The aim of study:

To be able to read
what is not written
and to hear what is
not said!
-----Zengyi Chang
http://www.bio.pku.edu.cn/lab/proteinsci/
Biochemistry (I & II)
Foundations and overview


Professor Zengyi Chang
(
[email protected]
Room 204, New Life Science Building
6275-8822
March 3, 2007
Definition of
Biochemistry
Biochemistry: seeks to understand the
structure, organization, and function of
living matter in chemical terms.
Biochemistry aims to understand how the lifeless
molecules interact to make the complexity and
efficiency of the life phenomena and to explain the
diverse forms of life in chemical terms.
It brought the occurrence of the molecular
revolution of biology in the 20th century and has
thus become the common language of biological
sciences.
What is common for all life forms (unity) and what
is unique for one particular form (diversification).
Kinds of questions asked by
biochemists
What are the chemical structures of the components of
living matter?
How do the interactions of these components give rise to
organized supramolecular structures, cells, multicellular
tissues, and organisms?
How does living matter extract energy from its
surroundings in order to remain alive?
How does an organism store and transmit the
information it needs to grow and to reproduce itself
accurately?
What chemical changes accompany the reproduction, aging,
and death of cells and organisms?
How are chemical reactions controlled inside living cells?
Three principle areas of
Biochemistry
Structural Chemistry: structure-function
relationship for proteins, carbohydrates,
DNA/RNA, lipids, etc.;
Metabolism: totality of chemical reactions that
occur in living organism, concerning catabolism &
anabolism of building blocks, as well as
management of cellular Energy;
Storage, transmission, and expression of
genetic information: DNA replication and protein
synthesis.
The Nobel Prize in Physiology or Medicine 1988
"for their discoveries of important
principles for drug treatment"


Sir James W. Black Gertrude B. Elion
George H. Hitchings
Biochemistry: contributes greatly to human health
Three examples of metabolic analogs designed by
biochemists and used as important drugs.
Leukemia
AIDS
Asthma
Many drugs were designed as a
result of our biochemical
understanding of living organisms
A consequence of accumulated knowledge
in central areas of biochemistry---protein
structure and function, nucleic acid
synthesis, enzyme mechanism, receptors
and metabolic control, vitamins, and
coenzymes, and comparative biochemistry.
Biochemistry: from the human Genome Project
to the Protein Research Plan
History of
Biochemistry

Some major events in the
history of Biochemistry
1828
Wohler synthesized urea from
ammonium cyanate in the lab.
1897
Buchner demonstrated fermentation with
cell extracts. In vitro (in glass) study began.
1926
Sumner crystallized urease.
1944
Avery, MacLeod, and McCarty showed DNA
to be the agent of genetic transformation.
1953
Watson and Crick proposed
the double helix for DNA
1959
Perutz determined 3-D structure of hemoglobin.
1966
Genetic codes unveiled.
1937
Krebs elucidated the
citric acid cycle.
Being dynamic for only about
100 years.
NH
4
CNO CO(NH
2
)
2
Inorganic organic
sugar ethanol

Ending vitalism,
beginning physics
and chemistry.

1869
Miescher isolated
nucleic acids.
1925
The glyclolytic
pathway revealed
The major types of
biomolecules were revealed
The major types of biomolecules found in ALL
types of living organism: proteins, carbohydrates,
lipids and nucleic acids.
Proteins, carbohydrates, and lipids were all
discovered before the 19
th
century.
Nucleic acids were the last of these to be
isolated, in 1868, by Johann Friedrich Miescher,
a Swiss, twenty-four years old.

