Biochemistry pt. 1

Fundamentals and
Societal Applications

Biochemistry is the
study of the structure,
composition, and
chemical reactions of
substances in living
systems.

 The importance of biochemistry can be seen
from the fact that it is used in many daily
activities.
 It is used in clinical diagnosis, manufacture of
various biological products, treatment of
diseases, in nutrition, agriculture etc.
 The study of biochemistry helps one understand
the actual chemical concepts of biology.
 That is the functioning of various body processes
and physiology by uses of biomolecules.

Biochemistry is a valuable subject in medicine without which
there would have been no such advancement in the field.
 Physiology: Biochemistry helps one understand the biochemical changes
and related physiological alteration in the body. Pathology of any disease
is studied through biochemical changes.
 Pathology: Based on the symptoms described by the patient, the
physician can get a clue on the biochemical change and
the associated disorder. For example, if a patient complains about
stiffness in small joints, then the physician may predict it to be gout and
get confirmed by evaluating uric acid levels in the blood. As uric acid
accumulation in blood results in gout.
 Nutrition deficiency: In the present scenario, many people rely on taking
multivitamin & minerals for better health. The function and role of
the vitamin in the body are described only by biochemistry.
 Hormonal deficiency: There are many disorders due
to hormonal imbalance in especially women and children. The formation,
role of hormones in the normal body function is taught in biochemistry by
which the physician can understand the concerned problem during
treatment.

Almost all the diseases or disorders have some biochemical
involvement. So the diagnosis of any clinical condition is easily
possible by biochemical estimations.
 Kidney function test: For example in kidney disorders, other
chemotherapy treatment etc urine test help understand the
extent of excretion of drugs or other metabolites, the change in
pH, the color of urine etc.
 Blood test: In diabetes, biochemical analytical test for blood
glucose level (above 150mg/ deciliter helps one understand the
severity of diabetes disorder. Another biochemical test for
ketones bodies in urine also indicates the stage of diabetes. The
appearance of ketone bodies or ketone urea is mostly the last
stage of diabetes.
 Liver function tests help understand the type of disease or
damage to the liver, the effect of any medication on liver etc.
 Serum cholesterol test: Evaluation of blood cholesterol level and
other lipoproteins helps understand the proneness of the patient
to cardiovascular diseases.

In agriculture, biochemistry plays a valuable role in farming, fishery,
poultry, sericulture, beekeeping etc.
 Prevent diseases: It helps for prevention, treatment of diseases and also increases
the production or yield.
 Enhance growth: Biochemistry gives an idea of how the use of fertilizers can
increase plant growth, their yield, quality of food etc.
 Enhance Yield: Some hormones promote growth, while other promote
flowering, fruit formation etc. In fisheries, use of substances to promote fish
growth, their reproduction etc can be understood.
 Adulteration: Even the composition of food material produced, their alteration or
adulteration for example in honey can be found by biochemical tests. Biochemistry
tests help prevent contamination.
 Biochemical tests for the pesticide residues or other toxic waste in plant, food
grain and soil can be evaluated. Hence during import and export of food grains a
biochemical check of the toxic residues is done to fix the quality.
 In animal husbandry, the quality of milk can be checked by biochemical tests. It
also helps diagnose any disease condition in animals and birds.
 In fisheries, the water quality is regularly monitored by biochemical tests. Any
drastic change in water chemistry & composition of fishery ponds can lead to the
vast death of fishes and prawns, hence the tests are done on regular basis to see
salt content (calcium content), pH, accumulation of waste due to not changing
water for long etc.

In nutrition, biochemistry describes the food chemistry. For
maintenance of health, optimum intake of many biochemicals
like macro, micronutrients, vitamins, minerals, essential fatty
acids & water is necessary.
 Food chemistry gives an idea of what we eat, i.e. it’ s
components like carbohydrates, proteins, fats,etc. and also the
possible physiological alteration due to their deficiency.
 The role of nutrients: Due to biochemistry the importance of
vitamins, minerals, essential fatty acids, their contribution to
health were known. Hence there is a frequent recommendation
for inclusion of essential amino-acids, cod liver oil, salmon fish
oil etc. by physicians and other health and fitness experts.
 The nutrients value of food material can also be determined by
biochemical tests.
 The physician can prescribe to limit usage of certain food like
excess sugar for diabetics, excess oil for heart &
lung problem prone patients etc. As these carbohydrate and fat
diets can inhibit the recovery rate from said disorder. This
knowledge is due to their idea of food chemistry and related

In a pharmacy, many drugs are stored for regular dispensing.
 Drug Constitution: Biochemistry gives an idea of
the constitution of the drug, its chances of degradation with
varying temperature etc. How modification in the medicinal
chemistry helps improve efficiency, minimize side effects etc.
 The half-life: This is a test done on biochemical drugs to know
how long a drug is stable when kept at so and so temperature.
 Drug storage: The storage condition required can be estimated
by the biochemical test.For example many enzymes, hormones
are stored for dispensing. These get deteriorated over time due
to temperature or oxidation, contamination and also due to
improper storage.
 Drug metabolism: It also gives an idea of how drug molecules
are metabolized by many biochemical reactions in presence of
enzymes. This helps to avoid drugs which have a poor metabolism
or those with excessive side effects from being prescribed or
dispensed to the patient.
 Biochemical tests: These tests helps fix the specific half-life or
date of expiry of drugs.

Biochemistry of plants gave way to the breakthrough of how food is synthesized in them and
the reason why they are autotrophs i.e. not dependent on other living beings for food.
Biochemistry in plants describes
 1. Photosynthesis: This describes how carbohydrates are synthesized by use of
sunlight, CO2, and water in the green leaves of plants. It goes on to explain about
different complex enzymes involved in the process to combine the energy of sun
within the molecules H2O+ CO2 in the form of carbohydrates.
 2. Respiration: By use of above photosynthesis pathway, plants leave out Oxygen
while taking up Carbon dioxide from the air.
 3. Different sugars: Biochemistry defines different types of carbohydrates formed in
plants like trioses (3 carbon sugars i.e. glyceraldehyde), tetroses (4), pentoses (5),
hexoses (6= glucose), heptuloses (7) etc. Heptuloses are the carbohydrates which go
on to form the nucleic acids i.e deoxyribonucliec acid (DNA), ribonucleic acid (RNA).
 4. Plants secondary metabolites: Biochemistry also describes how the plant
products like gums, tannins, alkaloids, resins, enzymes, phytohormones are formed
inside the plants.
 5. Other functions: It also describes how plants fruits get ripened, how plant seed
germinates, the respiration process inside the plant cell, how proteins and amino
acids are formed on rough endoplasmic reticulum and fats are formed on smooth
ER.

In Biology…
• Living organisms must work to stay alive, to
grow and to reproduce
• All living organisms have the ability to
produce energy and to channel it into
biological work
• Living organisms carry out energy
transductions, conversions of one form of
energy to another form

• Modern organisms use the chemical energy
in fuels (carbonhydrates, lipids) to bring
about the synthesis of complex
macromolecules from simple precursors
• They also convert the chemical energy into
concentration gradients and electrical
gradients, into motion and heat, and, in a
few organisms into light (fireflies, some
deep-sea fishes)

• Biological energy transductions obey the
same physical laws that govern all other
natural processes
• Bioenergetics is the quantitative study of
the energy transductions that occur in living
cells and of the nature and function of the
chemical process underlying these
transductions

The branch of physical chemistry known as
thermodynamics is concerned with the study of the
transformations of energy. That concern might seem
remote from chemistry, let alone biology; indeed,
thermodynamics was originally formulated by physicists
and engineers interested in the efficiency of steam
engines. However, thermodynamics has proved to be of
immense importance in both chemistry and biology. Not
only does it deal with the energy output of chemical
reactions but it also helps to answer questions that lie
right at the heart of biochemistry, such as how energy
flows in biological cells and how large molecules assemble
into complex structures like the cell.

• The first law of thermodynamics, also known as Law of
Conservation of Energy, states that energy can neither
be created nor destroyed; energy can only be transferred
or changed from one form to another. For example,
turning on a light would seem to produce energy;
however, it is electrical energy that is converted.
• A way of expressing the first law of thermodynamics is
that any change in the internal energy (∆E) of a system
is given by the sum of the heat (q) that flows across its
boundaries and the work (w) done on the system by the
surroundings: ΔE=q+w

• This law says that there are two kinds of processes, heat
and work, that can lead to a change in the internal
energy of a system. Since both heat and work can be
measured and quantified, this is the same as saying
that any change in the energy of a system must result in
a corresponding change in the energy of the
surroundings outside the system. In other words, energy
cannot be created or destroyed. If heat flows into a
system or the surroundings do work on it, the internal
energy increases and the sign of q and w are positive.
Conversely, heat flow out of the system or work done by
the system (on the surroundings) will be at the expense
of the internal energy, and q and w will therefore be
negative.

• The second law of thermodynamics says that the entropy
of any isolated system always increases. Isolated systems
spontaneously evolve towards thermal equilibrium—the
state of maximum entropy of the system. More simply put:
the entropy of the universe (the ultimate isolated system)
only increases and never decreases.
• A simple way to think of the second law of
thermodynamics is that a room, if not cleaned and tidied,
will invariably become more messy and disorderly with
time - regardless of how careful one is to keep it clean.
When the room is cleaned, its entropy decreases, but the
effort to clean it has resulted in an increase in entropy
outside the room that exceeds the entropy lost.

The third law of thermodynamics states that the
entropy of a system approaches a constant value as
the temperature approaches absolute zero. The
entropy of a system at absolute zero is typically zero,
and in all cases is determined only by the number of
different ground states it has. Specifically, the
entropy of a pure crystalline substance (perfect
order) at absolute zero temperature is zero. This
statement holds true if the perfect crystal has only
one state with minimum energy.

Living organisms and the second
law
• The reacting system is the collection of matter that is
undergoing a particular chemical or physical process; it may be
an organism, a cell, or two reacting compounds. The reacting
system and its surroundings together constitute the universe. In
the laboratory, some chemical or physical processes can be
carried out in isolated or closed systems, in which no material
or energy is exchanged with the surroundings. Living cells and
organisms, however, are open systems, exchanging both
material and energy with their surroundings; living systems are
never at equilibrium with their surroundings, and the constant
transactions between system and surroundings explain how
organisms can create order within themselves while operating
within the second law of thermodynamics.

