BIOCHEMISTRY-I

3 SEMESTER
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ANT MIT BMLT OTT
BIOCHEMISTRY..?
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Biochemistry is, literally, the study of the chemistry of life.
Although it overlaps other disciplines, including cell biology, genetics, immunology,
microbiology, pharmacology, and physiology, biochemistry is largely concerned with a
limited number of issues:
1. What are the chemical and three-dimensional structures of biological molecules?
2. How do biological molecules interact with one another?
3. How does the cell synthesize and degrade biological molecules?
4. How is energy conserved and used by the cell?
5. What are the mechanisms for organizing biological molecules and coordinating their
activities?
6. How is genetic information stored, transmitted, and expressed?
Biochemistry, like other modern sciences, relies on sophisticated instruments to dissect
the architecture and operation of systems that are inaccessible to the human senses.
In addition to the chemist’s tools for separating, quantifying, and otherwise analyzing
biological materials, biochemists take advantage of the uniquely biological aspects of
their subject by examining the evolutionary histories of organisms, metabolic systems,
and individual molecules.
In addition to its obvious implications for human health, biochemistry reveals the
workings of the natural world, allowing us to understand and appreciate the unique and
mysterious condition that we call life
1 The Origin of Life
Biological Molecules Arose from Inanimate Substances
Complex Self-Replicating Systems Evolved from Simple Molecules
2 Cellular Architecture
Cells Carry Out Metabolic Reactions
There Are Two Types of Cells: Prokaryotes and Eukaryotes
Molecular Data Reveal Three Evolutionary Domains of Organisms
Organisms Continue to Evolve
3 Thermodynamics
The First Law of Thermodynamics States That Energy Is Conserved
The Second Law of Thermodynamics States That Entropy Tends to
Increase
The Free Energy Change Determines the Spontaneity of a Process
Free Energy Changes Can Be Calculated from Reactant and Product
Concentrations
Life Achieves Homeostasis While Obeying the Laws of Thermodynamics
Biological Molecules Arose from Inanimate Substances
Living matter consists of a relatively small number of elements.
For example, C, H, O, N, P, Ca, and S account for ∼97% of the dry weight of
the human body (humans and most other organisms are ∼70% water).
Living organisms may also contain trace amounts of many other elements,
including B, F, Al, Si, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Br, Mo, Cd, I, and W,
although not every organism makes use of each of these substances
The atmosphere of the early earth probably consisted of small, simple compounds
such as H2O, N2, CO2, and smaller amounts of CH4 and NH3.
In the 1920s, Alexander Oparin and J. B. S. Haldane independently suggested that
ultraviolet radiation from the sun or lightning discharges caused the molecules of
the primordial atmosphere to react to form simple organic (carbon-containing)
compounds.
This process was replicated in 1953 by Stanley Miller and Harold Urey, who
subjected a mixture of H2O, CH4, NH3, and H2 to an electric discharge for about a
week.
The resulting solution contained water-soluble organic compounds, including
several amino acids (which are components of proteins) and other biochemically
significant compounds
Whatever their actual origin, the
early organic molecules became
the precursors of an enormous
variety of biological molecules.
These can be classified in various
ways, depending on their
composition and chemical reactivity.
A familiarity with organic chemistry
is useful for recognizing the
functional groups (reactive
portions) of molecules as well as
the linkages (bonding
arrangements) among them, since
these features ultimately determine
the biological activity of the
molecules.
Some of the common functional
groups and linkages in biological
molecules are…
Complex Self-Replicating Systems Evolved
from Simple Molecules
During a period of chemical evolution, the prebiotic
era, simple organic molecules condensed to form more
complex molecules or combined end-to-end as
polymers of repeating units.
In a condensation reaction, the elements of water
are lost.
The rate of condensation of simple compounds to form
a stable polymer must therefore be greater than the
rate of hydrolysis (splitting by adding the elements of
water.
In this prebiotic environment, minerals such as clays
may have catalyzed polymerization reactions and
sequestered the reaction products from water.
The size and composition of prebiotic macromolecules
would have been limited by the availability of small
molecular starting materials, the efficiency with which
they could be joined, and their resistance to
degradation
A critical moment in chemical evolution was
the transition from systems of randomly
generated molecules to systems in which
molecules were organized and
specifically replicated.
Once macromolecules gained the ability to
self perpetuate, the primordial environment
would have become enriched in molecules
that were best able to survive and multiply.
The first replicating systems were no doubt
somewhat sloppy, with progeny molecules
imperfectly complementary to their parents.
Over time, natural selection, the
competitive process by which reproductive
preference is given to the better adapted,
would have favored molecules that made
more accurate copies of themselves.
2 Cellular Architecture
Cells Carry Out Metabolic Reactions
Early cells depended on the environment to supply building materials.
As some of the essential components in the prebiotic soup became scarce, natural
selection favored organisms that developed metabolic pathways, mechanisms for
synthesizing the required compounds from simpler but more abundant precursors.
The first metabolic reactions may have used metal or clay catalysts (a catalyst is a
substance that promotes a chemical reaction without itself undergoing a net change).
In fact, metal ions are still at the heart of many chemical reactions in modern cells.
Some catalysts may also have arisen from polymeric molecules that had the
appropriate functional groups.
In general, biosynthetic reactions require energy; hence the first cellular reactions
also needed an energy source.
The eventual depletion of preexisting energy-rich substances in the prebiotic
environment would have favored the development of energy-producing metabolic
pathways.
For example, photosynthesis evolved relatively early to take advantage of a practically
inexhaustible energy supply, the sun. However, the accumulation of O2 generated
from H2O by photosynthesis (the modern atmosphere is 21% O2 presented an
additional challenge to organisms adapted to life in an oxygen-poor atmosphere
There Are Two Types of Cells: Prokaryotes and Eukaryotes
Molecular Data Reveal Three Evolutionary Domains of
Organisms

