《分子生物图谱》PPT课件.ppt

Obligatory course for biology studentsPrerequisite:General biology,Biochemistry,Molecular Biology,Prokaryotic Cell(does not have nucleus)Archaebacteria and eubacteria*Archea:Methnogens(anaerobic)Extreme halophiles(dead sea)Extreme thermophiles(hot spring,geysers)Eukaryotic Cell(contain a nucleus)Protista,fungi,animals and plants,Cells:,Cytoplasm:proteins,ribosome,metabolites and ionsPlasma membrane:phospholipid bilyer,associated proteins and carbohydratesDNAs,mtDNA,Basic Cellular Components,Prokaryotic cells,Bacteria:Gram-negative-Cell wall(3 layers:Periplasmic space;peptidoglycan;outer membrane)Gram-positive-Cell wall(thicker peptidoglycan layer)*Quite sensitive to lysozyme and penicillinCapsule and slime:The hydrophilic gel surrounding the cell wall in most bacteriaFlagella:Long,rigid protein roads,facilitating the movement of motile bacteriaFimbriae and pili:Short hair-like structure and attach other cells(essential infecting other organisms)Spores:A small,often unicelluar,reproductive unit of plants,algae,fungi,protoza,and bacteria,Organization of Eukaryotic Cells,Endoplasmic reticulum,Biomembrane,Nucleus,Nuclear envelope NucleolusNucleoplasm,Chromosome and karyotypeLong arm:q(for queue)Short arm:p(for petit)Gimsa(Quinacrine)Dark band:G band or G+band(AT rich)Light band:R band or G band(GC rich),Organelles in the Cytoplasm,(The membrane-bound structure in a cell)MitochondriaChloroplastsEndoplasmic reticulumGolgi apparatusPeroxisomesLysosomesVacuolesGlyoxisomes,Mitochondria,Size:1.5-2.0 in length,0.5-1.0 um in diameterApprox the same as E.coliMaternal inheritanceMany copies:occupying of the cytoplasmic volumeRole:produce ATPEncode:proteins and RNAs,mtDNA,Chloroplasts,Thylakoloids 类囊体Chlorophylls:located on the Thylakoloid membrane to absorb light for photosynthesis,Light 2H2O-O2+4H+4e-H+ADP 3-+Pi 2-ATP 4-+H2O,Endoplasmic reticulum,Rough ER:process newly synthesized peptides from ribosomeSmooth ER:involved in the synthesis and metabolism of lipids,Golgi apparatus,Major site for sorting and modifications of proteins and lipidsrough ER-transport vesicles-Golgi-Glycoproteins,Peroxisomes,Peroxisome:contain enzymes for degrading amino acids and fatty aidsCatalase2H202-2H20+02,Lysosomes,Lysosomes:1)nuclease for degrading DNA and RNA 2)Protease for degrading proteins and other enzymes for degrading polysacchrides and lipids 3)lysosomes exist only in animal cells(plant-vacuoles for degrading macromolecules),Glyoxisomes 乙醛酸循环体,Found mainly in plant seedsFatty acids-Acetyl CoAMicrobodies:Peroxisomes+Glyoxisomes,Viruses,Baltimore ClassificationStructureLife Cycles,The life cycle of Viruses,1)Attachment:viral surface protein-host cell receptor e.g:HIV GP120-CD4&Chemokine receptor(T cell)Penetration:endocytosisUncoating:viral capsid degraded by viral enzyme or host enzymeReplication:assembly viral proteins and DNA or RNAsRelease:escape from host cell by causing cell rupture(lysis),Bacteriophages,Bacteriophages are viruses infect bacteriadsDNA phages with contractile tails,such as T4dsDNA phages with long flexible tails,such as dsDNA phages with stubby tails,such as P22ssDNA phages,such as Phi X174ssRNA phages,such as MS2,Lytic cycle:phages replicate rapidly and eventually cause lysis of the host cell Lysogenic cycle:the viral DNA circularizes and integrates into the host DNA,Life cycle,Anthrax and Biological WeaponsBacterium:Bacillus anthracisCutaneous(skin)GastrointestinalInhalation,Pathogenesis of Anthrax,Gram+2 major virulence factors:Poly-D-glutamic acid capsule:protecting from being killed by phagocyteAnthrax toxins:lethal factor edema factor protective antigenLethal factor-cleaves members of mitogen-activated protein kinase kinase(MAPKK),interrupting the signaling pathways