LEARNING OBJECTIVES

Definition and meaning

Scope of BMB and related to Medicine

History and Time Line of BMB

Techniques in BMB

Origin of Life

Water & Functional Groups

Introduction
What is :
Biochemistry ?
Molecular Biology ?
Biochemistry and Molecular Biology ?
(BMB)

Biochemistry is the Chemistry of Life

Biochemistry can be defined as

the science of the chemical basis of life

( biological chemistry )

study of life at molecular level

life in its most basic level is a biochemical phenomenon

The Cell is the structural unit of living systems. Thus,

biochemistry can also be described as the science of the

chemical constituents of living cells and of the reactions
and processes they undergo.

By this definition, biochemistry encompasses large areas

of

Biochemistry Is Multidisciplinary
interdiciplinary sciences

One of the goals of biochemists is to integrate a large body

of knowledge into a molecular explanation of life.

This has been, and continues to be, a challenging task but, in

spite of the challenges, biochemists have made a great deal
of progress toward defining and understanding the basic
reactions common to all cells.

The discipline of biochemistry does not exist in a vacuum.

We have already seen how physics, chemistry, cell biology,

and evolution contribute to an understanding of
biochemistry.

Biochemistry is the science concerned with the various

molecules that occur in living cells and organisms and
with their chemical reactions.

. Anything more than an extremely superficial

comprehension of life, in all manifestations _ demands a

knowledge of biochemistry

In additon, medical students who acquire

of biochemistry
will be in strong position to deal with two central concerns
of the health sciences:
1. Understanding and maintenance of health and
2. Understanding and effective treatmen of disease.

Biochemistry is largely concerned with :

What are chemical and 3D structure of biological molecules ?

How do biological molecules (BM)

interact each other ?

How does the cell synthesize & degrade BM?

How is energy conseved and used by cell ?
What are the mechanism for organizing BM and coordinating
their activity ?

Molecular Biology

The name was coined by Warren Weaver of the Rockefeller

Foundation in 1938 and popularized by William T. Astbury

Pioneers: Erwin Schrodinger, Niels Bohr, Max Delbrukm

Paul Dirac, Max Perutz, Maurice Wilkins, Francis Crick

Is the study of biology at a molecular level.

Chiefly concerns itself with understanding the interactions between
the various systems of a cell, including the interactions between
DNA, RNA and protein biosynthesis as well as learning how these
interactions are regulated.

Study of gene expression and its regulation

There is not a defined line between Biochemistry and

Molecular Biology.

These two disciplines overlap and complement each other.

It can be said that the biochemistry and molecular biology
can not afford inseparable, like two sides of the same coin

1991 IUB become International Union of Biochemistry

and Molecular Biology (IUBMB)
The journals: Biochemistry and Molecular Biology
Education , BioEssays, BioFactors, Biotechnology and
Applied Biochemistry, IUBMB Life, Molecular Aspects of
Medicine and Trends in Biochemical Sciences

The Aim of BMB Is to Describe & Explain,

in Molecular Terms, All Chemical
Processes of Living Cells

The major objective of biochemistry is the complete

understanding, at the molecular level, of all of the chemical

processes associated with living cells.

To achieve this objective, biochemists have sought to

isolate the numerous molecules found in cells, determine

their structures, and analyze how they function.

Many techniques have been used for these purposes; some

of them are summarized in Table 1.

