CHEM 160 MODULE 3.

PROTEINS

RESOURCE 1: AMINO ACIDS

Basic Structure of Amino Acids

Amino acids are the monomers that make up proteins. Each amino acid has the same fundamental
structure (Figure 1), which consists of a central carbon atom, also known as the alpha (α) carbon
(Cα), bonded to an amino group (NH2), a carboxyl group (COOH), and to a hydrogen atom. Every
amino acid also has another atom or group of atoms bonded to the central atom known as the R
group (side chain).

Figure 1. General structure of an amino acid (OpenStax College, Biology (CC BY 3.0)).

Stereochemistry of Amino Acids

Twenty amino acids are naturally incorporated into polypeptides and are encoded by the universal
genetic code. These are called proteinogenic or standard amino acids. Except for glycine, all the 19
other standard amino acids have a uniquely different functional group on the tetrahedral Cα. The Cα
is termed "chiral" to indicate there are four different substituents and that the Cα is asymmetric.
Since the Cα is asymmetric there exists two possible, non-superimposable, mirror images of the
amino acids (i.e. enantiomers) (Figure 2):

Figure 2. Stereoisomerism in α-amino acids.

The absolute configurations of simple sugars and amino acids are specified by the D, L system, based
on the absolute configuration of the three-carbon sugar glyceraldehyde (Figure 3). For all chiral
compounds, stereoisomers having a configuration related to that of L-glyceraldehyde are designated
L, and stereoisomers related to D-glyceraldehyde are designated D. All standard amino acids are
found in the L-form in living systems. L-Amino acids are those with the α-amino group on the left,
and D-amino acids have the α-amino group on the right.

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 Figure 3. Steric relationship of the stereoisomers of alanine to the
absolute configuration of L- and D-glyceraldehyde.

Structure, Nomenclature and Classification of the Standard Amino Acids

The 20 standard amino acids are structurally and chemically different and differ in size and volume.
Some are branched, some are linear, some have ring structures. The structure, nomenclature and
classification of the 20 standard amino acids are shown in Table 1. The structural formulas are the
state of ionization that would predominate at pH 7.0. Amino acids are represented by a single
uppercase letter or a three-letter abbreviation. A typical grouping of their chemical nature is based
on the properties of their R groups, particularly, their polarity, or tendency to interact with water at
biological pH (near pH 7.0)

• Nonpolar, Aliphatic R Groups – contain nonpolar and hydrophobic side chains, participate in
hydrophobic interactions
• Aromatic R Groups – contain aromatic side chains, relatively nonpolar (hydrophobic),
participate in hydrophobic interactions
• Polar, Uncharged R Groups – contain polar and hydrophilic side chains, form hydrogen bonds
with water
• Negatively Charged (Acidic) R Groups – contain a carboxylic acid functional group with a
negative charge at neutral pH, can form H-bond with water, can form ionic interactions
• Positively Charged (Basic) R Groups – nitrogen-containing bases (e.g. guanidino, imidazole or
amino groups) with a net positive charge at neutral pH, form ionic interactions

Ten of these amino acids are considered essential in humans because these cannot be synthesized
by the human metabolic processes or are not readily available for normal metabolism (e.g. arginine),
thus, must be obtained from the diet.

Table 1. Structure, nomenclature and classification of the 20 standard amino acids.

Name Structure Notes Nutritional
Requirement
Non-polar, Aliphatic R Groups
Glycine alkyl non-essential
(Gly, G) achiral
no real contribution to
hydrophobic interactions

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Alanine alkyl non-essential
(Ala, A) methyl group

Valine alkyl essential

(Val, V) isopropyl group

Leucine alkyl essential

(Leu, L) isobutyl group

Isoleucine alkyl essential

(Ile, I) sec-butyl group

Proline alkyl non-essential

(Pro, P) imino acid
pyrrolidine ring

Methionine sulfur-containing essential

(Met, M) (thioether)

Aromatic R Groups
Phenylalanine phenyl ring essential
(Phe, F)

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Tyrosine hydroxyl group non-essential
(Tyr, Y) can form H-bonds

Tryptophan aromatic essential

(Trp, W) indole ring
can form H-bonds

Polar, Uncharged R Groups

Serine alcohol non-essential
(Ser, S) primary hydroxyl group

Threonine alcohol essential

(Thr, T) secondary hydroxyl group

Cysteine sulfur-containing (thiol) non-essential

(Cys, C) sulfhydryl group

Asparagine amide non-essential

(Asp, N)