Three thermodynamic quantities that describe the
energy changes occurring in a chemical reaction
1.Gibbs free energy, G, expresses the amount of energy
capable of doing work during a reaction at constant
temperature and pressure.
When a reaction proceeds with the release of free energy
(that is, when the system changes so as to possess less
free energy), the free-energy change, G, has a negative
value and the reaction is said to be exergonic. In
endergonic reactions, the system gains free energy and
G is positive.
The units of ΔG are expressed in joules/mole or
calories/mole (1 calorie: 4.184 J)

2. Enthalpy, Δ H, is the heat content of the
reacting system. It reflects the number and
kinds of chemical bonds in the reactants and
products.
• When a chemical reaction releases heat, it is
said to be exothermic; the heat content of the
products is less than that of the reactants and
Δ H has, by convention, a negative value.
• Reacting systems that take up heat from their
surroundings are endothermic and have
positive values of Δ H.
The units of ΔH are expressed in joules/mole or
calories/mole (1 calorie: 4.184 J)

Entropy, S, is a quantitative expression for
the randomness or disorder in a system
When the products of a reaction are
less complex and more disordered than
the reactants, the reaction is said to
proceed with a gain in entropy.
*Units of entropy are expressed in
joules/mole x K
Relationship of entropy and enthalpy expressed in:
Δ G = Δ H - T Δ S

Relationship of free energy, entropy, enthalpy expressed in:
Δ G = Δ H - T Δ S
Δ G = change in Gibbs free energy of the reacting
system
Δ H =change in enthalpy of the system/total energy
of the system
Δ T = absolute temperature
Δ S =change in entropy of the system.
• Δ S has a positive sign when entropy increases
• Δ H, has a negative sign when heat is released by
the system to its surroundings.
• Either of these conditions, which are typical of
favorable processes, tend to make G negative. In
fact, G of a spontaneously reacting system is
always negative.

• The second law of thermodynamics states that the
entropy of the universe increases during all
chemical and physical processes
• Does not require that the entropy increase take
place in the reacting system itself.
• The order produced within cells as they grow and
divide is more than compensated for by the
disorder they create in their surroundings in the
course of growth and division.
• In short, living organisms preserve their internal
order by taking from the surroundings free energy
in the form of nutrients or sunlight, and returning to
their surroundings an equal amount of energy as
heat and entropy.

Cells Require Free Sources of Energy
• Cells are isothermal systems—they function at essentially
constant temperature (they also function at constant
pressure). Heat flow is not a source of energy for cells, because
heat can do work only as it passes to a zone or object at a
lower temperature. The energy that cells can and must use is
free energy, described by the Gibbs free-energy function G,
which allows prediction of the direction of chemical reactions,
their exact equilibrium position, and the amount of work they
can in theory perform at constant temperature and pressure.
Heterotrophic cells acquire free energy from nutrient
molecules, and photosynthetic cells acquire it from absorbed
solar radiation. Both kinds of cells transform this free energy
into ATP and other energy-rich compounds capable of
providing energy for biological work at constant temperature.

Relationship of Standard Free Energy
Change and Equilibrium Constant
• The composition of a reacting system tends to continue
changing until equilibrium is reached. At the equilibrium
the rates of the forward and revers reactions are equal
and no further change occurs in the system. The Keq is
defined by the molar concentrations of products and
reactants at equilibrium
• aA+bB cC+ dD
• [C]c [D]d
• Keq = ------------------
• [A]a [B]b
• Where [A], [B], [C], and [D] are the molar concentrations
of the reaction components at the point of equilibrium.

• When a reacting system is not at equilibrium, the
tendency to move toward the equilibrium
represents a driving force. The magnitude of this
driving force is expressed as free energy change
(ΔG).
•
• Under standard conditions (250C), when
reactants and products are initially at the 1 M
concentrations the force driving the system
toward equilibrium is defined as the standard
free energy change (ΔG0)

• By this definiation, standart state for reactions
involves [H+] = 1M or pH=0.
• However most biochemical reactions occur in well-
buffered aqueous solutions near pH=7
• For convenience of calculations, biochemists define
a different standard state in which the
concentration of [H+] is 10-7 M , and for reactions
that involve Mg2+ (available in most reactions
involving ATP), its concentration in solution is
commonly taken to be constant at 1mM
•

• Physical constants based on this
biochemical standard state are called
standard transformed constants and
written as ΔG'0 and K'eq to distinguish
them from the untransformed constants
which are used by chemists.

• ΔG'0 is the difference between the free energy
content of the products and the free energy
contents of the reactants under standard
conditions
• ΔG'0 = ΔG'0
products– ΔG'0
reactives)
• When ΔG'0 is negative, the products contain less
free energy than the reactants and the reaction
will proceed spontaneously under standard
conditions
• When ΔG'0 is positive, the products contain more
free energy than the reactants and the reaction
will tend to go in the revers direction under
standard conditions

• Each chemical reaction has a characteristic
standard free energy change which may be
positive, negative or zero depending on the
equilibrium constant of the reaction
• ΔG'0 tell us in which direction and how far a
given reaction must go to reach equilibrium when
the initial concentration of each component is
1M, the pH is 7, the temparature is 250C.
• Thus ΔG'0 is a constant; a characteristic for a
given reaction

• Actual free energy change (ΔG) is a function of
reactant and product concentrations and of
the temparature prevailing during the reaction
which will not necessarily match the standard
conditions as defined before

• ΔG of any reaction proceeding spontaneously
toward its equilibrium is always negative,
become less negative as the reaction proceeds,
and is zero at he point of equilibrium, indicating
that no more work can be done by the reaction
• ΔG and ΔG'0 for a reaction like that
• A+B C+D
• is written as
• [C] [D]
• ΔG=ΔG'0 + RTln
• [A] [B]

• An example:
• A+B C+D
• Reaction is taking place at the standard
temparature and pressure
• But the concentrations of A,B,C and D are not
equal and none of them at the 1M concentration
• In order to determine actual ΔG under these non-
standard concentrations as the reaction proceeds
from left to right, we enter the actual
concentrations of A,B,C and D in this equation.

• Rest of the terms in the equation (R,T, ΔG'0 ) are
standard values
• When the reaction is at equilibrium there is no
force driving the reaction in either direction and
ΔG is zero, thus equation reduces to
• [C] [D]
• 0= ΔG'0 + RTln
• [A] [B]
• ΔG'0 = -RT lnK'eq ΔG'0

• The criteria for spontaneity of a reaction is the
value of ΔG not ΔG'0
• Standard free energy changes are additive.
• In the case of two sequential chemical reactions,
• A B ΔG'0
1
• B C ΔG'0
2

• Since the two reactions are sequential, we
can write the overall reaction as
• A C ΔG'0
total
• The ΔG'0 values of sequential reactions are
additive.
• ΔG'0
total = ΔG'0
1 + ΔG'0
2

• A B ΔG'0
1
• B C ΔG'0
2
• Sum: A C ΔG'0
1 + ΔG'0
2
• This principle of bioenergetics explains how a
thermodynamically unfavorable (endergonic)
reaction can be driven in the forward direction by
coupling it to a highly exergonic reaction through
a common intermediate

• The main rule in biochemical reactions in
living organisms:
• All endergonic reactions are coupled to an
exergonic reaction. There is an energy cycle
in cells that links anabolic and catabolic
reactions.

Glycolysis
• Glykys = Sweet, Lysis = splitting
• During this process one molecule of glucose (6 carbon molecule)
is degraded into two molecules of pyruvate (three carbon
molecule).
• Free energy released in this process is stored as 2 molecules of
ATP, and 2 molecules of NADH.
• Glucose + 2NAD+ = 2Pyruvate + 2NADH + 2H+ d= -146 kJ/mol
• 2ADP + 2Pi = 2ATP + 2H2O dGo = 2X(30.5 kJ/mol) = 61 kJ/mol
• -----------------------------------------------------
• dGo (overall) = -146+61 = -85 kJ/mol
• In standard condition glycolysis is an exergonic reaction
which tends to be irreversible because of negative dGo.

→ It is also called as Embden-Meyerhof Pathway
(EMP)
→ it is defined as the sequence of reactions converting
glucose or glycogen to pyruvate or lactate with
production of ATP.
→ Enzymes takes place in cytosomal fraction of the
cell.
→ major pathway in tissues lacking mitochondria like
erythrocytes, cornea, lens etc.
→ it is essential for brain which is dependent in
glucose for energy.
→ under anaerobic condition = glu + 2ADP + 2iP -----
2 Lactate + 2ATP

Glucose + 6O2 = 6CO2 + 6H2O
dGo= -2840 kJ/mol
Glucose + 2NAD+ = 2Pyruvate
+ 2NADH + 2H+ dGo = -146
kJ/mol
5.2% of total free energy that
can be released by glucose is
released in glycolysis.
Fate of Glucose in Living Systems

•Glycolysis was the very first biochemistry or oldest biochemistry
studied.
•It is the first metabolic pathway discovered.
•Louis Pasture 1854-1864: Fermentation is caused by
microorganism. Pastuer’s effect: Aerobic growth requires less
glucose than anaerobic condition.
•Buchner; 1897: Reactions of glycolysis can be carried out in cell-
free yeast extract.
•Harden and Young 1905: 1: inorganic phosphate is required for
fermentation. 2: yeast extract could be separated in small
molecular weight essential coenzymes or what they called Co-
zymase and bigger molecules called enzymes or zymase.
•1940: with the efforts of many workers, complete pathways for
glycolysis was established.
History of Glycolysis

Net Gain of Glycolysis
Basically in the process of glycolysis, the
following are invested:
Which will yield

• There are 10 enzyme-catalyzed reactions in glycolysis. There are
two stages
• Stage 1: (Reactions 1-5) A preparatory stage in which glucose is
phosphorylated, converted to fructose which is again forphorylated
and cleaved into two molecules of glyceraldehyde-3-phosphate. In
this phase there is an investment of two molecules of ATP.
• Stage 2: (Reactions 6-10) The two molecules of glyceraldehyde-3-
phosphate are converted to pyruvate with concomitant generation
of four ATP molecules and two molecules of NADH. Thus there is a
net gain of two ATP molecules per molecule of Glucose in
glycolysis.
Importance of phosphorylated intermediates:
1. Possession of negative charge which inhibit their diffusion through
membrane.
2. Conservation of free energy in high energy phosphate bond.
3. Facilitation of catalysis.

