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…