Proteins and amino acids
Marlou Snelleman
2012
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
N
C
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 which
interact with each other
Anti-parallel
Parallel
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 have to interact with each other to
form dimers or multimers to get their functionality
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!
Amino acids – Structure
 Every amino acid has the same basic structure: the
backbone with
 an amino group
 a Cα
 a carboxyl group
α
Amino acids - Structure
 The Cα is bound to an R group: the side chain
 different for each amino acid
 YASARA uses different colors for each kind of atom
 Note that the hydrogens are not shown in this picture
α
Amino acids - Structure
 The Cα is bound to an R group: the side chain
 different for each amino acid
 YASARA uses different colors for each kind of atom
 Note that the hydrogens are not shown in this picture
α
Nitrogen
Carbon
Oxygen
Amino acids - Structure
 The Cα is bound to an R group: the side chain
 different for each amino acid
 YASARA uses different colors for each kind of atom
 Note that the hydrogens are not shown in this picture
α
Amino acids - Structure
 The Cα is bound to an R group: the side chain
 different for each amino acid
 YASARA uses different colors for each kind of atom
 Note that the hydrogens are not shown in this picture
α
Amino acids - Structure
 The Cα is bound to an R group: the side chain
 different for each amino acid
 YASARA uses different colors for each kind of atom
 Note that the hydrogens are not shown in this picture
Side chain
α
Amino acids – Peptide bond
 The amino acids can make polymers via peptide bonds
 Note that there remains a charge on the ends of the
dipeptide
Amino acids – Codes
 There are 20 different amino acids
One
letter
Three
letter
Name
A
C
D
E
F
G
H
I
K
L
M
N
P
Q
R
S
T
V
W
Y
Ala
Cys
Asp
Glu
Phe
Gly
His
Ile
Lys
Leu
Met
Asn
Pro
Gln
Arg
Ser
Thr
Val
Trp
Tyr
Alanine
Cysteine
Aspartate
Glutamate
Phenylalanine
Glycine
Histidine
Isoleucine
Lysine
Leucine
Methionine
Asparagine
Proline
Glutamine
Arginine
Serine
Threonine
Valine
Tryptophan
Tyrosine
Amino acids – Properties
 Each side chain has different structural and chemical
properties










Hydrophobicity
Electric charge
Size
Sulfur containing
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 (hydrophilic)
 Asp, Glu, His, Lys, Asn, Gln, Arg
 Some amino acids like to stick to each other (hydrophobic)
 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
 Water molecules are quite happy on their own
 Introduction of a fatty acid makes the waters around it
unhappy
 They cannot make all hydrogen bonds
 They are bound in a “cage” around the
fatty acid tail
Hydrophobic tail
Hydrophilic head
Amino acids - Hydrophobicity
 More fatty acids will glue together
 The total hydrophobic surface will be smaller
 More waters will be happy
(Not scaled!!!)
Amino acids - Hydrophobicity
 More fatty acids will glue together
 The total hydrophobic surface will be smaller
 More waters will be happy
(Not scaled!!!)
Amino acids – Electric charge
 Positive: Lys, Arg
 Blue nitrogens
 Positive, neutral and negative:
Lys
Arg
His
 Depending on the environment
 Negative: Asp, Glu
 Red oxygens
Asp
His
Glu
Amino acids – Size
 Small amino acids
 Ala, Cys, Gly, Pro, Ser, Thr, Val
 Smallest: Gly
Gly
 Inbetween
 Asp, Ile, Leu, Asn
 Large amino acids
 Glu, Phe, Lys, Gln, Arg, Trp, Tyr
 Largest: Trp
Trp
Amino acids – Sulfur containing
 Cys and Met contain sulfur
Cys
Met
Sulfur bridge
 The sulfur of Cys is very reactive
 can make sulfur bridges with other cysteines
Amino acids – Secondary structure preference
 Most amino acids have a secondary structure
preference for
 helices
 strands
 or turns
Amino acids – Secondary structure preference
 Residues that are good for a helix
 Ala, Met, Glu, Leu, Lys (KAMEL)
 Residues that are good for strands
 Val, Ile, Thr, Trp, Tyr, Phe (WYFI-TV)
 Residues that are good for turns
 Pro, Ser, Asp, Asn, Gly (PSDNG)
It is all about amino acids
Sequence
MSQSTQTNEF
LSPEVFQHIW
DFLEQPIC
All different properties
MSQSTQTNEF
FQHIW
DFLEQPRIC
LSPEV
Secondary
structure
preference
Tertiary structure
Secondary structure elements
(folded protein)
Hydrophobicity
Hydrogen bonds
Charge interactions