1. Hexokinase reaction: Phosphorylation of
hexoses (mainly glucose)
I. This enzyme is present in most cells. In liver
Glucokinase is the main hexokinase (both
ISOENZYMES) which prefers glucose as substrate.
II. It requires Mg-ATP complex as substrate. Un-
complexed ATP is a potent competitive inhibitor of
this enzyme.
III. Enzyme catalyses the reaction by proximity effect;
bringing the two substrate in close proximity.
IV. This enzyme undergoes large conformational
change upon binding with Glucose. It is inhibited
allosterically by G6P.

Diagram of Hexokinase reaction

Difference between Hexokinase &
Glucokinase

2. Phosphoglucose Isomerase or
Phosphohexose Isomerase:
Isomerization of G6P to Fructose 6
phosphate.
I. This enzyme catalyzes the reversible
isomerization of G6P (an aldohexose) to
F6P (a ketohexose).
II. This enzyme requires Mg ++ for its activity.
III.It is specific for G6P and F6P.

3. Phosphofructokinase-1 Reaction: Transfer of
phosphoryl group from ATP to C-1 of
F6P to produce Fructose 1,6 bisphosphate.
I. This step is an important irreversible, regulatory
step.
II. The enzyme Phosphofructokinase-1 is one of the
most complex
regulatory enzymes, with various allosteric
inhibitors and
activators.
III. ATP is an allosteric inhibitor, and Fructose 2,6
biphosphate
is an activator of this enzyme.
IV. ADP and AMP also activate PFK-1 whereas citrate
is an inhibitor.

Aldolase Reaction: Cleavage of Fructose
1,6 bisphosphate into glyceraldehyde 3
phosphate (an aldose) and dihydroxy
acetone phosphate (a ketose).
I. This enzyme catalyses the cleavage of F1,6
biphosphate by aldol condensation
mechanism.
II. As shown below, the standard free energy
change is positive in the forward direction,
meaning it requires energy. Since the
product of this reaction are depleted very
fast in the cells, this reaction is driven in
forward direction by the later two reactions.

5. Triose phosphate mutase reaction:
Conversion of Dihydroxyacetone
phosphate to glyceraldehyde 3
Phosphate.
I. This a reversible reaction catalysed by
acid-base catalysis in which Histidine-95
and Glutamate -165 of the enzyme are
involved.

6. Glyceraldehyde-3-phosphate dehydrogenase
reaction (GAPDH): Conversion of GAP to
Bisphosphoglycerate.
I. This is the first reaction of energy yielding
step. Oxidation of aldehyde derives the
formation of a high energy acyl phosphate
derivative.
II. An inorganic phosphate is incorporated in
this reaction without any expense of ATP.
III.NAD+ is the cofactor in this reaction which
acts as an oxidizing agent. The free energy
released in the oxidation reaction is used in
the formation of acylphosphate.

The mechanism of GAPDH reaction:
Evidence for the mechanism;
I. Iodoacetate inhibits this reaction, indicating the involvement of Cysine
residue of enzyme.
II. Tritium from GAP is transferred to NAD, indicating transfer of hydide
ion in oxidation reaction.
III. 32P exchanges with PO4
- - indicating acyl enzyme intermediate.
Steps in reaction mechanism:
1. Glceraldehyde- 3- phosphate (GAP) binding to the enzyme.
2. Nucleophilic attack by SH group (sulfhydril group) on CHO group
forming a thiohemiacytal.
3. Direct transfer of hydride to NAD+ leading to the formation of thioester.
Energy of this oxidation is conserved in synthesis of thioester and
NADH.
4. Another molecule of NAD+ replaces NADH from enzyme site.
5. Nucleophilic attack on thioester by PO4
– - to form 1,3
bisphosphoglycerate

7. Phosphoglycerate kinase Reaction: Transfer of phosphoryl
group fron 1,3 bisphosphoglycerate to ADP generating
ATP.
I. The name of this enzyme indicates its function for reverse
reaction.
II. It catalyses the formation by proximity effect. ADP-Mg
bind on one domain and 1,3BPG binds on the other and a
conformational change brings them together similar to
hexokinase.
III. This reaction and the 6th step are coupled reaction
generating ATP from the energy released by oxidation of
3-phosphoglyceraldehyde.
IV. This step generates ATP by SUBSTRATE-LEVEL
PHOSPHORYLATION.

8. Phosphoglycerate Mutase Reaction: Conversion of 3-
phosphoglycerate to 2-phosphoglycerate (2-PG).
I. In active form, the phosphoglycerate mutase is
phosphorylated at His-179.
II. There is transfer of the phosphoryl group frm enzyme to
3-PG, generating enzyme bound 2,3-biphosphoglycerate
intermediate. This compound has been observed
occasionally in reaction mixture.
III. In the last step of reaction the phosphoryl group from the
C-3 of the intermediate is transferred to the enzyme and
2-PG is released.
IV. In most cells 2,3BPG is present in trace amount, but in
erythrocytes it is present in significant amount. There it
regulates oxygen affinity to hemoglobin.

9. Enolase Reaction: Dehydration of 2-
phosphoglycerate (2-PG) to
phosphoenolpyruvate (PEP).
I. Dehydration of 2-PG by this reaction
increases the standard free enrgy change of
hydrolysis of phosphoanhydride bond.
II. Mechanism: Rapid extraction of proton from
C-2 position by a general base on enzyme,
generating a carbanion. The abstracted
proton is readily exchanges with solvent.
III.The second rate limiting step involves
elimination of OH group generating PEP

10. Pyruvate Kinase Reaction:
Transfer of phosphoryl group from
PEP to ADP generating ATP and
Pyruvate.
I. This is the second substrate level
phosphorylation reaction of glycolysis.
II. This enzyme couple the free enrgy of
PEP hydrolysis to the synthesis of ATP
III.This enzyme requires Mg++ and K+

• A tautomer is a separate type isomer by an organic
compound that has the property that it can quickly
change their isomeric form by chemical reaction
called tautomerization. Typically, this occurs as the
migration of hydrogen atoms (protons) by an
exchange of one single bond with a double bond.

From one molecule of Glucose:
1Gl+2ATP+2NAD++ 4ADP+ 4Pi = 2pyruvate+2NADH+4ATP+ 2ADP+
2Pi
After balancing: 1Gl + 2NAD++ 2ADP + 2Pi = 2pyruvate+2ATP +
2NADH
2 molecules of ATP generated can directly be used for doing work or
synthesis.
The 2 NADH molecules are oxidized in mitochondria under aerobic
condition and the free energy released is enough to synthesize 6
molecules of ATP by oxidative phosphorylation.
Under the aerobic condition, pyruvate is catabolized further in
mitochondria through pyruvate dehydrogenase and cytric acid cycle
where all the carbon atoms are oxidized to CO2. The free energy
released is used in the synthesis of ATP, NADH and FADH2.
Under anaerobic condition: Pyruvate is converted to Lactate in
homolactic fermentation or in ethanol in alcohalic fermentation.

Energetics of Glycolysis Pathway
ATP FORMED:
1. Gly-3-PO4--- 1,3 Bisphosphoglycerate = 6
ATP
2. 1,3 Bisphosphoglycerate-3-Phosphoglycerate = 2
ATP
3. Phosphoenolpyruvate-- Enol pyruvate = 2
ATP
ATP CONSUMED:
4. Glucose---- Glucose-6-PO4 = 1
ATP
5. Fru-6-PO4---- Fru-1,6 bisphosphate = 1ATP
-----------------------
Net ATP synthesized 10 – 2 = 8 ATP

1. Insulin stimulate Hexokinase & Glucokinase
by converting glucose to glu-6-PO4
2. Insulin stimulate Phosphofructokinase
converting fru-6-PO4 to Fru-1,6 bisphosphate
3. Glucagon stimulate liver glu-6-PO4 by
converting glu-6-PO4 to glucose & fru-1,6-
bisphosphate.
4. Fru-1,6- bisphosphate is converted to fru-6-
PO4

1. Iodoacetate inhibit Gly-3-PO4
dehydrogenase involved in gly-3-PO4 to
1,3-bisphosphoglycerate
2. Arsenate inhibit sysnthesis of ATP in the
conversion of 1,3 bisphosphoglycerate to
3-phosphoglycerate.
3. Fluoride inhibit enolase in conversion of
2-Phosphoglycerate to phosphoglycerate

In an anaerobic condition or in the
need of sudden need of high amount
of ATP, glycolysis is the main source for
generation of ATP.
NAD+ is one of the crucial cofactor
required for GAPDH reaction. In order
to regenerate NAD+ from the reduced
form (NADH), this reaction takes place
in muscle cells.
Lactate dehydrogenase (LDH) reduces
pyruvate to lactate using NADH and
thereby oxidizing it to NAD+ .
Other than regenerating NAD+ for
running GAPDH reaction, LDH reaction
is a waste of energy, and its product
lactic acid brings the pH lower and
causes fatigue.

Glycolysis can generate sudden burst of
ATP without oxygen, using glucose and
glycogen storage of muscle and liver.
NAD+ is regenerated by lactic
fermentation to carry out GAPDH
reaction of glycolysis.

Alcoholic fermentation:
Microorganisms and yeast convert
pyruvate to alcohol and carobon
dioxide to regenerate NAD+ for
glycolysis (step 6, GAPDH).
It is a two step process:
1. Pyruvate decarboxylase (PDC)
reaction: This enzyme is Mg++-
dependent and requires an enzyme-
bound cofactor, thiamine
pyrophosphate (TPP). In this
reaction a molecule of CO2 is
released producing acetaldehyde.
2. Alcohal dehydrogenase reaction:
Acetaldehyde is reduced to ethanol
using NADH as reducing power, thus
regenerating NAD+ .

