Marlou Snelleman 2011 Proteins and amino acids. Overview Proteins Primary structure Secondary...

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Transcript of Marlou Snelleman 2011 Proteins and amino acids. Overview Proteins Primary structure Secondary...

  • Marlou Snelleman2011Proteins and amino acids

  • Overview

    ProteinsPrimary structureSecondary structureTertiary structureQuaternary structure

    Amino acidsBuilding blocks of proteinsProperties

  • ProteinsPrimary structureThe sequence

    Secondary structure-helices-strandsTurnsLoops

    Tertiary structureInteractions between the secondary structure elements to form the structured protein

    Quaternary structureDimers or multimers of proteins

  • Primary structure

    Proteins are polymers The monomers (residues) are amino acids

    The sequence:is the order of the amino acids in the proteinstarts at the amino (N) terminus and ends at the carboxy (C) terminusFor example: Met-Val-Lys-Leu-Cys-Ala

    NC

  • ProteinsPrimary structurethe sequence

    Secondary structure-helices-strandsTurnsLoops

    Tertiary structureInteractions between the secondary structure elements to form the structured protein

    Quaternary structureDimers or multimers of proteins

  • Secondary structureThe amino acids form four different secondary structure elements:-helices-strandsTurnsLoops

  • Secondary structure -helixN-terminus C-terminus

  • Secondary structure -strand A -sheet consists of at least two -strands interact with each otherAnti-parallelParallel

  • Secondary structure TurnTurns connect the secondary structure elements

  • Secondary structure - LoopA loop is everything that has no defined secondary structure

  • ProteinsPrimary structurethe sequence

    Secondary structure-helices-strandsTurnsLoops

    Tertiary structureInteractions between the secondary structure elements to form the structured protein

    Quaternary structureDimers or multimers of proteins

  • Tertiary structureThe secondary structure elements interact to form the structured protein

  • ProteinsPrimary structurethe sequence

    Secondary structure-helices-strandsTurnsLoops

    Tertiary structureInteractions between the secondary structure elements to form the structured protein

    Quaternary structureDimers or multimers of proteins

  • Quaternary structureSome proteins can interact with each other to form dimers or multimers

  • Amino acidsThe (secondary and tertiary) structure of the protein depends on the primary structureand therefore on the sequenceand therefore on the amino acids

    When you understand the amino acids, you understand everything!

  • Every amino acid has the same basic structure: the backbone withan amino groupan Can carboxyl group

    Amino acids StructureTextbook pictureIn the cytosol (water)

  • Amino acids StructureThe C is bound to an R group: the side chaindifferent for each amino acidthe atoms are labeled

  • Amino acids Peptide bondThe amino acids can make polymers via peptide bonds

  • Amino acids CodesThere are 20 different amino acids

    One letterThree letterNameAAlaAlanineCCysCysteineDAspAspartateEGluGlutamateFPhePhenylalanineGGlyGlycineHHisHistidineIIleIsoleucineKLysLysineLLeuLeucineMMetMethionineNAsnAsparaginePProProlineQGlnGlutamineRArgArginineSSerSerineTThrThreonineVValValineWTrpTryptophanYTyrTyrosine

  • Amino acids PropertiesEach side chain has different structural and chemical propertiesHydrophobicityElectric chargeSizeSulfur containingRigiditySecondary structure preferencePolarAlcoholicAliphaticAromaticEtc.

  • Amino acids PropertiesAmino acids are not easily put into boxes according to their propertiesEvery amino acid belongs to several categoriesEvery amino acid is unique

  • Amino acids HydrophobicityHydro = water; phobe = fear; phile = love

    Some amino acids like to stick into water (hydrophile)Asp, Glu, His, Lys, Asn, Gln, Arg

    Some amino acids like to stick to each other (hydrophobe)Ala, Cys, Phe, Ile, Leu, Met, Pro, Val, Trp

    And some are inbetweenGly, Ser, Thr, Tyr

  • Amino acids HydrophobicityHydrophobicity is the most important property

    It drives the folding of a proteinThe sticky amino acids glue togetherThe non-sticky amino acids point to the waterThe waters must be happy

  • Amino acids - Hydrophobicity(Not scaled!!!)

  • Some amino acids carry a charge

    Positive: Lys, Arg

    Negative: Asp, GluAmino acids Electric chargeLysArgAspGluPositive, neutral and negative: HisDepending on the environmentHis

  • Amino acids Size

    Small amino acidsAla, Cys, Gly, Pro, Ser, Thr, ValSmallest: Gly

    InbetweenAsp, Ile, Leu, Asn

    Large amino acidsGlu, Phe, Lys, Gln, Arg, Trp, TyrLargest: TrpGlyTrp

  • Amino acids Sulfur containingCys and Met contain sulfur

    The sulfur of Cys is very reactivecan make sulfur bridges with other cysteinesCysMetSulfur bridge

  • Especially rigidPro: an imino acid

    Especially flexibleGly: no side chainAmino acids RigidityGlyProRigid guanidinium groupArg

    ArgFlexible side chainLysLys

  • Amino acids Secondary structure preferenceMost amino acids have a secondary structure preference for helicesstrandsor turns

  • Residues that are good for a helixAla, Met, Glu, Leu, Lys (AMELK)

    Residues that are good for strandsVal, Ile, Thr, Trp, Tyr, Phe (VITWYF)

    Residues that are good for turnsPro, Ser, Asp, Asn, Gly (PSDNG)Amino acids Secondary structure preference

  • It is all about amino acidsMVKLCA

    *Turns alleen beta-turns?*Turns alleen beta-turns?

    *******Polair, alifatisch lehninger*Happy waters lehninger**Waarop wordt indeling van size bepaald?****