The archaea (also known as archaebacteria) are a group of prokaryotes that are as
distantly related to other prokaryotes (the bacteria, sometimes called eubacteria) as
both groups are to eukaryotes (eukarya). The archaea include some unusual
organisms: the methanogens (which produce CH4), the halobacteria (which thrive in
concentrated brine solutions), and certain thermophiles (which inhabit hot springs). The
pattern of branches in Woese’s diagram indicates the divergence of different types of
organisms (each branch point represents a common ancestor). The three-domain
Organisms Continue to Evolve
The natural selection that guided prebiotic evolution continues to direct the
evolution of organisms.
Small mutations (changes in an individual’s genetic material) arise at
random as the result of chemical damage or inherent errors in the DNA
replication process.
A mutation that increases the chances of survival of the individual increases
the likelihood that the mutation will be passed on to the next generation.
Beneficial mutations tend to spread rapidly through a population;
deleterious changes tend to die along with the organisms that harbor them
Principles of evolution:
1. Evolution is not directed toward a particular goal.
2. Variation among individuals
3. The past determines the future
4. Evolution is ongoing
3 Thermodynamics
• Energy must be conserved, but it can take different forms.
• In most biochemical systems, enthalpy is equivalent to heat.
• Entropy, a measure of a system’s disorder, tends to increase.
• The free energy change for a process is determined by its changes in
both enthalpy and entropy.
• A spontaneous process occurs with a decrease in free energy.
• The free energy change for a reaction can be calculated from the
temperature and the concentrations and stoichiometry of the reactants
and products.
• Biochemists defi ne standard state conditions as a temperature of 25°C,
a pressure of 1 atm, and a pH of 7.0.
• Organisms are nonequilibrium, open systems that constantly exchange
matter and energy with their surroundings while maintaining homeostasis.
• Enzymes increase the rate at which a reaction approaches equilibrium
Enzymes Catalyze Biochemical Reactions.
Nearly all the molecular components of an organism can potentially react
with one another, and many of these reactions are thermodynamically
favored (spontaneous).
However, only a subset of all possible reactions actually occur to a significant
extent in a living organism., the rate of a particular reaction depends not on
the free energy difference between the initial and final states but on the
actual path through which the reactants are transformed to products.
Living organisms take advantage of catalysts, substances that increase the
rate at which the reaction approaches equilibrium without affecting the
reaction’s ΔG and without themselves undergoing a net change.
Biological catalysts are referred to as enzymes, most of which are proteins
(RNA catalysts are also called ribozymes).
Enzymes accelerate biochemical reactions by physically interacting
with the reactants and products to provide a more favorable
pathway for the transformation of one to the other. Enzymes increase
the rates of reactions by increasing the likelihood that the reactants can
interact productively. Enzymes cannot, however, promote reactions whose ΔG
values are positive
BIOMOLECULES
 Biomolecules
Biomolecules are molecules that occur naturally in living organisms.
Biomolecules include macromolecules like proteins, carbohydrates, lipids and
nucleic acids.
It also includes small molecules like primary and secondary metabolites
and natural products.
Biomolecules consists mainly of carbon and hydrogen with nitrogen,
oxygen, sulphur, and phosphorus.
Biomolecules are very large molecules of many atoms, which are covalently
bound together

