrane and
is converted to the carnitine ester in the intermembrane space
or the carnitine ester is formed on the cytosolic face of the
intermembrane space.

 The fatty acyl-carnitine ester then enters the matrix through

facilitated diffusion through the acyl carnitine/carnitine transporter
(carnitine acyl carnitine translocase) of the inner membrane.
 Acyl carnitine enters as carnitine leaves. (it is an antiporter)
 The fatty acyl group is enzymatically transferred from carnitine to
intramitochondrial CoA by carnitine acyl transferase II. The
isozyme, located on the inner face of the inner mitochondrial
membrane, regenerates fatty acyl-CoA and releases it along with
free carnitine into the matrix.
 The carnitine released leaves matrix via acyl-carnitine/carnitine
transporter.
 The fatty-acyl CoA then undergoes subsequent beta-oxidation.

OXIDATION OF FATTY ACIDS
 Oxidation of fatty acids to acetyl-CoA

 In this process the beta-carbon is oxidized via a ketone
intermediate to a thioester.
 Mitochondrial oxidation of fatty acids takes place in 3 stages

 In the first stage- Beta oxidation- fatty acids undergo oxidative

removal of successive 2-carbon units in the form of acetyl-CoA
starting from the carboxyl end of the fatty acyl chain.
 For example, the 16-carbon palmitic acid (palmitate at pH7)
undergoes 7 passes through each pass losing 2 carbons as acetyl
CoA
 At the end of seven cycles the last 2 carbons of palmitate (originally
C15 and C16) remain as acetyl CoA
 The overall result is the conversion of the 16-carbon chain of
palmitate to 8 two-carbon acetyl groups of acetyl CoA molecules.
 Formation of each acetyl-CoA requires removal of 4 hydrogen
atoms (two pairs of electrons and four H+) from the fatty acyl moiety
by dehydrogenases.
 In the second stage of fatty acid oxidation, the acetyl groups of
acetyl-CoA are oxidized to carbon dioxide in the citric acid cycle,
which also takes place in the mitochondrial matrix.
 The first 2 stages of fatty acid oxidation produce the reduced
electron carriers NADH and FADH2, which in the third stage donate
electrons to the mitochondrial respiratory chain, through which the
electrons pass to oxygen with the concomitant phosphorylation of
ADP to ATP.
 The energy released by fatty acid oxidation is thus conserved as
ATP.


STEP 3: BETA OXIDATION OF SATURATED FATTY ACIDS
 Has four enzyme catalyzed reactions
1. DEHYDROGENATION of fatty acyl-CoA

 This produces a double bond between the alpha and beta carbon
atoms (C2 and C3) yielding a trans Δ2 enoyl CoA (the symbol Δ2
designates the position of the double bond)
 This reaction is catalyzed by the enzyme acyl-CoA dehydrogenase
which is FAD dependant.
 The isozymes of acyl-CoA dehydrogenase are specific for a range

of fatty acid lengths:
 Very long chain acyl-CoA dehydrogenase (VLCAD) acting
on fatty acids of 12 to 18
 Medium-chain acyl-CoA dehydrogenase (MCAD) acting on
fatty acids of 4 to 14
 Short-chain acyl-CoA dehydrogenase (SCAD) acting on fatty
acids of 4 to 8 carbons.

 MCAD deficiency is one of the most common error of

metabolism resulting in sudden infant death syndrome.
2. HYDRATION
 Water is added to the double bond of the trans-2-enoyl-CoA to
form the L stereoisomer of -hydroxyacyl-CoA (3-hydroxyacyl-
CoA)
 The addition is a trans addition
 The reaction is catalyzed by enoyl-CoA hydratase.
3. OXIDATION
 L--hydroxyacyl-CoA is dehydrogenated to form -ketoacyl-CoA
by the action of L--hydroxyacyl-CoA dehydrogenase which is
NAD+ dependent

4. THIOLYSIS
 In the last step of oxidation cycle an acyl-CoA acetyl transferase
(thiolase) promotes the reaction of -ketoacyl-CoA with a
molecule of free coenzyme A to split off the carboxyl terminal 2-
carbon fragment of the original fatty acid as acetyl-CoA.
 The other product is the co-enzyme A thioester of the fatty acid,
now shortened by 2 carbon atoms
 This reaction is called thiolysis.
 The reaction of beta-oxidation continue until the entire fatty acyl

residue is degraded to acetyl-CoA.

ENERGY YIELD FROM PALMITOYL-CoA
 Complete Beta-oxidation of palmitoyl CoA thus requires 7 cycles

𝑛
( − 1) 𝑤ℎ𝑒𝑟𝑒 𝑛 = 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑐𝑎𝑟𝑏𝑜𝑛𝑠
2
 In 7 cycles:
𝑛
 8 acetyl CoA molecules are produced ( )
2
 7 FADH2 are produced
 7 NADH + 7H+ are produced

 The 8 acetyl-CoA molecules produced enter the TCA cycle.
TOTAL ENERGY YIELD
PRODUCT CALCULATION ATP EQUIVALENCE
8 ACETYL CoA (in TCA)
NADH 3NADH x 8= 24 24 NADH x 2.5= 60ATP

FADH2
1FADH2 x 8= 8 8 FADH2 x 1.5= 12 ATP
GTP 1 GTP x 8= 8 8ATP
FROM -oxidation reducing equivalents (7 CYCLES)
NADH 1 NADH x 7=7 7 NADH x 2.5= 17.5 ATP
FADH2 1 FADH2 x 7= 7 7 FADH2 x 1.5= 10.5 ATP

TOTAL ENERGY YIELD 108 ATP
NET PRODUCTION (-2 ATP from 106ATP

activation)
BETA-OXIDATION OF UNSATURATED FATTY ACIDS WITH

CIS DOUBLE BOND AT ODD-NUMBERED CARBON ATOMS
 Consider the oxidation of palmitoleate (16:1) with a double bond at

carbon 9.
 Palmitoleoyl CoA then undergoes 3 cycles of degradation, which
are carried out by the same enzymes as in the oxidation of
saturated fatty acids.
 However, the Cis-3-enoyl CoA formed in the third round is not a
substrate for acyl dehydrogenase.
 The presence of a double bond between carbon 3 and carbon 4
prevents the formation of another double bond between carbon 2
and carbon 3.
 The impasse is then resolved by a new reaction that shifts the
position and configuration of the Cis-3 double bond.
 An isomerase converts this double bond into a trans-2 double
bond.
 The subsequent reactions are those of the saturated fatty acid
oxidation pathway in which the trans-2-enoyl CoA is a regular
substrate.

 The implication of such means in one cycle the first reaction which
requires FAD is bypassed producing 8 acetyl-CoAs, 6FADH2 and
7NADH + 7H+

OXIDATION OF POLYUNSATURATED FATTY ACIDS

WITH CIS DOUBLE BONDS AT EVEN-NUMBERED CARBON
ATOMS

 Two accessory enzymes make the -oxidation of polyunsaturated

fatty acids containing a cis double bond at an even-numbered
carbon atom possible.
 The 2 accessory enzymes are:
1. 2,4 dienoyl CoA reductase
2. Cis 3 enoyl isomerase
 -oxidation occurs until the double bond of the unsaturated acid
reaches position 4 of the acyl-CoA
 After the acyl-CoA dehydrogenase creates the trans double bond
between carbon 2 and 3, the enzyme 2,4-dienoyl CoA reductase
reduces the 2 double bonds into one, generating a trans  double
bond. The trans double bond is then isomerized to trans  so
that the normal steps of beta-oxidation can then proceed.
 The enzyme 2,4-dienoyl CoA reductase requires NADPH + H+ as
a cofactor


ODD CHAIN FATTY ACIDS YIELD PROPIONYL COENZYME

A IN THE FINAL THIOLYSIS
 Fatty acids having an odd number of carbon atoms are minor

species
 They are oxidized in the same way as fatty acids having an even
number, except that propionyl CoA and acetyl CoA rather than 2
molecules of acetyl CoA are produced in the final round of
degradation.
 The activated 3 carbon unit in propionyl CoA enters the citric acid
cycle after it is converted into succinyl-CoA.

KETOGENESIS
FORMATION OF KETONE BODIES
 Ketogenesis is the formation of acetoacetate, D-3 hydroxybutyrate

and acetone from acetyl CoA in the liver
 Ketone bodies are formed from acetyl CoA when fat breakdown
predominates carbohydrate degradation (glycolysis)
 Acetoacetate is a major fuel in some tissues
 Acetoacetate spontaneously decarboxylates to form acetone.
SYNTHESIS OF KETONE BODIES
 Occurs in liver mitochondria when fatty acids are in high

concentration in the blood (during fasting, starvation, or as a result
of a high-fat diet)
1. Beta oxidation
 Produces NADH and ATP and results in the accumulation of
acetyl-CoA, owing to allosteric inhibition of TCA cycle
 The liver also producing glucose using oxaloacetate (OAA),
so there is decreased condensation of acetyl CoA with OAA
to form citrate.
2. Two molecules of acetyl CoA
 Condense to produce acetoacetyl coA
 The reaction is catalyzed by thiolase or an isozyme of
thiolase
3. Acetoacetyl-CoA and acetyl CoA form hydroxymethylglutaryl
CoA (HMG-CoA) in a reaction catalyzed by HMG-CoA
synthase.
4. HMG-CoA is cleaved by HMG-CoA lyase to form acetyl CoA
and acetoacetate.

