Download The amino acids

Amino Acids
“When you understand the amino acids,
you understand everything”
©CMBI 2001
Amino Acids
Backbones run from the amino to the carboxy end, or in other
words, from N-terminus to C-terminus.
©CMBI 2001
Di-peptide
Amino acids bind, to form a
protein. Upon binding, two
protons from the NH3 and
one oxygen from the
carboxyl join to form a water.
So the peptide bond has at
the one side a C=O and at
the other side an N-H.
Only the ends of the chain
are NH3 or carboxylic.
©CMBI 2001
Amino Acid Sequence
The amino acid sequence (also called primary structure) of a
protein is the order of the amino acids in the protein chain.
The sequence is always read from the N-terminus to the Cterminus of the protein.
For example:
+H3N-Lys-Val-Phe-Ala-Met-Cys-Leu-Leu-Arg-Val-COO-
Or (in one-lettercode):
KVFAMCLLRV
©CMBI 2001
The 20 Amino Acids
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
Aspartic acid (Aspartate)
Glutamic acid (Glutamate)
Phenylalanine
Glycine
Histidine
Isoleucine
Lysine
Leucine
Methionine
Asparagine
Proline
Glutamine
Arginine
Serine
Threonine
Valine
Tryptophan
Tyrosine
©CMBI 2001
The 20 Amino Acids
©CMBI 2001
Amino Acid Characteristics
There are many of ways to characterize the properties of amino
acids. The ones most useful and most commonly used are:
Hydrophobicity
Size
Charge
Secondary structure preference
Alcoholicity
Aromaticity
And on top of that there are some special characteristics like bridge
forming by cysteines, rigidity of prolines, titrating at physiological
pH of histidine, flexibility of glycines, etc.
©CMBI 2001
Secondary Structure Preferences
Alanine
Arginine
Aspartic Acid
Asparagine
Cysteine
Glutamic Acid
Glutamine
Glycine
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Proline
Serine
Threonine
Tryptophan
Tyrosine
Valine
helix
1.42
0.98
1.01
0.67
0.70
1.39
1.11
0.57
1.00
1.08
1.41
1.14
1.45
1.13
0.57
0.77
0.83
1.08
0.69
1.06
strand
0.83
0.93
0.54
0.89
1.19
1.17
1.10
0.75
0.87
1.60
1.30
0.74
1.05
1.38
0.55
0.75
1.19
1.37
1.47
1.70
turn
0.66
0.95
1.46
1.56
1.19
0.74
0.98
1.56
0.95
0.47
0.59
1.01
0.60
0.60
1.52
1.43
0.96
0.96
1.14
0.50
©CMBI 2001
Sequence Alignment
Now that we know everything about the amino acids, we can look
at the real goal of this whole excercise: sequence alignments.
Which of the following alignments is better, left or right:
CWPSAAFPWC
CWPT---PWC
CWPSAAFPWC
CWP---TPWC
CWPYAAWPWC
CWP---FPWC
CWPYAAWPWC
CWPF---PWC
©CMBI 2001
Sequence Alignment
Don’t forget that we still want to gather information about an
unknown protein for which we determined the sequence.
To gather that information, we will need databases and sequence
alignments.
To do these sequence alignments, we need to know everything
about the amino acids.
And that is what we are working on right now.
©CMBI 2001