Biochemistry Chapter 1 and 2

8/11/2019 Biochemistry Chapter 1 and 2

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The aim of study:

To be able to readwhat is not written

and to hear what is

not said!-----Zengyi hang

http://www.bio.pku.edu.cn/lab/proteinsci/



Biochemistry (I & II)Foundations and overview

Professor Zengyi Chang

( 昌增益教授[email protected]

Room 204, New Life Science Building6275-8822

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 thediverse forms of life in chemical terms.

It brought the occurrence of the molecular

revolution of biology in the 20th century and hasthus become the common language of biologicalsciences.

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 ofliving matter?

How do the interactions of these components give rise toorganized 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 itselfaccurately?

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 thatoccur in living organism, concerning catabolism &anabolism of building blocks, as well asmanagement of cellular Energy;

Storage, transmission, and expression ofgenetic information: DNA replication and proteinsynthesis.



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: contr ibutes 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---proteinstructure and function, nucleic acid

synthesis, enzyme mechanism, receptors

and metabolic control, vitamins, and

coenzymes, and comparative biochemistry.



Biochemistry: f rom the human Genome Project

to the Protein Research Plan



History of

Biochemistry

S j i h



Some major events in the

history of Biochemistry

1828 Wohler synthesized urea fromammonium cyanate in the lab.

1897Buchner demonstrated fermentation with

cell extracts. In vitro (“in glass”) study began.

1926Sumner crystallized urease.

1944 Avery, MacLeod, and McCarty showed DNA

to be the agent of genetic transformation.

1953Watson and Crick proposed

the double helix for DNA

1959Perutz determined 3-D structure of hemoglobin.

1966Genetic codes unveiled.

1937Krebs elucidated the

citric acid cycle.

Being dynamic for only about100 years.

NH4CNO→ CO(NH2)2

Inorganic → organic

sugar → ethanol

Ending vitalism,beginning physics

and chemistry.

1869Miescher isolated

nucleic acids.

1925The glyclolytic

pathway revealed

http://scienceworld.wolfram.com/biography/photo-credits.html



The major types of

biomolecules were revealed

The major types of biomolecules found in ALLtypes of living organism: proteins, carbohydrates,lipids and nucleic acids.

Proteins, carbohydrates, and lipids were alldiscovered before the 19th century.

Nucleic acids were the last of these to be

isolated, in 1868, by Johann Friedrich Miescher,a Swiss, twenty-four years old.



Biochemistry isinterdisciplinary



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 tostudy the structures of biomolecules.

Medical research, which increasingly seeks tounderstand disease states in molecular terms.

Nutrition, which has illuminated metabolism bydescribing the dietary requirements for maintenance ofhealth.



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 regulatorymechanisms.

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 forBiochemical

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 onproteins, 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 FrederickHopkins: growth-stimulating vitamins.

1930, Hans Fischer: haemin and chlorophyll.

1931, Otto Warburg: nature and mode of action of the

respiratory enzyme.





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.





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.





matter (4) 1962, Max F. Perutz and John C. Kendrew: structures

of globular proteins.

1964, Dorothy Crowfoot Hodgkin: structures ofimportant 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.





matter (5) 1972, Christian Anfinsen: amino acid sequence and the

biologically active conformation; Stanford Moore andWilliam H. Stein: catalytic activity of the active centre of theribonuclease.

1975, John Corforth: stereochemistry of enzyme-catalyzedreactions.

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.

N b l P i i li th





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 ofRNA.

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.





matter (7)

2003, Peter Agre, Roderick MacKinnon: channels in

cell membranes.

2004, Richard Axel, Linda B. Buck: odorant

receptors.




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 anteriorpituitary lobe in the metabolism of sugar.

1953, Hans Krebs: citric acid cycle; Fritz Lipmann: role of co-

enzyme A in metabolism.




Metabolism of living matter (2) 1961, Melvin Calvin: carbon dioxide assimilation in plants.

1964, Konrad Bloch, Feodor Lynen: cholesterol and fattyacid metabolism.

1978, Peter Mitchell: chemiosmotic theory of biologicalenergy transfer.

1985. Michael S. Brown, Joseph L. Goldstein: regulation ofcholesterol 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.