5. Acetoacetate can be reduced by an NAD-requiring

dehydrogenase to 3-hydroxybutyrate
 The reaction is reversible and catalyzed by the enzyme 3-
hydroxybutyrate dehydrogenase
6. Acetoacetate is also spontaneously decarboxylated in a non
enzymatic reaction forming acetone (the source of the order on
the breath of ketotic diabetic patients)
 The liver lacks the enzyme needed to metabolize ketone bodies
(succinyl CoA acetoacetate CoA transferase, a thiotransferase) so
it can not use the ketone bodies it produces. Therefore,
acetoacetate and 3 hydroxybutyrate are released into the blood by
the liver.
LIPID BIOSYNTHESIS

 Lipids dissolve well in organic solvents but they are insoluble in

water
 A family of compounds that includes:
 Triglycerides (fats and oils)
o Fats: lipids that are solid at room temperature
o Oils: lipids that are liquid at room temperature
 Phospholipids
 Sterols (e.g. cholesterol)
 Biological function of lipids include:
 They are major components of cell membranes
 Nourishes skin and hair
 Insulates the body from extreme temperatures
 Cushions the vital organs in order to protect them from shock
 Lipids are important sources of energy- they serve as
metabolic fuel
 Some of them are substrates for synthesis of other compounds
(hormones, eicosanoids, bile acids)
 Lipids can be classified into
a. Simple lipids
 Triacylglycerols TAG (fats)
 Waxes
b. Complex lipids
 Phospholipids
 Sphingophospholipids
 Glycolipids
c. Isoprenoids and steroids

 Isoprenoids: vitamins A, D, E, K
 Steroids: sterols (cholesterol), bile acids, steroid hormones
BIOSYNTHESIS OF FATTY ACIDS
 Fatty acid biosynthesis takes place in the cytoplasm

 The body can synthesize all of the fatty acids it needs from
carbohydrates, fat or protein except for two
1. Linoleic acid
2. Linolenic acid
 PUFAs
 Found in plant and fish oils
 Excess food -> acetyl CoA-> fatty acids-> lipid (fat)
 Biosynthesis of fatty acids is catalyzed by a multi-enzyme complex
 Acyl carrier protein (ACP) has a side chain that carries the growing
fatty acid
 ACP rotates counterclockwise and its side chain sweeps over the
multienzyme system (empty spheres)
 At each enzyme, one reaction of chain is catalyzed

 Step 1: ACP picks up an acetyl group from acetyl CoA and

delivers to the first enzyme (a synthase)

 Step 2: ACP-malonytransferase reaction
 Step 3: condensation reaction
 Step 4: the first reduction
 Step 5: dehydration
 Step 6: the second reduction

 The second cycle then takes place.

 The maximum length of the fatty acid that can be synthesized
through this pathway is 16C (palmitic acid)
BIOSYNTHESIS OF MEMBRANE LIPIDS
SYNTHESIS OF GLYCEROPHOSPHOLIPID
 Step 1: reduction of dihydroxyacetone phosphate to glycerol 1-

phosphate

 Step 2: condensation reaction: esterification of fatty acids to

glycerol
BIOSYNTHESIS OF CHOLESTEROL
 Cholesterol is synthesized from cytosolic acetyl-CoA by a

sequence of reactions
 Glucose is the major source of carbon for acetyl-CoA
 Cytosolic acetyl-CoA forms acetoacetyl CoA, which condenses
with another acetyl-CoA to from hydroxylmethylglutaryl CoA
(HMG-CoA)

 Acetyl-CoA undergoes similar reactions in the mitochondria where

HMG-CoA is used for ketone body biosynthesis.
 Cytosolic HMG-CoA, a key intermediate in cholesterol
biosynthesis is reduced in the endoplasmic reticulum to mevalonic
acid by the regulatory enzyme hydroxymethylglutaryl-CoA
reductase
a. HMG-CoA reductase is inhibited by cholesterol
b. HMG-CoA reductase is also inhibited by phosphorylation by
AMP-activated protein kinase
c. In the liver HMG-CoA reductase is also inhibited by bile salts
and is induced when blood insulin levels are elevated.
 Mevalonic acid is phosphorylated and decarboxylated to form the

five-carbon (C5) isoprenoid, isopentenyl pyrophosphate
 Two isopentenyl pyrophosphate units condenses forming a C-10

compound, geranyl pyrophosphate which reacts with another C-5
to form a C-15unit compound, famesyl pyrophosphate.

 Squalene is formed from two C15 units and then oxidized and
cyclized to form lanosterol
 Lanosterol is converted to cholesterol (C-27) in a series of at least
25 steps.

 The ring structure of cholesterol cannot be degraded in the body.

The bile salts in the feces are the major form in which the steroid
nucleus is excreted.
REGULATION OF LIPID METABOLISM
 Regulation of lipid metabolism can be done at several levels

 High glycolysis rates result in an increased concentration of acetyl-
CoA in the mitochondrion, this leads to the inhibition of lipid
degradation and facilitate lipid biosynthesis.
 On the other hand as glycolysis rates decrease significantly due to
insufficient carbohydrate supply beta oxidation predominates in
the mitochondrial matrix which produces acetyl-CoA that can enter
the TCA and produce energy.
 Citrate formed in the TCA activates cytosolic acetyl-CoA
carboxylase thus promoting fatty acid synthesis.
 Acyl-CoAs inhibit acetyl-CoA carboxylase preventing further
breakdown of lipids. The malonyl CoA formed in fatty acid
biosynthesis can inhibit carnitine-palmitoyltransferase I preventing
fatty acyl-CoA molecules from entering the mitochondrial matrix
for beta oxidation

HORMONAL REGULATION OF FATTY ACID METABOLISM
 Major hormones:
1. Glucagon
2. Epinephrine
3. Insulin
REGULATION OF FATTY ACID SYNTHESIS
 Insulin activates phosphodiesterase that converts cAMP to AMP

this inactivates hormone sensitive lipase and activates acetyl-CoA
carboxylase promoting fatty acid biosynthesis.
 Epinephrine and glucagon inhibit fatty acid biosynthesis through
the cAMP cascade.
REGULATION OF FATTY ACID DEGRADATION
 Glucagon and epinephrine activate adenylyl cyclase which

catalyzes the conversion of ATP to cAMP which in turn activates
protein kinase that inhibits acetyl CoA carboxylase by
phosphorylation and activates lipase by phosphorylation and this

increases lipolysis and release of fatty acids
 Regulation of fatty acid metabolism prevents a futile cycle.

SUMMARY
 Lipids play an important role in human beings
 Among their various functions, fats can be used as an alternative
source of energy
 In production of energy, fats are broken down to free fatty acids
under the influence of epinephrine and glucagon.
 Medium chained and short chained fatty acids undergo beta-
oxidation in the mitochondria which contains 4 steps
(dehydrogenation, hydration, oxidation and thiolysis) to produce
large amounts of acetyl-CoA

 Some acetyl-CoA molecules formed react with each other to form

ketone bodies which are used as an alternative source of fuel in
some tissue
 Fatty acids can also be synthesized in the body by a multi-enzyme
complex (acyl carrier protein-ACP)
 The essential fatty acids linoleic and linolenic acid cannot be
synthesized by the body and have to be taken in through diet.
 Membrane lipids such as phospholipids and cholesterol are also
synthesized in multiple step reactions
 Breakdown and synthesis of fatty acids is under the influence of
epinephrine, glucagon and insulin.
o Epinephrine and glucagon stimulate fat degradation
o Insulin inhibits fat degradation
NUCLEOTIDE METABOLISM
OBJECTIVES
1. Synthesis and breakdown of purine nucleotides.
2. Synthesis and breakdown of pyrimidine nucleotides
3. Disorders of nucleotide metabolism
 Nucleotides are the biological monomers of nucleic acids that are

contained in the nucleus. These nucleotides are important in a
variety of pathways some biological functions of nucleotides
include:
1. They are building blocks of nucleic acids (DNA and RNA)

2. They are involved in energy storage (ATP), muscle contraction,

active transport, maintenance of ion gradient.
3. The activated intermediates in biosynthesis (e.g. UDP-glucose,
UPD-glucoronic acid, S-adenosylmethionine)
4. Components of co-enzyme (NAD+, NADP+, FAD, FMN and CoA)
5. Metabolic regulators
 Second messengers (cAMP, cGMP)
 Phosphate donors in signal transduction (ATP)
 Regulation of some enzymes via adenylation and uridylation.
 Allosteric regulation by AMP, ATP, GTP
NUCLEOTIDES
 Nucleotides consist of:
1. A phosphate group
2. A pentose sugar
 In DNA the pentose sugar is Deoxyribose (which lacks an –
OH group at carbon atom number 2’)
 In RNA the pentose sugar is ribose
3. A nitrogenous base that can either be a purine or pyrimidine
base.
 The bond between the phosphate group and the sugar is a
phosphodiester bond
 The bond between the nitrogenous base and the pentose sugar is a
-N-glycosidic bond
 NOTE: a nucleoside is a dephosphorylated nucleotide. i.e. it only
has a nitrogenous base and a pentose sugar

NITROGENOUS BASES
 The nitrogenous bases found in nucleotides that make up DNA and

RNA are planar, aromatic and heterocyclic compounds making
them easy to stack one on top of the other.
 They are heterocyclic in the sense that the carbon ring skeleton
contains different atoms i.e. nitrogen and carbon.
 Nitrogenous bases are derived from purine or Pyrimidines.
 Purines have double rings.

 Pyrimidines have single rings
 Numbering of bases is “unprimed” and the bases are numbered as

follows
PURINES
 The nitrogen atoms occupy N1, N3, N7 and N9
PYRIMIDINE
 The nitrogen atoms occupy N1 and N3
NUCLEIC ACID BASES
 There are 3 common bases found in both DNA and RNA these
include:
 Guanine (G)
 Adenine (A)
 Cytosine (C)
 The nitrogenous base Thymine (T) is only found in DNA.
 Thymine is also known as 5-methly-uracil.
 Uracil is only found in RNA
 The nitrogenous bases are also classified as either Pyrimidines and
purines
 The purines include: Guanine and Adenine

 The pyrimidine bases include: Cytosine (C), Uracil (U) and

thymine (T)
 These bases pair up in nucleic acids by hydrogen bonding.

SUGARS
 The pentose sugars are 5C sugars

 In RNA sugar is D-ribose
 In DNA sugar is 2’-deoxyribose
 Numbering of the sugars is “primed” hence we have 3’ and 5’ ends
in DNA and RNA
 NOTE: the carbons in the sugar are primed to differentiate them

from the carbons in the nitrogenous bases

NOMENCLATURE OF BASES, NUCLEOTIDES AND

NUCLEOSIDE
PURINE AND PYRIMIDINE METABOLISM

 There are two major pathways that lead to nucleotide synthesis
these include: the de novo pathways and the salvage pathways.
 De novo synthesis of nucleotides begins with their metabolic
precursors: amino acids, ribose-5-phosphate, carbon dioxide and
NH3.
 Salvaged pathways recycle the free bases and nucleosides released
from nucleic acid breakdown.

