生化-北大-曾-2

nullnullTeaching arrangements for Biochemistry I 2007 (Drs. Zengyi Chang, Xiaodong Su, Daochun Kong, Yongmei Qin) Saturdays, 8:00 - 11:00AM; 电教112 nullChapter 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.null 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. nullPrinciples 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)nullATPnullFrom Petras P. Dzeja and Andre Terzic The Journal of Experimental Biology 206, 2039-2047 (2003)nullnullDG = DH - TDSnullErwin Schrödinger (1887 – 1961)The Nobel Prize in Physics 1933 "for the discovery of new Productive forms of atomic theory" nullWhat is protein? Components of organisms: Enzymes (metabolism) Transport (O2, membrane …) Movements (muscles) Antibodies (immunity ) Brain … … Protections (horns, skins…)nullHe’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. Berzelius coined (命名了) the words isomerism, allotropy, and protein. Where does the name PROTEIN come from?nullYearInterweaving of the historical traditions of biochemistry, cell biology, and genetics. Proteins were thought to carry genetic information 182818971944Miescher discovered DNAnullnullThe Nobel Prize in Physiology or Medicine 1953 "for his discovery of the citric acid cycle"Hans Adolf Krebs (1900-1981) Sheffield University, Sheffield, United Kingdom 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. 1953nullThe 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 material" Francis H. C. Crick Maurice H. F. Wilkins James D. Watson nullThe central dogma 中心法则 Flow of information in gene expressionnullnullEveryday homework for biologists – Evolution！nullCurrent phylogeny tree of life (by Carl Woese)nullMetabolism 新成代谢合成代谢分解代谢nullMetabolism Pathways or Networksnull Amino AcidsProteins can be reduced to their constituent amino acids by a variety of methods. nullCommon Structural Features a carboxyl group(羧基) an amino group（氨基） side chains, or R groups null When the R group contains additional carbons in a chain, they are designated β,γ, δ, ε, etc., proceeding out from the a carbon.Rnullenantiomers or stereoisomers （立体异构） D, L system nullnullnullThe classifies of standard amino acidsbased on R groupFive main classes of amino acids: nonpolar and aliphatic aromatic (generally nonpolar) polar but uncharged negatively charged positively charged nullnullnullnullnullnullnullnullnullnullnull3.1.3 Nonstandard amino acids 4－羟(基)脯氨酸5－羟(基)赖氨酸硒代半胱氨酸链霉素6－N－甲基赖氨酸γ －羟基谷氨酸null鸟氨酸瓜氨酸About 300 kinds of a. a. not occurring in proteins Selenocysteine - the 21st amino acidSelenocysteine - the 21st amino acidSecThe occurrence of Selenocysteine (Sec) was first demonstrated for protein A of glycine reductase Cone 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硒代半胱氨酸Prokaryotic selenocysteine incorporationProkaryotic selenocysteine incorporation4 genes are essential: SelA selenocysteine synthase SelB elongation factor SelB SelC tRNASec SelD seleno- phosphate synthasenull22nd AMINO ACID IDENTIFIED in 2002 Methanogen uses stop codon to genetically encode l-pyrrolysine [Science, 296, 1459 and 1462 (2002)]. nullAmino Acids ---Acids and Bases Zwitterion(两性离子)Nonionic and zwitterionic forms of amino acids两性离子形式非离子形式nullCharacteristic titration curves of amino acids nullEffect of the chemical environment on pKanullTitration curve for glutamatenullTitration curve for histidinenull Peptides and proteinsPeptide bond formation by CONDENSATION 缩水反应nullThe structure of a pentapeptide(五肽)nullnullProteins And Prosthetic groups (辅基)nullLevels of structure in proteinsnullEveryday homework for biologists – Evolution！nullProtein sequences and Evolution！ Introduction to Bioinformatics: Sequence alignment; Homologs; Paralogs; orthologs; Blosum (blocks substitution matrix) ; Signature sequences; nullCurrent phylogeny tree of life (by Carl Woese) Working with proteins Working with proteinsMethods 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. 1. Proteins can be separated and purified nullJames B. Sumner Cornell Medical School Född 1887 Nobelpris 1946Lyckades mot allas förväntningar rena och kristallisera ett enzym, ureas 1926. Proteiner måste ha en välordnad struktur!nullJohn H. Northrop Columbia university Född 1891 Nobelpris 1946Isolerade och kristalliserade bl a pepsin (1929)nullnull蛋白质可以通过各种生物化学技术纯化 利用蛋白质的溶解度、净电荷、大小以及与配体结合特异性上的微小差异。有透析、凝胶过滤、离子交换层析、亲和层析、电泳（垂直板电泳、等电聚焦电泳、双向电泳）等分离纯化方法。透析Salting out and dialysis(透析)Column chromatography Column chromatography Ion-exchange chromatography Size-exclusion chromatography Affinity chromatography . . . . . . nullnullIon-exchange Chromatography 离子交换null 分离氨基酸常用的是带有耐酸性非常强的磺酸根SO3－Na＋（以盐的形式出现）的强阳离子交换树脂。首先将这种树脂填充到柱子中，然后注入含有样品的流动相，样品中含有阳离子成分X＋，通过静电吸引，与树脂中的带电基团相互作用，结果X＋与Na＋交换，即发生阳离子交换后，形成SO3－X＋。nullSize-exclusion 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. nullAffinity Chromatography 亲和层析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. 谢谢大家!