Download Amino Acids and Proteins

Amino Acids and Proteins
sidechain -R
Basic
NH
–(CH2)3 NH
arginine (arg, R)
NH2
Neutral, CH
glycine (gly, G)
alanine (ala, A)
valine (val, V)
leucine (leu, L)
isoleucine (ile, I)
sidechain -R
-H
-CH3
-CH(CH3)2
-CH2CH(CH3)2
-CH(CH3)CH2CH3
Neutral, S
cysteine (cys, C)
methionine (met, M)
-CH2SH
-CH2CH2SCH3
lysine (lys, K)
-(CH2)4NH2
Aromatic
phenylalanine
(phe, F)
CH2
tyrosine (tyr, Y)
CH2
OH
Heterocyclic
Neutral, OH
serine (ser, S)
threonine (thr, T)
CO2
proline (pro, P)
-CH2OH
-CH(OH)CH3
Acidic
aspartic acid (asp, D)
glutamic acid (glu, E)
asparagine (asn, N)
glutamine (gln, Q)
NH2 H
N
CH2
histidine (his, H)
HN
-CH2CO2H
-CH2CH2CO2H
-CH2CONH3+
-CH2CH2CONH3+
CH2
tryptophan (trp, W)
N
H
Peptide Bonds
2 +H3NCHCO2–
– H2O
O
a dipeptide
+
H3NCHC NHCHCO2
R
R
–
more amino acids: polypeptide
lots of amino acids: protein
R
Protein Chain Interactions
hydrogen bonding
sidechain interactions
H2 O H 2 O H 2 O
R
C
O
H
N
H
R
O
N
N C
N C
H
O
H
R
O
R
H
O
C N
C N
C
R
H
O
R
CO2
CO2
H3N
OH
S
S
S
O
ionic/polar H-bond -stack disulfide
bridge
S
Zn
S
N
NH
metals
Licensed by WSM under a Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Canada Licence.
H2 O H2 O H2 O
hydrophobic
Amino Acid Sidechains as Ligands
alcohol
alkoxide
amine
pKa
~16
HOH
OSer
H not lost
~10.5
H+ lost if
M-bound
NLys
~10.5
N-terminus
H+ lost if
M-bound
SCys
thioether
SMet
~8.5
H+ lost if
M-bound
NHis
OAsp
carboxylate
OGlu
C-terminus
H+ lost at
physio pH
~4
O
M
H
~110-140º
 (+ )
donor
-donor
H
O
M
N
M
H
~110-120º
 +  donor
 (+ )
donor
~6
imidazole
-donor
+
OTyr
thiolate
~110-140º
 donor,
 acceptor
S
M
M
S
CH3
H
N
 (+ )
donor
N
O
O
H+ lost at
physio pH
M
M
O
M
 +  donor
O
Weak vs Strong Field
SCys < SMet < OAsp, OGlu < H2O, OSer < NLys < NHis < CO, CN–
weaker
stronger
Hard vs Soft Donor
CO, CN– < SMet < SCys < NHis < NLys < H2O, OSer < OTyr < OAsp, OGlu
softer
harder
Licensed by WSM under a Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Canada Licence.
Levels of Protein Structure
Primary Structure (1º)



MET
SER
ASP
ASN
GLU
LYS
the sequence of amino acids
determined by nucleic acid sequence in DNA/RNA
can be altered by site-directed mutagenesis (Chem NP 1993 to Michael Smith)
GLY
ILE
ASP
GLU
HIS
SER
PHE
ILE
ASN
GLN
GLU
TRP
PRO
ASP
ALA
VAL
THR
LEU
ILE
ASP
ASP
LEU
PHE
VAL
PRO
GLU
ASN
MET
ILE
ASN
ASP
HIS
LEU
GLN
HIS
HIS
PRO
LYS
GLY
ALA
ALA
ILE
TYR
THR
GLU
SER
LEU
LYS
VAL
LEU
LEU
GLN
ASP
THR
TRP
PHE
ARG
TYR
ASN
ILE
ASP
ASN
ARG
GLN
TRP
ASP
PRO
GLY
CYS
PHE
LYS
PHE
SER
ILE
THR
TYR
GLY
LYS
PHE
PHE
GLY
ASP
ASP
TYR
ARG
HIS
LYS
GLU
VAL
LYS
THR
LEU
HIS
HIS
LYS
GLY
PHE
ALA
PHE
LYS
TRP
LYS
TYR
ILE
LEU
LYS
ALA
ILE
Secondary Structure (2º)




local conformation of polypeptide chain
determined primarily by H-bonding interactions
somewhat affected by sidechain interactions
e.g. -helix, -sheet
Tertiary Structure (3º)


-helix
entire 3D structure of one polypeptide chain
strongly affected by sidechain interactions
e.g. H-bonding / ionic / dipole / -stacking /
hydrophobic and -philic interactions /
covalent bonds (e.g. S-S links, M centres)
Quaternary Structure (4º)

potential amalgamation of multiple protein
chains into larger structures
-sheet
8×
3º structure
4º structure
Licensed by WSM under a Creative Commons Attribution-NonCommercial-ShareAlike 2.5 Canada Licence.