Proteins and amino acids
Marlou Snelleman
2011
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 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 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!
Amino acids – Structure
 Every amino acid has the same basic structure: the
backbone with
 an amino group
 an Cα
 an carboxyl group
α
α
“Textbook picture”
In the cytosol (water)
Amino acids – Structure
 The Cα is bound to an R group: the side chain
 different for each amino acid
 the atoms are labeled
δ
ζ
ε
β
γ
α
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
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
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!!!)
Amino acids – Electric charge
 Some amino acids carry a charge
 Positive: Lys, Arg
 Positive, neutral and negative:
His
 Depending on the environment
Lys
Arg
 Negative: Asp, Glu
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 – Rigidity
 Especially rigid
 Pro: an imino acid
 Rigid guanidinium group
 Arg
Pro
 Especially flexible
 Gly: no side chain
Gly
Arg
 Flexible side chain
 Lys
Lys
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 (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)
It is all about amino acids
MVKLCA…