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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
ΔG=ΔH-TΔS
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
• [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
• A B ΔG'01
• B C ΔG'02
• Since the two reactions are sequential, we
can write the overall reaction as
• A C ΔG'0total
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.
Mn cluster in
the OEC
Herbicides that
inhibit
Photosystem II
by blocking the
transfer of
electrons to
QH2:
Electron Flow through PSII: Electron Flow through Cytochrome bf:
Plastocyanin:
• Photosystem I:
Photosystem I:
700nm
photon
Biochem 3070 - Photosynthesis
Ferredoxin Structure
Lumen
(Thylakoid
Space)
Stroma
Lumen
Inner-membrane
Space
Matrix
What about CO2?
From light-driven
reactions
Ribulose 1,5-bisphosphate carboxylase/oxygenase [“rubisco”]:
• 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
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
Gluconeogenesis
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.
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