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Glutamine amide non-essential
(Gln, Q)

Negatively Charged (Acidic) R Groups

Aspartic acid second carboxylic group non-essential
(Aspartate)
(Asp, D)

Glutamic acid second carboxylic group non-essential

(Glutamate)
(Glu, E)

Positively Charged (Basic) R Groups

Lysine second primary amino essential
(Lys, K) group (ε-amino)

Arginine guanidino group essential

(Arg, R)

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Histidine imidazole group essential
(His, H)

Uncommon Amino Acids

In addition to the 20 standard amino acids, there are several uncommon ones found:
• Hydroxylysine and hydroxyproline. These are found in the protein collagen. Collagen is a
fibrous protein made up of three polypeptides that form a stable assembly, but only if the
proline and lysine residues are hydroxylated. (requires vitamin C for reduction of these
amino acids to hydroxy form)
• Thyroxine, an iodinated derivative of tyrosine, found in thyroglobulin (produced by thyroid
gland; requires iodine in diet)
• γ-carboxyglutamic acid (i.e. glutamic acid with two carboxyl groups) found in certain blood
clotting enzymes (requires vitamin K for production)
• N-methyl arginine and n-acetyl lysine. Found in some DNA binding proteins known as
histones

Amino Acids as Buffers

When an amino acid is dissolved in water, it exists in solution as the dipolar ion, or zwitterion
(German for “hybrid ion”), as shown in Figure 4. A zwitterion can act as either an acid (proton donor)
or as a base (proton acceptor):

high [H+] low [H+]

Cationic Zwitterionic Anionic

Figure 4. Protonic equilibria of amino acids.

Since amino acids, as well as peptides and proteins, incorporate both acidic and basic functional
groups, the predominant molecular species present in an aqueous solution will depend on the pH of
the solution. In order to determine the nature of the molecular and ionic species that are present in
aqueous solutions at different pH values, we make use of the Henderson-Hasselbalch Equation,
written below. Here, the pKa represents the acidity of a specific conjugate acid (HA). When the pH of
the solution equals pKa, the concentrations of HA and A– must be equal (log 1 = 0). The pKa values of
the standard amino acids are given in Table 2.

[𝐻𝐴]
𝑝𝐾𝑎 = 𝑝𝐻 + 𝑙𝑜𝑔10
[𝐴− ]

The titration curve for glycine in Figure 4 demonstrates this relationship. At very low pH, the
predominant ionic species of glycine is the fully protonated form, +H3N-CH2-COOH. At the midpoint

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(point of inflection) in the first stage of the titration, in which the -COOH group of glycine loses its
proton, equimolar concentrations of the proton-donor (+H3N-CH2-COOH) and proton-acceptor (+H3N-
CH2-COO-) species are present. The pH at the midpoint is 2.34, thus its -COOH group has a pKa
(labeled pK1) of 2.34. As the titration proceeds, another important point is reached at pH 5.97
(labeled as pI). Here, there is another point of inflection, at which removal of the first proton is
essentially complete and removal of the second has just begun. At this pH glycine is present largely
as the dipolar ion (+H3N-CH2-COO-). The second stage of the titration corresponds to the removal of a
proton from the -NH3+ group of glycine. The pH at the midpoint of this stage is 9.60, equal to the pKa
(labeled pK2) for the -NH3+ group. The titration is essentially complete at a pH of about 12, at which
point the predominant form of glycine is H2N-CH2-COO-.

Figure 4. Titration curve of glycine (Lehninger et al., 2005).

We can derive several important pieces of information from the titration curve of glycine. First, it
gives a quantitative measure of the pKa of each of the two ionizing groups: 2.34 for the -COOH group
and 9.60 for the -NH3+ group. Second is that glycine has two regions of buffering power. One of
these is the relatively flat portion of the curve, extending for approximately 1 pH unit on either side
of the first pKa of 2.34, indicating that glycine is a good buffer near this pH. The other buffering zone
is centered around pH 9.60. (Note that glycine is not a good buffer at the pH of intracellular fluid or
blood, about 7.4.). Third, is the relationship between the net electric charge of glycine and the pH of
the solution. At pH 5.97, glycine is present predominantly as its dipolar form, fully ionized but with
no net electric charge. The characteristic pH at which the net electric charge is zero is called the
isoelectric point or isoelectric pH, designated pI. Since glycine has no ionizable group in its side
chain, the pI is simply the arithmetic mean of the two pKa values {i.e. ½ (2.34 + 9.60) = 5.97}.