 The de novo pathways for purine and pyrimidine biosynthesis

seem to be nearly identical in all living organisms.
 The bases are not synthesized and then attached to ribose as might
be expected
 The purine ring structure is instead built up one or a few atoms at a
time, attached to ribose throughout the process.
 The pyrimidine ring is synthesized as orotate, attached to ribose

phosphate and then converted to common pyrimidine nucleotides
required in nucleic acid synthesis
 Although free bases are not intermediates in the de novo pathways,
they are intermediates in some of the salvage pathways
 Several important precursors are shared by the de novo pathways
for synthesis of Pyrimidines and purines.
 Phosphoribosyl pyrophosphate (PRPP) is important in both and in
the product nucleotide.
 An amino acid is an important precursor in each type of pathway:
 Glycine for purines and aspartate for Pyrimidines.
 Glutamine again is the most important source of amino groups in 5
different steps in the de novo pathways.
 Aspartate is also used as a source of an amino group in the purine
pathways in 2 steps
DE NOVO PURINE SYNTHESIS

 The order of addition of atoms in the purine ring does not follow
the numbering:
1. N9 is added first from glutamine
2. Glycine then donates 2 carbons and a nitrogen to form C4, C5
and N7
3. N10-formyl-tetrahydrofolate donates C8
4. Glutamine then starts the formation of the other ring by adding
N3
5. Carbon dioxide donates C6
6. Aspartate donates N1 and
7. N10-formyl-THF donates C2 to complete the ring
 The ring on the right of the purine is synthesized in a clockwise
direction starting with N9 and ending withC8.
 The ring on the left is synthesized in an anticlockwise direction

from C4 through to C6 then N1 and C2.
REACTIONS IN THE SYNTHESIS OF PURINE RINGS
 Before the ring can be attached to PRPP, ribose-5-phosphate has to

be activated to form PRPP (phosphoribosyl pyrophosphate).
 This is done by hydrolysis of 2 ATP bonds catalyzed by the
enzyme ribose phosphate pyrophosphokinase (PRPP synthetase)

 In the first committed step of the pathway an amino group is

donated by glutamine. This amino group is attached at C1 of PRPP
resulting in 5’-phosphoribosylamine
o The nitrogen donated is N9 of the purine ring
 There is a conformation change from alpha to beta
 The enzyme that catalyzes this reaction is amidophosphoribosyl
transferase
 The enzyme is inhibited by adenosine monophosphate (AMP) and
guanosine monophosphate (GMP)

 The second is the addition of 3 atoms from glycine.

 An ATP is consumed to activate the glycine carboxyl group (in the
form of an acyl phosphate) for this condensation.
 Glycine adds C4, C5 and N7
 The reaction is catalyzed by glycine amide ribobucleotide
(ribotide) synthetase
 The product of the reaction is glycine amide ribonucleotide

 In step 3 N10-formyl tetrahydrofolate adds C8

 This forms formyl glycinamide ribonucleotide(FGAR) and is
catalyzed by the enzyme glycinamide ribonucleotide
transformylase

 In step 4 nitrogen is contributed to form formylglycinamidine

ribonucleotide (FGAM)
 The reaction requires an ATP molecule and is catalyzed by
formylglycinamidine synthetase.

 In step 5 dehydration and ring closure yields the five membered

imidazole ring of the purine nucleus, as 5-aminoimidazole
ribonucleotide (AIR)
 This cyclizatiom reaction requires ATP and is catalyzed by formyl
glycinamidine ribonucleotide cyclase [also known as
aminoimidazole ribonucleotide (AIR) synthetase]

 In step 6 the product (5-aminoimidazole ribonucleotide) is

carboxylated to carboxyaminoimidazole ribonucleotide
 The enzyme catalyzing this reaction is Aminoimidazole
carboxylase

 In step 7 and 8 aspartate donates its amino group

 In step 7 the formation of an amide bond is catalyzed by N-
succinyl-5-aminoimidazole-4-carboxamide ribonucleotide
(SAICAR) synthetase, this requires ATP, followed by
 Step 8 where the carbon skeleton is eliminated as fumarate
catalyzed by the enzyme N-succinyl-5-aminoimidazole-4-
carboxamide ribonucleotide (SAICAR) lyase.

 In step 9 the final carbon is contributed by N10-

formyltetrahydrofolate. The reaction is catalyzed by 5-
aminoimidazole carboxiamide (AICAR) transformylase.
 The product formed in this step is N-formylaminoimidazole-4-
carboxamide ribonucleotide (FAICAR)
 A second ring closure takes place to yield the second fused ring of
the purine nucleus (step 10)
 The first intermediate with a complete purine ring is inosinate
(IMP)
 The reaction is catalyzed by inosinate synthase (IMP)
 Inosine monophosphate (IMP) which contains the base

hypoxanthine is generated
 IMP can be converted in the liver to the free base, hypoxanthine or
the nucleoside (by dephosphorylation)
 Hypoxanthine or inosine travels to various tissue, where it is
reconverted to the nucleotide
CONVERSION OF IMP TO AMP and GMP
 Conversion of inosinate to adenylate requires the insertion of an

amino group derived from aspartate.

 GTP is the source of the high energy phosphate in synthesizing

adenylosuccinate.
 This reaction is catalyzed by adenylosuccinate synthetase.
 The subsequent reaction is an elimination of fumarate by
adenylosuccinate lyase to form adenylate (AMP)
 In the formation of AMP, IMP is converted first to
adenylosuccinate by the enzyme adenylosuccinate synthetase
and finally to AMP by the action of adenylosuccinase
 In the conversion of inosinate to guanylate (GMP) NAD+-requiring
IMP dehydrogenase oxidizes carbon 2 forming xathylate (XMP)
followed by the addition of an amino group from glutamine to
form guanylate (GMP) in a reaction catalyzed by XMP-glutamine
amidotransferase which requires hydrolysis of two ATP bonds.
 In the formation of GMP, IMP is converted first to

xanthosine monophosphate by the enzyme IMP
dehydrogenase and finally to GMP by the action of GMP
synthetase

PURINE CATABOLISM
 When DNA and RNA are degraded nucleotides are released these
nucleotides can be catabolized to nucleosides (by
dephosphorylation) releasing their bases (adenine, guanine) which
can be used in the salvage pathway of synthesis of other
nucleotides or broken down to uric acid.
 In the degradation of the purine nucleotides, phosphate and
ribose are removed first, then the nitrogenous base is
oxidized.

DEGRADATION OF AMP
 AMP is degraded to adenosine by the removal of the phosphate by

a 5’-nucleotidase
 Adenosine is converted to inosine by enzyme adenosine deaminase
(ADA)
 Degradation of inosine by PNP (purine nucleoside phosphorylase)
produces hypoxanthine and ribose 1-phosphate

 Hypoxanthine is oxidized to xanthine by xanthine oxidase, this

enzyme requies molybdenum
 Xanthine is oxidized to uric acid by xanthine oxidase
 Uric acid, which is not very water soluble is excreted by the
kidneys


DEGRADATION OF GMP
 GMP is degraded to guanosine by the removal of the phosphate by

a 5’-nucleotidaase
 Guanosine is degraded to guanine and ribose-1-phosphate by
purine nucleoside phosphorylase (PNP)
 Guanine is then converted to xanthine
PYRIMIDINE BIOSYNTHESIS
 The pyrimidine base is synthesized before addition of the ribose

moiety

 In the first reaction, glutamine reacts with carbon dioxide and two
ATP molecules to form carbamoyl phosphate
 This reaction is analogous to the first reaction of the urea
cycle
 However for pyrimidine synthesis, glutamine provides the
nitrogen, and the reaction occurs in the cytosol, where it is
carbamoyl phosphate synthetase II which is inhibited by UTP
 An aspartate molecule adds to carbamoyl phosphate. The
molecules close to yield a ring which is forming orotate
 Orotate reacts with PRPP producing orotidine 5’-phosphate (OMP)
which is decarboxylated to form UMP.
 Both reactions are catalyzed by UMP synthase which functions
both as orotate phosphoribosyl transferase and OMP decarboxylase

 UMP is phosphorylated to UTP which obtains an amino group

from glutamine to form cytidine triphosphate (CTP). UTP and CTP
are used for RNA synthesis


 The ribose moiety of cytidine diphosphate (CDP) is reduced to

deoxyribose, forming deoxycytidine diphosphate (dCDP).
Ribonucleotide reductase is the enzyme
o dCDP is dephosphorylated and deaminated to form
deoxyuridine monophosphate
o dUMP is converted to thymidine monophosphate (dTMP) by
thymidylate synthase which requires methylene
tetrahydrofolate

o Phosphorylations produce dCTP and dTTP which are

precursors of DNA

PYRIMIDINE CATABOLISM
 In pyrimidine degradation, the carbons produce carbon dioxide and

a variety of water-soluble (beta-alanine and beta-aminoisobutyrate)
and some nitrogens released as ammonium ion, are used to
produce urea
 Excretion of beta-aminoisobutyrate increases in leukemia and
severe X-ray radiation exposure due to increased destruction of
DNA
 Humans probably transaminate beta-aminoisobutyrate to
methylmalonate semialdehyde which then forms succinyl-CoA



DISORDERS OF NUCLEOTIDE METABOLISM

GOUT
 Gout is a metabolic disorder of purine metabolism

 Various genetic defects in PRPP synthetase (reaction 1) present
clinically as gout
 Each defect—e.g. an elevated V max, increased affinity for ribose
5-phosphate, or resistance to feedback inhibition—results in
overproduction and over-excretion of purine catabolites.
 When serum urate levels exceed the solubility limit, sodium urate
crystalizes in soft tissues and joints and causes an inflammatory
reaction, gouty arthritis.

