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Lecture 5

BCH210 2014 Lecture 5.pdf

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Stavroula Andreopoulos

Lecture 5 Protein Structure Special ProteinsHow do Polypeptides Fold into 3D Protein Structures Several important principlesSecondary structures form wherever possible due to formation of large numbers of H bonds Hbonds induces coopertivityHelices and sheets often pack close together Peptide segments between secondary structures tend to be short and direct Proteins fold so as to form the most stable structuresStability arises fromFormation of large numbers of intramolecular hydrogen bonds Reduction in the surface area accessible to solvent that occurs upon folding Stability decreases energy associated with the structure Tertiary Structure of Proteins Folding of a polypeptide comprised of regions of alpha helices and beta structures into a closely packed 3D structureAmino acids great distances apart can be brought into close proximity Tertiary structure stabilized by covalent and noncovalent interactions Recognizable combinations of alphahelices betastrands and loops that appear in different proteins are called super secondary structures or MOTIFS Domains several discrete independently folded compact units consisting of combinations of motifsglobular proteins are made of 2 or more recognizable and distinct structuresdomainsEvolutionary Conservation Cytochrome C o Very homologous protein in all living organismswe all need it to live o The primary and tertiary structure is very alike across organisms o Very preserved o Binds the heme prosthetic groupLactate Dehydrogenase and Malate Dehydrogenaseo These 2 have homologous 3D structures o But the primary sequence is very different20 similarity o Carry out similar functionsPart of the same family of enzymesBoth carry out oxidationreduction actions o Still considered homologous proteins because of similar 3D structure4 Categories of Domains 1classentirely alpha helices and loops2classentirely beta sheets and nonrepeptitive structures linking beta strands3classhave supersecondary structures such as themotif andor regions of alternating alpha and beta 4classlocal clusters of alpha helices and beta sheets where each arises from separate continuous regions of the polypeptide chain with each foldscombination of secondary structures that form the core of a domain ie betabarrel beta helixQuaternary Structure of ProteinsRefers to organization and arrangement of subunits in a protein with multiple subunits ex HemoglobinEach subunit is a separate polypeptide chain Multisubunit protein is referred to as a oligomer Eg Heterodimermade up of two different and distinct subunits A dimer 2 subunits that interact extensivelyTrimmers interact through noncovalent interactionsProtein Subunit CompositionEssential step in the physical description of a protein MW of the native oligomer using gel filtration Subunits can be separated by SDSPAGEo For individual sizes of subunits o Need to add in betamercaptoethanol to remove disulfide bridges 4 Advantages of Mutisubunit ProteinsOligomers are more stableo Protection against proteasesActiveSites BindingofLigandsChangesinconformation Different proteins can share the same subunits Denaturation Leads to Loss of Protein Structure and FunctionThe cellular environment is suited to maintaining the weak forces that preserve protein structure and function External stressesheat chemical treatment etccan disrupt these forces in a process termed denaturationthe
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