I. Nucleophilic attack
on cabonyl gp carbon
of pyruvate by TPP
anion.
II. Departure of CO2
leaving the
carbanion-TPP
adduct.
III. Protonation of
carbanion
IV. Release of
acetaldehyde
following
regeneration of TPP

Two types controls for metabolic reactions:
a) Substrate limited : When concentrations of reactant and
products in the cell are near equilibrium, then it is the
availability of substrate which decides the rate of reaction.
b) Enzyme-limited: When concentration of substrate and products
are far away from the equilibrium, then it is activity of enzyme
that decides the rate of reaction. These reactions are the one
which control the flux of the overall pathway.
There are three steps in glycolysis that have enzymes which
regulate the flux of glycolysis.
I. The hexokinase (HK)
II. The phoshofructokinase (PFK)
III. The pyruvate kinase

Its activity is controlled by a complex allosteric regulation.
This reaction commits the cells to channel glucose to glycolysis.
ATP is the end product of glycolysis as well as it is substrate for PFK-
1. In presence of high concentration of ATP, ATP binds to inhibition
site of PFK, and thereby decreases the activity of enzyme.
AMP, ADP and Fructose 2, 6 biphosphate act as allosteric activators of
this enzyme.
Activation of enzyme by AMP overcomes the inhibitory effect of ATP.
Two other enzymatic activities are involved in the regulation of PFK.
a) Adnylate kinase: It readily equilibrates 2 ADP molecules to one ATP
and 1 AMP: 2ADP = ATP + AMP, K = [ATP][AMP] / [ADP] = 0.44
Any decrease in ATP and increase in ADP results in an increase in
AMP concentration, which activates PFK.
b) Fructose 1,6-bisphosphatase (FBPase): It catalyzes conversion of
FBP to Fructose 6-phosphate, thus reverting back the PFK reaction.

Substrate cycle or futile cycle: In order to control the flux of
glycolysis and to have better regulation, cells have FBPase which
keeps degrading the product of PFK reaction (FBP) to its substrate
(F-6-P). This is called substrate cycle. This is a futile exercise where,
cells invest an ATP to produce FBP which is hydrolysed back to F6-P
by FBPase. This is a price cells pay to keep glycolysis in check.
AMP acts as a potent inhibitor of FBPase. Thus the rate of
glycolysis can be increased many fold by AMP as it activates PFK
and at the same time it inhibits FBPase activity.
Hexokinase: It is allosterically inhibited by its product Glucose 6
phosphate. In liver Glucokinase is inhibited by Fructose 6
Phosphate. Uncomplexed ATP acts as a competitive inhibitor of
this enzyme.
Pyruvate Kinase: It is allosterically inhibited by ATP. ATP binding to
the inhibitor site of pyruvate kinase decxreases its ability to bing to
phosphoenol pyruvate (PEP) the substrate.It is also inhibited by
Acetyl coenzyme A and long chain fatty acid.

The citric acid cycle is the central
metabolic hub of the cell.
 It is the final common pathway for the
oxidation of fuel molecule such as amino
acids, fatty acids, and carbohydrates.
In eukaryotes, the reactions of the citric
acid cycle take place inside mitochondria,
in contrast with those of glycolysis, which
take place in the cytosol.

The citric acid cycle (Krebs cycle,
tricarboxylic acid cycle) includes a series of
oxidation-reduction reactions in
mitochondria that result in the oxidation of
an acetyl group to two molecules of carbon
dioxide and reduce the coenzymes that are
reoxidized through the electron transport
chain, linked to the formation of ATP.

A four- carbon compound (oxaloacetate) condenses with
a two-carbon acetyl unit to yield a six-carbon tricarboxylic
acid (citrate).
An isomer of citrate is then oxidatively decarboxylated.
The resulting five-carbon compound (α-ketoglutarate)
also is oxidatively decarboxylated to yield a four carbon
compound (succinate).
Oxaloacetate is then regenerated from succinate.
Two carbon atoms enter the cycle as an acetyl unit and
two carbon atoms leave the cycle in the form of two
molecules of carbon dioxide.

o Three hydride ions
(hence, six electrons) are
transferred to three molecules
of nicotinamide adenine
dinucleotide (NAD+), whereas
one pair of hydrogen atoms
(hence, two electrons) are
transferred to one molecule of
flavin adenine dinucleotide
(FAD) .
oThe function of the citric acid
cycle is the harvesting of high-
energy electrons from carbon
fuels.

Oxygen is required for the citric acid cycle
indirectly in as much as it is the electron
acceptor at the end of the electron-transport
chain, necessary to regenerate NAD+ and FAD.

o The citric acid cycle itself neither generates a
large amount of ATP nor includes oxygen as a reactant.
oInstead, the citric acid cycle removes electrons from
acetyl CoA and uses these electrons to form NADH and
FADH2 .
oIn oxidative phosphorylation, electrons released in the
reoxidation of NADH and FADH2 flow through a series of
membrane proteins (referred to as the electron-transport
chain) to generate a proton gradient across the
membrane
oThe citric acid cycle, in conjunction with oxidative
phosphorylation, provides the vast majority of energy
used by aerobic cells in human beings, greater than
95%.

•The four-carbon molecule, oxaloacetate
that initiates the first step in the citric
acid cycle is regenerated at the end of
one passage through the cycle.
•The oxaloacetate acts catalytically: it
participates in the oxidation of the acetyl
group but is itself regenerated.
•Thus, one molecule of oxaloacetate is
capable of participating in the oxidation
of many acetyl molecules

Step-1 Formation of Citrate- The citric
acid cycle begins with the condensation
of a four-carbon unit, oxaloacetate, and
a two-carbon unit, the acetyl group of
acetyl CoA. Oxaloacetate reacts with
acetyl CoA and H2O to yield citrate and
CoA.
This reaction, which is an aldol
condensation followed by a hydrolysis,
is catalyzed by citrate synthase.

Oxaloacetate first condenses with acetyl
CoA to form citryl CoA, which is then
hydrolyzed to citrate and CoA..

Citrate is isomerized into isocitrate to enable
the six-carbon unit to undergo oxidative
decarboxylation.
The isomerization of citrate is accomplished
by a dehydration step followed by a hydration
step.
The result is an interchange of a hydrogen
atom and a hydroxyl group.
The enzyme catalyzing both steps is called
Aconitase because cis-aconitate is an
intermediate.

Aconitase is an iron-sulfur protein, or
nonheme iron protein. It contains four iron
atoms that are not incorporated as part of
a heme group.

•The poison Fluoroacetate is toxic, because
fluoroacetyl-CoA condenses with
oxaloacetate to form fluorocitrate, which
inhibits Aconitase, causing citrate to
accumulate.
•The mode of inhibition is suicidal inhibition

•Isocitrate undergoes dehydrogenation catalyzed by
isocitrate dehydrogenase to form, initially, Oxalo
succinate, which remains enzyme-bound and
undergoes decarboxylation to α -ketoglutarate.
• The decarboxylation requires Mg++ or Mn++ ions.
•There are three isoenzymes of isocitrate
dehydrogenase.
•One, which uses NAD+, is found only in
mitochondria.
•The other two use NADP+ and are found in
mitochondria and the cytosol.

Respiratory chain-linked oxidation of
isocitrate proceeds almost completely
through the NAD+-dependent enzyme.

The conversion of isocitrate into α-
ketoglutarate is followed by a second oxidative
decarboxylation reaction, the formation of
Succinyl CoA from α-ketoglutarate.

• α-Ketoglutarate undergoes oxidative
decarboxylation in a reaction catalyzed by a
multi-enzyme complex similar to that involved
in the oxidative decarboxylation of pyruvate.
•The α--ketoglutarate dehydrogenase complex
requires the same cofactors as the pyruvate
dehydrogenase complex—thiamine
diphosphate, lipoate, NAD+, FAD, and CoA—
and results in the formation of succinyl-CoA.

•The equilibrium of this reaction is so
much in favor of succinyl-CoA formation
that it must be considered to be
physiologically unidirectional.
•As in the case of pyruvate oxidation,
arsenite inhibits the reaction, causing
the substrate, α -ketoglutarate, to
accumulate.

•Succinyl CoA is an energy-rich thioester
compound
•The cleavage of the thioester bond of
succinyl CoA is coupled to the
phosphorylation of a purine nucleoside
diphosphate, usually GDP.
•This reaction is catalyzed by succinyl
CoA synthetase (succinate thiokinase).

oThis is the only example in the citric acid cycle of
substrate level phosphorylation.
o Tissues in which gluconeogenesis occurs (the liver
and kidney) contain two isoenzymes of succinate
thiokinase, one specific for GDP and the other for ADP

•The GTP formed is used for the
decarboxylation of oxaloacetate to
phosphoenolpyruvate in gluconeogenesis,
and provides a regulatory link between
citric acid cycle activity and the
withdrawal of oxaloacetate for
gluconeogenesis. Nongluconeogenic
tissues have only the isoenzyme that uses
ADP.

•The first dehydrogenation reaction, forming
fumarate, is catalyzed by succinate
dehydrogenase, which is bound to the inner
surface of the inner mitochondrial membrane.
•The enzyme contains FAD and iron-sulfur (Fe:S)
protein, and directly reduces ubiquinone in the
electron transport chain.

Fumarase
(fumarate hydratase)
catalyzes the addition
of water across the
double bond of
fumarate, yielding
malate.

•Malate is converted to oxaloacetate by malate
dehydrogenase, a reaction requiring NAD+.
•Although the equilibrium of this reaction
strongly favors malate, the net flux is to
oxaloacetate because of the continual removal
of oxaloacetate (to form citrate, as a substrate
for gluconeogenesis, or to undergo
transamination to aspartate) and also the
continual reoxidation of NADH.
.

•As a result of oxidations catalyzed by the dehydrogenases
of the citric acid cycle, three molecules of NADH and one of
FADH2 are produced for each molecule of acetyl-CoA
catabolized in one turn of the cycle.
• These reducing equivalents are transferred to the
respiratory chain, where reoxidation of each NADH results in
formation of 3, and 2 ATP of FADH2.
•Consequently, 11 high-transfer-potential phosphoryl groups
are generated when the electron-transport chain oxidizes 3
molecules of NADH and 1 molecule of FADH2,
• In addition, 1 ATP (or GTP) is formed by substrate-level
phosphorylation catalyzed by succinate thiokinase.
.

•1 acetate unit generates approximately 12 molecules
of ATP.
• In dramatic contrast, only 2 molecules of ATP are
generated per molecule of glucose (which generates 2
molecules of acetyl CoA) by anaerobic glycolysis.
•Molecular oxygen does not participate directly in the
citric acid cycle.
•However, the cycle operates only under aerobic
conditions because NAD+ and FAD can be regenerated
in the mitochondrion only by the transfer of electrons to
molecular oxygen.

•Regulation of the TCA cycle like that of
glycolysis occurs at both the level of entry of
substrates into the cycle as well as at the key
reactions of the cycle.
•Fuel enters the TCA cycle primarily as acetyl-
CoA. The generation of acetyl-CoA from
carbohydrates is, therefore, a major control
point of the cycle.
•This is the reaction catalyzed by the PDH
complex.

