Introduction to Biochemistry

Biochemistry, sometimes called biological chemistry, is the study of chemical processes in

living organisms, including, but not limited to, living matter. The laws of biochemistry govern
all living organisms and living processes. By controlling information flow through
biochemical signaling and the flow of chemical energy through metabolism, biochemical
processes give rise to the complexity of life.
Much of biochemistry deals with the structures, functions and interactions of cellular
components such as proteins, carbohydrates, lipids, nucleic acids and other biomolecules —
although increasingly processes rather than individual molecules are the main focus. Among
the vast number of different biomolecules, many are complex and large molecules (called
biopolymers), which are composed of similar repeating subunits (called monomers). Each
class of polymeric biomolecule has a different set of subunit types.[1] For example, a protein
is a polymer whose subunits are selected from a set of 20 or more amino acids.
Biochemistry studies the chemical properties of important biological molecules, like
proteins, and in particular the chemistry of enzyme-catalyzedreactions.
The biochemistry of cell metabolism and the endocrine system has been
extensively described. Other areas of biochemistry include the
genetic code (DNA, RNA), protein synthesis, cell membrane transport and
signal transduction.
Over the last 40 years biochemistry has become so successful at explaining
living processes that now almost all areas of the life sciences from botany
to medicine are engaged in biochemical research. Today the main focus of
pure biochemistry is in understanding how biological molecules give rise to
the processes that occur within living cells, which in turn relates greatly to
the study and understanding of whole organisms.
Contents
1 History
2 Starting materials: the chemical elements of life
3 Biomolecules
3.1 Carbohydrates
3.2 Lipids
3.3 Proteins
3.4 Nucleic acids
4. Carbohydrates
4.1 Monosaccharides
4.2 Disaccharides
4.3 Oligosaccharides and polysaccharides
4.4 Use of carbohydrates as an energy source
4.4.1 Glycolysis (anaerobic)
4.4.2 Aerobic
4.4.3 Gluconeogenesis
5 Proteins
6 Lipids
7 Nucleic acids
8 Biochemical Processes
History
Gerty Cori and Carl Cori jointly won the Nobel Prize in 1947 for their discovery of the Cori cycle
at RPMI.
It once was generally believed that life and its materials had some essential property or
substance distinct from any found in non-living matter, and it was thought that only living
beings could produce the molecules of life. Then, in 1828, Friedrich Wöhler published a paper
on the synthesis of urea, proving that organic compounds can be created artificially.
The dawn of biochemistry may have been the discovery of the first enzyme, diastase (today
called amylase), in 1833 by Anselme Payen. Eduard Buchner contributed the first
demonstration of a complex biochemical process outside of a cell in 1896:
alcoholic fermentation in cell extracts of yeast. Although the term “biochemistry” seems to
have been first used in 1882, it is generally accepted that the formal coinage of biochemistry
occurred in 1903 by Carl Neuberg, a German chemist. Previous to this time, this area would
have been referred to as physiological chemistry. Since then, biochemistry has advanced,
especially
History continued….
since the mid-20th century, with the development of new techniques such as chromatography,
X-ray diffraction, dual polarisation interferometry, NMR spectroscopy, radioisotopic labeling,
electron microscopy, and molecular dynamics simulations. These techniques allowed for the
discovery and detailed analysis of many molecules and metabolic pathways of the cell, such as
glycolysis and the Krebs cycle (citric acid cycle).
Another significant historic event in biochemistry is the discovery of the gene and its role in the
transfer of information in the cell. This part of biochemistry is often called molecular biology. In
the 1950s, James D. Watson, Francis Crick, Rosalind Franklin, and Maurice Wilkins were
instrumental in solving DNA structure and suggesting its relationship with genetic transfer of
information. In 1958, George Beadle and Edward Tatum received the Nobel Prize for work in
fungi showing that one gene produces one enzyme. In 1988, Colin Pitchfork was the first
person convicted of murder with DNA evidence, which led to growth of forensic science. More
recently, Andrew Z. Fire and Craig C. Mello received the 2006 Nobel Prize for discovering the
role of RNA interference (RNAi), in the silencing of gene expression.
Starting materials: the chemical elements of life

Main articles: Composition of the human body and Dietary mineral

Around two dozen of the 92 naturally-occurring chemical elements are essential to
various kinds of biological life. Most rare elements on Earth are not needed by life
(exceptions being selenium and iodine), while a few common ones (aluminum and
titanium) are not used. Most organisms share element needs, but there are a few
differences between plants and animals. For example ocean algae use bromine but land
plants and animals seem to need none. All animals require sodium, but some plants do
not. Plants need boron and silicon, but animals may not (or may need ultra-small
amounts).
Just six elements—carbon, hydrogen, nitrogen, oxygen, calcium, and phosphorus—
make up almost 99% of the mass of a human body (see composition of the human body
for a complete list). In addition to the six major elements that compose most of the
human body, humans require smaller amounts of possibly 18 more.]
Biomolecules

The four main classes of molecules in biochemistry are

carbohydrates, lipids, proteins, and nucleic acids. Many
biological molecules are polymers: in this
terminology, monomers are relatively small micromolecules that
are linked together to create large macromolecules, which are
known as polymers. When monomers are linked together to
synthesize a biological polymer, they undergo a process called
dehydration synthesis. Different macromolecules can assemble in
larger complexes, often needed for biological activity.
Carbohydrates
Monosaccharides/ Disaccharides/ Polysaccharides

A molecule of sucrose (glucose + fructose), a disaccharide.