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.




information pathway (1) 1962, Francis Crick, James Watson, Maurice Wilkins: molecular

structure of nucleic acids.

1958,George Beadle, Edward Tatum: genes act by regulatingdefinite chemical events;Joshua Lederberg: genetic

recombination and the organization of the genetic material ofbacteria.

1959, Severo Ochoa, Arthur Kornberg: biological synthesis ofribonucleic 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 inprotein synthesis.




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 ofthe 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: partitionchromatography.

1980, Paul Berg: recombinant-DNA; Walter Gilbert,Frederick Sanger: nucleic acid sequencing.

1984, Bruce Merrifield: chemical synthesis of polypeptidesand 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 biologicalmacromolecules).

B k th hi t f Bi h i t



Books on the history of Biochemistry:

1.昌增益（译者）《蛋白质酶和基因化学与生物

学的交互作用

》，清华大学出版社，2005年1月。 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.昌增益（译者）《二十世纪生物学的分子革命分

子生物学所走过的路

》，科学出版社，2002年2

月。



2002

年

科学出版社

356 pages



701 pages, with over

7000 references cited!

March 3 2006

http://www.amazon.com/gp/product/images/0300076088/ref=dp_image_0/102-7721229-3341762?%5Fencoding=UTF8&n=283155&s=books



The Foundations ofBiochemistry

(Chapters 1-2 )

To be lectured by Professor Zengyi Chang( 昌增益教授

March 3, 2006



Living organisms are

classified into varioustypes

Organisms can be classified into



Inhabit extreme

environments

Common

progenitor

g

three domains based on genetic

relationships

Organisms can also be classified based on their



Organisms can also be classified based on their

biochemical differences (energy and carbon sources)

Energy

sources

Carbon sources



Major features ofliving organisms

Li i i diff f



Living organisms differ from

inanimate objects in certain aspects

Being chemically complex and highly organized.

Extract, transform and use energy (matter) fromtheir 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 intheir surroundings.

Being formed by evolution.

L ife 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

Cellular Foundations:



Universal

features ofa living cell.

Cellular Foundations:



Bi l l d bi h i l ti



Cells are the basic

structural and functional

life units where biomolecules

are produced (and degraded)

and function, with thousands

of biochemical reactions

occur in regulated ways.

Biomolecules and biochemical reactions are

meaningful only when viewed in the context

of biological structure!



Prokaryotic (“before

nucleus” ) cells lack an

internal membrane system

(i.e., having no

organelles).

An

E. coli

cell



Escherichia col

(E. coli) is

the best-studied

prokaryote.

CytoplasmContains many metabolic

enzymes and metabolites.

in dividing



The cytoplasm (shown being E. coli) is crowded wi

all types of biomolecules or biomolecular complex

thus el-like.



Eukaryotic cells have

evolved a complicated

internal membrane system,

thus forming all kinds of

organelles including a

nucleus.

An animal cell



A plant cellThe cytoplasm of an

eukaryotic cell is crowded,

highly ordered and dynamic

There exists a cytoskeleton system in eukaryotic cells



y y y

Prokaryotes are more efficient than eukaryotes in many a



compartmentalization

Both are well adapted to their respective lifestyles



Cellular components are

first isolated for

biochemical studies

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 extendingin vitro

results toin vivo

situations, where

the biomolecules are highly organized.



Viruses



are supramolecular complexes of mainl

ucleic acids and proteins that can replicate

themselves only in appropriate host cells,

Viruses have played important roles in understandi

the biochemistry (molecular biology) of life proce

Chemical Foundations:



Life molecules are

made of six principle

elements : C, H, N, O,P, and S.

(revealed by around the end of

the f irst half of 19

th

century)

Chemical Foundations:



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



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 linearchains, 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 likeproteins, nucleic acids, carbohydrates, lipids and

etc.).

V tilit f



Versatility of

carbon bonding:

Carbon is able to

form covalent

bonds with

H, O, N and itself.

An enormous

diversity of l i fe

molecules canthus be made.

Functional groups

f d i bi l lOH



found in biomoleculesO

P

H

N

S





Carbon

compounds are

three

dimensional!