The Principal Methods and Preparations Used

in Biochemical Laboratories

Methods for Separating and Purifying Biomolecules:

Salt fractionation :eg, ammonium sulfate
Chromatography :Paper,IEX, Affinity,TLC, GC, HPLC,Gel Filtration
Electrophoresis : Paper, high-voltage, agarose, cellulose acetate,
starch gel, polyacrylamide gel, SDS-PAGE
Ultracentrifugation :
Methods for Determining Biomolecular Structures:
Elemental analysis:
UV, visible, infrared, and NMR spectroscopy
Use of acid, alkaline or enzymes to degrade the biomolecule:
CD : Circular Dichroism Spectroscopy (Secondary structure)
Mass Spectrometry: MS/MS MALDI-TOF
X-ray crystallography
Specific sequencing methods (eg, for proteins and nucleic acids)

 Preparations for Studying Biochemical Processes

Whole animal (includes transgenic or animals with gene knockouts)
Homogenate
Isolated cell organelles
Subfractionation of organelles : Ultracentrifugation
Isolated perfused organ
Tissue slice; Whole cells
Single Cell Analysis (SCA): Individual cells can differ dramatically in
size, protein levels, and expressed RNA transcripts. These variations
are key to answering irresolvable questions in cancer research, stem
cell biology, immunology, developmental biology, and neurology.
Purified metabolites and enzymes
Isolated genes (including PCR and site-directed mutagenesis)

A Knowledge of Biochemistry Is Essential to

Life Sciences
Biochem
of the nucleic acids lies at the heart of genetics, in
All
turn, the use of genetic approaches has been critical for
elucidating many areas of biochem.

Physiology, overlaps with biochemistry almost completely.

Immunology employs numerous biochemical techniques,
and many immunologic approaches have found wide use
by biochemists.

Pharmacology and pharmacy rest on a sound knowledge of

biochemistry and physiology; in particular, most drugs are

 Poisons act on biochemical reactions or processes; this is

the subject matter of toxicology.

Biochemical approaches are being used increasingly to

study basic aspects of pathology (the study of disease), such

as inflammation, cell injury, and cancer.

Many workers in microbiology, zoology, and botany

employ biochemical approaches almost exclusively. These

relationships are not surprising, because life as we know it
depends on biochemical reactions and processes.

In fact, the old barriers among the life sciences are breaking
down, and biochemistry is increasingly becoming :

A Reciprocal Relationship Between Biochemistry &

Medicine Has Stimulated Mutual Advances

In fact, the interrelationship of BMB and medicine is a wide, two-

way street. BMB studies have illuminated many aspects of health

and disease, and conversely, the study of various aspects of health
and disease has opened up new areas of BMB.

NORMAL BIOCHEMICAL PROCESSES ARE THE BASIS OF

HEALTH & All Diseases Have a Biochemical Basis

Impact of the Human Genome Project (HGP)

on BMB, Medicine and many areas of
Research

History of BMB
and
Time Line
20 - 34

Some major events in the

history of Biochemistry
Being dynamic for only about
100 years.

Ending vitalism,
beginning physics
and chemistry.
1966
1959

Genetic codes unveiled.

Perutz determined 3-D structure of hemoglobin.

Watson and Crick proposed 1953
the double helix for DNA
1944 Avery, MacLeod, and McCarty showed DNA
Krebs elucidated the 1937
to be the agent of genetic transformation.
citric acid cycle.
1926 Sumner crystallized urease.
The glyclolytic
pathway revealed 1925 1897 Buchner demonstrated fermentation with
cell extracts. In vitro (in glass) study began.
Miescher isolated 1869
sugar ethanol
nucleic acids.
Inorganic organic
1828 Friedrich Wohler synthesized urea from
ammonium cyanate in the lab.
NH4CNO CO(NH2)2

Molecular Search Tools: Blots

- 1975 Edwin Southern - Southern blots
DNA immobilized on solid support
- 1977 JC Alwine - Northern blots
RNA immobilized on solid support
- 1981 W Neal Burnette - Western blots
Proteins immobilized on solid support
- 1998 Ishikawa & Taki Far-Eastern blots
_
Lipid detection
2001 Ethan Signer Eastern Blots
PTM protein

Southern Blot Applications

Reverse Genetics:
Start with a protein and work backwards in order to isolate the
structural gene for that protein.
Restriction Fragment Length Polymorphisms:
To map the genes responsible for inherited diseases.
Criminology: DNA fingerprinting
Clinical Diagnosis:
AIDS testing
Genetics, oncology (translocations, gene rearrangements)
Typing/classification of organisms
Forensic, parentage testing

Northern Blot Applications

Used

to determine when, where, and by how much genes

are expressed.
Can be used to investigate whether a mRNA is present in a

specific cell or tissue type.

