Biochemistry (I & II)


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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
  • (昌增益 教授)
  • changzy@pku.edu.cn
  • 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.
  • NH4CNO→ CO(NH2)2
  • Inorganicorganic
  • 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 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 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. 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 Interplay 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!

The Foundations of Biochemistry (Chapters 1-2)

  • To be lectured by
  • Professor Zengyi Chang
  • (昌增益 教授)
  • 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 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).

  • 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.

Eukaryotic cells have evolved a complicated internal membrane system, thus forming all kinds of organelles including a nucleus.

  • 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!!!

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 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 19th century)

  • Chemical Foundations:
  • The biologically most
  • abundant elements
  • are mostly only minor
  • constituents of the
  • earth’s 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 (构型)---fixed spatial arrangements of atoms.
  • A biomolecule can have counterless or limited three dimensional structures, i.e., having different conformations (构象), 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.
  • (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)
  • An asymmetric (chiral) carbon, linking to four different
  • substituents, can have two configurations, producing
  • a pair of stereoisomers called enantiomers (对映体).
  • 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 2n 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.

  • 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 (ΔG) 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 (ΔG‡ ): 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 (1010
  • to 1014 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 water—hydrophobic 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
  • H2O: 0 oC 100 oC
  • H2S: -85.5oC -60.7oC
  • 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 O2) 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!
  • It 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 (昌增益), Ph.D., Prof.
  • Director of Biochemitry I and II;
  • changzy@pku.edu.cn
  • Xiaodong Su (苏晓东), Ph.D., Prof.
  • su-xd@pku.edu.cn
  • Daochun Kong (孔道春),Ph.D., Prof.
  • daochun_kong@yahoo.com
  • Dr. Yongmei Qin (秦咏梅), Assoc. Prof.
  • qinym@pku.edu.cn

Teaching Assistants: 康瑞玉:raymank@126.com; 陈方圆faye@pku.edu.cn; 雷剑leijian@pku.edu.cn

  • Date
  • Chapter
  • Lecturer
  • Mar. 3
  • Chapter 1-2 Foundations of Biochemistry, water
  • Dr. Chang
  • Mar. 10
  •  
  • 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; 电教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
  • 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.



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