Biochemistry is
interdisciplinary
Biochemistry: a modern science of
interdisciplinary nature

Efforts of chemists and physicists in
understanding the mystery of life;
Application of investigation tools and theories of
physics and chemistry in life Sciences.
Biochemistry: Draws its major
themes from many other fields
Organic chemistry, which describes the properties of
biomolecules.
Biophysics, which applies the techniques of physics to
study the structures of biomolecules.
Medical research, which increasingly seeks to
understand disease states in molecular terms.
Nutrition, which has illuminated metabolism by
describing the dietary requirements for maintenance of
health.
Biochemistry draws its major
themes from other fields (Cont)
Microbiology, which has shown that single-celled
organisms and viruses are ideally suited for the
elucidation of many metabolic pathways and regulatory
mechanisms.
Physiology, which investigates life processes at the
tissue and organism levels.
Cell biology, which describes the biochemical division
of labor within a cell.
Genetics, which describes mechanisms that give a
particular cell or organism its biochemical identity.
Nobel prizes for
Biochemical
studies
1901-2006
A remarkable number of
Nobel prizes have been won by
biochemists
Two categories: Physiology or Medicine;
Chemistry.
See website: nobelprize.org.


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.
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.


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).
Books on the history of Biochemistry:


1.
20051
Fruton, J. S. (1999). Proteins, Enzymes, Genes: The
I nterplay of Chemistry and Biology. New Heaven
and London: Yale University Press.
electronic version of this book is available in the
library of Peking University).

2.
20022

2002

356 pages
701 pages, with over
7000 references cited!
The Foundations of
Biochemistry
(Chapters 1-2)

To be lectured by
Professor Zengyi Chang
(
March 3, 2006
Living organisms are
classified into various
types
Inhabit extreme
environments
Common
progenitor
Organisms can be classified into
three domains based on genetic
relationships
Organisms can also be classified based on their
biochemical differences (energy and carbon sources)
Energy
sources
Carbon sources
Major features of
living organisms
Living organisms differ from
inanimate objects in certain aspects
Being chemically complex and highly organized.
Extract, transform and use energy (matter) from
their environment (metabolism, being never at
equilibrium with their environment ).
Be capable of precise self-reproduction and self-
assembly (heredity and self-perpetuation).
Being able to sense and respond to alterations in
their surroundings.
Being formed by evolution.

Life depends on creating & duplicating order in a chaotic environment.
Cell is the structural and functional unit of living organisms
made up of thousands of different types of molecules in highly
organized self-assembled structures.
The whole is greater than the sum of the parts!
Fig. 3-26
Universal
features of
a living cell.
Cellular Foundations:
Structure of
prokaryotic
and eukaryotic
Cells
Cells
.
Biomolecules and biochemical reactions are
meaningful only when viewed in the context
of biological structure!

Escherichia coli
(E. coli) is
the best-studied
prokaryote.
Cytoplasm
Contains many metabolic
enzymes and metabolites.
An E. coli cell
in dividing
The cytoplasm (shown being E. coli) is crowded with
all types of biomolecules or biomolecular complexes,
thus gel-like.

An animal cell
A plant cell
The cytoplasm of an
eukaryotic cell is crowded,
highly ordered and dynamic
There exists a cytoskeleton system in eukaryotic cells

compartmentalization
Prokaryotes are more efficient than eukaryotes in many aspects
Both are well adapted to their respective lifestyles!!!
Subcellular particles of various sizes or
density are usually separated into fractions
via centrifugations.
Biomolecules are then further purified for
biochemical studies usually via
chromatography and electrophoresis.
Extreme care needs to be taken when extending
in vitro results to in vivo situations, where
the biomolecules are highly organized.
Viruses
Viruses are supramolecular complexes of mainly
nucleic acids and proteins that can replicate
themselves only in appropriate host cells,
Viruses have played important roles in understanding
the biochemistry (molecular biology) of life processes.
Life molecules are
made of six principle
elements : C, H, N, O,
P, and S.
(revealed by around the end of
the first half of 19
th
century)
Chemical Foundations:
The biologically most
abundant elements
are mostly only minor
constituents of the
earths crust (which
contains 47% O,
28% Si, 7.9% Al,
4.5% Fe, and 3.5% Ca).

