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Chapter 3 Proteins: Shape, Structure, and Function Proteins Execute Cell Functions Enzymes ► Channels and pumps ► Signal Molecules ► Messengers ► Molecular Machines ► Structural Support ► Cell Recognition ► Protein Shape and Structure Peptide Bond Links Amino Acids into Polypeptide Chain Protein Shape and Structure Evolution fine-tuned structure and chemistry ► Shape dictated by amino acid sequence ► polypeptide backbone side chains Protein Shape and Structure Sequence Determines Structure Protein Shape and Structure Weak Noncovalent Bonds/Interactions important to the folding of polypeptide chain Protein Shape and Structure ► ► Fold into Conformation of Lowest Energy Common Folding Patterns alpha helix Beta Sheet Coiled Coils Protein Shape and Structure Levels of organization protein structure primary= aa seqeunce ► secondary= stretches of alpha helix, beta sheets ► tertiary=3d organization ► quartenary=complete structure of protein w/ > 1 polypeptide chain ► Protein Shape and Structure ► ► Protein Domain= Fundamental Unit of Organization independently folding unit 40-350 aa modular unit; combine to form larger proteins different domains have different functions Fold= central core of domain; comprised of beta sheets and alpha helices in various combinations; limited number Short signature sequences identify homologous protein domains Protein Shape and Structure Domain shuffling during the course of evolution Percentage of total genes in respective genomes containing one or more copies of a particular protein domain Protein Shape and Structure Protein Module ► ► ► Smaller than an average domain, generally 40-200 aa Particular versatile structures Easily integrated into other proteins; form parts of many different proteins Protein Shape and Structure Protein Families Evolved ► ► ► similar 3d structure portions or aa sequence conserved non-conserved portions impart new functionality serine proteases homeodomain proteins kinases immunoglobulins Protein Shape and Structure ► Sequence Homology Searches ► Amino Acids Sequence Threading ► Modules form parts of many different proteins Protein Shape and Structure Protein Shape and Structure Larger proteins can assemble from identical monomeric subunits Protein Shape and Structure ► ► ► Larger proteins often contain more than one polypeptide Proteins can serve as subunits for assembly of large structures Self Assembly Protein Function ► Function of protein dictated by physical interactions w/ other molecules specificity and ligand affinity governed by multiple weak noncovalent bonds active/binding site often cavity on protein surface formed by neighboring aa or aa that may belong to different portions of polypeptide Protein Function Conformation determines chemistry Regions adjacent to active or ligand binding site may restrict water to increase ligand binding ► Clustering of polar or chged residues can alter chemical reactivity ► Type and orientation of exposed aa side chains govern chemical reactivity ► Protein Function “Evolutionary tracing” to determine sites critical to protein function 3d structure of protein family members are similar even when aa homology falls to 25% ► Map unchg aa or nearly unchg from all known family members onto 3d structure of one family member ► Most invariant positions often on surface and represent ligand binding site ► Protein Function Proteins Bind to other Protein Through Several Types of Interfaces Protein Function Equilibrium Constant Describes Binding Strength Steady state or equilibrium: # association events/sec = # dissociation/sec ► From conc of two molecules and complex equilibrium constant can be calculated ► Protein Function Enzymes as Catalysts Make or break covalent bonds ► Speed up chemical reactions > 106 fold ► ► Stabilize transition state Decrease activation energy Increase local conc of substrate at catalytic site Hold reactants in proper orientation for chem rxn Binding energy contributes directly to catalysis Not consumed or changed during process Protein Function Common Types of Enzymes Hydrolases Nuclease Proteases Phosphatases Isomerases Polymerases Kinases OxidoReductases ATPases Synthases Protein Function Enzyme Kinetics Vmax= how fast enzyme can process substrate, pt at which enzyme saturated w/substrate ► Turnover Number= Vmax/[enzyme] turnover ranges from 1-10,000 substrate molec/sec ► Km= substrate conc at Vmax/2; measure of affinity ► Protein Function Lysozyme ► ► Natural antibiotic