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BIOL 200 Exam.pdf

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McGill University
Biology (Sci)
BIOL 200
Richard Roy

BIOL 200 ExamProtein Structure and FunctionAmino Acids Can be Dexter or Laevus D or L isomers enantiomers with a central alpha carbon Amino Acids differ by their R functional groupsSpecial Amino AcidsCysteine has a sulfhydryl group SH that can form disulphide bonds SS with another cysteine This creates intra and inter crosslinking that stabilize folded structure Proline has a rigid ring structure that can create kinks or make bulges that disrupt structureGlycine has a symmetrical R group R group is a hydrogenProtein function is derived from the three dimensional structure and the three dimensional structure is specified by the aminoacid sequence The threedimensional structure is also known as the proteins conformationLevels of Protein Structure Primary sequenceSecondarylocal foldingTertiary long range foldingQuaternary multimeric structureSupramolecular largescale assemblyTertiary Quaternary and Supramolecular all form a functional protein These functions include Regulation on and off Structure microtubules Movement Catalysis enzymatic proteins Transport and Signaling Not all proteins form a quaternary structure because some do not consist of subunitsPrimary Sequence Amino End HN is also called the Nterminus and the Carboxy End COO is also 3called the Cterminus The positive Nterminus will form a peptide bond with the negative Cterminus Often the amino acids incorporated in a polypeptide are referred to as residuesSecondary Structures Folding of localized regions of a polypeptide chain that form stabilizing noncovalent Hbonding is used interactions for instancealpha helicesbeta sheetsbeta turnsmotifs No noncovalent interactions will result in a random coil In an alpha helix the direction of the Rgroup pointing inwards or outwards IS VERY IMPORTANTIn beta pleated sheets theyare laterally packed beta strands A beta strand a short 5 to 8 residue nearly extended polypeptide segmentHbonding between backbone of the beta strands The beta sheets have directionalitycan be parallel same orientation or antiparallel opposite orientation Rgroups project outwards whereas in alpha helices they project inwards AND outwards Beta turns are produced by amino acid R groups that are very compact eg LysineProline It is hydrogen bonding that forms the beta turn MotifsCombination of secondary structures form the motifsCoiledcoils the internal R groups pointing upward are very hydrophobic These form hydrophobic interactions with the hydrophobic residueseg Keratin stabilized by these hydrophobic interactions and other fibrous proteins used in structure Two alpha helicesEFhandhelixloophelix HLH motif Referred to as the calciumbinding motif 2 Ionic bonds inside the loop to bind Ca Alpha helixbeta loopalpha helixZincfinger motif Specific for the interaction with zinc Very important for DNAbinding and RNAbinding proteinsAlpha helixbeta loopssheetsHistidine and cysteine interact with the zinc molecule through ionic bondingTertiary StructureForms domainsLong range folding within a polypeptide chain Stabilized by hydrophobic interactions between nonpolar side chains hydrogen bonds between polar side chains and disulfide bridges between cysteine residuesProvide a compact structure of alpha helices beta sheets and beta turns secondary structures Difference between motifs and domains motifs are still very localized interactions very small components of the polypeptide Determines specific activities but doesnt tell the whole story of the protein Domains do determine the function of the protein Domains are modularmany polypeptides are composites of different combinations of domains There are a finite set of domains and the swapping of domains between polypeptides allows for different shapes like alternative gene splicingmany products from just a couple domains The combination of all the domains determines the actual function of the polypeptideStructural Domains A region of the protein which is selfstabilizing and can fold independently Functional Domain A region of the protein that exhibits a particular activityeven when isolated from the rest of the protein This is important in determining catalytic activity Quaternary Structuremany subunits of tertiary structure coming together Example hemoglobin has 2 identical alpha subunits and two identical beta subunits Homotrimer polypeptide of 3 identical subunitsSupramolecular StructureMacromolecular assemblies Usually greater than 1 mega Dalton in size Tens to hundreds of polypeptide chains as well as other macromoleculesExample the transcription preinitiation complex formed of the RNA Polymerase general transcription factors and mediator complexDescription Level oLinear sequence 1 oalpha helices 2 beta pleated sheets beta loops and Uturns motifs odomains 3 omultimeric domains 4 Supramolecular macromolecular assemblies molecular machinery
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