Elements found in living organisms
The first tier elements
are all able to form
covalent bonds!
Most of the elements in living matter have relatively low atomic
numbers; H, O, N and C are the lightest elements capable of forming
one, two, three and four bonds, respectively.
The lightest elements form the
strongest covalent bonds in general.
Fig. 3-1
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 O
P
H
N
S
Multiple functional groups are usually
found in one biomolecule.
Structure of Acetyl-coenzyme A
(Acetyl-CoA)
Carbon
compounds are
three
dimensional!
The four single bonds around
a carbon have a characteristic
tetrahedral arrangement.
Carbon-carbon single
bonds are free to rotate.
The two double-bonded
carbons and atoms attached
to them all lie in the same
rigid (non-rotatable) plane.
Life is thus
three-dimensional!
A carbon-based biomolecule may
have stereoisomers of different
configuration or conformation
Two compounds having the same formula can
have different spatial arrangements in
covalent bond linkages, i.e., having different
configurations ()---fixed spatial
arrangements of atoms.
A biomolecule can have counterless or limited
three dimensional structures, i.e., having different
conformations , due to the rotating
feature of C-C bonds (with the same covalent
linkages).
Configuration may result from
the presence of a C=C bond
Much input of energy
is needed for their
interconversion (via
breakage/formation
of covalent bonds.
(
Each is a well-defined
compound with unique
chemical properties
and distinct biological
roles.
They are
geometric isomers
(i.e., 2-dimensional)
An asymmetric (chiral) carbon, linking to four different
substituents, can have two configurations, producing
a pair of stereoisomers called enantiomers ().
The two are enantiomers The two are the same

Configuration may also result from the
presence of asymmetric carbons.
Enantiomers, discovered by
Louis Pateur in 1848,
demonstrate almost identical
chemical properties, but rotate
the plane of plane-polarized
light in opposite directions with
the same degree of rotation;
racemic mixtures show no such
optical activity.
For a pair of optically active
enantiomers, each will rotate
the plane of polarized light in
equal and opposite directions.
A molecule having n asymmetric
carbons may have 2
n
stereoisomers
Fig. 3-10
A biomacromolecule usually exhibit a
limited number of stable conformations
among the many possible ones
The function of a biomolecule
usually depends on its specific
tree-dimensional structure, a
combination of its
configuration and conformation.
Carbon-based
biomolecules vary in sizes:
from small ones to
biomacromolecules
(biopolymers)
Supplying molecules for a multitude of biological functions;
Modular construction of the biomacromolecules;
One single DNA molecule
of 4.64 million nucleotide
Pairs (the E. coli genome)
A sultisubunit protein molecule
(pyruvate dehydrogenase complex)
Carbohydrates, proteins and nucleic acids
can be biomacromolecules.
DNA and protein molecules are visible via electron miscroscopy
Biomolecules
interact
Biomolecules interact
covalently and noncovalently
Biomolecules are transformed into new molecules via
covalent interaction (i.e., chemical reaction), in which
old bonds are broken and new ones formed
(metabolism).
A covalent bond is formed by the sharing of a pair of
electrons between adjacent atoms.
Biomolecules also specifically interact reversibly via
noncovalent interaction, including electrostatic
interaction, hydrogen bonds, and van der Waals
interaction (molecular recognition).
The thousands of enzyme-catalyzed chemical reactions occurring
in a living organism are collectively called metabolism.
Interactions between biomolecules
are usually stereospecific
For biomolecules having an asymmetric carbon,
usually only one of the two enantiomers will be
produced and used by the cell, as a result of the
asymmetry of the enzymes catalyzing such
transformations.
The human taste receptors distinguish these
two stereoisomers as sweet and bitter!
Biochemistry
is precise!
Five general types of
chemical
transformations occur in
living organisms
You should have studied them all
in taking Organic Chemistry!
Oxidation-reduction: reactions
involve electron transfers.
Oxidation of biomolecules often occurs as
dehydrogenation (), electron acceptors are
needed for such reactions to occur.
Carbons in biomolecules exist
in five oxidation states.
Oxidation
Nucleophilic substitution reactions involve
the attack of an electron-rich nucleophile
towards an electron-poor center.
Nucleophile
Leaving group
ATP
Isomerization reactions involve electron
transfers within the same molecule.
Here, electrons are transferred
from carbon 2 to carbon 1.
Group transfer reactions are common
for activating metabolic intermediates
These are actually nucleophilic
substitution reactions.
(Leaving group: ADP)
(Nucleophile)
Condensation reactions join
two molecules into one
Nucleophilic
substitution
again!
Energy for life
Energy is extracted, channeled,
and consumed very effectively
in living organisms!
Physical Foundations:
Cells are
consummate
transducers
of
energy!