in egg white, tears, saliva Hydrolyzes polysaccharide chains residing in cell wall of bacteria Protein Function Specific Mechanism of Lysozyme Hydrolysis Enzyme positions substrate bending critical chem bonds that participate in chem rxn ► Positions acidic side chain of Glu w/in active site to provide high conc of acidifying H+ ions ► Negatively chged Asp stabilizes positive chged transition state ► Protein Function General Mechanism for Enzyme Activity Active site contains atoms that speed up rxn ► Substrate driven towards transition state upon binding to enzyme; shape of substrate chgs & critical bonds bent ► Covalent bond sometimes formed btwn substrate and side chain of enzyme ► Restoration of side chain to original state ► Protein Function Small Molecules Add Extra Functions to Proteins ► ► ► Chromophores detect light; retinal Metal atoms assist w/ catalytic functions; Zn, Mg, Fe Coenzymes (sm organic molec) provide functional grps; biotin Protein Function Multienzyme Complexes Increase the rate of cell metabolism ► Product of enzyme A passed directly to enzyme B; product of enzyme B passed to enzyme C; and so on ► Simulates intracellular membrane compartment; effectively increasing substrate conc at site of enzyme activity ► Protein Function Regulation of Catalytic Activity Negative Feedback ► Positive Regulation ► Allosterism ► Protein Function Allosterism Protein Function Symmetric Protein Assemblies and Cooperative Allosterism: sm chgs in ligand conc switches enzyme assembly from fully active to fully inactive state via conformation changes that are transmitted across neighboring subunits Protein Function Allosteric Transition in Aspartate Transcarbamoylase ► ► ► ► 6 catalytic subunits and 6 regulatory subunits all or none transition between T-tense and R-relaxed state Active R state driven by binding of carbamoylphosphate and aspartate Inactive T state driven by binding of CTP to regulatory dimers Protein Function Regulation by Phosphorylation/Dephosphorylation ► ► Addition or removal of P grp carrying (2) negative chgs can cause major conformation chg in protein Phosphorylation/dephosphorylation of proteins= response to signals that specify chg in cell state Protein Function Protein Kinase transfers terminal P of ATP to OH grp of SER, Thr, or Tyr ► 100’s ea specific for particular target ► Kinases share 250 aa catalytic domain ► Non-conserved aa flanking catalytic site or in loops w/in kinase domain confer specificity ► Protein Function Protein Phosphatases ► ► Catalyzes the removal of P grp Some specific; some act on broad range of proteins Protein Function Protein can Function as Microchip Cdk= cyclin dependent protein kinase activity dependent upon 3 events: 1. binding of second protein cyclin 2. phosphorylation of Thr side chain 3. dephosphorylation of Tyr side chain Cdk monitors specific set of cell components acting as input-output device Protein Function GTP Binding Proteins Analogous to Proteins regulated by P/de-P ► Active when GTP bound; inactive when GTP hydrolyzed ► Protein Function Regulatory Proteins Control Activity of GTP Binding Proteins ► ► GAP= GTPase activating protein; binds and induces hydrolysis GEF= Guanine nucleotide exchange factor; binds to GDP protein causing it to release GDP in exchange for GAP Protein Function Large Protein Movements Generated from Small Ones ► EF-Tu 1. 2. 3. = elongation factor in protein synthesis, GTPase tRNA complexes w/ GTP bound form of EF-Tu w/ aa masked GTP hydrolysis occurs when tRNA binds to mRNA on ribosome; tRNA disassociates GTP hydrolysis causes “Swtich helix” to swivel unmasking aa Protein Function Motor Proteins ► Produce lg movements in cells such as: muscle contraction crawling and swimming of cells movement of chromosomes movement of organelles enzymes on DNA ► Possess moving parts as force generating machines Protein Function ATP hydrolysis allows unidirectional series of conformational chgs to propel proteins along DNA Protein Function Allosteric proteins harness energy derived from ATP hydrolysis, ion gradients, electron transport processes to pump ions or sm molecules across membranes Ca2+ Pump of Sarcoplasmic Reticulum Protein Function Mechanism of Ca2+ Pump Protein Function Structure of Ca2+ Pump 10 transmembrane helices ► 4 transmembrane helices provide Ca2+ binding sites for pump ► helices that bind Ca2+ wind around ea other forming cavity btwn helices for Ca2+ ► ATP hydrolysis causes conformation chgs that later cavity enabling Ca2+ to be pushed through ►