Introduction

Biochemistry is the study of the chemical substances and processes that occur in plants,
animals, and microorganisms and of the changes they undergo during development and life.
It deals with the chemistry of life, and as such it draws on the techniques of analytical,
organic, and physical chemistry, as well as those of physiologists concerned with the
molecular basis of vital processes. All chemical changes within the organism−either
the degradation of substances, generally to gain necessary energy or the buildup of complex
molecules necessary for life processes−are collectively termed metabolism. These chemical
changes depend on the action of organic catalysts known as enzymes, and enzymes, in turn,
depend for their existence on the genetic apparatus of the cell. It is not surprising that
biochemistry enters into the investigation of chemical changes in disease, drug action, and
other aspects of medicine, as well as in nutrition, genetics, and agriculture.

The term biochemistry is synonymous with two somewhat older terms: physiological
chemistry and biological chemistry. Those aspects of biochemistry that deal with the
chemistry and function of very large molecules (e.g., proteins and nucleic acids) are often
grouped under the term molecular biology. Biochemistry is a young science, having been
known under that term only since about 1900. Its origins, however, can be traced much
further back; its early history is part of the early history of both physiology and chemistry.

Branches of Biochemistry:
 Structural biochemistry
 Bio-organic Chemistry
 Enzymology
 Metabolic Biochemistry
 Xenobiotics
 Immunology
 Endocrinology
 Neurochemistry
 Chemotaxonomy
 Chemical ecology
 Virology
 Molecular genetics and Genetic engineering
 Molecular biology
 Cell biology
Structural Biochemistry:
An area of biochemistry which aims to understand the chemical architecture of biological
macromolecules, especially proteins and nucleic acids (DNA and RNA) and attempting to
meet the peptide sequences, and conformal structure and physico-chemical atomic
interactions that enable these structures. One of the greatest challenges is to determine the
structure of a protein knowing only the amino acid sequence, which would be essential for
the rational design of proteins (protein engineering) base.

Bio-organic Chemistry:
An area of chemistry that deals with the study of organic compounds (ie, those having
carbon-carbon or carbon-hydrogen covalent bonds) that come specifically from living
things. It is a science closely related to the classical biochemistry, since in most carbon
biological compounds involved. While classical biochemical helps to understand the
biological processes based on knowledge of structure, chemical bonding, molecular
interactions and reactivity of organic molecules, the bioorganic chemistry tries to integrate
the knowledge of organic synthesis, reaction mechanisms, structural analysis and analytical
methods with primary and secondary metabolic reactions, biosynthesis, cell recognition and
chemical diversity of living organisms. From there arises Natural Products
Chemistry (Secondary metabolism).

Enzymology:
This area studies the behavior of biological catalysts or enzymes, such as certain proteins and
certain catalytic RNA and the coenzymes and cofactors, such as metals and vitamins. So the
mechanisms of catalysis is questioned, the processes of interaction of enzymes-substrate
catalytic transition states, enzymatic activities, reaction kinetics and mechanisms of
enzymatic regulation and expression, all from a biochemical point of view. Studies and tries
to understand the essential elements of the active site and those who are not, and catalytic
effects that occur in the modification of these elements; in this sense, techniques frequently
used as directed mutagenesis.

Metabolic Biochemistry:
An area of biochemistry which claims to know the different types of metabolic pathways at
the cellular level and organic context. Thus they are essential skills enzymology and cell
biology. Study all cellular biochemical reactions that make life possible, and as well as
healthy organic biochemical indices, the molecular basis of metabolic diseases or metabolic
intermediates flows globally.

From here arise academic disciplines such as bioenergetics (the study of energy flow in living
organisms), Nutritional Biochemistry (study of the processes of nutrition associated with
metabolic pathways) and clinical biochemistry (the study of biochemical alterations in
disease states or trauma). The metabolism is the set of science and techniques dedicated to
complete study of the system comprising the set of molecules that are metabolic
intermediates, primary and secondary metabolites, which can be found in a biological system.