Edema factor-adenylate cyclaseProtective antigen-mediates two factors by binding to a cellular receptor,Protein structure and function,Building Blocksamino acidsPeptidesSecondary structureThree dimensional structureEnzymesMembrane proteinMiscellaneous proteins,The 20 amino acids of proteins,Acidic:aspartic acid;glutamatic acidsBasic:lysine,arginine&histidineAromatic:tyrosine,tryptophan and phenylalanineSulfur:cysteine,methionineUncharged hydrophilic:serine,threonine,asparagine,glutamineInactive hydrophobic:glycine,alanine,valine,leucine,isoleucineSpecial structure:prolineSalt bridge:interaction between+&-R groups,important stabilizing force in proteinsDisufide bonds:strong force for stabilizing the globular structureMethionine:synthesis of all peptide chains starts from methionineProline:the only amino acid has its R group and amino group directly connected-often located at the turn of a peptide in the 3-D structure of a protein,Peptide is a chain of amino acids linked together by peptide bonds.Polypeptides usually refer to long peptides whereas oligopeptides are short peptides(10 amino acids).Proteins are made up of one or more polypeptides with more than 50 amino acids,Peptides,Primary structureThe primary structure of a protein refers to its amino acid sequences.The amino acid in a peptide is also called a residue,Secondary structure,Alpha helixBeta strand,beta sheet and beta barrelMotif,Every 3.6 residues make one turnThe distance between the two terns is 0.54 nmThe C=O(or N-H)of one turn is hydrogen bonded to N-H(or C=O)of the neighboring turn,Alpha helix,Protein motifs and domains,Motif:a characteristic domain structure consisting of 2 or more helices or strandsCommon examples:coiled coil,helix-loop-helix,zinc finger,leucine zipper,Three dimensional structure,3 D structure is also called tertiary structureIf a protein consists of more than one polypeptide,it also has the quanternary structureX-ray crystallography and nuclear magnetic resonance(NMR)Protein data bank:“PDB ID”of a macromolecules,Enzymes,Enzyme are the catalysts of biochemical reaction in the cellsNumerous drugs are enzyme inhibitors:HIV protease:essential for HIV replication.Its inhibitor-control AidsAngiotension converting enzyme(ACE):promotes contraction of blood vessels-Its inhibitor-treat hypertension and congestive heart failurecGMP phosphodiesterase:catalyzes the conversion of cGMP into GMP-target of ViagraCalcineurin:the target of the immunosuppressive drugs PK506 and cyclosporin A,Classification of Enzyme,International Union of Biochemistry and Molecular Biology,IUBMBNomenclature,1)Oxidoreductase:dehydrogenase,oxidase,reductase,catalse2)Transferases:transfer of acetal,methyl,phosphase3)Hydrolases:protease nucleases:exonuclease endonuclease phosphatase:calcineurin4)Lyases:decarboxylase5)Isomerase:atomic rearrangements,rotamase6)Ligases:DNA ligase,EC(Enzyme Commission)numberEC1.11.1.6:the first digit indicates that the enzyme belongs to oxidoreductase(class 1)Subsequent digits represent subclass and sub-subclass.,Membrane protein,1-Transmembrane proteinsG-protein-coupled receptors Immunoglobulin family:Immunoglobulin,CD3,CD4,CD8,Fc receptor,MHC I,MHC II2-Transport proteins Ion channels:1)Ca,K,Na etc 2)Voltage-gated ion channel;ligand-gated ion channel Others:porins3-Membrane attached proteins Ras,v-Src,others:myristate,farnesyl,glycosylphosphatidylinositol,Ras:One of the large family of GPT-binding proteins that help relay signals from cell-surfaces receptors to the nucleus.Named for the ras gene,first identified in viruses cause rat sarcomaV-Src:Name of the first retroviral oncogene discovered(v-src)and its precursor proto-oncogene(c-src).The product of these genes is a membrane-associated protein kinase that phosphorylates many target proteins on tyrosine residues.