Can

reveal the size or sizes of the mRNA encoded by a

gene.
Sometimes, a number of different mRNA species are encoded by

the same gene

Different promoter sites
Alternative mRNA processing
Different terminator sites

Nobel prizes for

Biochemical
studies
1901-2012

Nobel Prizes in revealing the

structural chemistry of living matter (1)

1902, Emil Fischer: chemical syntheses of sugar and purine.

1910, Albrecht Kossel: cell chemistry made through work on proteins,
including the nucleic substances.
1915, Richard Willstatter: plant pigments.
1923, Frederick G. Bantiing and John Macleod: insulin.
1927, Heirich Wieland: bile acids.
1928, Adolf Windaus: sterols.
1929, Christiaan Eijkman: antineuritic vitamin; Sir Frederick Hopkins:
growth-stimulating vitamins.
1930, Hans Fischer: haemin and chlorophyll.
1931, Otto Warburg: nature and mode of action of the respiratory
enzyme.

Nobel Prizes in revealing the

structural chemistry of living
matter (2)

1937, Norman Haworth: carbohydrates and vitamin C; Paul

Karrer: carotenoids, flavins and vitamins A and B2.
1938, Richard Kuhn: carotenoids and vitamins.
1939. Adolf Butenandt: sex hormones; Leopold Ruzicka:
terpenes.
1943, Henric Dam, Edward A. Doisy: vitamin K.
1945, Sir Alexander Fleming, Ernst B. Chain, Sir Howard
Florey: penicillin.
1946, James B. Sumner, John H. Northrop, Wendell M.
Stanley: enzyme and protein cystallization.
1947, Sir Robert Robinson: alkaloids.

Nobel Prizes in revealing the

structural chemistry of living
matter (3)

1950, Edward C. Kendall, Tadeus Reichstein, Philip S. Hench:

hormones of the adrenal cortex.
1952, Selman A. Waksman: streptomycin.
1953, Hermann Staudinger: macromolecular chemistry.
1954, Linus Pauling: structure of complex substances-proteins.
1955, Hugo Theorell: nature and mode of action of oxidation
enzymes.
1955, Vincent du Bigneaud: biochemically important sulphur
compounds.
1957, Lord Todd: nucleotides and nucleotide co-enzymes.
1958, Frederick Sanger: structure of proteins.

Nobel Prizes in revealing the

structural chemistry of living
matter (4)
1962,

Max F. Perutz and John C. Kendrew: structures

of globular proteins: Hb & Mb
1964, Dorothy Crowfoot Hodgkin: structures of
important biochemical substances.
1970, Luis Leloir: sugar nucleotides.
1971, Earl W. Sutherland, Jr.: mechanisms of the
action of hormones.
1972, Gerald M. Edeman, Rodney R. Porter: chemical
structure of antibodies.

Nobel Prizes in revealing the

structural chemistry of living
matter (5)

1972, Christian Anfinsen: amino acid sequence and the

biologically active conformation; Stanford Moore and William H.
Stein: catalytic activity of the active centre of the ribonuclease.
1975, John Corforth: stereochemistry of enzyme-catalyzed
reactions.
1977, Roger Guillemin, Andrew V. Schally, Rosalyn Yalow:
peptide hormones.
1978, Werner Arber, Daniel Nahans, Hamilton O. Smith:
restriction enzymes.
1982, Sune K. Bergstrom, Bengt, I. Samuelsson, John R. Vane:
prostaglandins.