1) Regulation of PDH Complex
a) Allosteric modification-PDH complex is inhibited by acetyl-
CoA and NADH and activated by non-acetylated CoA
(CoASH) and NAD+.
b) Covalent modification-The pyruvate dehydrogenase
activities of the PDH complex are regulated by their state
of phosphorylation. This modification is carried out by a
specific kinase (PDH kinase) and the phosphates are
removed by a specific phosphatase (PDH phosphatase).
PDH kinase is activated by NADH and acetyl-CoA and
inhibited by pyruvate, ADP, CoASH, Ca2+ and Mg2+.
The PDH phosphatase, in contrast, is activated by Mg2+
and Ca2+

2) Regulation of TCA cycle enzymes
The most likely sites for regulations are the
nonequilibrium reactions catalyzed citrate
synthase, isocitrate dehydrogenase, and α-
ketoglutarate dehydrogenase. The
dehydrogenases are activated by Ca2+,
which increases in concentration during
muscular contraction and secretion, when
there is increased energy demand.

a) Citrate synthase- There is allosteric
inhibition of citrate synthase by ATP and long-
chain fatty acyl-CoA.
b) Isocitrate dehydrogenase- is allosterically
stimulated by ADP, which enhances the
enzyme's affinity for substrates. In contrast,
NADH inhibits iso-citrate dehydrogenase by
directly displacing NAD+. ATP, too, is inhibitory.

a) α-ketoglutarate dehydrogenase -α- Ketoglutarate
dehydrogenase is inhibited by succinyl CoA and
NADH. In addition, α-ketoglutarate dehydrogenase is
inhibited by a high energy charge. Thus, the rate of
the cycle is reduced when the cell has a high level of
ATP.
d) Succinate dehydrogenase is inhibited by
oxaloacetate, and the availability of oxaloacetate, as
controlled by malate dehydrogenase, depends on the
[NADH]/[NAD+] ratio.

•Since three reactions of the TCA cycle as well as PDH
utilize NAD+ as co-factor, the cellular ratio of NAD+/NADH
has a major impact on the flux of carbon through the TCA
cycle.
•The activity of TCA cycle is immediately dependent on
the supply of NAD+, which in turn, because of the tight
coupling between oxidation and phosphorylation, is
dependent on the availability of ADP and hence,
ultimately on the rate of utilization of ATP in chemical and
physical work.
•Thus, respiratory control via the respiratory chain and
oxidative phosphorylation primarily regulates citric acid
cycle activity.

Excess of ATP
depicts energy rich state
of the cell, hence TCA
cycle is inhibited while
reverse occurs when the
cell is in a low energy
state with excess of
ADP.

•The citric acid cycle is not only a pathway for
oxidation of two-carbon units, but is also a
major pathway for interconversion of
metabolites arising from transamination and
deamination of amino acids, and providing the
substrates for amino acid synthesis by
transamination, as well as for gluconeogenesis
and fatty acid synthesis.
•Because it functions in both oxidative and
synthetic processes, it is amphibolic.

•The citric acid cycle is the final common
pathway for the oxidation of carbohydrate,
lipid, and protein because glucose, fatty acids,
and most amino acids are metabolized to
acetyl-CoA or intermediates of the cycle.
•The function of the citric acid cycle is the
harvesting of high-energy electrons from
carbon fuels.
• 1 acetate unit generates approximately 12
molecules of ATP per turn of the cycle.

As a major metabolic hub of the cell, the
citric acid cycle also provides intermediates
for biosynthesis of various compounds.
i) Role in Gluconeogenesis- All the
intermediates of the cycle are potentially
glucogenic, since they can give rise to
oxaloacetate, and hence net production of
glucose (in the liver and kidney, the organs
that carry out gluconeogenesis.

The key enzyme that catalyzes net transfer out of the cycle
into gluconeogenesis is phospho-enol-pyruvate carboxy
kinase, which catalyzes the decarboxylation of oxaloacetate
to phosphoenolpyruvate, with GTP acting as the phosphate
donor.

Since the transamination reactions are reversible, the
cycle also serves as a source of carbon skeletons for the
synthesis of some amino acids like Alanine, aspartate,
Asparagine Glutamate , glutamine etc.

Aspartic acid is a precursor of Asparagine, Lysine,
Methionine, Threonine and Isoleucine. These amino acid
except Asparagine are essential amino acids, they are
synthesized only in plants.

iii) Role in fatty acid synthesis- Acetyl-CoA,
formed from pyruvate by the action of
pyruvate dehydrogenase, is the major
substrate for long-chain fatty acid synthesis .
Acetyl-CoA is made available in the
cytosol from citrate synthesized in the
mitochondrion, transported into the cytosol,
and cleaved in a reaction catalyzed by ATP-
citrate lyase.

Citrate is transported out of
the mitochondrion when
Aconitase is saturated with
its substrate.
This ensures that citrate is
used for fatty acid synthesis
only when there is an
adequate amount to ensure
continued activity of the
cycle
Acetyl co A can also be
used for the synthesis of
cholesterol, steroids etc.

Succinyl co A
condenses with
amino acid
Glycine to form
Alpha amino beta
keto Adipic acid,
which is the first
step of haem
biosynthesis.

Glutamate and Aspartate derived from
TCA cycle are utilized for the synthesis of
purines and pyrimidines.

•Riboflavin, in the form of flavin adenine dinucleotide (FAD), a
cofactor for succinate dehydrogenase
•Niacin, in the form of nicotinamide adenine dinucleotide
(NAD), the electron acceptor for isocitrate dehydrogenase, α-
ketoglutarate dehydrogenase, and malate dehydrogenase;
•Thiamine(vitamin B1) , as thiamine pyro phosphate, the
coenzyme for decarboxylation in the α -ketoglutarate
dehydrogenase reaction;
•Pantothenic acid, as part of coenzyme A such as acetyl-CoA
and succinyl-CoA and
•Biotin- in CO2 fixation reaction to compensate oxaloacetate
concentration.

•Anaplerosis is the act of replenishing TCA cycle
intermediates that have been extracted for biosynthesis
(in what are called cataplerotic reactions).
•The TCA Cycle is a hub of metabolism, with central
importance in both energy production and biosynthesis.
•Therefore, it is crucial for the cell to regulate
concentrations of TCA Cycle metabolites in the
mitochondria.
•Anaplerotic flux must balance cataplerotic flux in order
to retain homeostasis of cellular metabolism

1) Formation of oxaloacetate from pyruvate
In case oxaloacetate is converted into amino acids
for protein synthesis or used for gluconeogenesis
and, subsequently, the energy needs of the cell rise.
The citric acid cycle will operate to a reduced extent
unless new oxaloacetate is formed, because acetyl
CoA cannot enter the cycle unless it condenses with
oxaloacetate.
Even though oxaloacetate is recycled, a minimal
level must be maintained to allow the cycle to
function.

Oxaloacetate is formed by –
a)Carboxylation of pyruvate, by
pyruvate carboxylase
b)Through formation of malate
from pyruvate by Malic
enzyme
c)From malate to oxaloacetate
by malate dehydrogenase
Mammals lack the enzymes for the net
conversion of acetyl CoA into oxaloacetate or
any other citric acid cycle intermediate.

2) Formation of oxaloacetate from Aspartate-
Oxaloacetate can also be formed from Aspartate by
transamination reaction.
3) Formation of Alpha keto glutarate- Alpha
ketoglutarate can be formed from Glutamate
dehydrogenase or from transamination reactions.
4) Formation of Succinyl co A – Succinyl co A can
be produced from the oxidation of odd chain fatty
acid and from the metabolism of methionine and
isoleucine (through carboxylation of Propionyl co A
to Methyl malonyl co A and then Succinyl co A)

•fats burn in the flame of carbohydrates means
fats can only be oxidized in the presence of
carbohydrates.
•Acetyl co A represents fat component, since
the major source is fatty acid oxidation.
•Acetyl co A is completely oxidized in the TCA
cycle in the presence of oxaloacetate.

Pyruvate is mainly used up for Anaplerotic reactions
to compensate for oxaloacetate concentration.
Thus without carbohydrates (Pyruvate), there would
be no Anaplerotic reactions to replenish the TCA-
cycle components.
With a diet of fats only, the acetyl CoA from fatty
acid degradation would not get oxidized and build
up due to non functioning of TCA cycle.
Thus fats can burn only in the flame of
carbohydrates.

• Bacteria are capable of growth on fatty
acids and lipids. Lipids are part of the
membranes of living organisms and if
available (usually because the organism
that was using them dies) can be used as a
food source. Lipids are large molecules and
cannot be transported across the
membrane. A class of extracellular
enzymes called lipases are responsible for
the breakdown of lipids.

• Lipases attack the bond between the glycerol
molecule oxygen and the fatty acid. Phospholipids
are attacked by phospholipases. There are four
classes of phospholipases given different names
depending upon the bond they cleave.
Phospholipases are not particular about their
substrate and will attack a glycerol ester linkage
containing any length fatty acid attached to it. The
result of this digestion is a hydrophillic head
molecule, glycerol and fatty acids of various chain
lengths. The head can be one of several small organic
molecules that are funneled into the TCA cycle by one
or two reactions that we won't cover here. Glycerol is
converted into 3-Phosphoglycerate (depending upon
the action of phospholipase C or phospholipase D)
and eventually pyruvate via glycolysis. This leaves the
fatty acids to deal with.

• Fatty acids are degraded by a four step process
called b-oxidation. The fatty acid is first
activated by the addition of Coenzyme-A to the
end. This activation requires energy in the form
of ATP, but is only performed once per fatty acid
degraded. The b carbon (see figure) is then
oxidized from CH2 to C=O (a ketone) by three
reactions. (This is where the pathway gets its
name.) The oxidized b group is now susceptible
to attack. An enzyme called b-
ketothiolase splits the fatty acid into acetyl-CoA
and adds another Coenzyme-A to the previously
oxidized b group on the fatty acid.

• The fatty acid is now two carbons shorter and
an Acetyl-CoA has been generated which can
be fed into the TCA cycle. The smaller fatty
acid moves through the b-oxidation pathway
again, producing another Acetyl-CoA and
shrinking by 2 carbons. By performing
successive rounds of beta oxidation on a fatty
acid, it is possible to convert it completely to
Acetyl-CoA. The perceptive reader might
notice that for fatty acids with odd numbers of
carbons, the final reaction will yield acetyl-CoA
and Coenzyme-A hooked to a three carbon
fatty acid (propionyl-CoA). Propionyl-CoA is
handled differently by different bacteria. In E.
coli it is converted into pyruvate.