(From sarcoma,the type of cancer that the src virus causes;pronounced“SARK”),Miscellaneous proteins,ChaperoneInterleukinsInterferonsTumor Necrosis FactorsChemokins,Chaperone:Proteins that helps other proteins avoid misfolding pathways that produce inactive and aggregated states,Conjugated protein:Glycoproteins,metalloproteins,Cytokines,Regulate immunity,inflammation,apoptosis,and hematopoiesise.g:InterleukinsInterferonsTumor Necrosis FactorsChemokins,Hormones:insulin,growth hormone,and prolactin Structural proteins:collagen,myosinTranscirptional factors:zinc fingers,leucine zipper,helix-turn-helix,helix-loop-helixUbiquitin:the marker for protein degradation.If a protein binds to ubiquitin,it will be degraded by proteasome,Nucleic Acids,Genomics and Proteomics,1:Building blocks-nucleotides2:DNA structure3:RNA structure 4:Chromatin Structure5:The genetic code6:Genes7:Repetitive DNA sequences8:Genomics and proteomics,Section B Protein Structure,Molecular Biology Course,B1 Amino acids-basic structure,4.A few proteins contain nonstandard amino acids that are formed by post-translational modification of proline and lysine.,proline,Common structure of 19 AAs,a-carbon is chiral(asymmetric)except in glycine(R is H),2.Amino acids are dipolar ions(zwitterions 兼性离子)in aqueous solution and are amphoteric(兼性的同时有酸碱性或正负电荷的),3.The side chains(R)differ in size,shape,charge and chemical reactivity,Protein structure,B1Amino acids:structure,side chains(charged,polar uncharged,nonpolar aliphatic,aromatic)B2Protein structure and function:Structure:size and shapes,primarysecondary tertiary quaternary,prosthetic groups Domains,motif,and family FunctionB3Protein analysis Purification Determine sequence,mass,and structure(X-ray crystallography and NMR),1.“Acidic”amino acids(2):containing additional carboxyl groups which are usually ionized,Form salt bridges,are hydrophilic(亲水),aspartic acid(Asp,D，天冬氨酸),glutamic acid(Glu,E，谷氨酸),Protein structure,B1 Amino acids-charged(5),2.“Basic”amino acids(3):containing positively charged groups,Lysine(Lys,K,赖氨酸),The imidazole group(咪唑基)has a pKa near neutrality.This group can be reversibly protonated under physiological conditions,which contribute to the catalytic mechanism of many enzymes.,Arginine(arg,R,精氨酸),d,e,a guanidino group(胍基）,Histidine(His,H，组氨酸),Protein structure,Contain groups that form hydrogen bonds with water,hydrophilic,Contain hydroxyl groups.,Asparagine(Asn,N，天冬酰氨),B1 Amino acids-polar uncharged(5),Serine(Ser,S，丝氨酸),Threonine(Thr,T，苏氨酸),Glutamine(Gln,Q，谷氨酰氨),Protein structure,Cysteine(Cys,C，半胱氨酸)has a thiol(巯醇)group，which is often oxidizes to cystine(胱氨酸),x-S-S-x,Protein structure,Glycine(Gly,G，甘氨酸),Proline(Pro,P，脯氨酸):imino acid(亚氨基酸),Methionine(Met,M，甲硫氨酸):contains a sulfur atom,Protein structure,B1 Amino acids-nonpolar aliphatic(7),(hydrophobic 疏水),Alkyl(烷基)side chains,Alanine(Ala,A，丙氨酸),Valine(Val,V，缬氨酸),Leucine(Leu,L，亮氨酸),Isoleucine(Ile,I，异亮氨酸),Protein structure,Phenylalanine(Phe,F，苯丙氨酸),Tyrosine(Tyr,Y，酪氨酸),Tryptophan(Trp,W，色氨酸),Protein structure,B1 Amino acids-aromatic(3),Accounts for most of UV absorbance of proteins at 280 nm hydrophobic（疏水的),B2Protein structure and function,Molecular Biology Course,Structure:size and shapes,primarysecondary tertiary quaternary,prosthetic groups(辅基，nonprotein molecules of conjugated proteins(结合蛋白)Domains,motif,and family Protein function,B2Protein structure Sizes,A few thousands Daltons(x 103)to more than 5 million Daltons(x 106)Some proteins contain bound nonprotein materials(prosthetic groups or other macromolecules),which accounts for the increased sizes and functionalities of the protein complex.,Protein structure,Globular proteins:enzymes,Complementary fit