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Chapter 4: Amino Acids

Amino acid structure
General properties
Peptide bonds
Classification and characteristics
Acid-base properties
Nomenclature
Stereochemistry
Nonstandard amino acids
Amino acid derivatives
D-amino acids
Biologically active amino acids
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Backbone of an amino acid is
composed of the N, Co, and C
Amino acid structures and
sequences are written from
left to right, starting with the
N-terminus (amino) and
finishing with the C-terminus
(carboxyl)
The thing that differentiates
each amino acid is the R
group
Co is chiral, except in Gly
o
Please carefully note the
charged ends (termini).
At physiological pH, the
ends of an amino acid are
charged. Certain R
groups will also be charged
at pH 7.
Amino acid
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General Properties
The backbone of individual amino acids are zwitterionic
(i.e. has both a positively charged and a negatively
charged group)
Some amino acids have ionizable (i.e., charged) side
chains
Because of these ionizable groups (backbone and some
side chains), amino acids can have a number of different
charge states
The R group in an amino acid is called the side chain
An amino acid is often called a residue (i.e., an amino
acid residue, especially in polypeptides and proteins)
There are 20 standard amino acids - they all differ in R
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Amino Acids: Protein Legos, But Cheaper!
Condensation Reaction = Peptide Bond
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Classification
Non-polar
Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine
(Leu, L), Isoleucine (Ile, I), Methionine (Met, M), Proline
(Pro, P), Phenylalanine (Phe, F), Tryptophan (Trp, W)
Polar
Serine (Ser, S), Threonine (Thr, T), Asparagine (Asn, N),
Glutamine (Gln, Q), Tyrosine (Tyr, Y), Cysteine (Cys, C)
Charged
Aspartic acid (Asp, D, -1); Glutamic acid (Glu, E, -1)
Lysine (Lys, K, +1); Arginine (Arg, R, +1), Histidine (His, H,
+1)
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7
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9
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Nomenclature: o-amino acids because carboxylic and amino groups
Are connected to the a-carbon.
pK
1
and pK
2
respectively pK
R
is for R group pKs

pK
1
~ 2.2 while pK
2
~ 9.4 pKas of the termini for ALL AAs
pK
1
pK
2

At physiological pH, carboxylic and amino groups are
completely ionized!!! Try drawing structure of amino
acids at different pHs!
pK
R

Acid - Base Properties of Amino Acids
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Acid - Base Properties of Amino Acids
|
|
.
|

\
|
+ =
[HA]
] [A
log pK pH
-
( )
j i
pK pK
2
1
pI + =
Henderson-Hasselbalch Eq.

Isoelectric point: the pH where a
protein carries no net electrical
charge
The observed pKa of an amino acid side
chain is dependent on its environment in the
protein - standard pKas can be substantially
shifted by the protein environment
Glycine
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Isoelectric Point
pI = 0.5(pK
i
+ pK
j
) for 2 ionizable groups (Average)
If amino acid has ionizable side chain, then it must be
taken into account when computing pI!
If the side chain is negatively charged when ionized
(Asp, Glu), then pI = 0.5(pK
1
+ pK
R
) (remember pK
1
is
the pK
a
of the C-terminus, -COOH)
e.g., pI of Asp = 0.5(2.20 + 3.90) = 3.05 (the total charge from
the side chain and C-term at pH=3.05 is 1 which balances
with the +1 charge of the N-term to give a total charge of 0)
If the side chain is positively charged when ionized (Arg,
Lys, His), then pI = 0.5(pK
R
+ pK
2
) (remember pK
2
is
the pK
a
of the N-terminus, -NH
2
)
E.g., pI of Lys = 0.5(10.54 + 9.4) = 9.97
Practical pI Calculations: Asp
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K
a1
= 2.0 A- = HA log(1) pH = 2.0 = pK
10A-, 1HA log(10) pH = 3.0
100A-, 1HA log(100) pH = 4.0
1000A-, 1HA log(1000) pH = 5.0