Some amino acids have additional acidic or basic groups in their side chains. A third pKa,
representing these groups (pKaR) is listed in the fourth column of Table2. The pI values (fifth column
of Table 2) of these amino acids are often very different from those amino acids without ionizable R
groups. As expected, such compounds display three inflection points in their titration curves, as
illustrated by the titration curves of glutamate (Figure 5) and histidine (Figure 6). For each of these
compounds four possible charged species are possible, one of which has no overall charge. Formulas
for these species are written above the titration curves, together with the net charge of each
species.

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 Figure 5. Titration curve of glutamic acid (Lehninger et al., 2005).

Figure 6. Titration curve of histidine (Lehninger et al., 2005).

If additional acidic or basic groups are present in the side chain, the pI is the average of the pKa
values of the two most similar acids. To assist in determining similarity we define two classes of
acids. The first consists of acids that are neutral in their protonated form (e.g. –COOH & –SH). The
second includes acids that are positively charged in their protonated state (e.g. –NH3+). In the case of
glutamic acid, the similar acids are the α-carboxyl group (pKa = 2.19) and the side chain carboxyl
group (pKa = 4.25), so pI = ½ (2.19 + 4.25) = 3.22. For histidine, the similar acids are the amino group
in the imidazole ring on the side chain (pKa = 6.0) and the α-amino group (pKa = 9.17), so the
calculated pI = ½ (6.0 + 9.17) = 7.59.

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 Table 2. pKa and pI values of the standard amino acids (Lehninger et al., 2005).

pKa1 pKa2 pKaR pI

Amino acid
(-carboxyl) (protonated -amino) (side chain)
Gly 2.34 9.60 5.97
Ala 2.34 9.69 6.01
Val 2.32 9.62 5.97
Leu 2.36 9.60 5.98
Ile 2.36 9.68 6.02
Pro 1.99 10.96 6.48
Phe 1.83 9.13 5.48
Tyr 2.20 9.11 10.07 5.66
Trp 2.38 9.39 5.89
Ser 2.21 9.15 5.68
Thr 2.11 9.62 5.87
Cys 1.96 10.28 8.18 5.07
Met 2.28 9.21 5.74
Asn 2.02 8.80 5.41
Gln 2.17 9.13 5.65
Asp 1.88 9.60 3.65 2.77
Glu 2.19 9.67 4.25 3.22
Lys 2.18 8.95 10.53 9.74
Arg 2.17 9.04 12.48 10.76
His 1.82 9.17 6.00 7.59

References/ Attributions

This resource is a modified derivative work that includes materials from the following sources:

“Proteins” by OpenStax College, Biology (CC BY 3.0):

https://cnx.org/contents/GFy_h8cu@11.10:2zzm1QG9@8/Proteins. The Openstax book can be
downloaded for free at https://openstax.org/details/books/biology.

“Nomenclature of Amino acids” by LibreTexts (CC BY-NC-SA 3.0):

https://chem.libretexts.org/Bookshelves/Biological_Chemistry/Supplemental_Modules_(Biological_
Chemistry)/Proteins/Amino_Acids/Nomenclature_of_Amino_acids

“Stereochemistry of Amino Acids” by LibreTexts (CC BY-NC-SA 3.0):

https://chem.libretexts.org/Bookshelves/Biological_Chemistry/Supplemental_Modules_(Biological_
Chemistry)/Proteins/Amino_Acids/Properties_of_Amino_Acids/Stereochemistry_of_Amino_Acids

“Amino Acids, the Henderson-Hasselbalch Equation, and Isoelectric Points” by LibreTexts (CC BY-NC-
SA 3.0):
https://chem.libretexts.org/Bookshelves/Organic_Chemistry/Map%3A_Organic_Chemistry_(McMur
ry)/26%3A_Biomolecules-
_Amino_Acids%2C_Peptides%2C_and_Proteins/26.04%3A_Amino_Acids%2C_the_Henderson-
Hasselbalch_Equation%2C_and_Isoelectric_Points

Lehninger, A. L., Nelson, D. L., & Cox, M. M. (2005). Lehninger Principles of Biochemistry (4th ed.).
New York, N.Y., Basingstoke: W.H. Freeman

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