of a substrate molecule to the catalytic site on an enzyme molecule.,Protein structure,B2Protein structure Shapes,Fibrous proteins:important structural proteins(silk fibroin,keratin in hair and wools),keratin in hair,Keratin(角蛋白),Protofibril(初原纤维),microfibril(微管),Protein structure,Polypeptides contain N-and C-termini and are directional,usually ranging from 100-1500 aa,Formation of a peptide bond(shaded in gray)in a dipeptide.,Protein structure,B2Protein structure Primary,Structure of the pentapeptide Ser-Gly-Tyr-Ala-Leu.,N terminus,C terminus,Protein structure,a-helix right-handed 3.6 aa per turn hydrogen bond N-HO=C,Collagen triple helix:three polypeptide intertwined,A stereo,space-filling representation,Protein structure,B2Protein structure Secondary,b-sheet:hydrogen bonding of the pepetide bond N-H and C=O groups to the complementary groups of another section of the polypeptide chain,A stereo,space-filling representation of the six-stranded antiparallel b sheet.,Parallel b sheet:sections run in the same directionAntiparallel b sheet:sections run in the opposite direction,Protein structure,Protein structure,B2Protein structure Tertiary,The different sections of a-helix,b-sheet,other minor secondary structure and connecting loops of a polypeptide fold in three dimensions,Noncovalent interaction between side chains that hold the tertiary structure together:van der Waals forces,hydrogen bonds,electrostatic salt bridges,hydrophobic interactionsCovalent interaction:disulfide bonds,Denaturation of protein by disruption of its 2o and 3o structure will lead to a random coil conformation,Protein structure,Many proteins are composed of two or more polypeptide chains(subunits).These subunits may be identical or different.The same forces which stabilize tertiary structure hold these subunits together.This level of organization called quaternary structure.,The quaternary structure of hemoglobin。a1-yellow;b1-light blue;a2-green;b2-dark blue;heme-red,back,Protein structure,B2Protein structure Quaternary,Advantages of the quaternary structure:It allows very large protein molecules to be made,such as tubulin.It can provide greater functionality to a protein by combining different activities into a single entity.The interactions between the subunits can often be modified by binding of small molecules and lead to the allosteric effects seen in enzyme regulation.,Protein structure,Covalently or noncovalently attached to many conjugated proteins,and give the proteins chemical functionality.Many are co-factors in enzyme reactions.Examples:heme groups in hemogobin(Figure),Protein structure,B2Protein structure Prosthetic groups,Protein structure,B2Protein structure Domains,motifs and families,Domains:structurally independent units(tertiary)of a protein,being connected by sections with limited higher order structure within the same polypeptide.(Figure)They can also have specific function such as substrate binding,Protein structure,Structural motifs:Groupings of secondary structural elements that frequently occur in globular proteins Often have functional significance and represent the essential parts of binding or catalytic sites conserved among a protein family,bab motif,Protein families:structurally and functionally related proteins from different sources,The primary structures of c-type cytochromes from different organisms,Protein structure,Motif,The tertiary structures of the above c-type cytochromes,Cys,Met and His side chains covalently linked to the heme to the protein,Protein structure,Domain,Back,Enzymes:substrate binding,side chain in catalysisSignaling:cell membrneTransport and storage:hemoglobin transports oxygenStructure and movement:collagen,keratin,tubulin in cytoskeleton,actin and myosin for