Amino Acids (18.1-18.

3)
Amino acids have the same basic structure
20 common amino acids combine in different sequences to form thousands of
different proteins
Amino acids differ here
H R
All amino acids have C
H3N COO-

Cg General Structure
gamma carbon
H R Beta and gamma carbons
O
C
R C C C C O H3N COO-

beta carbon alpha carbon alpha carbon

Cb Ca Ca 1
Carboxylic acid amino acid
Which of the following are alpha amino acids and which are not?

2
 Classification of Amino Acids
O O O O O
Nonpolar H3N CH C O H3N CH C O H3N CH C O H3N CH C O H3N CH C O
amino acids H CH3 CH CH3 CH CH3 CH2
glycine alanine CH3 CH2 CH CH3
O valine CH3 CH3
H3N CH C O O O isoleucine
O leucine
CH2 H3N CH C O H3N CH C O
CH2 C O
CH2 CH2
S
H2N
CH3 proline
HN
methionine phenylalanine tryptophan
O O O O O O
Polar H3N CH C O H3N CH C O H3N CH C O H3N CH C O H3N CH C O H3N CH C O
uncharged CH2 CH2 CH2 CH2 CH CH3 CH2
amino acids C O CH2 SH OH OH
NH2 C O cysteine serine threonine
asparagine NH2
glutamine tyrosine OH
O
Polar
O O
Polar O
H3N CH C O
H3N CH C O H3N CH C O H3N CH C O O
charged CH2 CH2
charged CH2 CH2 H3N CH C O
acidic CH2 C O basic CH2 CH2 CH2
amino acids C O O amino acids CH2 CH2
CH2 N
O NH
glutamic acid aspartic acid
arginine C NH2 NH3 3 NH
(glutamate) (aspartate) histidine
NH2 lysine
 Amino Acid Abbreviations
3-letter Single-letter
Name
abbreviation abbreviation
Glycine Gly G
Alanine Ala A
Valine Val V
Leucine Leu L
Isoleucine Ile I
Proline Pro P
Phenylalanine Phe F
Tyrosine Tyr Y
Tryptophan Trp W
Cysteine Cys C
Methionine Met M
Lysine Lys K
Arginine Arg R
Histidine His H
Aspartate Asp D
Glutamate Glu E
Asparagine Asn N
Glutamine Gln Q
Serine Ser S
4
Threonine Thr T
 Amino acids are weak polyprotic acids (18.4)
both the amino and carboxy
many protons
groups are protonated at low
pH. Carboxy loses proton first
and then amino loses at high pH.
H H O H H O H O
H N C C O H H N C C O H N C C O
H R H R H R

lower pH neutral pH higher pH

Amino acids are zwitterions (dipolar)

zwitterions have charged residues but are electrically neutral
the amino and carboxy charges cancel each other out at neutral pH so aa wo/
charged side chains are uncharged at neutral pH

Isoelectric point, pI
H R pH where amino acid is electrically neutral
C depends on the R group also
-
H3N COO
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 Amino Acid pKas
a-carboxylic Side
Amino Acid a-amino
acid chain
Alanine 2.34 9.69
Arginine 2.17 9.04 12.48
Asparagine 2.02 8.80
Aspartic Acid 2.09 9.82 3.86
Cysteine 1.71 10.78 8.33
Glutamic Acid 2.19 9.67 4.25
Glutamine 2.17 9.13
Glycine 2.34 9.60
Histidine 1.82 9.17 6.00
Isoleucine 2.36 9.68
Leucine 2.36 9.68
Lysine 2.18 8.95 10.53
Methionine 2.28 9.21
Phenylalanine 1.83 9.13
Proline 1.99 10.60
Serine 2.21 9.15
Threonine 2.63 10.43
Tryptophan 2.38 9.39
Tyrosine 2.20 9.11 10.07
Valine 2.32 9.62 6
 Titration of Amino Acids
Amino acids have titration curves like diprotic or triprotic acids

net charge
+1 0 -1

pK2
X O
H2N CH C O
Net H
charge O
+1 Net
pI X H3N CH C O charge
O H -1

H3N CH C OH Net
H charge
0
X
pK1

7
Alanine
similar to diprotic acid

8
 Histidine
similar to triprotic acid

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Amino Acid Questions. Explain in detail with structures and equations where applicable.
1. Given a peptide with the following amino acid sequence, identify the polar amino
acids, the aromatic amino acids, and the sulfur-containing amino acids.

