Marlou Snelleman 2011 Proteins and amino acids

Overview Proteins Primary structure Secondary structure Tertiary structure Quaternary structure Amino acids Building blocks of proteins Properties

Proteins Primary structure The sequence Secondary structure α-helices β-strands Turns Loops Tertiary structure Interactions between the secondary structure elements to form the structured protein Quaternary structure Dimers 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 protein starts at the amino (N) terminus and ends at the carboxy (C) terminus For example: Met-Val-Lys-Leu-Cys-Ala NC

Proteins Primary structure the sequence Secondary structure α-helices β-strands Turns Loops Tertiary structure Interactions between the secondary structure elements to form the structured protein Quaternary structure Dimers or multimers of proteins

Secondary structure The amino acids form four different secondary structure elements: α-helices β-strands Turns Loops

Secondary structure – α-helix N-terminus C-terminus

Secondary structure – β-strand A β-sheet consists of at least two β-strands interact with each other Anti-parallelParallel

Secondary structure – Turn Turns connect the secondary structure elements

Secondary structure - Loop A loop is everything that has no defined secondary structure

Proteins Primary structure the sequence Secondary structure α-helices β-strands Turns Loops Tertiary structure Interactions between the secondary structure elements to form the structured protein Quaternary structure Dimers or multimers of proteins

Tertiary structure The secondary structure elements interact to form the structured protein

Proteins Primary structure the sequence Secondary structure α-helices β-strands Turns Loops Tertiary structure Interactions between the secondary structure elements to form the structured protein Quaternary structure Dimers or multimers of proteins

Quaternary structure Some proteins can interact with each other to form dimers or multimers

Amino acids The (secondary and tertiary) structure of the protein depends on the primary structure and therefore on the sequence and therefore on the amino acids When you understand the amino acids, you understand everything!

Every amino acid has the same basic structure: the backbone with an amino group an C α an carboxyl group Amino acids – Structure α “Textbook picture”In the cytosol (water) α

Amino acids – Structure The C α is bound to an R group: the side chain different for each amino acid the atoms are labeled α β γ δ ε ζ

Amino acids – Peptide bond The amino acids can make polymers via peptide bonds

Amino acids – Codes There are 20 different amino acids One letter Three letter Name AAlaAlanine CCysCysteine DAspAspartate EGluGlutamate FPhePhenylalanine GGlyGlycine HHisHistidine IIleIsoleucine KLysLysine LLeuLeucine MMetMethionine NAsnAsparagine PProProline QGlnGlutamine RArgArginine SSerSerine TThrThreonine VValValine WTrpTryptophan YTyrTyrosine

Amino acids – Properties Each side chain has different structural and chemical properties Hydrophobicity Electric charge Size Sulfur containing Rigidity Secondary structure preference Polar Alcoholic Aliphatic Aromatic Etc.

Amino acids – Properties Amino acids are not easily put into boxes according to their properties Every amino acid belongs to several categories Every amino acid is unique

Amino acids – Hydrophobicity Hydro = 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 inbetween Gly, Ser, Thr, Tyr

Amino acids – Hydrophobicity Hydrophobicity is the most important property It drives the folding of a protein The sticky amino acids glue together The non-sticky amino acids point to the water The 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 LysArg Asp Glu Positive, neutral and negative: His Depending on the environment His

Amino acids – Size Small amino acids Ala, Cys, Gly, Pro, Ser, Thr, Val Smallest: Gly Inbetween Asp, Ile, Leu, Asn Large amino acids Glu, Phe, Lys, Gln, Arg, Trp, Tyr Largest: Trp Gly Trp

Amino acids – Sulfur containing Cys and Met contain sulfur The sulfur of Cys is very reactive can make sulfur bridges with other cysteines CysMetSulfur bridge

Especially rigid Pro: an imino acid Especially flexible Gly: no side chain Amino acids – Rigidity Gly Pro Rigid guanidinium group Arg Flexible side chain Lys

Amino acids – Secondary structure preference Most amino acids have a secondary structure preference for helices strands or turns

Residues that are good for a helix Ala, Met, Glu, Leu, Lys (AMELK) Residues that are good for strands Val, Ile, Thr, Trp, Tyr, Phe (VITWYF) Residues that are good for turns Pro, Ser, Asp, Asn, Gly (PSDNG) Amino acids – Secondary structure preference

It is all about amino acids MVKLCA …