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					              Teaching arrangements for Biochemistry I 2007
           (Drs. Zengyi Chang, Xiaodong Su, Daochun Kong, Yongmei Qin)
                     Saturdays, 8:00 - 11:00AM; 电教112
    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. 18*             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                                       Dr. Chang
May 12           Chapter 8 Nucleotides and nucleic acids                 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
    Chapter 3 pp 75-115
    Amino Acids, Peptides
       and Proteins

Nelson, D. L., and Cox, M. M. (2005)
Lehninger Principles of Biochemistry,
             4th edition.
    Biochemistry asks how the remarkable
properties of living organisms arise from the
thousands of different lifeless biomolecules. When
these molecules are isolated and examined individually,
they conform to all the physical and chemical laws
that describe the behavior of inanimate matter—as do
all the processes occurring in living organisms.

     The study of biochemistry shows how the
collections of inanimate molecules that constitute living
organisms interact to maintain and perpetuate life
animated solely by the physical and chemical laws that
govern the nonliving universe.
             Principles of

1. The total energy of the universe is
   constant (能量守恒定律);
2. The total entropy(熵) is continually
—Rudolf Clausius, The Mechanical Theory of
 Heat with Its Applications to the Steam-Engine
 and to the Physical Properties of Bodies,1865
From Petras P. Dzeja and Andre Terzic The Journal of Experimental Biology 206,
2039-2047 (2003)
Erwin Schrödinger
(1887 – 1961)
 The Nobel Prize in
 Physics 1933
 "for the discovery of new
 Productive forms of
 atomic theory"
What is protein?
Components of organisms:
Enzymes (metabolism)
Transport (O2, membrane …)
Movements (muscles)
Antibodies (immunity )
Brain … …
Protections (horns, skins…)
Where does the name PROTEIN come from?

           Jöns JACOB Berzelius (1779-1848)
            Berzelius coined (命名了)
            the words isomerism, allotropy,
            and protein.
            He’s a Swedish chemist, a student
            of Dalton. He developed the
            concepts of the ion and ionic
            compounds. He introduced the
            classical system of chemical
            symbols in 1811, and discovered a
            number of elements.

  1944                                       Proteins were thought to
                                             carry genetic information

       Miescher discovered DNA

  1828                           Interweaving of the
                                 historical traditions
                                   of biochemistry,
                                     cell biology,
                                    and genetics.
The Nobel Prize in Physiology or Medicine
1953 "for his discovery of the citric acid cycle"
           The research I have been doing - studying how
           foodstuffs yield energy in living cells - does not lead
           to the kind of knowledge that can be expected to
           give immediate practical benefits to mankind. I
           have chosen this field of study, it was because I
           believed in its importance in spite of its theoretical
           character. My reason for this belief was that all
           living things must be continuously fed with energy
           and I am convinced that an understanding of the
           process of energy production will eventually help us
           in solving some of the practical problems of
           medicine. – Nobel Banquet Speech, Dec. 1953
            Hans Adolf Krebs (1900-1981)
            Sheffield University, Sheffield, United Kingdom
         The Nobel Prize in Physiology or
         Medicine 1962
         "for their discoveries concerning the
         molecular structure of nucleic acids and its
         significance for information transfer in living

Francis H. C.         James D.         Maurice H. F.
Crick                 Watson           Wilkins
    The central dogma 中心法则
Flow of information in gene expression
Everyday homework for biologists – Evolution!
Current phylogeny tree of life (by Carl Woese)
Metabolism 新成代谢

Metabolism Pathways or Networks
 Amino Acids

Proteins can be reduced to their
constituent amino acids by a variety
of methods.
Common Structural Features

a carboxyl group(羧基)
an amino group(氨基)

side chains, or R groups
• When the R group contains additional carbons in a
  chain, they are designated β,γ, δ, ε, etc., proceeding out
  from the a carbon.

•enantiomers or stereoisomers (立体异构)
       D, L system
The classifies of standard amino acids

    based on R group
Five main classes of amino acids:
nonpolar and aliphatic
aromatic (generally nonpolar)
polar but uncharged
negatively charged
positively charged
3.1.3 Nonstandard amino acids

                         γ -羟基谷氨酸




About 300 kinds of a. a. not occurring in proteins


Selenocysteine - the 21st amino acid
          H   •The occurrence of Selenocysteine
              (Sec) was first demonstrated for
              protein A of glycine reductase
              Cone et al. 1976

H             •Sec is used in the active site of
     Cb H
              some redox enzymes:
                 •formate dehydrogenase
    Ca           •glutathione peroxidase
                 •iodothyronine 5'-deiodinase
    Sec       •The only genetically coded non-
              standard amino acid
  Prokaryotic                        SelC

  selenocysteine                   Seryl tRNA
  incorporation                          H            Selenide
                                      l              SelD
4 genes are essential:              O-C-C-CH2-OH
                                        I            ATP
•SelA selenocysteine        SelA        NH
        synthase                         H
•SelB   elongation factor             I

              SelB          SelB        I
•SelC   tRNASec             GTP          2

•SelD   seleno-                               Selenoprotein
        phosphate                  UGA        mRNA
      Methanogen uses stop codon
   to genetically encode l-pyrrolysine
    [Science, 296, 1459 and 1462 (2002)].
Amino Acids ---Acids and Bases

                非离子形式                       两性离子形式

  Nonionic and zwitterionic forms of amino acids
Characteristic titration curves of amino acids
Effect of the chemical environment on pKa
Titration curve for glutamate
Titration curve for histidine
  Peptides and proteins
Peptide bond formation by CONDENSATION 缩水反应
The structure of a pentapeptide(五肽)
Proteins And Prosthetic groups (辅基)
Levels of structure in proteins
Everyday homework for biologists – Evolution!
Protein sequences and Evolution!

Introduction to Bioinformatics:
•Sequence alignment;
•Paralogs; orthologs;
•Blosum (blocks substitution matrix) ;
•Signature sequences;
Current phylogeny tree of life (by Carl Woese)
   Working with proteins
1. Proteins can be separated and purified
 • Methods for separating proteins take
   advantage of properties such as charge,
   size, and solubility, which vary from one
   protein to the next. Because many
   proteins bind to other biomolecules,
   proteins can also be separated on the
   basis of their binding properties.
                 James B. Sumner
                 Cornell Medical School
                 Född 1887
                 Nobelpris 1946

Lyckades mot allas förväntningar
rena och kristallisera ett enzym,
ureas 1926.

Proteiner måste ha en
välordnad struktur!
            John H. Northrop
            Columbia university
            Född 1891
            Nobelpris 1946

Isolerade och
kristalliserade bl a
pepsin (1929)

Salting out and dialysis(透析)
Column chromatography

•   Ion-exchange chromatography

•   Size-exclusion chromatography

•   Affinity chromatography

•   ......
 Chromatography 分子筛

This method separates proteins
according to size. The column
contains a cross-linked polymer
with pores of selected size.
Larger proteins migrate faster
than smaller ones, because they
are too large to enter the pores
in the beads and hence take a
more direct route through the
column. The smaller proteins
enter the pores and are slowed
by the more labyrinthian path
they take through the column.
Affinity chromatography
separates proteins by their
binding specificities. The proteins
retained on the column are those
that bind specifically to a ligand
cross-linked to the beads. (In
biochemistry, the term "ligand" is
used to refer to a group or
molecule that is bound. ) After
nonspecific proteins are washed
through the column, the bound
protein of particular interest is
eluted by a solution containing
free ligand.

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