The flow of
electrons (i.e.,
oxidation-
reduction
reactions)
provides
energy for
organisms.
The common form of energy
for life is free energy (G)
Biological processes usually take place at
constant temperature and pressure, thus only
free energy is available to do work.
The flow of electrons in oxidation-reduction
reactions underlies energy transduction in
living cells.
Living organisms extract energy from either
fuels or sunlight.
Life obeys the laws of thermodynamics.

Interaction between
biomolecules are
usually understood in
thermodynamic and
kinetic terms.
The thermodynamics and kinetics for a
chemical reaction deal with its free energy
change and activation energy respectively.
For a chemical reaction A B, the
free energy change (G) will
determine towards which direction the
reaction will occur: it occurs towards
the direction of decreasing free
energy.
The actual rate of the reaction is
determined by the activation energy
(G

): free energy difference between

the transition state and the ground
state of the reactants.
Direction of
chemical reaction
Determing the rate of
chemical reaction
Enzymes will only speed up (catalyze) reactions (10
10

to 10
14
fold) that are thermodynamically favorable!
Actual free energy change vs
standard free energy change;
Reversible vs irreversible reactions.
Noncovalent
interactions
Noncovalent interactions between
biomolecules are essential to life
Such individually weak, accumulatively
large interactions play essential roles
in many life processes.
The three types of interactions
(electrostatic interactions, hydrogen
bonding, and van der Waals interactions)
differ in geometry, strength, and
specificity, and are greatly affected in
different ways by the presence of water.

Genetic
Foundations

The information
to make
functional
proteins are
stored in
DNA and
expressed via
RNA.
Folding is Aided by Molecular Chaperones
Assembly is Aided by Molecular Chaperones
Evolutionary Foundations
Life has to be understood
in evolutionary terms
Leading to the production of mostly harmful
mutations, but occasionally beneficial ones.
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!
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 point
H
2
O: 0
o
C 100
o
C
H
2
S: -85.5
o
C -60.7
o
C
Each water can
Form H-bond
with 4 other
water molecules.
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.
Amphipathic molecules
tend to spontaneously
rearrange themselves in
water.
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 O
2
) is
fundamental to photosynthesis.
Organic biomolecules are believed to be
produced abiotically early on the earth
All biological molecules (proteins,
nucleic acids, carbohydrates and lipids)
in all organisms are made from the same
set of subunits (amino acids,
nucleotides, monosaccharides, and fatty
acids).
Such subunits have been successfully
produced in the laboratory by simulating
the conditions of the early times of the
earth.
Biomolecues first arose by
chemical evolution before
subject to biological
evolution:
Building blocks of
biomacromolecules need to
be formed during prebiotic
evolution.
A typical animal or plant cell contains
approximately 100,000 kinds of biomolecules!
Proteins and polysaccharides from
all sources are made of simple
building blocks.
Building blocks of
nucleic acids and
lipids
A simulating
experiment
for the abiotic
production of
biomolecules:
Simulated what might
happened in a billion
years in one week.
Devoid of oxygen!
Hypothesized by
Aleksandr I. Oparin
in 1922.
Tested by
Stanley Miller
in 1953.
(but not thymine)
The RNA World
hypothesis of
evolution.
Evolution:
The eons of time
made the improbable
inevitable!
Self replicating RNA
Protein
DNA
Polymerization
(condensation)
Replication via
complementarity
Lipids membrane
cell
Which came first, DNA
or Protein?
Answer: Neither!
I t is RNA!
Peptides
Some scientific journals and
organizations in the field of Biochemistry



International Union of
Biochemistry and Molecular Biology
Chinese Society of Biochemistry
and Molecular Biology
(Dr. Zengyi Chang is an Executive
Council Member)
Dr. Zengyi Chang is an
Editorial Advisory Board Member
Dr. Zengyi Chang is an
Associate Editor-in-Chief
Instructors for
Biochemistry I








Zengyi Chang (), Ph.D., Prof.
Director of Biochemitry I and II;
[email protected]


