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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.

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  1. 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 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

  2. Chapter 3 pp 75-115 Amino Acids, Peptides and Proteins 氨基酸、肽及蛋白质 Nelson, D. L., and Cox, M. M. (2005) Lehninger Principles of Biochemistry, 4th edition.

  3. Biochemistryasks 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 lawsthat 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.

  4. Principles of Bioenergetics/Biochemistry • The total energy of the universe is constant (能量守恒定律); • The total entropy(熵) is continually increasing(熵增加原理). • —Rudolf Clausius, The Mechanical Theory of Heat with Its Applications to the Steam-Engine and to the Physical Properties of Bodies,1865 (trans.1867)

  5. ATP

  6. From Petras P. Dzeja and Andre TerzicThe Journal of Experimental Biology206, 2039-2047 (2003)

  7. DG = DH - TDS

  8. Erwin Schrödinger (1887 – 1961) The Nobel Prize in Physics 1933 "for the discovery of new Productive forms of atomic theory"

  9. What is protein? Components of organisms: Enzymes (metabolism) Transport (O2, membrane …) Movements (muscles) Antibodies (immunity ) Brain … … Protections (horns, skins…)

  10. Where does the name PROTEIN come from? Berzelius coined (命名了) the words isomerism, allotropy, andprotein. 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 ofelements.

  11. Year 1944 Proteins were thought to carry genetic information 1897 Miescher discovered DNA Interweaving of the historical traditions of biochemistry, cell biology, and genetics. 1828

  12. 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

  13. The Nobel Prize in Physiology or Medicine 1962 "for their discoveries concerning the molecular structure of nucleic acids and its significance forinformationtransfer in living material" Francis H. C. Crick James D. Watson Maurice H. F. Wilkins

  14. The central dogma 中心法则 Flow of information in gene expression

  15. Everyday homework for biologists – Evolution!

  16. Current phylogeny tree of life (by Carl Woese)

  17. Metabolism 新成代谢 分解代谢 合成代谢

  18. Metabolism Pathways or Networks

  19. Amino Acids Proteins can be reduced to their constituent amino acids by a variety of methods.

  20. Common Structural Features a carboxyl group(羧基) an amino group(氨基) side chains, or R groups

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

  22. enantiomers or stereoisomers (立体异构) • D, L system

  23. 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

  24. 3.1.3 Nonstandard amino acids γ-羟基谷氨酸 4-羟(基)脯氨酸 5-羟(基)赖氨酸 链霉素 6-N-甲基赖氨酸 硒代半胱氨酸

  25. About 300 kinds of a. a. not occurring in proteins 鸟氨酸 瓜氨酸

  26. H Se H H Cb Ca Selenocysteine - the 21st amino acid 硒代半胱氨酸 • The occurrence of Selenocysteine (Sec) was first demonstrated for protein A of glycine reductaseCone et al. 1976 • Sec is used in the active site of some redox enzymes: • formate dehydrogenase • glutathione peroxidase • iodothyronine 5'-deiodinase • The only genetically coded non-standard amino acid Sec

  27. SelC Seryl tRNA synthetase Selenide SelD ATP SelA Selenomono- phosphate H H I l O-C-C-CH2-Se- O-C-C-CH2-OH I NH2 I NH2 SelB GTP Selenoprotein mRNA UGA Selenocysteine Prokaryotic selenocysteine incorporation • 4 genes are essential: • SelAselenocysteine synthase • SelB elongation factor SelB • SelC tRNASec • SelDseleno- phosphate • synthase

  28. 22nd AMINO ACID IDENTIFIED in 2002 Methanogen uses stop codonto genetically encode l-pyrrolysine [Science, 296, 1459 and 1462 (2002)].

  29. Amino Acids ---Acids and Bases Zwitterion(两性离子) 两性离子形式 非离子形式 Nonionic and zwitterionic forms of amino acids

  30. Characteristic titration curves of amino acids

  31. Effect of the chemical environment on pKa

  32. Titration curve for glutamate

  33. Titration curve for histidine

  34. Peptides and proteins Peptide bond formation by CONDENSATION 缩水反应

  35. The structure of a pentapeptide(五肽)

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