Nobel Prizes in revealing the

structural chemistry of living
matter (6)

1982, Aaron Klug: structural elucidation of biologically important

nucleic acid-protein complexes.
1986, Stanley Cohn, Rita Levi-Montalcini: growth factors.
1989, Sidney Altman, Thomas E. Cech: catalytic properties of RNA.
1991, Erwin Neher, Bert Sakmann: single ion channels.
1992, Edmond H. Fischer, Edwin G. Krebs: reversible protein
phosphorylation.
1994, Alfred G. Gilman, Martin Rodbell: G-proteins.
1997, Stanley B. Prusiner: Prions.
1997,Jens C. Skou: ion-transporting enzyme.
1998, Robert F. Furchgott, Louis J. Ignarro, Ferid Murad: nitric oxide.

Nobel Prizes in revealing the

structural chemistry of living
matter (7)
2003, Peter Agre, Roderick MacKinnon: channels in cell
membranes.
2004, Richard Axel, Linda B. Buck: odorant receptors.
2006. Roger D. Konberg: Molecular basis of
Eukaryotic transcription.
2008. O. Shimomura, M. Chalfie, R.Y. Tsien: discovery of GFP
2009. V. Ramakrishnan, T.A Steitz, A.F Yonath:
Structure & function ribosomes
2012. Robert. J Lefkowitz & Brian K. Kobilka: Studies of
G-protein-Coupled Receptors.

Nobel Prizes in revealing the

Metabolism of living matter (1)

1907, Eduard Buchner: cell-free fermentation.

1922, Archibald B. Hill: production of heat in the muscle?; Otto
Meyerhof: fixed relationship between the consumption of oxygen and the
metabolism of lactic acid in the muscle.
1929, Arthur Harden, Hand von Euler-Chelpin: fermentation of sugar
and fermentative enzymes.
1937, Albert Szent-Gyorgyi: biological combustion, vitamin C and the
catalysis of fumaric acid.
1947, Carl Cori and Gerty Cori: catalytic conversion of glycogen;
Bernardo Houssay: hormone of the anterior pituitary lobe in the
metabolism of sugar.
1953, Hans Krebs: citric acid cycle; Fritz Lipmann: role of co-enzyme A
in metabolism.

Nobel Prizes in revealing the

Metabolism of living matter (2)

1961, Melvin Calvin: carbon dioxide assimilation in plants.

1964, Konrad Bloch, Feodor Lynen: cholesterol and fatty acid metabolism.
1978, Peter Mitchell: chemiosmotic theory of biological energy
transfer.
1985. Michael S. Brown, Joseph L. Goldstein: regulation of cholesterol
metabolism.
1988, Sir James W. Black, Gertrude B. Elion, George H. Hitchings:
principles for drug treatment.
1988, Johann Deisenhofer, Robert Huber, Hartmut Michel: photosynthetic
reaction centre.
1997, Paul D. Boyer, John E .Walker: synthesis of ATP.
1999, Gunter Blobel: protein localization.

Nobel Prizes in revealing the

Metabolism of living matter (3)

2000, Arvid Carlsson, Paul Greengard, Eric R. Kandel:

signal transduction in the nervous system.
2001, Leland H. Hartwell, Tim Hunt, Sir Paul Nurse:
regulators of the cell cycle.
2002, Sydney Brenner, H. Robert Horvitz, John E.
Sulston: regulation of organ development and
programmed cell death.
2004, Aaron Ciechanover, Avram Hershko, Irwin Rose:
ubiquitin-mediated protein degradation.

Nobel Prizes in revealing the

information pathway (1)

1962, Francis Crick, James Watson, Maurice Wilkins: molecular

structure of nucleic acids.
1958,George Beadle, Edward Tatum: genes act by regulating
definite chemical events;Joshua Lederberg: genetic
recombination and the organization of the genetic material of
bacteria.
1959, Severo Ochoa, Arthur Kornberg: biological synthesis of
ribonucleic acid and deoxyribonucleic acid.
1965, Francois Jacob, Andre Lwoff, Jacques Monod: genetic
control of enzyme and virus synthesis.
1968, Robert W. Holley, H. Gobind Khorana, Marshall W.
Nirenberg: interpretation of the genetic code and its function in
protein synthesis.

