1. Amino acids R-groups non-polar polar acidic basic proteins
condensation between
carboxylic acids and amines + +
H2O
carboxylic acid
amine
amide

2. Amides amides resonance structure dipeptide alanine glycine Ala-Gly
+H2O

3. Polypeptides _ “backbone” _ H _ R _ H _ R _ H _ R H N1- C1- C1- N2-OH = O = O = O
peptide bonds
C-terminal
residue
N-terminal
residue
biological activity
= structure
protein structure
4 levels

4. 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

5. Secondary structure hydrogen bonding backbone groups N1- C1- C1- N2-_ H = O OH R
H-bond donors
H-bond acceptors
Two main secondary structures:
-helix
-sheet

6. 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 C = O N H
proline
no H-bonding
breaks helix = O C

7. 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

8. Proteins Fibrous 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)
-sheet
insoluble in H2O
keratin
collagen
hair
skin
- helix
non-polar residues

9. Disulfide bonds cysteine -CH2-SH C H N C C H N C S-H H-S reduced [O]
oxidized

10. Tertiary structure Primary structure sequence of amino acids Non-polar
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
Serine
Glutamic acid
Phenylalanine
Histidine
Arginine
Valine
Aspartic acid
Isoleusine
Asperagine
Methionine
Glycine

11. Tertiary structure arrange these in an -helix polar non-polar
Ala-Phe-Ser-Ser-Val-Glu-His-Ile-Met-Arg-Asp-Val-His-Asn-Gly
arrange these in an -helix
Asp 11
Ser 4
His 7
Gly 15
polar
Ser 3
non-polar
Ile 8
interior
Val 12
Asn 14
Arg 10
Glu 6
Phe 2
His 13
Ala 1
Val 5
Met 9
exterior

12. Tertiary structure interaction of the R-groups globular proteins+
globular proteins
proteins fold around
non-polar groups
hydrophobic residues
inside
polar and charged residues
outside

13. Tertiary structure interactions of R-groups LDF
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

14. C-terminus N-terminus His Arg NH+ Asp -O-CH O = His Fe2+ Phe Ala CH3
Cys S
Cys
N-terminus
Pro
Pro

15. Denaturing treatments
1. Heat
above 50-60oC
frying egg
sunburn
2. pH
disrupt salt bridges
approach pHI
3. detergents
unfold globular proteins
SDS - +
Na+
SO4-

16. Denaturing treatments
4. reducing agents
S-S SH HS
oxidizing agents
5. Metal salts
Hg+, Pb+, Ag+
S-Hg C = O _ O-
Hg+
6. H-bonding solvents
alcohol
acetone
7. “Chaotropes”
urea
guanidine