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?****