Nobel Prizes in revealing the

information pathway (2)

1969, Max Delbruck, Alfred D. Hershey, Salvador E. Luria:

replication mechanism and the genetic structure of viruses.
1975, David Baltimore, Renato Dulbecco, Howard M. Temin:
interaction between tumour viruses and the genetic material of
the cell.
1983, Barbara McClintock: mobile genetic elements.
1987, Susumu Tonegawa: generation of antibody diversity.
1989, J. Michael Bishop, Harold E. Varmus: oncogenes.
1993, Richard J. Roberts, Philip A. Sharp: split genes.
1995, Edward B. Lewis, Christiane Nusslein-Volhard, Eric, F.
Wieschaus: genetic control of early embryonic development.

Nobel Prizes in inventing important

methods for biochemical studies

1948, Arne Tiselius: electrophoresis, serum proteins.

1952, Archer J. P. Martin, Richard L. M. Synge: partition
chromatography.
1980, Paul Berg: recombinant-DNA; Walter Gilbert, Frederick
Sanger: nucleic acid sequencing.
1984, Bruce Merrifield: chemical synthesis of polypeptides and
polynucleotides.
1993, Kary B. Mullis: polymerase chain reaction; Michael Smith:
site-directed mutagenesis.
2002, John B. Fenn, Koichi Tanaka : mass spectrometry; Kurt
Wuthrich: NMR ( structure analyses of biological
macromolecules).

Techniques in
Biochemistry and Molecular Biology

Spectroscopic Methods
Spectroscopy:
Study of interaction between radiation (or
other forms of energy) and matter (a branch of
science).
Spectrometry:
Analytical methods based on atomic and
molecular spectroscopy
43

THE ELECTROMAGNETIC
SPECTRUM

Emission, Luminescence, and

Scattering Methods

46

Molecular Search Tools: Blots

- 1975 Edwin Southern - Southern blots
DNA immobilized on solid support
- 1977 JC Alwine - Northern blots
RNA immobilized on solid support
- 1981 W Neal Burnette - Western blots
Proteins immobilized on solid support
- 1998 Ishikawa & Taki Far-Eastern blots
_
Lipid detection
2001 Ethan Signer Eastern Blots
PTM protein

Southern Blot Applications

Reverse Genetics:
Start with a protein and work backwards in order to isolate the
structural gene for that protein.
Restriction Fragment Length Polymorphisms:
To map the genes responsible for inherited diseases.
Criminology: DNA fingerprinting
Clinical Diagnosis:
AIDS testing
Genetics, oncology (translocations, gene rearrangements)
Typing/classification of organisms
Forensic, parentage testing

Northern Blot Applications

Used

to determine when, where, and by how much genes

are expressed.
Can be used to investigate whether a mRNA is present in a

specific cell or tissue type.

Can

reveal the size or sizes of the mRNA encoded by a

gene.
Sometimes, a number of different mRNA species are encoded by

the same gene

Different promoter sites
Alternative mRNA processing
Different terminator sites

The Origin of Life

Certain biochemical feature are common to all
organism

Biological Molecules Arose from Inorganic

Materials

Complex Self-replicating Systems Evolved from

Simple Molecules

Definitions of Life:
Any

population of entities which has the properties of

multiplication, heredity, and variation. John Maynard Smith

Life

is an expected, collectively self-organized property of

catalytic polymers. Stuart Kauffman

Life

possesses the properties of replication, catalysis, and

mutability. Norman Horowitz

1. Life must be chemical

As a result, computer generated artificial intelligence
is excluded.
2. Life sustains itself by gathering atoms and energy form
its environment.
If it doesnt eat, its not alive. Life requires
metabolism.
3. Living organisms must display variation.
No two people, bunnies, or bacteria are necessarily the
same. Life requires reproduction and genetic
variability.