 However, most cases of gout reflect abnormalities in renal

handling of uric acid.
LESCH-NYHAN SYNDROME
 Hyperuricemia characterized by frequent episodes of uric acid

lithiasis and a bizarre syndrome of self-mutilation, reflects a defect
in hypoxanthine-guanine phosphoribosyltransferase (HGPRT),
an enzyme of purine salvage pathway.
 The accompanying rise in intracellular PRPP results in purine
overproduction.
 Mutations that decrease or abolish HGPRT activity include
deletions, frameshift mutations, base substitutions, and aberrant
mRNA splicing.
 Allopurinol is used to treat gout and Lesch nyhan syndrome

o Inihibition of xanthine oxidase by alloxanthine is the
mechanism involved in allopurinol treatment of gout and
lesch-nyhan syndromes

HYPOURICEMIA
 Hypouricemia and increased excretion of hypoxanthine and

xanthine are associated with xanthine oxidase deficiency due to a
genetic defect or to severe liver damage.
 Patients with a severe enzyme deficiency may exhibit xanthinuria
and xanthine lithiasis.
ADENOSINE DEAMINASE (ADA) AND PURINE NUCLEOSIDE

PHOSPHORYLASE (PNP) DEFICIENCY
 ADA deficiency is associated with an immunodeficiency disease

in which both thymus-derived lymphocytes (T cells) and bone
marrow-derived lymphocytes (B cells) are sparse and
dysfunctional
 PNP deficiency is associated with a severe deficiency of T cells

but apparently normal B cell function. Immune dysfunctions
appear to result from accumulation of dGTP and dATP, which
inhibit ribonucleotide reductase and thereby deplete cells of DNA
precursors
OVERPRODUCTION OF PYRIMIDINE CATABOLITES IS

ONLY RARELY ASSOCIATED WITH CLINICALLY
SIGNIFICANT ABNORMALITIES
 Since the end products of pyrimidine catabolism are highly water-

soluble, pyrimidine overproduction results in few clinical signs or
symptoms.
 In hyperuricemia associated with severe overproduction of PRPP,
there is overproduction of pyrimidine nucleotides and increased
excretion of β-alanine.
 Since N5, N10-methylene-tetrahydrofolate is required for
thymidylate synthesis, disorders of folate and vitamin B12
metabolism result in deficiencies of TMP.
OROTIC ACIDURIA
 The orotic aciduria that accompanies Reye’s syndrome probably

is a consequence of the inability of severely damaged mitochondria
to utilize carbamoyl phosphate, which then becomes available for
cytosolic overproduction of orotic acid.
 Type I oroticaciduria reflects a deficiency of both orotate
phosphoribosyl transferase and orotidylate decarboxylase
(reactions 5 and 6)
 The rarer type II orotic aciduriais due to a deficiency only of
orotidylate decarboxylase (reaction 6).
SUMMARY
 Ingested nuclei acids are degraded to purines and pyrimidines.

New purines and pyrimidines are formed from amphibolic
intermediates and thus are dietarily nonessential
 Several reactions of IMP biosynthesis require folate derivatives
and glutamine. Consequently, antifolate drugs and glutamine
analogs inhibit purine biosynthesis
 Oxidation and amination of IMP forms AMP and GMP, and
subsequent phosphoryl transfer from ATP forms ADP and GDP.
 Further phosphoryl transfer from ATP to GDP forms GTP. ADP is
converted to ATP by oxidative phosphorylation. Reduction of
NDPs forms dNDPs.
 Hepatic purine nucleotide biosynthesis is stringently regulated by
the pool size of PRPP and by feedback inhibition of PRPP-
glutamyl amidotransferase by AMP and GMP.
 Coordinated regulation of purine and pyrimidine nucleotide
biosynthesis ensures their presence in proportions appropriate for
nucleic acid biosynthesis and other metabolic needs.
 Humans catabolize purines to uric acid (pKa 5.8), present as the
relatively insoluble acid at acidic pH or as its more soluble sodium
urate salt at a pH near neutrality.
 Urate crystals are diagnostic of gout. Other disorders of purine
catabolism include Lesch- Nyhan syndrome, von Gierke’s disease,
and hypouricemias.
 Since pyrimidine catabolites are water-soluble, their
overproduction does not result in clinical abnormalities.
 Excretion of pyrimidine precursors can, however, result from a
deficiency of ornithine transcarbamoylase because excess
carbamoyl phosphate is available for pyrimidine biosynthesis.
NUCLEIC ACID METABOLISM

OBJECTIVES
1. DNA synthesis
2. RNA synthesis
3. Disorders of nucleic acid synthesis
 There are two types of nucleic acids found in all living cells of the
body.
 These include DNA and RNA
o The difference between the two is that DNA contains
deoxyribose sugar which does not have an –OH group at
carbon 2 while the ribose sugar in RNA contains an –OH
group at carbon two
o The other difference lies within the nucleotides contained in
each, RNA has uracil in place of thymine
 These nucleic acids are the storages of genetic information that is
inherited through generations
 These nucleic acids are greatly diverse and they function in
controlling cell activities including synthesis of certain products
such proteins (which make hormones, enzymes and structural
components of the cell), replication and differentiation of cells
 Fundamentally all the genetic material in every somatic cell in an
individual is the same however, due to different expressions of
genes by different cells; different cells have different functions and
structures
 Because of their importance it is fundamental to study and know
how these nuclei acids are formed and replicated because failure in

metabolism of these nucleic acids leads to certain disorders,

syndromes and diseases.
DNA METABOLISM
 DNA is the chemical basis of heredity and it is organized into
genes, the fundamental units of genetic information
 Genes are the parts of DNA that code for proteins

 Genes do not function independently, their replication and function
are controlled by various gene products, often in collaboration with
components of various signal transduction pathways e.g.
hormones.
 Knowledge of the structure and function of nuclei acids is essential
in understanding genetics and many aspects of pathophysiology as
well as the genetic basis of disease
STRUCTURE OF DNA
 DNA in human cell nuclei is a linear double stranded helical

structure that contains nucleotides.
o In bacteria DNA is double stranded but it is circular, this type
of DNA is analogous to DNA found in the mitochondria of
human cells
 The nucleotides of DNA have the following components:
nitrogenous bases, a deoxyribose sugar and a phosphate group
o NOTE: the difference between a nucleotide and a nucleoside
is that a nucleotide is a phosphorylated nucleoside. Meaning
that a nucleotide has a ribose/deoxyribose sugar, nitrogenous
base and a phosphate group while a nucleoside only contains
a ribose/deoxyribose sugar and a nitrogenous base.
 The nitrogenous bases in DNA include:
 Purines Guanine and adenine (have 2 rings)
 Pyrimidines: cytosine and thymine (have 1 ring)
 Remember that nucleotides in one strand of DNA form
complementary base pairs with nucleotides of the opposite strands:
o Guanine forms 3 hydrogen bonds with cytosine

o Adenine forms 2 hydrogen bonds with thymine
 It is also worth knowing that the backbone of DNA is held together

by a 5’3’ phosphodiester bond
o This phosphodiester bond links the 5’-hydroxyl group of one
pentose and the 3’ hydroxyl group of the next
 The strands in DNA are antiparallel. One chain runs in a 5’ to 3’
direction and the other chain runs in a 3’ to 5’ direction
 The 5’ end has the phosphate group
 The 3’ end has the carbon of the deoxyribose sugar

 DNA contains genes (a part of DNA that codes for proteins)

 Genes consist of both introns and exons
o Introns are the non-coding regions of DNA
o Exons are the coding regions of DNA
o Only 1.5% of total human DNA is “coding” or exon DNA

DNA SYNTHESIS AND REPLICATION
 Every human cell that undergoes mitosis has a cell cycle consists
of:
 Interphase which consists of:
o G1 Phase: replication of organelles
o S Phase: replication of DNA
o G2 Phase: synthesis of proteins for cell division.
 Some cells enter into G0 phase (terminally
differentiated cells e.g. nerve cells)
 M Phase: consists of prophase, metaphase, anaphase, and
telophase
 Cytokinesis

 DNA replication is managed in such a way that there are minimal

errors in DNA.
 In DNA replication each strand of DNA acts as a template onto
which the new strand is synthesized
 For DNA replication to occur successfully certain rules have to be
followed:
1. DNA replication is semiconservative
 Each DNA strand serves as a template for the synthesis of a
new strand, producing two new DNA molecules, each with
one new strand and one old strand. This is semiconservative
replication

2. Replication begins at an origin and usually proceeds bidirectionally

 DNA is opened at a site rich in A-T this place is called the
origin of replication (OriC)
 Once DNA is opened at the origin of replication a replication
bubble is formed and the ends of each bubble are called
replication forks
 The formation of new DNA happens at each replication fork
 Prokaryotes have one site of origin on each chromosome
 Eukaryotes have multiple sites of origin on each chromosome
3. DNA synthesis proceeds in a 5’ to 3’ direction and is semi-

discontinuous
 Since DNA strands are antiparallel. There is a strand that is
synthesized in a 5’ to 3’ direction this strand is called the
leading strand (it is synthesized from the strand of parental
DNA running from 3’ to 5’ direction) and it is synthesized in
a continuous manner
 The other strand that is synthesized in the 3’ to the 5’
direction is called the lagging strand and it is synthesized in
sections called okazaki fragments which are eventually
joined together forming phosphodiester bonds

4. DNA is synthesized by DNA polymerase

 DNA polymerase adds nucleotides to the growing chain of
DNA
 Prokaryotes have 3 DNA polymerases: pol I, II, III.
o Pol III is the major replicative enzyme
o Pol I is involved in both DNA replication and repair
PROPERTIES OF DNA POLYMERASES (I, II AND III)
DNA POLYMERASE A (I)
 Exhibits 3’ to 5’ exonuclease activity (proofreading)

 It also exhibits 5’ to 3’ exonuclease activity
 It has the slowest polymerization rate (nucleotides/second) and
processivity (nucleotides added before polymerase dissociates)
than polymerase II and III.