Carbohydrates are made from monomers called monosaccharides. Some of these
monosaccharides include glucose (C6H12O6), fructose (C6H12O6), anddeoxyribose
(C5H10O4). When two monosaccharides undergo dehydration synthesis, water is
produced, as two hydrogen atoms and one oxygen atom are lost from the two
monosaccharides' hydroxyl group.
 The function of carbohydrates includes energy storage and providing
structure. Sugars are carbohydrates, but not all carbohydrates are
sugars. There are more carbohydrates on Earth than any other known
type of biomolecule; they are used to store energy and genetic
information, as well as play important roles in cell to cell interactions
and communications.
One important carbohydrate is glucose. Glucose is the major energy
source in most life forms. For instance, polysaccharides are broken
down into their monomers (glycogen phosphorylase removes glucose
residues from glycogen). Disaccharides like lactose or sucrose are
cleaved into their two component monosaccharides.
Lipids

A triglyceride with a glycerol molecule on the left and three fatty acids coming off it.
Lipids are usually made from one molecule of glycerol combined with other molecules.
In triglycerides, the main group of bulk lipids, there is one molecule of glycerol and
three fatty acids. Fatty acids are considered the monomer in that case, and may be
saturated (no double bonds in the carbon chain) or unsaturated (one or more double
bonds in the carbon chain).
Lipids, especially phospholipids, are also used in various pharmaceutical products, either
as co-solubilisers (e.g., in parenteral infusions) or else as drug carrier components (e.g.,
in a liposome or transfersome).
Lipids are an integral part of our daily diet. Most oils and milk products that we
use for cooking and eating like butter, cheese, ghee etc., are composed of fats.
Vegetable oils are rich in various polyunsaturated fatty acids (PUFA). Lipid-
containing foods undergo digestion within the body and are broken into fatty
acids and glycerol, which are the final degradation products of fats and lipids.
Proteins

The general structure of an α-amino acid, with the amino group

on the left and the carboxyl group on the right.
Proteins are very large molecules – macro-biopolymers – made from monomers
called amino acids. There are 20 standard amino acids, each containing acarboxyl group,
an amino group, and a side-chain (known as an "R" group). The "R" group is what makes
each amino acid different, and the properties of the side-chains greatly influence the
overall three-dimensional conformation of a protein. When amino acids combine, they
form a special bond called a peptide bond through dehydration synthesis, and become a
polypeptide, or protein.
In order to determine whether two proteins are related, or in other words to decide
whether they are homologous or not, scientists use sequence-comparison methods.
Methods like Sequence Alignments and Structural Alignments are powerful tools that help
scientists identify homologies between related molecules.
A schematic representation of hemoglobin.
The red and blue ribbons represent the
protein globin; the green structures
are the heme groups.

Like carbohydrates, some proteins perform

largely structural roles. For instance, movements of the proteins actin and myosin ultimately
are responsible for the contraction of skeletal muscle.
Antibodies are an example of proteins that attach to one specific type of molecule. In fact,
the enzyme-linked immunosorbent assay(ELISA), which uses antibodies, is currently one of
the most sensitive tests modern medicine uses to detect various biomolecules. Probably the
most important proteins, however, are the enzymes. These molecules recognize specific
reactant molecules called substrates; they then catalyze the reaction between them. By
lowering the activation energy, the enzyme speeds up that reaction by a rate of 1011 or more:
a reaction that would normally take over 3,000 years to complete spontaneously might take
less than a second with an enzyme.
NUCLEIC ACIDS

The structure of deoxyribonucleic acid (DNA);

the picture shows the monomers being put together.
Nucleic acids are the molecules that make up DNA,
an extremely important substance that all cellular organisms
use to store their genetic information.
The most common nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid
(RNA). Their monomers are called nucleotides. The most common nucleotides are
adenine, cytosine, guanine, thymine, and uracil. Adenine binds with thymine and uracil;
Thymine binds only with adenine; and cytosine and guanine can bind only with each
other.
Schematic relationship between biochemistry,
genetics, and molecular biology

Researchers in biochemistry use specific techniques native

to biochemistry, but increasingly combine these with
techniques and ideas developed in the fields of
genetics, molecular biology and biophysics.
There has never been a hard-line between these
disciplines in terms of content and technique.
Today, the terms molecular biology and biochemistry are nearly interchangeable.
The figure above right is a schematic that depicts one possible view of the
relationship between the fields:
Biochemistry is the study of the chemical substances
and vital processes occurring in living organisms.
Biochemists focus heavily on the role, function, and
structure of biomolecules. The study of the chemistry
behind biological processes and the synthesis of
biologically active molecules are examples of
biochemistry.

Genetics is the study of the effect of genetic

differences on organisms. Often this can be inferred by
the absence of a normal component (e.g., one gene). The
study of "mutants" – organisms with a changed gene that
leads to the organism being different with respect to
the so-called "wild type" or normal phenotype.
Genetic interactions (epistasis) can often confound
 Molecular biology is the study of molecular underpinnings of
the process of replication, transcription and translation of
the genetic material. The central dogma of molecular biology
where genetic material is transcribed into RNA and then
translated into protein, despite being an oversimplified
picture of molecular biology, still provides a good starting
point for understanding the field. This picture, however, is
undergoing revision in light of emerging novel roles for RNA.

 Chemical Biology seeks to develop new tools based on

small molecules that allow minimal perturbation of biological
systems while providing detailed information about their
function. Further, chemical biology employs biological systems
to create non-natural hybrids between biomolecules and
synthetic devices (for example emptied viral capsids that can
deliver gene therapy or drug molecules)