When comparing catabolism of fats and sugars two
points jump out.
Reuse of components - Whenever possible, the cell
will reuse a carrier, cofactor or enzyme. For example
in fatty acid breakdown, Coenzyme-A plays a major
role and the electron carriers FAD and NAD are
used.
Funneling - Cells also try to reuse common
pathways. A given substrate will be converted into a
common metabolite and then funneled into an
already existing pathway. Fatty acids are broken
down into Acetyl-Coenzyme-A and this is fed into the
TCA cycle.

• Oxidative phosphorylation is a highly
efficient method of producing large
amounts of ATP, the basic unit of
energy for metabolic processes. During
this process electrons are exchanged
between molecules, which creates a
chemical gradient that allows for the
production of ATP. The most vital part of
this process is the electron transport
chain, which produces more ATP than
any other part of cellular respiration.

The electron transport chain is the final component
of aerobic respiration and is the only part
of glucose metabolism that uses atmospheric oxygen.
Electron transport is a series of redox reactions that
resemble a relay race. Electrons are passed rapidly
from one component to the next to the endpoint of the
chain, where the electrons reduce molecular oxygen,
producing water. This requirement for oxygen in the
final stages of the chain can be seen in the overall
equation for cellular respiration, which requires both
glucose and oxygen.

• A complex is a structure consisting of a central
atom, molecule, or protein weakly connected to
surrounding atoms, molecules, or proteins. The
electron transport chain is an aggregation of four of
these complexes (labeled I through IV), together
with associated mobile electron carriers. The
electron transport chain is present in multiple
copies in the inner mitochondrial membrane of
eukaryotes and the plasma
membrane of prokaryotes.
See next slide for image

The electron transport chain
The electron transport chain is a series of electron transporters embedded in
the inner mitochondrial membrane that shuttles electrons from NADH and
FADH2 to molecular oxygen. In the process, protons are pumped from the
mitochondrial matrix to the intermembrane space, and oxygen is reduced to
form water.

To start, two electrons are carried to the first complex aboard
NADH. Complex I is composed of flavin mononucleotide (FMN)
and an enzyme containing iron-sulfur (Fe-S). FMN, which
is derived from vitamin B2 (also called riboflavin), is one of
several prosthetic groups or co-factors in the electron transport
chain. A prosthetic group is a non-protein molecule required for
the activity of a protein. Prosthetic groups can
be organic or inorganic and are non-peptide molecules bound to
a protein that facilitate its function.
Prosthetic groups include co-enzymes, which are the prosthetic
groups of enzymes. The enzyme in complex I is NADH
dehydrogenase, a very large protein containing 45 amino
acid chains. Complex I can pump four hydrogen ions across the
membrane from the matrix into the intermembrane space; it is
in this way that the hydrogen ion gradient is established and
maintained between the two compartments separated by the
inner mitochondrial membrane.

Complex II directly receives FADH2, which does not pass
through complex I. The compound connecting the first and
second complexes to the third is ubiquinone (Q). The Q
molecule is lipid soluble and freely moves through
the hydrophobic core of the membrane. Once it is reduced to
QH2, ubiquinone delivers its electrons to the next complex in
the electron transport chain. Q receives the electrons derived
from NADH from complex I and the electrons derived from
FADH2 from complex II, including succinate dehydrogenase.
This enzyme and FADH2 form a small complex that delivers
electrons directly to the electron transport chain, bypassing
the first complex. Since these electrons bypass, and thus do
not energize, the proton pump in the first complex, fewer ATP
molecules are made from the FADH2 electrons. The number
of ATP molecules ultimately obtained is directly proportional
to the number of protons pumped across the inner
mitochondrial membrane.

The third complex is composed of cytochrome b, another Fe-S
protein, Rieske center (2Fe-2S center), and cytochrome c
proteins; this complex is also called cytochrome
oxidoreductase. Cytochrome proteins have a
prosthetic heme group. The heme molecule is similar to the
heme in hemoglobin, but it carries electrons, not oxygen. As a
result, the iron ion at its core is reduced and oxidized as it
passes the electrons, fluctuating between
different oxidation states: Fe2+ (reduced) and Fe3+ (oxidized).
The heme molecules in the cytochromes have slightly
different characteristics due to the effects of the different
proteins binding them, which makes each complex. Complex
III pumps protons through the membrane and passes its
electrons to cytochrome c for transport to the fourth complex
of proteins and enzymes. Cytochrome c is the acceptor of
electrons from Q; however, whereas Q carries pairs of
electrons, cytochrome c can accept only one at a time.

The fourth complex is composed of cytochrome
proteins c, a, and a3. This complex contains two
heme groups (one in each of the cytochromes a
and a3) and three copper ions (a pair of CuA and
one CuB in cytochrome a3). The cytochromes hold
an oxygen molecule very tightly between the iron
and copper ions until the oxygen is completely
reduced. The reduced oxygen then picks up two
hydrogen ions from the surrounding medium to
produce water (H2O). The removal of the
hydrogen ions from the system also contributes
to the ion gradient used in the process
of chemiosmosis.

•Oxidative phosphorylation is the metabolic pathway
in which electrons are transferred from electron donors to electron
acceptors in redox reactions; this series of reactions
releases energy which is used to form ATP.
•There are four protein complexes (labeled complex I-IV) in the electron
transport chain, which are involved in moving electrons from NADH and
FADH2 to molecular oxygen.
•Complex I establishes the hydrogen ion gradient by pumping four
hydrogen ions across the membrane from the matrix into the
intermembrane space.
•Complex II receives FADH2 , which bypasses complex I, and delivers
electrons directly to the electron transport chain.
•Ubiquinone (Q) accepts the electrons from both complex I and complex II
and delivers them to complex III.
•Complex III pumps protons through the membrane and passes its
electrons to cytochrome c for transport to the fourth complex of proteins
and enzymes.
•Complex IV reduces oxygen; the reduced oxygen then picks up two
hydrogen ions from the surrounding medium to make water.

ATP synthase is one of the wonders of the molecular
world. ATP synthase is an enzyme, a molecular
motor, an ion pump, and another molecular motor
all wrapped together in one amazing nanoscale
machine. It plays an indispensable role in our cells,
building most of the ATP that powers our cellular
processes. The mechanism by which it performs this
task is a real surprise.

ATP synthesis is composed of two rotary
motors, each powered by a different fuel. The
motor at the top, termed F0, an electric motor.
It is embedded in a membrane (shown
schematically as a gray stripe here), and is
powered by the flow of hydrogen ions across
the membrane. As the protons flow through the
motor, they turn a circular rotor (shown in blue).
This rotor is connected to the second motor,
termed F1. The F1 motor is a chemical motor,
powered by ATP. The two motors are connected
together by a stator, shown on the right, so that
when F0 turns, F1 turns too.

So why have two motors connected together?
The trick is that one motor can force the other
motor to turn, and in this way, change the
motor into a generator. This is what happens in
our cells: the F0 motor uses the power from a
proton gradient to force the F1 motor to
generate ATP. In our cells, food is broken down
and used to pump hydrogen ions across the
mitochondrial membrane. The F0 portion of
ATP synthase allows these ions to flow back,
turning the rotor in the process. As the rotor
turns, it turns the axle and the F1 motor
becomes a generator, creating ATP as it turns.

Large, complex molecular machines
like ATP synthase pose difficult
problems for structural scientists, so
the structures of these machines are
often determined in parts. The
picture shown here is a composite of
four different structures, combining
structures determined by X-ray
crystallography and NMR
spectroscopy.

When operating as a generator, it uses the power of
rotational motion to build ATP, or when operating as
a motor, it breaks down ATP to spin the axle the
opposite direction. The synthesis of ATP requires
several steps, including the binding of ADP and
phosphate, the formation of the new phosphate-
phosphate bond, and release of ATP. As the axle
turns, it forces the motor into three different
conformations that assist these difficult steps. Two
states are shown here. The one on the left shows a
conformation that assists the binding of ADP, and
the one on the right shows a conformation that has
been forced open to release ATP. Notice how the
oddly-shaped axle forces the change in
conformation.
See next slide for figure

In this picture, we are looking down the axis of rotation, as if
we where looking down at the top of the picture on the first
page. The rotor is composed of 12 identical protein chains,
colored blue here, and the ion pump is a single chain, colored
red. The pump has an arginine amino acid that hands off a
hydrogen ion to aspartates on the rotor. Aspartate amino
acids typically have a negative charge, but since the rotor is
surrounded by membrane lipids, this would be very
unfavorable. So, the rotor only turns when the aspartates
have a hydrogen attached, neutralizing their charge.
Hydrogen ions take a convoluted path through the F0 motor,
turning the rotor in the process. They are gathered by a chain
of amino acids in the pump, and transferred to the arginine.
The arginine passes the hydrogen to the rotor, which turns all
the way around. Then the hydrogen is offloaded by other
amino acids on the pump, and finally passed to the opposite
side of the membrane. The exact path of the hydrogen ions
through the pump is still a matter of intense study.
See next slide for figure

PHOTOSYNTHESIS
In 1780 Joseph Priestly discovered
photosynthesis:
“…plants can “restore air which has
been injured by the burning of
candles.”
“…the air would neither extinguish
a candle, nor was it all
inconvenient to a mouse which I
put into it.”

•Photosynthesis provides essentially all
free energy in biological systems by
converting solar energy into chemical
energy.
•Carbohydrates are formed from light-
driven reactions that collectively
appear deceptively simple:
CO2 + H2O + light  CnH2nOn + O2

• Photosynthesis occurs in specialized organelles
called chloroplasts:

• Photosynthesis consists of two sets of
reactions:
the LIGHT and DARK reactions.
• The LIGHT-driven reactions are the primary
events of photosynthesis; these occur in the
thylakoid membrane.
• The DARK reactions occur in the stroma.

•The light-reactions of photosynthesis
generate high-energy electrons that are
used to form NADPH.
•On their way to NADPH, these high-
energy electrons flow through a
membrane-bound “electron transport”
pathway, generating a proton motive
potential (Δp) from which ATP is made.

Sunlight spectrum, Chlorophyll a and Bacteriochlorophyll a

• Light-harvesting Pigments help absorb wavelengths of light in the region of
the spectrum where chlorophyll pigments do not absorb light.
• Photons absorbed by these pigments also transfer energy to chlorophyll.
β-carotene helps protect plants from photochemical
reactions, expecially those involving oxygen; (it serves as an
“antioxidant.”)