Val-Met-Ser-Ile-Phe-Arg-Cys-Tyr-Leu

2. Write equations to show the ionic dissociation reactions of the following amino acids:
aspartic acid

valine

3. Draw the predominant ionized forms of the following amino acids at pH 7:

glutamic acid histidine arginine

4. Based on the pKa information for amino acids, is there any amino acid that could serve
as a buffer at pH 6? If so, which one(s)? 10
Amino acid questions continued.
5. Sketch a titration curve for the amino acid cysteine; indicate the pKa values for all
titratable groups.

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 Amino acids have handedness (18.5-18.6)
Chirality - an object or molecule that cannot be superimposed
on its mirror image image is chiral
your left and right hands are mirror images of each other.
They are non-superimposable mirror images.
You cannot exactly superimpose your left and right hands.

non-superimposable
mirror images - chiral
Molecular handedness
Molecules with carbon are frequently chiral
carbon must have 4 different groups bound to it - called
a chiral carbon or chiral center.

The presence of one chiral carbon always produces a chiral

molecule

A molecule with more than one chiral carbon may or may not
be chiral overall superimposable
mirror images - achiral

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In the type of chiral center we are intersted in, carbon must have 4 different groups attached:
The chiral atom that
makes
Examples: the overall molecule
chiral

Propane Has 2 sets of Chloroethane Has 2 identical

CH3 Cl atoms attached
identical groups
attached (the (the hydrogens)
H C H H C H
hydrogens and the achiral
methyl groups) CH3
CH3
achiral
Amino acids

Groups attached to Ca of amino acids

NH3+
H R
NH3+
C - Ca
CH3
H3N COO Ca CH3 H
COO-
H
1. COO- 4 different groups attached COO-

2. H in all amino acids except

3. NH3+ glycine (the R group is hydrogen) Alanine
4. R group enantiomers 13
Label the chiral center in the following molecules if one is present.

OH O NH3 NH3
H2
H3C CH C OH H3C C CH3 H3C C C CH3

Cl Cl
H2 H2 H2 H2
H3C C CH C CH3 H3C CH C C CH3

Two of the 20 common amino acids have two chiral carbon atoms in their structures.
Identify these amino acids, draw their structures below, and label their chiral centers.

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Enantiomers - molecules that are non superimposable mirror images of each other

Enantiomers have the same name but are distinguished by a prefix

R vs. S system most commonly used
D vs. L is older nomenclature

only L amino acids are in making proteins (L for Life)

Enantiomers have many identical physical properties:

melting and boiling points
same pI
same solubility in water
same density

Enantiomers have some physical and chemical properities that differ

rotate plane polarized light in opposite directions
reactivity with other chiral molecules
**biological activity
**odors and tastes
**activity as drugs

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Examples of the differing biological activity of enantiomers:

CH3 CH3

Chiral O O
center
Chiral center

H2C C H H C CH2
CH3 H3C

L-Carvone D-Carvone
mirror
(in spearmint) (in caraway)

Chiral
center Chiral center

(R)-Limonene (S)-Limonene 16
(smell of oranges) mirror (smell of lemons)
 Chiral center Chiral center

O O
H H
O O
N N
HN NH
O O
O O

(R)-Thalidomide (S)-Thalidomide
(sedative) mirror (fetal abnormalities)

H CO2H HO2C H

CH3 H3C

H3CO OCH3

Must be sold
mirror as 97% S
(S)-Naproxen (R)-Naproxen enantiomer
(anti-inflammatory) (liver toxin)

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