Xenobiotics:
This is the discipline that studies the metabolic behavior of the compounds whose chemical
structure is not proper in the regular metabolism of a given organism. They may be secondary
metabolites of other organisms (e.g. mycotoxins, snake venom and phyto-chemicals when
they enter the human body) or non-existent in nature or infrequent
compounds. The Pharmacology is a discipline that studies benefiting xenobiotics cell
function in the organism due to its therapeutic or preventive effects (drugs).

Pharmacology has clinical applications when the substances are used in the diagnosis,
prevention, treatment and relief of symptoms of a disease and the rational development of
less invasive and more effective against specific biomolecular target substances. On the other
hand, the Toxicology is the study that identifies, studies and describes the dose, the nature,
incidence, severity, reversibility, and generally the mechanisms of adverse effects ( toxic
effects ) produced by xenobiotics.

Immunology:
This is one of the areas of biology, which is interested in the reaction of the organism to other
organisms such as bacteria and viruses. All this taking into account the reaction and immune
function of living things. It is essential in this area development and behavior studies
production of antibodies.

Endocrinology:
The study of internal secretions called hormones, which are produced by specialized cells
substances whose aim is to affect the function of other cells. Endocrinology is biosynthesis,
storage and function of hormones, cells and tissues secreting and hormone signaling
mechanisms. There are sub-disciplines such as medical endocrinology, the endocrinology
plant and animal endocrinology.

Neurochemistry:
The study of organic molecules involved in neuronal activity. This term is frequently used to
refer to neurotransmitters and other molecules such as neuro-active drugs influencing
neuronal function.

Chemotaxonomy:
The study of the classification and identification of bodies according to their demonstrable
differences and similarities in their chemical composition. The studied compounds can be
phospholipids, proteins, peptides, glycosides, alkaloids and terpenes. John Griffith Vaughan
was one of the pioneers of chemotaxonomy. Examples of applications can be cited
chemotaxonomy differentiation family Asclepiadaceae and Apocynaceae at the discretion of
the presence of latex; the presence of agarofuranos in the family Celastraceous; the sesqui
terpene lactones with skeleton germacrano that are characteristic of the family Asteraceae or
the presence of abietanos in the aerial parts of plants of the genus Salvia Old World as
opposed to the New World which have mainly neo–clerodanos.

Chemical ecology:
The study of the chemical compounds of biological origin involved in the interactions of
living organisms. It focuses on the production and response signaling molecules (semi
chemicals) and compounds that influence growth, survival and reproduction of other
organisms (allelo chemicals).

Virology:
This is one of the area of biology, dedicated to the study of elementary bio systems:
viruses. Both classification and recognition, and its operation and molecular structure. It aims
to recognize performance targets for potential drugs and vaccines to prevent direct or
preventive expansion. We also analyze and predict, in evolutionary terms, variation and
combination of viral genomes, which could eventually make them more dangerous. Finally
they represent a tool with a lot of projection as recombinant vectors, and have been already
used in gene therapy.
Molecular genetics and Genetic engineering:
An area of biochemistry and molecular biology that studies the genes, their heritage and their
expression. Molecularity, is dedicated to the study of DNA and RNA mainly, and uses tools
and powerful techniques in the study, such as PCR and its variants, mass sequencers,
translation, transcription-commercial kits for extracting DNA and RNA, processes in-vitro
and in-vivo, restriction enzymes, DNA ligases is an essential to know as the DNA is
replicated, transcribed and translated into proteins (Central Dogma of Molecular Biology),
and the mechanisms of basal expression and inducible gene genome.

It also studies the insertion of genes, gene silencing and the differential expression of genes
and their effect. Thereby overcoming barriers and boundaries between species in the sense
that the genome of a species can insert it in another and generate new species. One of their
top goals is to meet current regulatory mechanisms and gene expression, that is, obtain an
epigenetic code. It is an essential pillar in all life science disciplines, especially
biotechnology.