Xiaodong Su (), Ph.D., Prof.
[email protected]
Daochun Kong (),Ph.D., Prof.
[email protected]
Dr. Yongmei Qin (), Assoc. Prof.
[email protected]
Teaching Assistants:
:[email protected];
[email protected]
[email protected]

Date

Chapter

Lecturer

Mar. 3

Chapter 1-2 Foundations of Biochemistry, water

Dr. Chang

Mar. 10


Chapter 3. Amino acids, peptides and proteins

Dr. Su

Mar. 17


Chapter 3 Amino acids, peptides and proteins

Dr. Su

Mar. 24


Chapter 4 The three-dimensional structures of protein

Dr. Su

Mar. 31

Chapter 4 The three-dimensional structures of protein

Dr. Su

Apr. 7


Chapter 5 Protein Function

Dr. Chang

Apr. 14

Chapter 5 Protein Function
Dr. Chang

Apr. 21

Chapter 6 Enzymes

Dr. Chang

Apr. 28

Chapter 6 Enzymes
Chapter 8 Nucleotides and nucleic acids

Dr. Chang

May 12



Dr. Kong

May 19

Chapter 9 DNA-based information technoloogies

Dr. Kong
May 26

Chapter 7 Carbohydrates and Glycobiology Dr. Qin

June 2 Chapter 10 Lipid

Dr. Qin

Jun. 9

Chapter 11 Biological membranes and tansport

Dr. Qin

Jun. 16

Chapter 12 Biosignaling


Dr. Qin

Teaching arrangements for Biochemistry I
(Drs. Zengyi Chang, Xiaodong Su, Daochun Kong, and Yongmei Qin)
Saturdays, 8:00 - 11:00pm; 112
Date Chapter Lecturer
Over view of metabolism and Chapter 14: Principles of Bioenergetics Dr. Zengyi Chang
Chapter 15 Glycolysis & Catabolism of Hexoses Dr. Zengyi Chang
Chapter 16 The Citric Acid Cycle Dr. Zengyi Chang
Chapter 17 Oxidation of Fatty Acids Dr. Yongmei Qin
Chapter 18 Amino Acid Oxidation & Production of Urea Dr. Yongmei Qin
Chapter 18 Amino Acid Oxidation & Production of Urea Dr. Yongmei Qin
Chapter 20 Carbohydrate Biosynthesis Dr. Yongmei Qin
Chapter 20 Carbohydrate Biosynthesis Dr. Yongmei Qin
Chapter 21 Lipid biosynthesis Dr. Yongmei Qin
Chapter 21 Lipid biosynthesis Dr. Yongmei Qin
Chapter 19 Oxidative phosphorylation and photophosphorylation Dr. Zengyi Chang
Chapter 19 Oxidative phosphorylation and photophosphorylation Dr. Zengyi Chang
Chapter 22 Biosynthesis of amino acids, nucleotides and related molecules Dr. Zengyi Chang
Chapter 22 Biosynthesis of amino acids, nucleotides and related molecules Dr. Zengyi Chang
Chapter 23 Integration and hormonal regulation of mammalian metabolism Dr. Zengyi Chang
Textbook and reference books
Nelson, D. L., and Cox, M. M. (2005)
Lehninger Principles of Biochemistry, fourth
edition, Worth Publishers.
Berg, J. M., Tymoczko, J. L., and Stryer, L.
(2002) Biochemistry, Fifth edition, W. H.
Freeman and Company, New York.
Mathews, C. K., van Holde, K. E., and Ahern, K.
G. (2000) Biochemistry, third edition,
Benjamin/Cummings (www.aw-
bc.com/mathews/).

Grading policy for Biochemistry I
Tests (about one for each chapter) will
contribute 20% to the final grade.
Final exam will contribute 80% to the final
grade.

(Each student will be required to find, read
and orally present a research paper in
Biochemistry II)
Class discipline
Class attendance is required
(reflected in the test scores).
Academic misbehavior of any kind
(cheating on exams, uninvited talk
during lecture, etc.) will absolutely
not be tolerated!
Enjoy the molecular
trip of life!
Please study with a
historical perspective,
an interdisciplinary
spirit, and a
questioning mind.