The majority of chlorophyll molecules in a
photosynthetic unit do not get involved in
photosynthesis directly. Rather, they transfer their
absorbed energy to a reaction center complex.
C C C C C
C C C C C C C C C C
C C C C C C C C C C C
C C C C C C C C C C C C C
C C C C C C C C C C C C
C C C C C C C C C C C C C C
C C C C C C C C C C C
C C C C C C C C C C
C C C C C C C C C
C C C C C

Light energy
absorbed by antenna
chlorophyll molecules
and auxillary
pigments is
transferred to
specialized reaction
centers.
This energy transfer
(often called
“resonance energy
transfer” or “exciton
hopping”) is very
efficient, approaching
100%!

X-ray Structure of Photosystem II (S. elongatus)

Mn cluster in
the OEC
Schematic mechanism
of oxygen generation in
PSII:

Herbicides that
inhibit
Photosystem II
by blocking the
transfer of
electrons to
QH2:

Electron Flow through PSII: Electron Flow through Cytochrome bf:
Plastocyanin:

Biochem 3070 - Photosynthesis
Ferredoxin Structure
Stryer, et.al., Biochemistry, 5th ed.

“Z-Scheme” of Photosynthesis:

Andre Jagendorf and
Ernest Uribe’s classic
experiment, showing
the production of ATP
from an artificially
induced proton
gradient across
isolated chloroplasts
in the absence of any
light!
(First Reported in 1965)

Stroma
Lumen
(Thylakoid
Space)

Stroma
Lumen
Inner-membrane
Space
Matrix

What about CO2?
CO2 + H2O + light  CnH2nOn + O2

Melvin Calvin discovered the CO2 acceptor by using C-
14 radioactive labeled carbon dioxide:
He discovered that the reactions of CO2 fixation are almost
identical to reactions of the phosphate shunt:

The Calvin Cycle:
From light-driven
reactions

Ribulose 1,5-bisphosphate carboxylase/oxygenase [“rubisco”]:
Rubisco consitutes more
than 16% of all protein in
chloroplasts.
It is the most abundant
protein in the entire
biosphere!

Proposed mechanism for Rubisco:

References
• https://adapaproject.org/bbk_temp/tiki-
index.php?page=Leaf%3A+How+does+ATP+Synthase+Make+ATP%3F
• https://pdb101.rcsb.org/motm/72
• https://www.boundless.com/biology/textbooks/boundless-biology-
textbook/cellular-respiration-7/oxidative-phosphorylation-76/electron-
transport-chain-362-11588/
• http://www.slideshare.net/VBCOPS/glycolysis-ppt
• http://lecturer.ukdw.ac.id/dhira/Metabolism/RespFats.html

• http://www.namrata.co/tca-cycle-lecture-1/
• https://biochem.wisc.edu/sites/default/files/courses/501_sp2015_syllabus.pdf

Biosynthesis and Metabolic Regulation
• Cell Signaling and Metabolism
• Pentose Phosphate Pathway
• Regulation of Blood Glucose

Cell Signaling and Metabolism
Cells typically communicate using chemical signals. These
chemical signals, which are proteins or other molecules produced by
a sending cell, are often secreted from the cell and released into the
extracellular space. There, they can float – like messages in a bottle –
over to neighboring cells.
Not all cells can “hear” a particular chemical message. In order
to detect a signal (that is, to be a target cell), a neighbor cell must have
the right receptor for that signal. When a signaling molecule binds to its
receptor, it alters the shape or activity of the receptor, triggering a
change inside of the cell. Signaling molecules are often called ligands,
a general term for molecules that bind specifically to other molecules
(such as receptors).

The message carried by a ligand is often relayed through a chain of
chemical messengers inside the cell. Ultimately, it leads to a change in
the cell, such as alteration in the activity of a gene or even the induction
of a whole process, such as cell division. Thus, the
original intercellular (between-cells) signal is converted into
an intracellular (within-cell) signal that triggers a response.

Forms of signalling
Cell-cell signalling involves the transmission of a
signal from a sending cell to a receiving cell. However, not
all sending and receiving cells are next-door neighbors, nor
do all cell pairs exchange signals in the same way.
There are four basic categories of chemical
signalling found in multicellular organisms:
• Paracrine signalling
• Autocrine signalling
• Endocrine signalling
• Signalling by direct contact

Paracrine Signalling
Often, cells that are near one another communicate
through the release of chemical messengers (ligands that
can diffuse through the space between the cells). This type
of signaling, in which cells communicate over relatively
short distances, is known as paracrine signaling.
Paracrine signaling allows cells to locally coordinate
activities with their neighbors. Although they're used in
many different tissues and contexts, paracrine signals are
especially important during development, when they allow
one group of cells to tell a neighboring group of cells what
cellular identity to take on.

In order for paracrine
factors to successfully
induce a response in
the receiving cell, that
cell must have the
appropriate receptors
available on the cell
membrane to receive
the signals, also
known as
being competent.
Additionally, the
responding cell must
also have the ability to
be mechanistically
induced.

Autocrine Signalling
In autocrine signaling, a cell signals to itself, releasing a
ligand that binds to receptors on its own surface (or, depending on the
type of signal, to receptors inside of the cell). This may seem like an
odd thing for a cell to do, but autocrine signaling plays an important role
in many processes.
For instance, autocrine signaling is important during
development, helping cells take on and reinforce their correct identities.
From a medical standpoint, autocrine signaling is important in cancer
and is thought to play a key role in metastasis (the spread of cancer
from its original site to other parts of the body). In many cases, a signal
may have both autocrine and paracrine effects, binding to the sending
cell as well as other similar cells in the area.

Tumor development
is a complex process that
requires cell division,
growth, and survival. One
approach used by tumors
to upregulate growth and
survival is through
autocrine production of
growth and survival
factors.
Autocrine
signaling plays critical
roles in cancer activation
and also in providing self-
sustaining growth signals
to tumors.

Endocrine Signalling
When cells need to transmit signals over long distances, they
often use the circulatory system as a distribution network for the
messages they send. In long-distance endocrine signaling, signals
are produced by specialized cells and released into the bloodstream,
which carries them to target cells in distant parts of the body. Signals
that are produced in one part of the body and travel through the
circulation to reach far-away targets are known as hormones.
In humans, endocrine glands that release hormones include
the thyroid, the hypothalamus, and the pituitary, as well as the gonads
(testes and ovaries) and the pancreas. Each endocrine gland releases
one or more types of hormones, many of which are master regulators of
development and physiology.

For example, the
pituitary releases growth
hormone (GH), which
promotes growth,
particularly of the
skeleton and cartilage.
Like most hormones, GH
affects many different
types of cells throughout
the body. However,
cartilage cells provide
one example of how GH
functions: it binds to
receptors on the surface
of these cells and
encourages them to
divide.

Signalling by Direct Contact
Gap junctions in animals and plasmodesmata in plants are tiny
channels that directly connect neighboring cells. These water-filled channels
allow small signaling molecules, called intracellular mediators, to diffuse
between the two cells. Small molecules, such as calcium ions, are able to
move between cells, but large molecules like proteins and DNA cannot fit
through the channels without special assistance.
The transfer of signaling molecules transmits the current state of
one cell to its neighbor. This allows a group of cells to coordinate their
response to a signal that only one of them may have received. In plants,
there are plasmodesmata between almost all cells, making the entire plant
into one giant network. In another form of direct signaling, two cells may
bind to one another because they carry complementary proteins on their
surfaces. When the proteins bind to one another, this interaction changes
the shape of one or both proteins, transmitting a signal. This kind of
signaling is especially important in the immune system, where immune cells
use cell-surface markers to recognize “self” cells (the body's own cells) and
cells infected by pathogens.

Activity 1: Answer the following.
1. This is the general term for molecules that bind
specifically to other molecules.
2. The message carried by a ligand is often relayed through
__________ inside the cell.
3. In _____________, signals are produced by specialized
cells and released into the bloodstream, which carries them
to target cells in distant parts of the body.
4. These are water-filled channels that allow small signaling
molecules to diffuse between the two cells.
5. It is thought to be a key role in metastasis.

Similarly to some of the processes in cellular respiration, the
molecules that go through the pentose phosphate pathway are mostly
made of carbon. The easiest way to understand this pathway is to
follow the carbon.
The breakdown of the simple sugar, glucose, in glycolysis
provides the first 6-carbon molecule required for the pentose phosphate
pathway. During the first step of glycolysis, glucose is transformed by
the addition of a phosphate group, generating glucose-6-phosphate,
another 6-carbon molecule. The pentose phosphate pathway can use
any available molecules of glucose-6-phosphate, whether they are
produced by glycolysis or other methods.

Oxidative PhaseStep 1:
Glucose-6-phosphate is oxidized to form lactone. NADPH is produced
as a byproduct of this reaction as NADP+ is reduced as glucose-6-phosphate is
oxidized. Following the oxidation of glucose-6-phosphate, another reaction,
catalyzed by a different enzyme, uses water to form 6-phosphogluconate, the
linear product.
NADPH is similar in structure and function as the high energy electron
shuttle, NADH, mentioned in the cellular respiration articles. NADPH has an
added phosphate group and is used in the cell to donate its electrons, just like
NADH. Once NADPH has donated its electrons it is said to be oxidized
(oxidation = loss of electrons) and is now symbolized as, NADP+. NADPH is
often used in reactions that build molecules and occurs in a high concentration
in the cell, so that it is readily available for these types of reactions.
Step 2:
Next, a carbon is removed (cleaved) and CO2 is released. Once
again, the electrons released from this cleavage is used to reduce NADP+ to
NADPH. This new 5-carbon molecule is called ribulose-5-phosphate.

The “oxidative”
word of this phase
comes from the
process of
oxidation.
Oxidation is
the breakdown of
a molecule as it
loses at least one
of its electrons.

Non-Oxidative Phase
Step 3:
Ribulose-5-phosphate can be converted into two different 5-carbon
molecules. One is the sugar used to make up DNA and RNA called, ribose-5-
phosphate and this is the molecule we will focus on. Ribulose-5-phosphate isn’t
being divided because the carbon count is the same in the next step.
Step 4:
The rest of the cycle is now made up of different options that depend
on the cell’s needs. The ribose-5-phosphate from step 3 is combined with
another molecule of ribose-5-phosphate to make one, 10-carbon atom. Excess
ribose-5-phosphate, which may not needed for nucleotide biosynthesis, is
converted into other sugars that can be used by the cell for metabolism.
The 10-carbon atom is interconverted to create a 3-carbon molecule
and a 7-carbon molecule. The 3-carbon product can be shipped over to
glycolysis if it needs. That being said, recall that we can also work our way
back up to another molecule in this phase. So that 3-carbon molecule could
also be shipped over from glycolysis and transformed into ribose-5-phosphate
for DNA and RNA production.