Molecular biology:
This is the scientific discipline that aims to study the processes taking place in living
organisms from a molecular standpoint. Classical biochemical and metabolic cycles
investigated in detail and the integration and disintegration of the molecules making up living
beings, molecular biology aims set preferably in the behavior of biological macromolecules
(DNA, RNA, enzymes, hormones, etc.) within the cell and explains the biological functions
of the living being by these properties at the molecular level.

Cell biology:
(Formerly cytology, from citos = cell and logos = study or treaty) This is an area of biology
dedicated to the study of the morphology and physiology of prokaryotes and eukaryotes. Try
to know their properties, structure, biochemical composition, functions, containing
organelles, their interaction with the environment and their life cycle. It is essential in this
area know the intrinsic cellular life processes during the cell cycle, such as nutrition,
respiration, synthesis of components, defense mechanisms, cell division and cell death.
You must also understand the mechanisms of cell communication (especially in multicellular
organisms) or junctions. It is essentially an area of observation and experimentation in cell
cultures, which often target the identification and separation of cell populations and
recognition of cell organelles. Some techniques used in cellular biology are concerned with
the use of cytochemical techniques, plant cell cultures, observation by optical and electron
microscopy, immune cytochemistry, immune histo-chemistry, ELISA or flow cytometry. It is
closely linked to disciplines such as histology, microbiology and physiology.

The Molecular Logic of Life

The Chemical Unity of Diverse Living Organisms
Living organisms are composed of lifeless molecules. When these molecules are isolated and
examined individually, they conform to all the physical and chemical laws that describe the
behavior of inanimate matter. Yet living organisms possess extraordinary attributes not
shown by any random collection of molecules. First consideration is the properties of living
organisms that distinguish them from other collections of matter. After arriving at a broad
definition of life, we can describe a set of principles that characterize all living organisms.
These principles underlie the organization of organisms and the cells that make them up, and
they provide the framework for this book. They will help you to keep the larger picture in
mind while exploring the illustrative examples presented in the text.

Living Matter Has Several Characteristics

What distinguishes all living organisms from all inanimate objects? First, they are structurally
complicated and highly organized. They possess intricate internal structures (Fig. 1-la) and
contain many kinds of complex molecules. By contrast, the inanimate matter in our
environment-clay, sand, rocks, seawater-usually consists of mixtures of relatively simple
chemical compounds.

Second, living organisms extract, transform, and use energy from their environment (Fig. 1-
lb), usually in the form of either chemical nutrients or the radiant energy of sunlight. This
energy enables living organisms to build and maintain their own intricate structures and to do
mechanical, chemical, osmotic, and other types of work. By contrast, inanimate matter does
not use energy in a systematic way to maintain structure or to do work. Inanimate matter
tends to decay toward a more disordered state, to come to equilibrium with its surroundings.
The third and most characteristic attribute of living organisms is the capacity for precise self-
replication and self-assembly (Fig. 1-lc), a property that can be regarded as the quintessence
of the living state. A single bacterial cell placed in a sterile nutrient medium can give rise to a
billion identical "daughter" cells in 24 hours. Each of the cells contains thousands of different
molecules, some extremely complex; yet each bacterium is a faithful copy of the original,
constructed entirely from information contained within the genetic material of the original
cell. By contrast, mixtures of inanimate matter show no capacity to grow and reproduce in
forms identical in mass, shape, and internal structure, generation after generation.

The ability to self-replicate has no true analog in the nonliving world, but there is an
instructive analogy in the growth of crystals in saturated solutions. Crystallization produces
more material identical in lattice structure with the original "seed" crystal. Crystals are much
less complex than the simplest living organisms, and their structure is static, not dynamic as
are living cells. Nonetheless, the ability of crystals to "reproduce" themselves led the
physicist Erwin Schrodinger to propose in his famous essay "What Is Life?" that the genetic
material of cells must have some of the properties of a crystal. Schrodinger's 1944 notion
(years before the modern understanding of gene structure was achieved) describes rather
accurately some of the properties of deoxyribonucleic acid, the material of genes.