 It functions in gap filling following DNA replication and

recombination.
DNA POLYMERASE B (II)
 Exhibits 3’ to 5’ exonuclease (proofreading)

 It does not exhibit 5’ to 3’ exonuclease activity.
 It has a moderate polymerization rate and a moderate Processivity.
 It functions in proofreading and repair.
DNA POLYMERASE C (III)
 Exhibits 3’ to 5’ exonuclease activity

 It does not exhibit 5’ to 3’ exonuclease activity.
 It has a fast polymerization rate and a fast processivity.
 It functions in processivity, leading strand synthesis.
POL I (polA) POL II (polB) POL III (polC)
SUBUNITS 1 7 MORE THAN

10
3’ -> 5’ Yes Yes Yes

exonuclease
(proofreading)
3’ -> 5’ Yes no no
exonuclease

Polymerization 16-20 40 250- 1,000

rate
(nucleotides/s) ( Slow) (Moderate) (Fast)
Processivity 3-200 1, 500 ≥ 500,000

(nucleotides
added before (Fast) (Moderate) (Slow)
polymerase
dissociates)
 In eukaryotes there are at least 5 DNA polymerase enzymes

termed alpha, beta, gamma, delta and epsilon
o Alpha DNA polymerase is involved in replication of
nuclear DNA it acts in conjunction with delta DNA
polymerase
o Beta and epsilon function repair of nuclear DNA
o Gamma DNA polymerase function in mitochondria

 DNA polymerases can only copy a DNA template in the 3’ to

5’ direction and produce the newly synthesized strand in the
5’ to 3’ direction

 DNA replication happens in 3 stages

 Initiation
 Elongation
 Termination
INITIATION
 DNA replication is most studied in E. coli

 Initiation begins at replication origin (oriC) which consists of 245
base pairs
 This oriC is rich in A=T base pairs which are easy to open, the
nucleotide sequence in this region is called the consensus sequence
and it is the point at which DNA replication is initiated

 The initiator protein called DnaA recognizes the ori sequence and
opens DNA at this point this forms a replication bubble.
 Once the strands are separated they should be kept separated from
each other and stabilized by a protein called single strand binding
protein
o This protein prevents the DNA strands from coming back
together
o It also protects the single stranded DNA from the attack of
nucleases because single stranded DNA is more vulnerable to
breakdown by nucleases than is double stranded DNA.
 The replication bubble has 2 replication forks at each end
o DNA helicase uses a lot of ATP to further unwind the DNA
strand at the replication fork


 Unwinding DNA at the replication fork causes the DNA distal to

this point to become tight (super coil) and this provides a problem
in unwinding DNA further
o This problem is solved by DNA topoisomerase, which alters
the topology of DNA and relieves the torsional stress on the
super coiled DNA
o DNA topoisomerase can solve the problem of negative or
positive super coils (i.e. when the DNA is too “tight” or too
“loose”)
o DNA topoisomerase-I has two domains: a domain with
nuclease activity and a domain with ligase activity.
 The nuclease cuts one strand of DNA allowing it to
unwind around the intact strand and after this happens
the ligase fuses the cut strand reforming the broken
phosphodiester bond in the strand and thus changing the
topology of DNA
 Ciprofloxacin an example of an example of a quinolone
drug blocks the ligase domain of DNA topoisomerase
and so DNA is cut into many fragments without it being
rejoined. These are used in bacterial treatment
 Etoposides are also used in cancer cell treatment they
function like quinolones and work on human DNA
topoisomerase
o DNA topoisomerase-II (DNA gyrase) is also present and it
works on both strands of DNA
 DNA gyrase
ELONGATION
 DNA polymerase catalyzes the synthesis of DNA

 DNA polymerase adds nucleotides to the growing 3’ end of DNA
o Deoxyribonucleoside triphosphates e.g. deoxyadenosine

triphosphate (dATP), deoxyguanosine triphosphate (dGTP),
dexoythymidine triphosphate (dTTP) and deoxycytidine
triphosphate (dCTP) are the precursors for DNA synthesis
o Each precursor pairs with the corresponding base on the
template strand and forms a phosphodiester bond with the
hydroxyl group on the 3’ carbon on the sugar at the end of
the growing chain
o Pyrophosphate is produced and cleaved to two inorganic
phosphates
 DNA polymerase cannot synthesize a new DNA strand de novo, it
requires a primer.
 RNA serves as the primer for DNA polymerase in vivo. The RNA
primer, which contains about 10 nucleotides is formed by copying
the parental strand in a reaction catalyzed by primase
 DNA polymerase adds deoxyribonucleotides to the 3’ hydroxyls of
the RNA primers and subsequently to the ends of the growing
DNA strands

 DNA parental (template) strands are copied simultaneously at

replication forks although they run in opposite directions
 The leading strand is formed by continuous copying of the
parental strand that runs 3’ to 5’ toward the replication fork
 The lagging strand is formed by discontinuous copying of the
parental strand that runs 3’ to 5’ away from the replication
fork
o As more of the helix is unwound, synthesis of the
lagging strand begins from another primer. The short

fragments formed by this process are known as Okazaki

fragments
o The RNA primers are removed by nucleases and then
the resulting gaps are filled with the appropriate
deoxyribonucleotides by another DNA polymerase
o Finally, the okazaki fragments are joined by DNA

ligase, an enzyme that catalyzes formation of
phosphodiester bonds between two polynucleotide
chains

LAGGING STRAND SYNTHESIS
 Is accomplished by short okazaki fragments.

 First an RNA primer is synthesized by primase and as in leading
strand, DNA polymerase III binds to the RNA primer and adds
deoxyribonucleotides.
 Although the process seems simple the complexity lies in the
coordination of leading and lagging strand synthesis: both strands
are produced by a single asymmetric DNA polymerase III dimer
which is accomplished by looping the DNA of the lagging strand
bringing together the two point of polymerization.

 At the replication fork DnaB helicase and DnaG primase constitute

a functional unit within the replication complex, the primosome.
 DNA polymerase III uses one set of its core subunits to synthesize
the leading strand continuously, while the other set of core
subunits cycles from one okazaki fragment to the next on the
looped lagging strand.
 The DnaB helicase unwinds the DNA at the replication fork as it
travels along the lagging strand template in the 5’ to 3’ direction.
DNA primase occasionally associates with DnaB helicase and
synthesizes a short RNA primer.
 When the synthesis of an okazaki fragment has been completed,
replication halts and the core subunits of DNA polymeraseIII
dissociates from their beta sliding clump and associate with the
new clamp initiating synthesis of a new okazaki fragment.
 The entire complex responsible for coordinated DNA synthesis at a
replication fork is a replisome.
 Once an okazaki fragment has been completed, its RNA primer is
removed by nuclease and replace with DNA by DNA polymerase I
and the remaining Nick is sealed by DNA ligase by formation of a
phosphodiester bond between a 3’ hydroxyl end of one strand and
a 5’ phosphate end of another strand.
 The phosphate must be activated by adenylation.
 In eukaryotic cells, about 200 deoxyribonucleotides are added to

the lagging strand in each round of synthesis, whereas in
prokaryotes 1000 to 2000 are added
TERMINATION

 Termination utilization substance (Tus) binds to the ter site

 Tus inhibits helicase activity and thus prevents replication forks
continuing through this region
 Ter sites act as replication “blocks”

RNA METABOLISM
STRUCTURE OF RNA
 RNA is a product of DNA transcription, it is similar to DNA

except for the fact that RNA carries ribose sugar rather than
deoxyribose sugar and uracil (U) rather than thymine (T)
o A small amount of thymine is present in RNA
 RNA is generally single stranded in contrast to DNA which is

double stranded
 When the single strands loop back on themselves the bases on
opposite sides pair
o Guanine with cytosine: with 3 hydrogen bonds in between
o Adenine with uracil: with 2 hydrogen bonds in between
 RNA functions in protein synthesis
o In this process, a part of DNA is transcribed into a
complementary strand of mRNA (messenger RNA) which
then attaches to the ribosome (consisting of rRNA=
ribosomal RNA) in order to translate the sequence of
nucleotide bases into an amino acid sequence that eventually
makes a protein

 Note: only one strand of DNA is transcribed during RNA synthesis

and the 5’ end of the mRNA corresponds to the amino terminus of
the amino acid chain while the 3’ strand of the mRNA corresponds
to the carboxyl terminus of the amino acid chain.


 There are 4 types of RNA

 rRNA (ribosomal RNA): are components of ribosomes, the
complexes that carry out the synthesis of proteins
 tRNA (transfer RNA): are adapter molecules that faithfully
translate the information in mRNA into a specific sequence
of amino acids, they carry amino acids
 mRNA (messenger RNA): are intermediaries, carrying
genetic information from one or a few genes to a ribosome,
where the corresponding proteins can be synthesized
 small nuclear RNA (snRNA) and microRNA (miRNA):
together with proteins form small nuclear ribonucleoproteins
(snRNPS) that act as ribozymes
TRANSCRIPTION
 Transcription is a DNA-directed synthesis of RNA
 mRNA is transcribed from the template strand of a gene.
 RNA polymerase can initiate the synthesis of new chains. A primer
is not required
 RNA polymerase separates the DNA strands at the appropriate
point and bonds the RNA nucleotides as they base-pair along the
DNA template
 The DNA template is copied in the 3’ to 5’ direction and the RNA
chain grows in the 5’ to 3’ direction.
o Ribonucleotides (GTP, UTP, CTP, ATP) serve as the
precursors for the RNA chain. This process is similar to that
for DNA synthesis
 Transcription takes place in 3 stages
 Initiation
 Elongation
 Termination
 Specific sequences of nucleotides along the DNA mark where gene

transcription begins and ends
o RNA polymerase attaches and initiates transcription at the
promoter, “upstream” of the information contained in the
gene, the transcriptional unit.
o The terminator signals mark the end of transcription
 Bacteria have a single type of RNA polymerase that synthesizes all
RNA molecules
 In contrast, eukaryotes have 3 RNA polymerases (I, II and III) in
their nuclei
o RNA polymerase II is used for mRNA synthesis
INITIATION OF RNA TRANSCRIPT
 Transcription in eukaryotic cells varies from transcription in

prokaryotic cells
o In prokaryotes the presence of a promoter sequence
determines which strand of DNA helix is the template.
Within the promoter is the starting point for the transcription
of a gene
 The promoter also includes a binding site for RNA
polymerase several dozen nucleotides upstream of the
start
 In prokaryotes, RNA polymerase can recognize and
bind directly to the promoter region

o In eukaryotes, proteins called transcription factors recognize

the promoter region, especially a TATA box (TATAAAA)
and bind to the promoter
 After they have bound to the promoter, RNA
polymerase binds to transcription factors to create a
transcription initiation complex
 RNA polymerase then starts transcription

PROKARYOTES EUKARYOTES
 The presence of a promoter  In eukaryotes proteins called
sequence determines which transcription factors
strand of the DNA helix is recognize the promoter
the template region, especially a TATA
 Within the promoter is box (TATAAT) and bind to
the starting point for the promoter
the transcription of a  After they have bound to the
gene promoter, RNA polymerase
 The promoter also binds to transcription factors
includes a binding site to create a transcription
for RNA polymerase initiation complex
several dozens

nucleotides upstream  RNA polymerase then starts

of the start point. transcription
 RNA polymerase can
recognize and bind
directly to the promoter
region
ELONGATTION OF RNA TRANSCRIPT
 As RNA polymerase moves along the DNA, it untwists the double

helix, 10 to 20 bases at a time
 The enzyme adds nucleotides to the 3’ end of the growing strand
 Behind the point of RNA synthesis, the double helix re-forms and
the RNA molecule peels away.

