Marlou Snelleman

2011

Proteins and amino acids

Overview

ProteinsPrimary structureSecondary structureTertiary structureQuaternary structure

Amino acidsBuilding blocks of proteinsProperties

Proteins Primary structure

The sequence

Secondary structureα-helicesβ-strandsTurnsLoops

Tertiary structure Interactions 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

N C

Proteins Primary structure

the sequence

Secondary structureα-helicesβ-strandsTurnsLoops

Tertiary structure Interactions 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:α-helicesβ-strandsTurnsLoops

Secondary structure – α-helixN-terminus

C-terminus

Secondary structure – β-strand A β-sheet consists of at least two β-strands interact

with each other

Anti-parallel Parallel

Secondary structure – TurnTurns connect the secondary structure elements

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

structure

Proteins Primary structure

the sequence

Secondary structureα-helicesβ-strandsTurnsLoops

Tertiary structure Interactions between the secondary structure elements to form the

structured protein

Quaternary structureDimers or multimers of proteins

Tertiary structure• The secondary structure elements interact to form

the structured protein

Proteins Primary structure

the sequence

Secondary structureα-helicesβ-strandsTurnsLoops

Tertiary structure Interactions 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 Cα

an carboxyl group

Amino acids – Structure

α

“Textbook picture” In the cytosol (water)

α

Amino acids – StructureThe Cα is bound to an R group: the side chain

different for each amino acidthe atoms are labeled

α

β

γ

δ

ε

ζ

Amino acids – Peptide bondThe amino acids can make polymers via peptide

bonds

Amino acids – CodesThere are 20 different amino acids

One letter

Three letter

Name

A Ala AlanineC Cys CysteineD Asp AspartateE Glu GlutamateF Phe PhenylalanineG Gly GlycineH His HistidineI Ile IsoleucineK Lys LysineL Leu LeucineM Met MethionineN Asn AsparagineP Pro ProlineQ Gln GlutamineR Arg ArginineS Ser SerineT Thr ThreonineV Val ValineW Trp TryptophanY Tyr Tyrosine

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, Glu

Amino acids – Electric charge

Lys Arg

Asp Glu

Positive, neutral and negative: His

Depending on the environment

His

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: Trp

Gly

Trp

Amino acids – Sulfur containingCys and Met contain sulfur

The sulfur of Cys is very reactivecan make sulfur bridges with other cysteines

Cys Met Sulfur bridge

Especially rigidPro: an imino acid

Especially flexibleGly: no side chain

Amino acids – Rigidity

Gly

Pro

Rigid guanidinium groupArg

Arg

Flexible side chainLys

Lys

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…