Each component of a living organism has a specific function. This is true not only of
macroscopic structures such as leaves and stems or hearts and lungs, but also of microscopic
intracellular structures such as the nucleus or chloroplast. Even individual chemical
compounds in cells have specific functions. The interplay among the chemical components of
a living organism is dynamic; changes in one component cause coordinating or compensating
changes in another, with the result that the whole ensemble displays a character beyond that
of the individual constituents. The collection of molecules carries out a program, the end
result of which is the reproduction of the program and the self perpetuation of that collection
of molecules.
Figure 1-1 Some characteristics of living matter. (a) Microscopic complexity and organization are
apparent in this thin section of vertebrate muscle tissue, viewed with the electron microscope. (b) The
lion uses organic compounds obtained by eating other animals to fuel intense bursts of muscular
activity. The zebra derives energy from compounds in the plants it consumes; the plants derive their
energy from sunlight. (c) Biological reproduction occurs with near-perfect fidelity.

Biochemistry Seeks to Explain Life in Chemical Terms

The molecules of which living organisms are composed conform to all the familiar laws of
chemistry, but they also interact with each other in accordance with another set of principles,
which we shall refer to collectively as the molecular logic of life. These principles do not
involve new or as yet undiscovered physical laws or forces. Instead, they are a set of
relationships characterizing the nature, function, and interactions of biomolecules.

If living organisms are composed of molecules that are intrinsically inanimate, how do these
molecules confer the remarkable combination of characteristics we call life? How is it that a
living organism appears to be more than the sum of its inanimate parts? Philosophers once
answered that living organisms are endowed with a mysterious and divine life force, but this
doctrine (vitalism) has been firmly rejected by modern science. The basic goal of the science
of biochemistry is to determine how the collections of inanimate molecules that constitute
living organisms interact with each other to maintain and perpetuate life. Although
biochemistry yields important insights and practical applications in medicine, agriculture,
nutrition, and industry, it is ultimately concerned with the wonder of life itself.

Chemical Unity Underlies Biological Diversity

A massive oak tree, an eagle that soars above it, and a soil bacterium that grows among its
roots appear superficially to have very little in common. However, a hundred years of
biochemical research has revealed that living organisms are remarkably alike at the
microscopic and chemical levels (Fig. 1-2). Biochemistry seeks to describe in molecular
terms those structures, mechanisms, and chemical processes shared by all organisms and to
discover the organizing principles that underlie life in all of its diverse forms.

Figure 1-2 Diverse living organisms share common chemical features. The eagle, the oak tree, the
soil bacterium, and the human share the same basic structural units (cells), the same kinds of
macromolecules (DNA, RNA, proteins) made up of the same kinds of monomeric subunits
(nucleotides, amino acids), the same pathways for synthesis of cellular components, and the same
genetic code and evolutionary ancestors.
Although there is a fundamental unity to life, it is important to recognize at the outset that
very few generalizations about living organisms are absolutely correct for every organism
under every condition. The range of habitats in which organisms live, from hot springs to
Arctic tundra, from animal intestines to college dormitories, is matched by a correspondingly
wide range of specific biochemical adaptations. These adaptations are integrated within the
fundamental chemical framework shared by all organisms. Although generalizations are not
perfect, they remain useful. In fact, exceptions often illuminate scientific generalizations.

All Macromolecules Are Constructed from a Few Simple Compounds

Most of the molecular constituents of living systems are composed of carbon atoms
covalently joined with other carbon atoms and with hydrogen, oxygen, or nitrogen. The
special bonding properties of carbon permit the formation of a great variety of molecules.
Organic compounds of molecular weight (M r ) less than about 500, such as amino acids,
nucleotides, and monosaccharides, serve as monomeric subunits of proteins, nucleic acids,
and polysaccharides, respectively. A single protein molecule may have 1,000 or more amino
acids, and deoxyribonucleic acid has millions of nucleotides.

Each cell of the bacterium Escherichia coli (E. coli) contains more than 6,000 different kinds
of organic compounds, including about 3,000 different proteins and a similar number of
different nucleic acid molecules. In humans there may be tens of thousands of different kinds
of proteins, as well as many types of polysaccharides (chains of simple sugars), a variety of
lipids, and many other compounds of lower molecular weight.