TERMINATION OF TRANSCRIPTION
 Transcription proceeds until after the RNA polymerase transcribes

a terminator sequence in the DNA
 In prokaryotes, RNA polymerase stops transcription right at the
end of the terminator. Both the RNA and DNA are then released
 In eukaryotes, the polymerase continues for hundreds of
nucleotides past the terminator sequence AAUAAA. At a point
about 10 to 35 nucleotides past this sequence, the pre-mRNA is
cut from the enzyme
POST TRANSCRIPTIONAL MODIFICATION

 In eukaryote the mRNA modified after transcription

 Enzymes in the eukaryotic nucleus modify the pre-mRNA before

the genetic messages are dispatched to the cytoplasm
 At the 5’ end of the pre-mRNA molecule, a modified form of
guanine nucleotide is added, the 5’ cap
o This helps protect mRNA from hydrolytic enzymes
o It also functions as an “attach here” signal for ribosomes
 At the 3’ end, an enzyme adds 50 to 250 adenine nucleotides, the
poly (A) tail.
o In addition to inhibiting hydrolysis and facilitating ribosome
attachment, the poly(A) tail also seems to facilitate the export
of mRNA from the nucleus
o The mRNA molecule also includes non-translated leader and
trailer segments
 RNA splicing also takes place, it removes introns and joins exons
to create an mRNA molecule with a continuous coding sequence

o The pre-mRNA combines with snRNPs (small nuclear

ribonucleotide proteins) and other proteins to form a
spliceosome
o Within the spliceosome snRNA base-pairs with nucleotide at
the ends of the intron
o The RNA transcript is cut to release the intron and the exons
are spliced together, the spliceosome then comes apart,
releasing mRNA which now contains only exons

 RNA splicing appears to have several functions

 First, at least some introns contain sequences that control
gene activity in some way
 Splicing itself may regulate the passage of mRNA from the
nucleus to the cytoplasm
 One clear benefit of split genes is to enable a gene to encode
for more than one polypeptide
o Alternative RNA splicing gives rise to two or more
different polypeptides, depending on which segments
are treated as exons.

o Early results of the human Genome project indicate that

this phenomenon may be common in humans.
SUMMARY
 DNA and RNA are the nucleotides found in cells
 DNA in humans is linear and double stranded while in bacteria it is
circular and double stranded
 RNA functions in protein synthesis, there are about 4 types of
RNA: tRNA, mRNA, snRNA, rRNA
 DNA replication happens in the S phase of the cell cycle and it
follows 4 fundamental rules
 DNA replication is universal and if a part of DNA is opened for
replication then the entire genome is committed to replication
however if a part of DNA is opened for RNA formation
(transcription) it is only limited to that part of the DNA.
 DNA replication involves: initiation, elongation and termination
 RNA is formed by transcription which takes place in 3 stages:
 Initiation
 Elongation
 Termination
 Replication of DNA and formation of RNA has to be accurate to
prevent genetic mutations that could lead to genetic diseases.
PROTEIN SYNTHESIS
OBJECTIVES
1. Transcription

2. Translation
3. Post-translational modifications of proteins
 Proteins are macromolecules that consist of amino acid subunit

 Proteins are the end products of most information pathways
 A typical cell requires thousands of different proteins at any given
moment.
 These must be synthesized in response to the cell’s current needs,
transported (targeted) to their appropriate cellular locations and
degraded when no longer needed.
 Proteins serve various functions in animal cells, these functions
include:
 Proteins form part of the phospholipid of all cells where they
function as channels and carrier molecules
 Proteins function in the buffer system of the body: due to
their amphoteric nature proteins have the ability to resist pH
changes in the body.
 Proteins function as hormones in many signaling pathways
e.g. insulin
 Proteins function as immunoglobulins/ antibodies in the
immune system of the organism
 Proteins function as enzymes that catalyze metabolic
reactions
 Due to this versatile nature of proteins it is important to study how
these proteins are synthesized
 Every nucleated cell with protein synthesizing machinery (e.g.
ribosomes) has the ability to synthesize proteins
 In each nucleus of every cell, there are genes that code for proteins
 A gene is a part of DNA that codes for proteins
 The human body contain many genes that are currently being
studied and mapped out
 Not every part of DNA codes for proteins. Genes consist of 2
parts:
a. Introns: The “non-coding” areas on a gene
b. Exons: The “coding” areas on a gene, these account for
1.5% of the total human DNA.
 The entire process of protein synthesis starts in the nucleus of a

cell and is completed in the cytosol.
 A part on the single strand of DNA is used as a template in a
process called transcription to produce mRNA (messenger
RNA)
 This process produces a strand that is complementary to the
DNA template strand
 mRNA carries the genetic information from the nucleus and
through the nuclear pores to the protein machinery of the cell
(the ribosome)
 On the ribosome the sequence of nucleotide bases on the
mRNA is converted into a sequence of amino acids in a

process called translation that utilizes tRNA (transfer RNA)

and rRNA (ribosomal RNA)
 Due to the complexity of protein synthesis it was impossible to

understand or explain mutations before the genetic code was
elucidated
 The code provides a foundation for explaining the way in which
protein defects may cause genetic disease and for the diagnosis and
perhaps treatment of these disorders
 The letters A, G, T and C correspond to the nucleotides found in

DNA, the genetic code explains how these bases are arranged in
order to carry out proteins synthesis
 The properties of the genetic code include:
o The bases A, G, T and C (U in RNA) are arranged in triplets
to form what is called a codon this codon is found on mRNA
that is produced during transcription
 Remember there are 20 different amino acids that are
required for protein synthesis thus there must be at least
20 distinct codons that make up the genetic code
 Since there are only 4 different nucleotides in mRNA,
each code must consist of more than a single purine or
pyrimidine molecule.
 Codons consisting of 2 nucleotides each could provide
for only 16 (42) specific code, whereas codons of 3
nucleotides could provide 64 (43)
 It is now known that each codon consists of a sequence
of 3 nucleotides (a triplet code)
o It is a degenerate code
 Assuming that one codon codes for only one amino
acid then there would be 64 amino acids however, there
are only 20. This is brought about by the degeneracy of
this code
 An amino acid can be coded for by different codons
(but a codon cannot code for 2 different amino acids)
 Some codons do not even code for amino acids and
function as start (AUG) and stop (UAG, UGA, UAA)
codons.

o The code is non-overlapping

 It is always read from the 5’ end to the 3’ end e.g.
AGUAACUAC would be translated as AGU-AAC-
UAC and not AGU-UAA-ACU-UAC
o The genetic code is universal and functions the same in all
living organisms

 Since RNA has a role to play in protein synthesis it is essential to

known the type of RNA found in cells
 Ribosomal RNA (rRNA) are components of ribosomes, the
complexes that carry out the synthesis of proteins
 Messenger RNA (mRNA) are intermediaries, carrying
genetic information from one or a few genes to a ribosome,
where the corresponding proteins can be synthesized
 Transfer RNA (tRNA) adapter molecules that faithfully
translate the information in mRNA into a specific sequence
of amino acids

 Small nuclear RNA (snRNA) and microRNA (miRNA)

together with proteins form small nuclear ribonucleoproteins
(snRNPS) that act as ribozymes
TRANSFER RNA
 These are adapter molecules that carry amino acids to the site of
protein synthesis
 The consist of an amino acid arm (which carries the amino acid at
the 3’ end), a D arm, a TC arm, an extra arm and an arm bearing
the anticodon
 The anticodon on the tRNA arm is complementary to the codon on
the mRNA

 As it was deduced from the genetic code it is known that there are
64 codons (43) however there are only 32 anticodons on tRNA
 This can be explained by the wobble base theory:

 Wobble allow some tRNAs to recognize more than one

codon
 When several different codons specify one amino acid, the
difference between them usually lies at the third base position
(at the 3’ end) for example alanine is coded for by the triplets
GCU, GCC, GCA and GCG
 The codons for most amino acids can by symbolized by 𝑋𝑌𝐺𝐴
OR 𝑋𝑌𝐶𝑈
 The first two letters of each codon are the primary
determinants of specificity
 tRNAs base-pair with mRNA codons at a three-base
sequence of the anticodon
o The tRNA is arranged antiparallel to the mRNA
o The first base of the codon in mRNA (read in the 5’ ->
3’ direction) pairs with the third base of the anticodon
 Some tRNAs include the nucleotide inosinate (designated I)

which contains the uncommon base hypoxanthine

 The first two bases of an mRNA codon always form strong

base pairs with the corresponding bases of tRNA anticodon
and confer most of the coding specificity
 The first base of the anticodon (reading in the 5’ -> 3’) pairs
with the third base of the codon.
 When the first base of the anticodon is C or A, base paring is
specific and only one codon is recognized by that tRNA.
When the first base is U or G binding is less specific and two
different codons may be read.
 When inosine (I) is the first (wobble) nucleotide of an

anticodon, 3 different codons can be recognized.