Step 5:
The 3-carbon molecule and the 7-carbon molecule, from the interconversion
above in step 4, interconvert again to make a new 4-carbon molecule and 6-
carbon molecule. The 4-carbon molecule is a precursor for amino acids, while
the 6-carbon molecule can be used in glycolysis. The same reversal of steps in
option 4 can happen here as well.
The pentose phosphate pathway takes place in the cytosol of the cell, the same
location as glycolysis. The two most important products from this process are
the ribose-5-phosphate sugar used to make DNA and RNA, and the NADPH
molecules which help with building other molecules.

In summary
Oxidative phase:
• -1 H2O
• +2 NADPH
• +1 CO2
Non-oxidative phase:
• Ribose-5-phosphate for DNA/RNA building (also produced in the oxidative
phase)
Consider the following
NADPH is readily available to donate its electrons in the cell because
it occurs in such high concentration. Aside from helping build molecules, what
kind of benefit is this really for the cell? NADPH is able to donate its electrons
to compounds that fight dangerous oxygen molecules. These compounds are
called antioxidants and you’ve probably heard about them being in some foods.
Antioxidants donate electrons to neutralize dangerous oxygen radicals (super
reactive oxygen molecules). Once they have given away their electrons,
antioxidants need to quickly reload in case there are more oxygen radicals.
NADPH is able to give antioxidants their constant flow of electrons to fight
oxygen crime.

Activity: Write the correct order of the
Pentose Phosphate Pathway.
__ Ribulose-5-phosphate can be converted into two
different 5-carbon molecules.
__ Glucose-6-phosphate is oxidized to form lactone.
NADPH is produced as a byproduct of this reaction as
NADP+ is reduced as glucose-6-phosphate is oxidized.
__ The pentose phosphate pathway takes place in the
cytosol of the cell, the same location as glycolysis.
__ A carbon is removed (cleaved) and CO2 is released.
Once again, the electrons released from this cleavage is
used to reduce NADP+ to NADPH.
__ The 10-carbon atom is interconverted to create a 3-
carbon molecule and a 7-carbon molecule.

Regulation of Blood Glucose
• Gluconeogenesis
• Glycogen Metabolism
• Hormonal Control

Step 1 - the first irreversible step:
We start with the two pyruvate molecules that came from
a non-carbohydrate source. Pyruvate (3 carbons) is combined
with bicarbonate to create oxaloacetate (4 carbons). This
reaction requires ATP. Another GTP is then used to transform
oxaloacetate into phosphoenolpyruvate, a 3-carbon molecule
with a phosphate group attached.
Steps 1 through 4 will occur twice, each time with a
pyruvate molecule. We need enough carbons to eventually get a
6 carbon molecule. As we mentioned before, detours are
required in gluconeogenesis to get around the irreversible
reactions of the glycolysis pathway. The reactions in step 1,
converting pyruvate into oxaloacetatete, and oxaloacetate into
phosphoenolpyruvate, are the first detour.

Step 2: A hydroxyl group is
used to change the 3-carbon
molecule, preparing for a
phosphate group to be
transferred to another carbon
in the molecule.
Step 3: ATP is used to add
another phosphate group to
the 3-carbon molecule.
Step 4: The high energy
electrons carried by NADH are
used to remove one of the
phosphate groups. Once
NADH has lost its high energy
electrons (a process which is
called “oxidation”) it’s called
NAD^+.

Glycogen degradation and synthesis are
relatively simple biochemical processes.
Glycogen degradation consists of three
steps: (1) the release of glucose 1-
phosphate from glycogen, (2) the
remodeling of the glycogen substrate to
permit further degradation, and (3) the
conversion of glucose 1-phosphate into
glucose 6-phosphate for further
metabolism. The glucose 6-phosphate
derived from the breakdown of glycogen
has three fates: (1) It is the initial substrate
for glycolysis, (2) it can be processed by
the pentose phosphate pathway to
yield NAPDH and ribose derivatives; and
(3) it can be converted into free glucose
for release into the bloodstream. This
conversion takes place mainly in the liver
and to a lesser extent in the intestines and
kidneys.

Glycogen synthesis requires an activated form of glucose, uridine
diphosphate glucose (UDP-glucose), which is formed by the reaction
of UTP and glucose 1-phosphate. UDP-glucose is added to the
nonreducing end of glycogen molecules. As is the case for glycogen
degradation, the glycogen molecule must be remodeled for continued
synthesis.
The regulation of these processes is quite complex. Several
enzymes taking part in glycogen metabolism allosterically respond to
metabolites that signal the energy needs of the cell. These allosteric
responses allow the adjustment of enzyme activity to meet the needs of
the cell in which the enzymes are expressed. Glycogen metabolism is
also regulated by hormonally stimulated cascades that lead to the
reversible phosphorylation of enzymes, which alters their kinetic
properties. Regulation by hormones allows glygogen metabolism to adjust
to the needs of the entire organism. By both these mechanisms, glycogen
degradation is integrated with glycogen synthesis. We will first examine
the metabolism, followed by enzyme regulation and then the elaborate
integration of control mechanisms.

Regulation of Blood Glucose Levels:
Insulin and Glucagon
Cells of the body require nutrients in order to function. These nutrients are
obtained through feeding. In order to manage nutrient intake, storing excess
intake, and utilizing reserves when necessary, the body uses hormones to
moderate energy stores. Insulin is produced by the beta cells of the pancreas,
which are stimulated to release insulin as blood glucose levels rise (for
example, after a meal is consumed). Insulin lowers blood glucose levels by
enhancing the rate of glucose uptake and utilization by target cells, which use
glucose for ATP production. It also stimulates the liver to convert glucose to
glycogen, which is then stored by cells for later use. As insulin binds to its
target cell via insulin receptors and signal transduction, it triggers the cell to
incorporate glucose transport proteins into its membrane. This allows glucose
to enter the cell, where it can be used as an energy source. These actions
mediated by insulin cause blood glucose concentrations to fall, called a
hypoglycemic, or "low sugar" effect, which inhibits further insulin release from
beta cells through a negative feedback loop.

Impaired insulin function can lead to a condition called diabetes
mellitus, which has many effects on the body . It can be caused by
low levels of insulin production by the beta cells of the pancreas, or
by reduced sensitivity of tissue cells to insulin. This prevents glucose
from being absorbed by cells, causing high levels of blood glucose,
or hyperglycemia (high sugar). High blood glucose levels make it
difficult for the kidneys to recover all the glucose from nascent urine,
resulting in glucose being lost in urine. High glucose levels also result
in less water being reabsorbed by the kidneys, causing high amounts
of urine to be produced; this may result in dehydration. Over time,
high blood glucose levels can cause nerve damage to the eyes and
peripheral body tissues, as well as damage to the kidneys and
cardiovascular system. Oversecretion of insulin can
cause hypoglycemia, low blood glucose levels. This causes
insufficient glucose availability to cells, often leading to muscle
weakness. It can sometimes cause unconsciousness or death if left
untreated.

Regulation of Blood Glucose Levels:
Thyroid Hormones
The basal metabolic rate, which is the amount of calories required by the body
at rest, is determined by two hormones produced by the thyroid gland: thyroxine, also
known as tetraiodothyronine or T4, and triiodothyronine, also known as T3. T3 and T4
release from the thyroid gland are stimulated by thyroid-stimulating hormone (TSH),
which is produced by the anterior pituitary. These hormones affect nearly every cell in the
body except for the adult brain, uterus, testes, blood cells, and spleen. They are
transported across the plasma membrane of target cells where they bind to receptors on
the mitochondria, resulting in increased ATP production. In the nucleus, T3and
T4activate genes involved in energy production and glucose oxidation. This results in
increased rates of metabolism and body heat production. This is known as the hormone's
calorigenic effect.
Disorders can arise from both the underproduction and overproduction of
thyroid hormones. hypothyroidism, underproduction of the thyroid hormones, can cause a
low metabolic rate leading to weight gain, sensitivity to cold, and reduced mental activity,
among other symptoms. In children, hypothyroidism can cause cretinism, which can lead
to mental retardation and growth defects. Hyperthyroidism, the overproduction of thyroid
hormones, can lead to an increased metabolic rate, which may cause weight loss,
excess heat production, sweating, and an increased heart rate.

Activity: Identify the following.
1. They release from the thyroid gland and stimulated by
thyroid-stimulating hormone (TSH), which is produced
by the anterior pituitary.
2. A readily mobilized storage form of glucose.
3. Impaired insulin function can lead to a condition called
__________, which has many effects on the body.
4. It allows glycogen metabolism to adjust to the needs of
the entire organism.
5. It makes difficult for the kidneys to recover all the
glucose from nascent urine, resulting in glucose being
lost in urine.

References:
• https://www.boundless.com/biology/textbooks/boundless-biology-
textbook/the-endocrine-system-37/regulation-of-body-processes-
212/hormonal-regulation-of-metabolism-799-12035/
• https://www.ncbi.nlm.nih.gov/books/NBK21190/
• https://www.endocrineweb.com/conditions/diabetes/normal-regulation-
blood-glucose
• https://www.khanacademy.org/test-prep/mcat/biomolecules/carbohydrate-
metabolism/a/glycolysis-and-gluconeogenesis
• https://www.khanacademy.org/test-prep/mcat/biomolecules/carbohydrate-
metabolism/a/pentose-phosphate-pathway
• https://www.tamu.edu/faculty/bmiles/lectures/Pentose%20Phosphate%20Pa
thway.pdf
• https://www.khanacademy.org/science/biology/cell-signaling/mechanisms-
of-cell-signaling/a/introduction-to-cell-signaling

ANSWERS:
Activity 1
1. Ligands
2. A chain of chemical messengers
3. Endocrine signalling
4. Intracellular mediators
5. Autocrine signalling
Activity 2:
3, 1, 5, 2, 4
Activity 3:
1. tetraiodothyronine or T4, and triiodothyronine, also known as T3
2. Glycogen
3. diabetes mellitus
4. regulation by hormones
5. High blood glucose levels

Biochemistry pt. 1

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