K
a2
= 3.9 A- = HA log(1) pH = 3.9 = pK
10A-, 1HA log(10) pH = 4.9
100A-, 1HA log(100) pH = 5.9
1000A-, 1HA log(1000) pH = 6.9
|
|
.
|

\
|
+ =
[HA]
] [A
log pK pH
-
HA H
+
+ A
-
Practical pI Calculations: Asp
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|
|
.
|

\
|
+ =
[HA]
] [A
log pK pH
-
HB
+
B + H
+
K
a
= 9.9 B = HB
+
log(1) pH = 9.9 = pK
1B, 10HB
+
log(0.1) pH = 8.9
1B, 100HB
+
log(0.01) pH = 7.9
1B, 1000HB
+
log(0.001) pH = 6.9
B
HB
+
NOTE! At the pH values for the acids (pKa 2.0 and
3.9), the base above is almost completely (HB
+
)!
Therefore, the pI calculation focuses on the equivalent
numbers of acid groups that must be ionized!
(0.5(pKa1 + pKa2)) = 1.99 + 3.90 / 2 = 2.94
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Amino Acid Nomenclature
Greek lettering used to identify atoms in all amino acid side
chains - lysine and glutamate are shown as examples
Naming is for Carbon atoms - anything attached to the carbon
has the same Greek letter
For example, the NH
3
+ at the end of the Lys side chain is Nc
Glu has carbon for acid, so this is the o carboxylic acid
o
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Amino Acids: Protein Legos, But Cheaper!
Condensation Reaction = Peptide Bond
Polypeptide AYDG
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My Peptide
steven (my last name has a B, drat!)

Horse Myoglobin (154 amino acids)
mglsdgewqq vlnvwgkvea diaghgqevl irlftghpet
lekfdkfkhl kteaemkase dlkkhgtvvl talggilkkk
ghheaelkpl aqshatkhki pikylefisd aiihvlhskh
pgdfgadaqg amtkalelfr ndiaakykel gfqg

Titin
Over 30,000 amino acids total!
Polypeptide Sequences
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Disulfide Bonds
Amino acids in a poly-
peptide chain can also be
cross-linked via two Cys
residues
Cys residues have SH
groups at the end of their side
chains. Two of these groups
can be oxidized to form an S-
S (disulfide) bond.
Disulfide bonds can provide
stability to a protein structure
(hair perms!).
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Nomenclature
STANDARD CONVENTION! Write an amino acid sequence
from the N-terminus to the C-terminus.

N-terminus-AA
1
-AA
2
-AA
3
-AA
4
-AA
n
-C-terminus
Order DOES count left to right, N-term to C-term

Glx means either Gln or Glu; same for Asx (Asn or Asp)

Long name - drop -ine and add -yl and put amino acids in order
(e.g. alanine alanyl, lysine lysyl, etc.)

NOTE! The peptide is different, if named backwards!!!
KCAT (Lys-Cys-Ala-Thr) is different from TACK
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Protein Structure
DNA polymerase I
Adds nucleic acids to
the end of a DNA strand
(shown in red)
The protein undergoes a
conformational change
during reaction (blue
and black are before and
after conformations)
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Protein Structure
Leucyl tRNA synthetase
all organisms
One polypeptide chain that
folds into two functional
domains (green and purple)
The green domain does
editing/error correcting for
mistakes that occur in the
purple domain
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Protein Structure
Alanine racemase
(bacterial)
Homodimer (2
polypeptide
chains)
Purple molecule is
in the active site(s)
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Protein Structure
Pore (porin) protein (ompF) that is inserted through
cell membranes and selectively allows passage of
small molecules (blue barrel; red selectivity filter)
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Botulism toxin
(Clostridium
botulinum)
Nerve toxin
BoTox cosmetic
Wrinkles
Biowarfare defense
Kills by
suffocation
Protein Structure
For Next Time:
Finish Chapter 4 and Start Chapter 5.
We will not be covering Protein Purification yet.
Keep working problems in Textbook and Student
Companion for Chapters 4 and 5.
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