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Amino acids
R-groups
non-polar
polar
acidic
basic
proteins condensation between
carboxylic acids and amines
C
O
+ H N
C
N
OH
carboxylic acid
O
amine
amide
+ H2O
Amides
resonance structure
amides
O
O
C
C
N
N
dipeptide
H
H2N C C
O
OH
H
H2N C C
CH3
H
alanine
glycine
H
O
OH
H2N C C
CH3
O
H
N C C
H H
Ala-Gly
+H2O
O
OH
Polypeptides
“backbone”
_
_
_
_
_
_
H R
H R
H R
_
H N1-C1-C1-N2-C2-C2-N3-C3-C3- OH
O
O
O
peptide bonds
C-terminal
N-terminal
residue
residue
=
=
=
biological activity = structure
4 levels
protein structure
Primary structure
sequence of amino acids
hemoglobin transports O2 and CO2
4 protein chains 300 amino acids
Sickle cell anemia
6th amino acid from
N-terminus
R
Glu
Val
-CH2CH2-CO2H
-CH(CH3)2
water soluble
water insoluble
Secondary structure
hydrogen bonding backbone groups
=
=
=
H-bond donors
_
_
_
_
_
_
H R
H R
H R
_
H N1-C1-C1-N2-C2-C2-N3-C3-C3- OH
O
O
O
H-bond acceptors
Two main secondary structures:
-helix
-sheet
Alpha helix
Every C=O bonded to N-H 4 residues away
forms a helix
core is backbone
R-groups outside
3.6 amino acids per turn
H
proline
=
C
=
C
O
O
N
no H-bonding
breaks helix
Beta sheet
Every C=O bonded to N-H far apart in 1o structure
on different chains
peptide chains extended
side-by-side
maximal H-bonding for anti-parallel chains
small R-groups above and below the sheet
if not -helix or -sheet
random coil
Fibrous Proteins
1o structure amino acid sequence
2o structure - helix
-sheet
H-bonding between
C=O- and N-H+ of backbone


some proteins only have 1o and 2o structure:
fibroin (silk)
keratin hair
collagen skin
-sheet
- helix
insoluble in H2O
non-polar residues
Disulfide bonds
cysteine -CH2-SH
H
H
N C S-H
H-S C N
C
reduced
C
[O]
H
H
N C S
S C N
C
C
oxidized
Tertiary structure
Primary structure
sequence of amino acids
Ala-Phe-Ser-Ser-Val-Glu-His-Ile-Met-Arg-Asp-Val-His-Asn-Gly
Ala-Phe-Ser-Ser-Val- Glu-His-Ile-Met-Arg-Asp-Val-His-Asn-Gly-
Non-polar
Polar
Acidic or Basic
Alanine
Phenylalanine
Valine
Isoleusine
Methionine
Glycine
Serine
Histidine
Glutamic acid
Arginine
Aspartic acid
Asperagine
Tertiary structure
Ala-Phe-Ser-Ser-Val-Glu-His-Ile-Met-Arg-Asp-Val-His-Asn-Gly
arrange these in an -helix
polar
exterior
7
His
3
Ser
11
4
Asp Ser
15
Gly
8
Ile
14 Asn
Val 12
10 Arg
Ala 1
Glu
6
Phe His Met
2
9
13
Val 5
non-polar
interior
Tertiary structure
interaction of the R-groups
+
-
-
-
+
+
-
hydrophobic residues
inside
globular proteins
proteins fold around
non-polar groups
polar and charged residues
outside
Tertiary structure
interactions of R-groups
1. Hydrophobic interactions
non-polar R-groups
LDF
2. Hydrogen bonding
polar R-groups
between H-bond
donors and acceptors
3. Ionic bonds (salt bridges) acidic and basic R-groups
ion-ion
4. Covalent bonds (disulfide)
cysteins
C-terminus
His
NH+
-O-CH Asp
O
Ala
CH3
His
Fe2+
=
Arg
Phe
Cys
S
S Cys
N-terminus
Pro
Pro
Denaturing treatments
1. Heat
above 50-60oC
2. pH
disrupt salt bridges
approach pHI
frying egg
sunburn
3. detergents unfold globular proteins SDS
-
+
-
-
+
Na+
SO4-
Denaturing treatments
4. reducing agents
oxidizing agents
5. Metal salts
S-S
Hg+, Pb+, Ag+
SH HS
S-Hg
O Hg+
C O
6. H-bonding solvents alcohol
acetone
7. “Chaotropes”
H2N
O
NH
C
C
urea
NH2
H2N
NH2
guanidine