Early earth, a tiny speck

in the galaxy, contained
simple inorganic
molecules that gave rise
to the first biological
macromolecules.
These, in turn, gained
the ability to self
organize and selfreplicate, eventually
forming cellular life
forms

Universe : 13.7 Bys

Earth : 4.6 Bys
Early Life: 3.8 BYs

The Origin of Life

The Oparin-Haldane
Hypothesis
1924. A. Oparin & John
Haldane
Postulate:
Reducing Atmosphere:
- H20, CH4, NH3, CO2, H2
( primordial soup )

1953. Miller & Urey

Stanley Miller and

Harold Urey
mixture of H2O,
CH4, NH3, and H2
Apparatus for
emulating the
synthesis of organic
compounds on the
prebiotic Earth

Nucleic acid bases can also

be synthesized under
supposed prebiotic
conditions.
In particular, adenine is
formed by the condensation
of HCN, a plentiful
component of the
prebiotic atmosphere, in a
reaction catalyzed by NH3

26 Elements
Major elements:
C, H, O, N, P, S : 92%
By Wet Weight :
O - 65%
C - 18%
H - 10%
N - 3%
Minor elements: 3.95%
Trace elements: 0.05%

Al, As, Ga

H - 63%
O - 25.5% number of
C - 9.5%
atoms
N - 1.4%

Life molecules
are made
around
carbon.

Carbon is extremely versatile in

forming covalent bonds with other
atoms or itself
Carbon

accounts for more than half of the dry weight

of cells.
Covalently linked carbon atoms can form linear
chains, branched chains and cyclic structures.
All kinds of functional groups (e.g., alcohol, amino,
carboxyl) can be attached to the hydrocarbon
backbones (thus making the major biomolecules like
proteins, nucleic acids, carbohydrates, lipids and
etc.).

Versatility of
carbon bonding:
Carbon is able to
form covalent
bonds with
H, O, N and
itself.
An enormous
diversity of life
molecules can
thus be made.

Functional groups
found in biomolecules

P
S

Water and life

Life has been evolved in water

Water

is a polar molecule, forming H-bonds

between themselves (thus making water a highly
cohesive liquid) or with other molecules.
Water greatly weakens electrostatic forces and
hydrogen bonding between polar molecules, thus
being an excellent solvent for polar molecules.
hydrophobic groups are pushed away and
together by waterhydrophobic interactions
(driving proteins to fold and lipid bilayers to form).

Life undoubtedly could not have arisen in the

absence of water!

Each water can

Form H-bond
with 4 other
water molecules.

Thermal properties of water: high

boiling point, high melting point,
high heat of vaporization and high
heat capacity (thus a good
thermal buffer for the living
organisms).
Perhaps the most essential
property of water is that it is a
liquid at room temperature.
Melting point

Boiling

Amphipathic molecules
tend to spontaneously
rearrange themselves in
water.

Hydrophobic interaction is
a passive interaction
between hydrophobic
molecules due to the
hydrogen bonding between
water molecules.
Important for the
formation of
biomembranes (made of
amphipathic phospholipids)
and the folding of proteins.

Water is central to biochemistry

Nearly

all biomolecules assume their

shapes (and therefore their functions) in
response to the physical and chemical
properties of the surrounding water.
Water is the medium for the majority of
biochemical reactions.
Water actively participate in many
chemical reactions supporting life.
Oxidation of water (producing O2) is
fundamental to photosynthesis.

Reference Textbooks &

Journals

NCBI

PubMed

Stanford
HireWire

Voet & Voet 4Ed

Harpers Biochemistry 29th E

I. Structures & Functions of Proteins &
Enzymes
II. Bioenergetics & the Metabolism of
Carbohydrates & Lipids

III. Metabolism of Proteins & Amino Acids

IV. Structure, Function, & Replication of
Informational Macromolecules
V. Biochemistry of Extracellular &
Intracellular Communication
VI. Special Topics

Science should be as simple as

possible but not simpler.
Albert Einstein

The END
hasta la vista