Chapter 3.1:
Amino Acids
CHEM 7784
Biochemistry
Professor Bensley
CHAPTER 3.1
Amino Acids
Today’s Objective: to understand
• The structure and naming of amino acids
• The ionization behavior of amino acids
Proteins: Main Agents of
Biological Function




Catalysis
Transport
Structure
Motion
Proteins
monomer
amino acid
polymer protein subunit
Supramolecular Enzyme complex
structure
Amino Acids: Building Blocks
of Protein
carboxyl group
amino group
a-carbon
side chain
Amino Acids: Atom Naming
• Organic nomenclature: start from one end
• Biochemical designation: start from
a-carbon and go down the R-group
Proline
Nonpolar, Aliphatic R Groups
These amino
acid side
chains are
hydrophobic.
Aromatic R Groups
These amino
acid side
chains absorb
UV light at
270-280 nm.
Polar, Uncharged R Groups
•These amino
acids side chains
can form hydrogen
bonding
•Cysteine can form
disulfide bonds
Positively Charged (Basic) R Groups
Negatively Charged (Acidic) R Groups
• Amino Acid structure flash card template (pdf file)
available to download on course website
Amino Acid
Name
3 Letter
Abbreviation
One-Letter
Symbol
pI
Occurrence in
Proteins (%)
Glycine
Gly
G
5.97
7.2
Alanine
Ala
A
6.01
7.8
Proline
Pro
P
6.48
5.2
Valine
Val
V
5.97
6.6
Leucine
Leu
L
5.98
9.1
Isoleucine
Ile
I
6.02
5.3
Methionine
Met
M
5.74
2.3
Phenylalanine
Phe
F
5.48
3.9
Tyrosine
Tyr
Y
5.66
3.2
Tryptophan
Trp
W
5.89
1.4
Amino Acid
Name
3 Letter
Abbreviation
One-Letter
Symbol
pI
Occurrence in
Proteins (%)
Serine
Ser
S
5.68
6.8
Threonine
Thr
T
5.87
5.9
Cysteine
Cys
C
5.07
1.9
Asparagine
Asn
N
5.41
4.3
Glutamine
Gln
Q
5.65
4.2
Lysine
Lys
K
9.74
5.9
Histidine
His
H
7.59
2.3
Arginine
Arg
R
10.76
5.1
Aspartate
Asp
D
2.77
5.3
Glutamate
Glu
E
3.22
6.3
Essential Amino Acids
Amino Acid
Min.
Daily # of pathways - One
mg.
Pathway
1
Isoleucine*
10
1 - threonine --> isoleucine -
-
muscles
2
Leucine*
14
1 - keto-isovalerate -->
leucine
-
-
blood, muscle,
hormone
3
Lysine
12
2 - asparate --> lysine
-
calcium
herpes, triglycerides
4
Methionine
13
7 - homoserine -->
methionine
cysteine
selenium,
zinc
hair, skin, chelator
5
Phenylalanine 14
3 - chorismate -->
phenylalanine
tyrosine
B6
depression
6
Threonine
7
3 - aspartate --> threonine
glycine, serine
-
collagen, tooth
enamel
7
Tryptophan
3.5
1 - chorismate -->
tryptophan
niacin, seratonin -
depression
8
Valine*
10
1 - pyruvate --> valine
-
muscles
Generates
Works
With
(Against)
Augments
-
Food Sources: Fish - meat - poultry - cottage cheese - peanuts - lentils
*= BCAA, Branched-Chain Amino Acids, all important in muscle recovery
Uncommon Amino Acids
Ionization of Amino Acids
• At acidic pH  cationic form
• At neutral pH  Zwitterions
• At alkaline pH  anionic form
Chemical Environment Affects pKa Values
•a-carboxy group is much more acidic than in
carboxylic acids
•a-amino group is slightly less basic than in amines
Amino Acids Can Act as Buffers
•Amino acids with uncharged side-chains,
such as glycine, have two pKa values:
•The pKa of the a-carboxyl group is 2.34
•The pKa of the a-amino group is 9.6
•Therefore, Glycine can act as a buffer in two
pH regions. (See next slide)
Isoelectric Point, pI
•Amino Acids Carry a Net Charge of Zero at a
Specific pH
pK1  pK 2
pI 
2