 When an amino acid is specified by several different codons,

the codons that differ in either of the first two bases require
different tRNAs
 A minimum of 32 tRNAs are required to translate all 61
codons (31 to encode amino acids and 1 for initiation)
 In the process of protein synthesis pre-mRNA is formed, which is

eventually modified to mRNA through RNA processing. The

mRNA then leaves the nucleus and on the ribosome the mRNA is
translated into the protein.
TRANSCRIPTION
 Transcription is a DNA-directed synthesis of RNA
 mRNA is transcribed from the template strand of a gene.
 RNA polymerase can initiate the synthesis of new chains. A primer
is not required
 RNA polymerase separates the DNA strands at the appropriate
point and bonds the RNA nucleotides as they base-pair long the
DNA template

 The DNA template is copied in the 3’ to 5’ direction and the RNA

chain grows in the 5’ to 3’ direction.
o Ribonucleotides (GTP, UTP, CTP, ATP) serve as the
precursors for the RNA chain. This process is similar to that
for DNA synthesis
 Transcription takes place in 3 stages
 Initiation
 Elongation
 Termination
 Specific sequences of nucleotides along the DNA mark where gene
transcription begins and ends
o RNA polymerase attaches and initiates transcription at the
promoter, “upstream” of the information contained in the
gene, the transcriptional unit.
o The terminator signals mark the end of transcription
 Bacteria have a single type of RNA polymerase that synthesizes all
RNA molecules
 In contrast, eukaryotes have 3 RNA polymerases (I, II and III) in
their nuclei
o RNA polymerase II is used for mRNA synthesis
INITIATION OF RNA TRANSCRIPT
 Transcription in eukaryotic cells varies from transcription in

prokaryotic cells
o In prokaryotes the presence of a promoter sequence
determines which strand of DNA helix is the template.
Within the promoter is the starting point for the transcription
of a gene

 The promoter also includes a binding site for RNA

polymerase several dozen nucleotides upstream of the
start
 In prokaryotes, RNA polymerase can recognize and
bind directly to the promoter region
o In eukaryotes, proteins called transcription factors recognize

the promoter region, especially a TATA box (TATAAAA)
and bind to the promoter
 After they have bound to the promoter, RNA
polymerase binds to transcription factors to create a
transcription initiation complex
 RNA polymerase then starts transcription

ELONGATTION OF RNA TRANSCRIPT
 As RNA polymerase moves along the DNA, it untwists the double

helix, 10 to 20 bases at a time
 The enzyme adds nucleotides to the 3’ end of the growing strand
 Behind the point of RNA synthesis, the double helix re-forms and
the RNA molecule peels away.

TERMINATION OF TRANSCRIPTION
 Transcription proceeds until after the RNA polymerase transcribes

a terminator sequence in the DNA
 In prokaryotes, RNA polymerase stops transcription right at the
end of the terminator. Both the RNA and DNA are then released
 In eukaryotes, the polymerase continues for hundreds of
nucleotides past the terminator sequence AAUAAA. At a point
about 10 to 35 nucleotides past this sequence, the pre-mRNA is
cut from the enzyme
POST TRANSCRIPTIONAL MODIFICATION

 In eukaryote the mRNA modified after transcription

 Enzymes in the eukaryotic nucleus modify the pre-mRNA before

the genetic messages are dispatched to the cytoplasm
 At the 5’ end of the pre-mRNA molecule, a modified form of
guanine nucleotide is added, the 5’ cap
o This helps protect mRNA from hydrolytic enzymes
o It also functions as an “attach here” signal for ribosomes
 At the 3’ end, an enzyme adds 50 to 250 adenine nucleotides, the
poly (A) tail.
o In addition to inhibiting hydrolysis and facilitating ribosome
attachment, the poly(A) tail also seems to facilitate the export
of mRNA from the nucleus
o The mRNA molecule also includes non-translated leader and
trailer segments
 RNA splicing also takes place, it removes introns and joins exons
to create an mRNA molecule with a continuous coding sequence

o The pre-mRNA combines with snRNPs (small nuclear

ribonucleotide proteins) and other proteins to form a
spliceosome
o Within the spliceosome snRNA base-pairs with nucleotide at
the ends of the intron
o The RNA transcript is cut to release the intro and the exons
are spliced together, the spliceosome then comes apart,
releasing mRNA which now contains only exons

 RNA splicing appears to have several functions

 First, at least some introns contain sequences that control
gene activity in some way
 Splicing itself may regulate the passage of mRNA from the
nucleus to the cytoplasm
 One clear benefit of split genes is to enable a gene to encode
for more than one polypeptide
o Alternative RNA splicing gives rise to two or more
different polypeptides, depending on which segments
are treated as exons.

o Early results of the human Genome project indicate that

this phenomenon may be common in humans.
TRANSLATION
 Translation happens in the cytoplasm on ribosomes
 Ribosomes consist of a small subunit and a larger subunit that are
assembled during translation
 The ribosome found in prokaryotes are 70S and consist of a 50S
and a 30S subunit. These 70S ribosomes are also found in the
mitochondria of eukaryotic cells
 The ribosomes found in eukaryotes are mainly 80S and they
consist of a 60S subunit and 40S subunit

80S vs 70S RIBOSOMES

 Bacterial ribosomes contain about 65% rRNA and 38% proteins,
they have a diameter of about 18 nm and are composed of two
unequal subunits with sedimentation coefficients of 30S and 50s
and a combined sedimentation coefficient of 70S.
 Both subunits contain dozens of ribosomal proteins and at least one
large rRNA.
 The ribosomal subunits are huge RNA molecules
 In the 50S subunit the 5S and 23S rRNAs form the structural core.
 The 2 irregularly shaped ribosomal subunits fit together to form a
cleft through which the mRNA passes as the ribosome moves
along it during translation.
 The ribosomes in eukaryotic cells are larger and more complex
than bacterial ribosomes with a diameter of about 23nm and a
sedimentation coefficient of about 80S
 They also have 2 subunits which vary in size among species but on
average 60S and 40S
 Altogether eukaryotic ribosomes contain more than 80 different
proteins
 Ribosomal structure and function are strikingly similar in all
organisms and organelles
 Protein synthesis requires 4 stages: activation of amino acids,

initiation, elongation, termination + release and folding + post-
translational modifications

ACTIVATION OF AMINO ACIDS
 For synthesis of a polypeptide with a defined sequence, two

fundamental chemical requirements must be met:
1. The carboxyl group of each amino acid must be activated to
facilitate formation of a peptide bond

2. A link must be established between each new amino acid and

the information in the mRNA that encodes it
 Both these requirements are met by attaching the amino acid to a
tRNA in the first stage of protein synthesis.
 Attaching the right amino acid to the right tRNA is critical.
 This reaction takes place in the cytosol, not on the ribosome
 Each of the 20 amino acids is covalently attached to a specific
tRNA at the expense of ATP energy, using magnesium-dependent
activating enzyme known as aminoacyl-tRNA synthetase
 When attached to their amino acid (aminoacylated) the tRNAs are
said to be “charged”
 NOTE: “charging” of the tRNA is the same as activating the amino

acid
INITIATION
 The mRNA bearing the code for the polypeptide to be synthesized

binds to the smaller of two ribosomal subunits and to the initiating
aminoacyl-tRNA (which is usually methionine)
 The large ribosomal subunit binds to form an initiation complex

 The initiating aminoacyl-tRNA base-pairs with the mRNA codon

AUG that signals the beginning of the polypeptide.
 This process, which requires GTP is promoted by cytosolic

proteins called initiation factors
 In eukaryotes, methionyl-tRNAiMet binds to the small ribosomal
subunit
o The 5’ cap of the mRNA binds to the small subunit, and the
first AUG codon base pairs with the anticodon on the
methionyl-tRNAiMet
o The methionine that initiates protein synthesis is
subsequently removed from the N terminus of the
polypeptide

 In bacteria the methionine that initiates protein synthesis is

formylated and is carried by tRNAfMet
o Prokaryotes do not contain a 5’ cap on their mRNA. An
mRNA sequence upstream from the translation start (the
shine-Dalgarno sequence) binds to the 3’ end of 16S
ribosomal RNA (rRNA) to position the small ribosomal
subunit on the mRNA

 Initiation factors (IFs), ATP and GTP are required for formation of
the initiation complex
o The initiation factors are designated IF-1, IF-2, and IF-3 in
prokaryotes. In Eukaryotes, they are designated eIF-1, eIF-2
and so on. Seven or more may be present
o Release of the initiation factors involves hydrolysis of GTP
to guanosine diphosphate (GDP) and an inorganic phosphate


ELONGATION
 Cells use 3 steps to add each amino acid residue, and the steps are
repeated as many times as there are residues to be added
 Elongation step 1: binding of an incoming aminoacyl-tRNA
o The mRNA codon at the A site (Acceptor or
aminoacyl) determines which aminoacyl-tRNA will
bind
o The codon and the anticodon bind by base pairing that
is antiparallel
o Internal methionine residues in the polypeptide chain
are added in response to AUG codons. They are carried
by tRNAmMet, a second tRNA specific for methionine
o An elongation factor (EF) (EF-Tu in prokaryotes and
EF-1 in eukaryotes) and hydrolysis of GTP are required
for binding
 Elongation step 2: peptide bond formation

o A peptide bond forms between the amino acid group of
the aminoacyl-tRNA at the A site and the carbonyl of
the aminoacyl group attach to the tRNA at the P

(peptidyl) site. Formation of the peptide bond is

catalyzed by peptidyl transferase which is rRNA (23s)
o The tRNA at the P site now does not contain an amino
acid. It is “uncharged”
o The growing polypeptide chain is attached to the tRNA
in the A site
 Step 3: translocation
o The peptidyl-RNA (along with the attached mRNA)
moves from the A site to the P site
o Hydrolysis of GTP is required
o The next codon in the mRNA is now in the A site
o The elongation cycle in eukaryotes and prokaryotes are
quite similar
o 3 eukaryotic elongation factors (eEF1Eef1and
eEF2) have functions analogous to those of the bacterial
elongation factors (EF-Tu, EF-Ts and EF-G
respectively)
o Eukaryotic ribosomes do not have an E (exit) site,

uncharged tRNAs are expelled directly from the P site
o The elongation and translocation steps are repeated

until a termination codon moves into the A site.
TERMINATION
 When a termination codon (UGA, UAG or UAA) occupies the A

site, release factors cause the newly synthesized polypeptide to be
released from the ribosome
 The ribosomal subunits dissociate from the mRNA

POST-TRANSLATIONAL MODIFICATIONS OF
PROTEINS
 When insulin is synthesized it is preproinsulin
 In its modification the signal sequence is removed to form pro-
insulin
 Furthermore, a part of the polypeptide is cleaved off to release a C
polypeptide while disulfide bonds are introduced in the
polypeptide chain to form mature insulin.
 This post translational modification of insulin serves to:
a. Make insulin more water soluble given that it is a peptide
hormone and functions extracellularly in an aqueous
environment: (more positive and negative charges)

b. Activate insulin via preproinsulin and pro-insulin

 Newly synthesized polypeptide chains undergo folding and
processing such as:
 Amino-terminal and carboxyl-terminal modification
 Loss of signal sequences
 Modification of individual amino acids
 Attachment of carbohydrate side chains (glycosylation)
 Addition of isoprenyl groups
 Addition of prosthetic groups
 Proteolytic processing
 Formation of disulfide cross-links