To purify and to characterize thoroughly all of these molecules would be an insuperable task
were it not for the fact that each class of macromolecules (proteins, nucleic acids,
polysaccharides) is composed of a small, common set of monomeric subunits. These
monomeric subunits can be covalently linked in a virtually limitless variety of sequences
(Fig. 1-3), just as the 26 letters of the English alphabet can be arranged into a limitless
number of words, sentences, or books.
Figure 1-3 Monomeric subunits in linear sequences can spell infinitely complex messages. The
number of different sequences possible (S) depends on the number of different kinds of subunits (N)
and the length of the linear sequence (L): S = NL. For polymers the size of proteins (L ≈ 1,000), S is
very large, and for nucleic acids, for which L may be many millions, S is astronomical.

Deoxyribonucleic acids (DNA) are constructed from only four different kinds of simple
monomeric subunits, the deoxyribonucleotides, and ribonucleic acids (RNA) are composed
ofjust four types of ribonucleotides. Proteins are composed of 20 different kinds of amino
acids. The eight kinds of nucleotides from which all nucleic acids are built and the 20
different kinds of amino acids from which all proteins are built are identical in all living
organisms.
Most of the monomeric subunits from which all macromolecules are constructed serve more
than one function in living cells. The nucleotides serve not only as subunits of nucleic acids,
but also as energy carrying molecules. The amino acids are subunits of protein molecules,
and also precursors of hormones, neurotransmitters, pigments, and many other kinds of
biomolecules.
From these considerations we can now set out some of the principles in the molecular logic of
life:
• All living organisms have the same kinds of monomeric subunits.
• There are underlying patterns in the structure of biological macromolecules.
• The identity of each organism is preserved by its possession of distinctive sets of
nucleic acids and of proteins.

Origin, History, and Chemical Evolution of Life

Chemical evolution is the sequence of chemical changes in originally nonliving matter that
give rise to life. The phrase “chemical evolution” is also used, in astronomy and cosmology,
to describe the changing makeup of the Universe’s stock of chemical elements through deep
time since the Big Bang, from hydrogen and helium immediately after the Big Bang to the
full array of elements observed today. This article will restrict itself to the first meaning.

The first known living things on Earth were prokaryotes, a type of cell similar to present-day
bacteria. Prokaryote fossils have been found in 3.4-million-year-old rock in the southern part
of Africa, and in even older rocks in Australia, including some that appear to be
photosynthetic. All forms of life are theorized to have evolved from the original prokaryotes,
probably 3.5-4.0 billion years ago.

The primitive Earth

The chemical and physical conditions of the primitive Earth are invoked to explain the origin
of life, which was preceded by chemical evolution of organic chemicals. Astronomers believe
that about 14 billion years ago, all matter was concentrated in a single mass, and that it blew
apart with a “big bang.” In time, as the Universe expanded and temperatures became low
enough to permit the existence of atoms, stars and galaxies formed out of the primordial
hydrogen and helium produced by the big bang. The nuclear processes in the hearts of these
stars and in the explosions of some of them in novae produced heavier elements such as
carbon, iron, and oxygen. Eventually, in part of the Milky Way galaxy, a disk-shaped cloud
of dust condensed and formed the Sun and its planets, including the Earth. Heat produced by
compaction kept the Earth liquid as it formed. Then, as the planet cooled, Earth’s layers
formed. The first atmosphere was made up of hot hydrogen gas, too light to be held by
Earth’s gravity. Water vapor, carbon monoxide, carbon dioxide, nitrogen, and methane
replaced the hydrogen atmosphere. As Earth cooled, water vapor condensed and torrential
rains began cooling its surface, rising up as steam; eventually the Earth’s surface cooled
enough for the fallen rain to exist as water on the surface, whereupon it began to fill up the
low parts of the surface, forming the seas. Also present were lightning, volcanic activity,
and ultraviolet radiation. It was in this setting that life began.