Classes of Biomolecules
There are four major classes of biomolecules:
i. Carbohydrates
ii. Lipids
iii. Proteins
iv. Nucleic acids
 Carbohydrates

Carbohydrates are good source of energy.

Carbohydrates (polysaccharides) are long chains of sugars.
Monosaccharides are simple sugars that are composed of 3-7 carbon
atoms.
They have a free aldehyde or ketone group, which acts as reducing agents
and are known as reducing sugars.
Disaccharides are made of two monosaccharides. The bonds shared
between two monosaccharides are the glycosidic bonds.
Monosaccharides and disaccharides are sweet, crystalline and water
soluble substances.
Polysaccharides are polymers of monosaccharides. They are un-sweet and
complex carbohydrates. They are insoluble in water and are not in
crystalline form.

Example: glucose, fructose, sucrose, maltose, starch, cellulose etc.

 Lipids
Lipids are composed of long hydrocarbon chains.
Lipid molecules hold a large amount of energy and are energy
storage molecules. Lipids are generally esters of fatty acids
and are building blocks of biological membranes.
Most of the lipids have a polar head and non-polar tail. Fatty
acids can be unsaturated and saturated fatty acids.
Lipids present in biological membranes are of three classes
based on the type of hydrophilic head present:
ü Glycolipids are lipids whose head contains oligosaccharides
with 1-15 saccharide residues.
ü Phospholipids contain a positively charged head which are
linked to the negatively charged phosphate groups.
ü Sterols, whose head contain a steroid ring. Example steroid.
Example of lipids: oils, fats, phospholipids, glycolipids, etc.
 Nucleic Acids
Nucleic acids are organic
compounds with heterocyclic rings.
Nucleic acids are made of polymer
of nucleotides.
Nucleotides consist of nitrogenous
base, a pentose sugar and a
phosphate group.
Nucleoside is made of nitrogenous
base attached to a pentose sugar.
The nitrogenous bases are
adenine, guanine, thyamine,
cytosine and uracil.
Polymerized nucleotides form DNA
and RNA which are genetic
material.
 Proteins
Proteins are heteropolymers of stings of amino acids.
Amino acids are joined together by the peptide bond which is formed in
between the carboxyl group and amino group of successive amino acids.
Proteins are formed from 20 different amino acids, depending on the
number of amino acids and the sequence of amino acids.
There are four levels of protein structure:
(i) Primary structure of Protein - Here protein exist as long chain of amino
acids arranged in a particular sequence. They are non-functional proteins.
(ii) Secondary structure of protein - The long chain of proteins are folded and
arranged in a helix shape, where the amino acids interact by the formation
of hydrogen bonds. This structure is called the pleated sheet. Example: silk
fibres.
(iii) Tertiary structure of protein - Long polypeptide chains become more
stabilizes by folding and coiling, by the formation of ionic or hydrophobic
bonds or disulphide bridges, these results in the tertiary structure of protein.
(iv) Quaternary structure of protein - When a protein is an assembly of more
than one polypeptide or subunits of its own, this is said to be the quaternary
structure of protein. Example: Haemoglobin, insulin.