1. Amino Acids carboxylic acid amine R varies with amino acid R = HOH
carboxylic acid
H2N C H
amine  H R R
varies with amino acid
R = H
glycine

2. R-groups Nonpolar glycine -H alanine -CH3 valine -CH-CH3 CH3 proline
2o amine
leucine
-CH2-CH-CH3
CH3
phenylalanine
isoleucine
-CH-CH2-CH3
CH3
methionine
-CH2-CH2-S-CH3

3. Polar R-groups serine -CH2-OH asparagine -CH2-C-NH2 O threonine
-CH-CH3 OH
glutamine
-CH2-C-NH2 O
-CH2
tyrosine
tryptophan
cysteine
-CH2-SH

4. Acidic R-groups -CH2-CH2-C = O OH glutamic acid -CH2-C = O OH
aspartic acid

5. Basic R-groups = lysine -CH2-CH2-CH2-CH2-NH2 arginine
-CH2-CH2-CH2-NH-C-NH2 = NH
histadine

6. Amino acids glycine non-chiral all other -amino acids in proteins
H2N H O OH R O-
H3N+ H R
glycine
non-chiral
all other -amino acids in proteins
L-enantiomers
at neutral pH (pH = 7.0)
zwitterion
very high b.p. (> 200oC)
very soluble in water

7. acid-base chemistry low pH neutral pH high pH amine protonatedOH R C
H2N H O OH R C
H2N H O O- R O-
H3N+
low pH
neutral pH
high pH
amine protonated
amine and c.a.
deprotonated
amine and c.a.
protonated
c.a. deprotonated
no net charge
negative charge
positive charge
pH = pHI
isoelectric point
amino acids
diprotic acids
2 pKa

8. Titration of an amino acid
alanine
R = CH3 C
H3N+ H O OH R
pKa1 = 2.34
pKa2 = 9.69
Ka1 = =
4.57 x 10-3
CH3
Ka1 =
[H+][A-]
[H+] [A-] [HA]
0.1 M
[HA]
initial
0.1
change +x +x -x
equil.
4.57 x 10-3 = x2 +x +x
0.1-x
0.1 - x
pH = 1.87
X = 2.14 x 10-2 =
[H+]

9. × net charge pH equivalents of OH- +1 9.0 8.0 7.0 6.0 5.0 4.0 3.0 2.0
1.0
2.0
3.0
4.0
5.0
6.0
7.0
8.0
9.0 ×

10. × × pH equivalents of OH- net charge 0.05 M 0.05 M 0.05 M pH = pKa +
1.0
2.0
3.0
4.0
5.0
6.0
7.0
8.0
9.0 ×
net charge +1
+1/2
0.05 M
pKa1 = 2.34
0.05 M
0.05 M ×
pH =
pKa +
log [A-]
[HA]
0.05 M
1/2
pH = pKa
= 2.34

11. × × net charge at equivalence point: pH isoelectric point pH =+1
+1/2
pKa2 = 9.69
pKa1 = 2.34 pH
equivalents of OH-
1.0
2.0
3.0
4.0
5.0
6.0
7.0
8.0
9.0 × ×
isoelectric point
pH =
pKa1 + pKa2 2
pH = ( )/2
1/2 1
pH = pHI = 6.02

12. × × × × pH equivalents of OH- net charge at 2nd half-way point:
1.0
2.0
3.0
4.0
5.0
6.0
7.0
8.0
9.0 ×
net charge
at 2nd half-way point: +1
+1/2
-1/2 -1 × ×
pKa2 = 9.69 ×
pH = pKa2
= 9.69
1/2 1
3/2

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

14. Proteins _ “backbone” _ H _ R _ H _ R _ H _ R H N1- C1- C1- N2- C2-OH = O = O = O
peptide bonds
C-terminal
residue
N-terminal
residue
biological activity
= structure
protein structure
4 levels
Primary structure =
order of the amino acids

15. 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

16. 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

17. 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

18. = glutamic acid R = - CH2CH2COOH pKa1 = 3.20 (-COOH) pKa2 = 4.25
H3N+ H O OH R
pKa1 = 3.20
(-COOH)
CH2CH2C = O OH
pKa2 = 4.25
(R-COOH)
pKa3 = 9.67
(-NH3)
It will take ___ equivalents to titrate glutamic acid 3
1st group
2nd group
3rd group

19. = × × × × × pKa1 = 3.20 pKa2 = 4.25 pHI = 3.7 pKa3 = 9.67 3.2 + 4.25O -2 +1 -1 C 12 OH
H3N+ C H = O 10 ×
CH2CH2C OH 8
pKa1 = 3.20 × pH
pKa2 = 4.25
pHI = 3.7
pKa3 = 9.67 × 4 × ×
= 3.7 2 2
= 7.0 2 1 2 3
equivalents OH-