How life began

According to prevalent theory, chemical evolution occurred in four stages. In the first stage of
chemical evolution, molecules in the primitive environment formed simple organic
substances, such as amino acids. This concept was first proposed in 1936 in a book
entitled, “The Origin of Life on Earth,” by the Russian scientist, Aleksandr Ivanovich Oparin
(1894– 1980). He considered hydrogen, ammonia, water vapor, and methane to be
components in the early atmosphere. Oxygen was lacking in this chemically-reducing
environment. Oparin stated that ultraviolet radiation from the Sun provided the energy for the
transformation of these substances into organic molecules. Scientists today state that such
spontaneous synthesis occurred only in the primitive environment. Abiogenesis became
impossible when photosynthetic cells added oxygen to the atmosphere. The oxygen in the
atmosphere gave rise to the ozone layer, which then shielded Earth from ultraviolet radiation.
Newer versions of this hypothesis contend that the primitive atmosphere also
contained carbon monoxide, carbon dioxide, nitrogen, hydrogen sulfide, and hydrogen.
Present-day volcanoes emit these substances.

In 1957, Stanley Miller (1930–) and Harold Urey (1893–1981) provided laboratory evidence
that first-stage chemical evolution as described by Oparin could well have occurred. Miller
and Urey created an apparatus that simulated the primitive environment. They used a warmed
flask of water for the ocean and an atmosphere of water, hydrogen, ammonia, and methane.
Sparks discharged into the artificial atmosphere represented lightning. A condenser cooled
the atmosphere, causing rain that returned water and dissolved compounds back to the
simulated sea. When Miller and Urey analyzed the components of the solution after a week,
they found various organic compounds had formed. These included some of the amino acids
that compose the proteins of living things. Their results gave credence to the idea that simple
substances in the warm primordial seas gave rise to the chemical building blocks of
organisms.

In the second stage of chemical evolution, the simple organic molecules (such as amino
acids) that formed and accumulated joined together into larger structures (such as proteins).
The units linked to each other by the process of dehydration synthesis to form polymers. A
problem with this part of the hypothesis was that the abiotic synthesis of polymers had to
occur without the assistance of enzymes. In addition, these reactions give off water and
would, and would therefore not occur spontaneously in a watery environment. Sydney Fox of
the University of Miami suggested that waves or rain in the primitive environment splashed
organic monomers on fresh lava or hot rocks, which would have allowed polymers to form
abiotically. When he tried to do this in his laboratory, Fox produced proteinoids−abiotically
synthesized polypeptides.

In the third step in chemical evolution, it is suggested, polymers interacted with each other
and organized into aggregates known as protobionts. Protobionts are not capable of
reproducing, but had other properties of living things. Scientists have successfully produced
protobionts from organic molecules in the laboratory. In one study, proteinoids mixed with
cool water assembled into droplets or microspheres that developed membranes on their
surfaces. These are protobionts, with semi-permeable and excitable membranes, similar to
those found in cells.

In the final step of chemical evolution, protobionts developed the ability to reproduce and
pass genetic information from one generation to the next. Some scientists theorize RNA to be
the original hereditary molecule. Short polymers of RNA have been synthesized abiotically in
the laboratory. In the 1980s, Thomas Cech and his associates at the University of Colorado at
Boulder discovered that RNA molecules can function as enzymes in cells. This implies that
RNA molecules could have replicated in prebiotic cells without the use of protein enzymes.
Variations of RNA molecules could have been produced by mutations and by errors during
replication. Natural selection operating on the different RNAs would have brought about
subsequent evolutionary development. This would have fostered the survival of RNA
sequences best suited to environmental parameters, such as temperature and salt
concentration. As the protobionts grew and split, their RNA was passed on to off-spring. In
time, a diversity of prokaryote cells came into existence. Under the influence of natural
selection, the prokaryotes could have given rise to the vast variety of life on Earth.

As of 2006, most aspects of the chemical evolution scenario outlined above remained
speculative. The origin of life remains a topic of intense interest to scientists and is an area of
active research.