SUMMARY
 Proteins are biological polymers with diverse functions
 They are coded for by genes in the DNA
 The genetic code helps us understand protein synthesis
 Protein synthesis involves
 Transcription which has initiation, translation and
termination produces mRNA
 Post transcriptional modification and mRNA splicing (which
requires snRNPs)
 Translation forms the amino acid chain through the help of
tRNA and rRNA. It also has initiation, elongation and
termination phases
 Post-translational modification
HEME METABOLISM
OBJECTIVES
1. Heme synthesis
2. Heme breakdown
3. Bilirubin metabolism

HEME SYNTHESIS
STRUCTURE OF HEME
 Heme is a derivative of the porphyrin molecule

 Porphyrins are cyclic compounds formed by fusion of 4 pyrole
rings linked by methenyl bridges
 Heme consists of a porphyrin ring coordinated with iron and is

found mainly in hemoglobin but also present in myoglobin and the
cytochromes

BIOLOGICAL IMPORTANCE OF HEME
Protein Function
Hemoglobin Transport of oxygen in blood
Myoglobin Storage of oxygen in muscle
Cytochrome C Involvement in electron transport

chain
Cytochrome P450 Hydroxylation of xenobiotics
Catalase Degradation of hydrogen peroxide
Tryptophan pyrrolase Oxidation of tryptophan

 Heme is the prosthetic group of hemoproteins

 Hemoglobin (The oxygen carrier because of heme
 Heme and ferrous iron confer the ability to store and transport
oxygen
HEME BIOSYNTHESIS
 The substrates mainly include succinyl-CoA, glycine, Fe2+

 Heme can be synthesized by almost all the tissues in the body
which require hemoproteins
 Major sites of synthesis are in the liver and bone marrow
 The whole synthetic process takes place subcellularly in the
mitochondria and cytosol.
 Step 1:
 In the mitochondrion glycine and succinyl- CoA condense in
addition are decarboxylated to form -Aminolevulinic acid
(ALA)

 ALA synthase catalyzes this reaction

 Pyridoxal phosphate is the cofactor of ALA synthase
 ALA synthase is the regulatory enzyme for heme

biosynthesis
 ALA synthesis is the committed step of the heme synthesis
pathway and usually rate-limiting step for the overall
pathway.
 Regulation occurs through control of gene transcription
 Heme regulates its own synthesis in the liver, it functions as a
feedback inhibitor, repressing transcription of the ALA
synthase gene in most cells.
 Step 2
 The succeeding few reactions occur in the cytoplasm
 One ALA condenses with another molecule of ALA to form
porphobilinogen (PBG)
 The condensation involves removal of 2 molecules of water
and the enzyme is ALA dehydratase

 Porphobilinogen (PBG) is the first pathway intermediate that

includes a pyrole ring
 The porphyrin ring is formed by condensation of 4 molecules of

porphobilinogen

 Porphobilinogen Deaminase catalyzes successive PBG

condensations, initiated in each case by elimination the amino
group
 The four porphobilinogen form the first in a series of porphyrins;
these are hydroxymethylbilane, uroporphyrinogen III,
corproporphyrinogen III and protoporphyrinogen IX
 The porphyrins are altered by decarboxylation and oxidation and

protoporphyrin IX is formed.

 Heme is formed by incorporation of iron (Fe2+)

o This rection is partly spontaneous
o Ferrochelatase enhaces rate and it can be inhibited by lead
o Iron (II) is added to protoporphyrin IX via ferrochelatase, a
homodimeric enzyme containing 2 iron-sulfur clusters

 Iron obtained from the diet is transported via transferrin and is

stored as ferritin in the bone marrow
 Vitamin C increases the uptake of iron from the intestinal tract
 Excess iron is stored as hemosiderin
REGULATION OF HEME SYNTHESIS
1. ALA synthase
 This is the major site of regulation
 It is regulated by repression mechanism.
o Heme inhibits the synthesis of ALA synthesis by acting
as a corepressor.
o The feedback regulatory effect is a typical example of
end-product inhibition
 ALA synthase is also allosterically inhibited by hematin

o When there is excess of free heme without globin

chains to bind with, the iron (II) is oxidized to iron (III)
forming hematin.
o Hematin will inhibit ALA synthase to prevent excessive
unwanted production of heme
o Hematin will also inhibit the translocation of ALA
synthase from the cytoplasm into the mitochondria
where its substrate succinyl CoA is formed. Thus
synthesis is inhibited till there are sufficient globin
chain to bind with
 Lack of vitamin B6 will decrease the synthesis of ALA
o Drugs like NH (iisonicotinic acid hydrazide) that
decrease the availability of pyridoxal phosphate may
also affect heme synthesis
2. Heme synthesis may be inhibited by heavy metals. The steps
catalyzed by ALA dehydratase and ferrochelatase are inhibited by
lead
3. Erythropoietin
 The kidneys also secrete a hormone called erythropoietin
 The function of erythropoietin is to stimulate the production
of red blood cells.
 The kidney produces 85-95% of the body’s erythropoietin so
when the kidney is damaged (kidney disease or failure), not
enough erythropoietin is produced to maintain normal red
blood cell level. This leads to anemia.

HEME BREAKDOWN AND BILIRUBIN METABOLISM

 After red blood cells, which contain hemoglobin, reach their life
span of about 120 days, they are phagocytosed by cells of the
reticuloendothelial system
 Globin is released and converted to amino acids
 Heme is degraded to bilirubin, which is excreted in the bile
 Heme is oxidized and cleaved to produce carbon monoxide and
biliverdin, a green pigment
 Iron is released, oxidized and returned by transferrin to the iron
stores to the body
 Bilirubin which is produced by reduction of biliverdin, is carried
by the protein albumin to the liver
 In the liver, bilirubin reacts with UDP-glucoronate to form
bilirubin monoglucuronide which is converted to the diglucuronide
 Formation of diglucuronide increases the solubility of the pigment

and bilirubin diglucuonide is secreted into the bile
 Bacteria in the intestine convert bilirubin to urobilins and
stercobilins, which gives feces its brown color

SUMMARY
 Heme is a pigment found in many important molecules such as
hemoglobin, myoglobin and cytochromes
 Heme is synthesized by various steps which involve the
mitochondrion and the cytosol
 Old red blood cells are broken down by the reticuloendothelial
system

 The end products of heme breakdown are conjugated to UDP-

glucoronate and excreted in bile and eventually in urine as urobilin
and feces as stercobilin
ACKNOWLEDGMENTS
SPECIAL THANKS TO:
 Moses Kazevu (author)

 Dr Chimuka Mwaanga (lecturer)
The following books:
 Harper’s illustrated biochemistry

 Board review series: biochemistry, molecular biology and genetics
 Lehninger’s Principles of biochemistry
 Lippincott’s illustrated biochemistry
 Textbook of medical biochemistry
 Biochemistry by Voet and Voet
My colleagues
 Zebediya Phiri
 Amanda Saano
 Mwatu Kalombo
 Agness Mbela
 Faleny Sakala
 Gift Zimba
 Ruqaiyyah Sakala
 Savannah Kadisha
 Macraie Mudumuka
 Kunda Lapukeni
 Geoffrey Mulela
 Martha Mwaba
 Mubita Kennedy Mbangweta
 Classmates
LUSAKA APEX MEDICAL SCHOOL- BIOCHEMISTRY

DEPARTMENT 2016 ©


Biochemistry (Metabolism) by Moses K

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Biochemistry (Metabolism) by Moses K

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1ST EDITION BY: MOSES KAZEVU JR

2 PROPERTY OF MOSES KAZEVU

After studying through this material it is advisable also to pass through

This book provides a variety of useful information including simplified

MAKING UNAUTHORIZED COPIES OF THIS BOOK IS

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TRICARBOXYLIC ACID CYCLE ....................................................... 75

THE ELECTRON TRANSPORT CHAIN AND OXIDATIVE

GLYCOGEN METABOLISM ............................................................. 123

HEXOSE MONOPHOSPHATE SHUNT ............................................ 165

URONIC ACID PATHWAY ................................................................ 187

AMINO ACID METABOLISM ........................................................... 193

LIPID METABOLISM ......................................................................... 238

NUCLEOTIDE METABOLISM .......................................................... 281

NUCLEIC ACID METABOLISM ....................................................... 322

ACKNOWLEDGMENTS ..................................................................... 404

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exergonic i.e. ΔG<0 and energy is released as bonds between

NORMAL VS ABNORMAL METABOLISM

 Knowing normal metabolism enables understanding of

OUTLINE OF CATABOLIC PATHWAYS

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 The nature of diet sets the patterns of metabolism.

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 Dietary carbohydrates are broken down to simple sugars mainly

OVERVIEW OF CARBOHYDRATE METABOLISM

 Glucose is the chief in the metabolism of plants, animals and many

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c. Oxidation via the pentose phosphate (phosphogluconate)

OVERVIEW OF CARBOHYDRATE METABOLISM

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 Lipids are a heterogeneous group

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adipocytes, or transported in plasma in association with proteins,

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 Because of the insolubility of lipids in water ingested

OVERVIEW OF FATTY ACID METABOLISM

 The source of long chain fatty acids is either dietary lipids or de

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 Fatty acids can also be formed by lipogenesis which converts

 These compounds can be metabolized to carbon dioxide and water,

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CARBOHYDRATE AND PROTEIN METABOLIC PATHWAYS

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 Amino acids and glucose formed from digestion of proteins and

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LIPID METABOLIC PATHWAYS AT TISSUE/ORGAN LEVEL

 Lipids in the diet are mainly triacylglycerol and are hydrolyzed to

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 The other major source of long fatty acid is synthesis (lipogenesis)

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METABOLIC PATHWAYS AT SUBCELLULAR LEVEL

 Compartmentation of pathways in separate subcellular

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 In gluconeogenesis substrates such as lactate and Pyruvate which

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REGULATION OF METABOLIC REACTIONS

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