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Amino Acid Sidechains

CH3
CH3
Neutral - Nonpolar
C CH CH3
H CH3 CH CH3 H2
Glycine (Gly or G) Alanine (Ala or A) Valine* (Val or V) Leucine* (Leu or L)

H H2
C CH2 CH3 C C S CH3 C
H2 H2
C
CH3 H2
NH

Isoleucine* (Ile or I) Methionine* (Met or M) Phenylalanine* (Phe or F) Tryptophan* (Trp or W)


H
N
This is the entire Neutral - Polar H
OH
C O
amino-acid. The side
chain is circled C OH
OH H2
CH 3
Serine (Ser or S) Threonine* (Thr or W)
Proline (Pro or P)

O
O

C C NH2 H2 C OH
C C C NH2
C SH H2
H2 H2 H2
Asparagine (Asn or N) Glutamine (Gln or Q) Cysteine (Cys or C) Tyrosine (Tyr or Y)

Acidic O
O O O
H2 H2
C C OH C C O- C C C OH C C C O-
H2 H2 H2 H2

Aspartic Acid (Asp or D) (Ionized form of Asp) Glutamic acid (Glu or E) (Ionized form of Glu)

Basic
H2 H2 H2 H2 H2 H2
C C C C NH2 C C C C NH3
H2 H2

Lysine* (Lys or K) (Ionized form of Lys)


NH NH2

H2 H2 H H2 H2 H
C C C N C NH2 C C C N C NH2
H2 H2

Arginine (Arg or R) (Ionized form of Arg)


NH
NH C
H2
C
H2 N
N
H
Histidine (His or H) (Ionized form of His)

* These amino acids are essential in human nutrition (we can not synthesize them).

Reyes 1
Relationship of pK and pH to charge
Every acidic or basic group on a molecule has a different “pK” (K is the dissociation constant) value. The
relationship between the pH of the solution it is in and the pK of the ionizable group will determine the
predominant form of the ionizable group. Every acidic or basic group has an “acid form” (also known as the
“protonated form”) and a “base form” (also known as the “deprotonated form”). For carboxylic acids, the
protonated form (acid form) is –COOH and the deprotonated form (base form) is –COO-. Form amines, the
protonated form (acid form) is –NH3+ and the deprotonated form (base form) is –NH2.

If the pH of the solution equals the pK of the ionizable group, then the acid and base forms of that group
will be present in equal amounts.

If the pH of the solution is lower than the pK of the ionizable group, then the acid form of that group will
be more abundant than the base form. (The predominant form is the protonated form.)

If the pH of the solution is higher than the pK of the ionizable group, then the base form of that group will
be more abundant than the acid form. (The predominant form is the deprotonated form.)

Knowing the pH of the solution and using the previous three possible scenarios, you can determine if an ionizable
group will be neutral, positively or negatively charged. Once you have drawn all the ionizable groups in their
respective forms, you can add up all the charges present to give the overall charge of the amino acid or peptide you
are drawing.

pK values of ionizable groups in proteins.

Group Acid ⇌ Base + H+ Typical pK*

Terminal Carboxyl COOH COO- + H+ 3.1


H2 H2
Aspartic acid C COOH C COO - + H+ 3.9
H2 H2 H2 H2
Glutamic acid C C COOH C C COO - + H+ 4.0
H2 H2
C C
+ H+
Histidine N NH
6.0
HN NH

Terminal amino NH3 NH2 + H+ 8.0

Cysteine SH S- + H+ 8.2

Tyrosine 10.5
OH O- + H+

Lysine (CH2)4 NH3 (CH2)4 NH2 + H+ 10.5


NH 2 NH
H H
(CH2 )3 N C (CH2 )3 N C + H+
Arginine 12.5
NH 2 NH 2

*pK values depend on temperature, ionic strength, and the microenvironment of the ionizable group.

Reyes 2