The four single bonds around

a carbon have a characteristic



a carbon have a characteristic

tetrahedral arrangement.

Carbon-carbon single

bonds are free to rotate.

The two double-bonded

carbons and atoms attachedto them all lie in the same

rigid (non-rotatable) plane.

Life is thus

three-dimensional

A carbon-based biomolecule may



b b b yhave stereoisomers of different

configuration or conformation Two compounds having the same formula can

have different spatial arrangements in

covalent bond linkages, i.e., having differentconfigurations (构型

)--- fixed spatialarrangements of atoms.

A biomolecule can have counterless or limited

three dimensional structures, i.e., having differentconformations

（构象）, due to the rotatingfeature of C-C bonds (with the same covalentlinkages).

Configuration may result from



g ythe presence of a C=C bond

Much input of energyis needed for their

interconversion (via

breakage/formation

of covalent bonds.

(

顺丁烯二酸，马来酸）

（反丁烯二酸，富马酸）

Each is a well-defined

compound with unique

chemical properties

and distinct biological

roles.They are

geometric isomers

(i.e., 2-dimensional )

The two are enantiomers The two are the same



An asymmetr ic (chi ral) carbon, linking to four dif ferent

substituents , can have two conf igurations, producing

a pair of stereoisomers called enantiomers ( 对映

).

Configuration may also result from thepresence of asymmetric carbons.

Enantiomers discovered by



Enantiomers, discovered by

Louis Pateur in 1848,

demonstrate almost identical

chemical properties, but rotate

the plane of plane-polarizedlight in opposite directions with

the same degree of rotation;

racemic mixtures show no such

optical activity.

For a pair of optically active



p p y

enantiomers, each will rotate

the plane of polarized light inequal and opposite directions.

A molecule having n asymmetric



A molecule having n asymmetric

carbons may have 2n stereoisomers

Fig. 3-10

A biomacromolecule usually exhibit a



limited number of stable conformations

among the many possible ones



The function of a biomoleculeusually depends on its specific

tree-dimensional structure, acombination of its

configuration and conformation.

C b b d



Carbon-based

biomolecules vary in sizes:from small ones to

biomacromolecules(biopolymers )

Supplying molecules for a multi tude of biological functions;

Modular construction of the biomacromolecules;

DNA and protein molecules are visible via electron miscroscopy



One single DNA molecule

of 4.64 mill ion nucleotide

Pairs (the E. coli genome)

A sultisubunit protein molecule(pyruvate dehydrogenase complex)

Carbohydrates, proteins and nucleic acids

can be biomacromolecules.





Biomolecules

interact

Biomolecules interact



Biomolecules interactcovalently 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 occur r ing

in a living organism are collectively called metabolism .

I t ti b t bi l l



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 theasymmetry 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 inliving organisms

You should have studied them all

in taking Organic Chemistry

Oxidation-reduction:

reactions



involve electron transfers.

Oxidation of biomolecules often occurs as

dehydrogenation ( 脱氢作用 ), 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 transferredfrom carbon 2 to carbon 1.

Group transfer reactions are commonf ti ti t b li i t di t



for activating metabolic intermediates

These are actually nucleophilic

substitution reactions.

(

Leaving group: ADP)

(Nucleophile)

Condensation reactions join



two molecules into one

Nucleophilicsubstitution

again!



e s areconsummate



transducers

ofenergy!

The flow of

electrons (i.e.,oxidation-

reduction

reactions)provides

energy for

organisms.





Interaction between

biomolecules are

usually understood inthermodynamic and

kinetic terms.

The thermodynamics and kinetics for ah i l ti d l ith it f



chemical reaction deal with its free energy

change and activation energy respectively.

For a chemical reaction A B, thefree energy change ( G) will

determine towards which direction the

reaction will occur: it occurs towardsthe direction of decreasing freeenergy.

The actual rate of the reaction isdetermined by the activation energy

(

G

‡ ): free energy difference between

the transition state and the round

Enzymes will only speed up (catalyze) reactio



Direction of

chemical reaction

Determing the rate o

chemical reaction

to 10

14

fold) that are thermodynamically favor

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, accumulativelylarge interactions play essential rolesin many life processes.

The three types of interactions(electrostatic interactions, hydrogenbonding, and van der Waals interactions)

differ in geometry, strength, andspecificity, and are greatly affected indifferent ways by the presence of water.

Genetic

F d ti



Foundations

The informationto make

functional

proteins arestored in

DNA and

expressed viaRNA.

Folding is Aided by Molecular Chaperones

Assembly is Aided by Molecular Chaperones

Evolutionary FoundationsLife 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



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 andtogether by water — hydrophobic interactions

(driving proteins to fold and lipid bilayersife undoubtedly could not have arisen in the absence of

Each water can

Form H-bond

with 4 other



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 O: 0

o

C 100

o

C

water molecules.

Amphipathic moleculestend to spontaneously

h l i



Hydrophobic interaction is

a passive interaction

between hydrophobic

molecules due to the

hydrogen bonding between

water molecules.

Important for theformation of

biomembranes (made of

amphipathic phospholipids )

and the folding of proteins

rearrange themselves in water.

Water is central to biochemistry



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 sameset of subunits (amino acids,nucleotides, monosaccharides, and fattyacids).

Such subunits have been successfullyproduced in the laboratory by simulatingthe conditions of the early times of theearth.

Biomolecues first arose by



Biomolecues first arose by

chemical evolution beforesubject to biological

evolution:

Building blocks of

biomacromolecules need to

be formed during prebioticevolution.



A typical animal or plant cell contains

approximately 100,000 kinds of biomolecules



roteins and polysaccharides from

all sources are made of simple

building blocks.



Building blocks of

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.

http://www.evrimcilerinitiraflari.com/res/OPARIN.jpg



(but not thymine)

Polymerization(condensation)

Which came first, DNAor Protein?



The “RNA World”

hypothesis of

evolution.

Evolution:

The eons of time

made the improbable

inevitable

Self replicating RNA

Protein

DNA

( )

Replication viacomplementarity

Lipids

membrane

cell

Answer: Neither!

I t is RNA!

Peptides

Some scientific journals and

i ti i th fi ld f Bi h i t



organizations in the field of Biochemistry

International Union of

Biochemistry and Molecular Biology

Chinese Society of Biochemistryand Molecular Biology

(Dr. Zengyi Chang is an ExecutiveCouncil Member)

Dr. Zengyi Chang is anEditorial Advisory Board Member

Dr. Zengyi Chang is an Associate Editor-in-Chief

Instructors for

Biochemistry I

http://www.proteinscience.org/current.shtml


http://pubs.acs.org/journals/bichaw/articleWindow.html


http://asbmb.org/asbmb/site.nsf/web/7F6008CA94729FC5852570500068B279?OpenDocument

http://asbmb.org/asbmb/site.nsf/web/7F6008CA94729FC5852570500068B279?OpenDocument

http://www.jbc.org/current.shtml



Biochemistry I

Zengyi Chang (昌增益), Ph.D., Prof.

Director of Biochemitry I and II;

[email protected]

Xiaodong Su (苏晓东), Ph.D., Prof.

[email protected]

Daochun Kong (孔道春),Ph.D., Prof.

[email protected]

Dr. Yongmei Qin (秦咏梅), Assoc. Prof.

[email protected]



Teach ing Ass istants :

康瑞玉:[email protected];

陈方圆

[email protected]；

雷剑[email protected]

Teaching arrangements for Biochemistry I(Drs. Zengyi Chang, Xiaodong Su, Daochun Kong, and Yongmei Qin)

Saturdays 8:00 11:00pm; 112

mailto:%E9%99%88%E6%96%B9%E5%9C%[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

Saturdays, 8:00 - 11:00pm; 112

Date Chapter Lecturer

Over view of metabolism and Chapter 14: Principles of Bioenergetics Dr. Zengyi Chang



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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



Grading policy for Biochemistry I



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Tests (about one for each chapter) willcontribute 20% to the final grade.

Final exam will contribute 80% to the finalgrade.

( 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



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trip of life!Please study with a

historical perspective, an interdisciplinary

spirit, and a

Documents

Biochemistry Chapter 1 and 2