CHAPTER 3

Amino Acids

Outline
3.1 Proteins Are Built from a Repertoire of 20 Amino
Acids
3.2 Amino Acids Contain a Wide Array of Functional
Groups
3.3 Essential Amino Acids Must Be Obtained from the
Diet

1
 Two Different Ways of Depicting How
Biomolecules Will Be Used
• Fischer projections are useful • Stereochemical renderings are
for visualizing the constituent useful for visualizing the shape of
atoms of the molecule. the molecule
• Every atom is identified, and • Wedges are used to depict the
the bonds to the central atom direction of bond projection. A solid
are depicted as vertical and wedge shows the bond projecting
horizontal lines. The horizontal toward the viewer out of the plane. A
bonds are taken to project out dashed wedge shows the bond
of the plane toward the viewer, projecting behind the plane, away
whereas the vertical bonds from the viewer. The remaining
are assumed to project behind bonds are depicted as straight lines.
the plane away from the
viewer.

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 Section 3.1 Proteins Are Built from a Repertoire of 20
Amino Acids
Learning objective 1: Identify the main classes of amino acids.
• An α-amino acid is composed of a central carbon atom called the α-carbon.
• The α-carbon is linked to an amino group, a carboxylic acid, a hydrogen atom,
and a distinctive side chain, called the R group.
• When four different groups are bonded to the α -carbon, the amino acids are
chiral, which means that they exist as two mirror-image forms: the L isomer
and the D isomer.
• Only the L isomers are found in proteins.

Figure 3.1 The L and D isomers of amino acids. The

letter R refers to the side chain. The L and D isomers
are mirror images of each other. 3
All Amino Acids Have at Least Two Charged Groups
• Free amino acids in solution at neutral pH exist as dipolar ions.
• The amino group (NH3+) and the carboxyl group (COO−) are charged.
• The ionization state of amino acids vary as a function of pH

Figure 3.2 Ionization state as a function of pH. The ionization state of amino acids is
altered by a change in pH. The zwitterionic form predominates near physiological pH,
approximately 7.4 .
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 Section 3.2 Amino Acids Contain a Wide Array
of Functional Groups
• The 20 amino acids found in proteins contain unique side
chains that vary in size, shape, charge, hydrogen-bonding
capacity, hydrophobic character, and chemical reactivity.
• Amino acids have three-letter abbreviations and one-letter
symbols.
• Amino acids can be sorted into four groups on the basis of
the general characteristics of their R groups:
– Hydrophobic amino acids (9)
– Polar amino acids (6)
– Positively charged amino acids (3)
– Negatively charged amino acids (2)
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 Hydrophobic Amino Acids Have Mainly
Hydrocarbon Side Chains

• The amino acids having side chains consisting only of

hydrogen and carbon are hydrophobic.
• The hydrophobic amino acids, particularly the larger
aliphatic and aromatic ones, tend to cluster together inside
the protein away from the aqueous environment of the cell.

6
 Fischer projection and stereochemical
rendering of hydrophobic amino acids
Mnemonic
Glycine Go
Alanine And
Valine Vote
Leucine Like
Isoleucine It
Methionine Matters
Proline Please
Phenylalanine For
Tryptophan Wellness

7
 Hydrophobic Amino Acids
Glycine and Alanine
GAVLIMPFW
Mnemonic
Glycine Go
Alanine And
Valine Vote
Leucine Like
Isoleucine It
Methionine Matters
Proline Please
Phenylalanine For
Tryptophan Wellness

8
 Hydrophobic Amino Acids
Valine, Leucine, and Isoleucine
GA VLI MPFW
Mnemonic
Glycine Go
Alanine And

Valine Vote
Leucine Like
Isoleucine It

Methionine Matters
Proline Please
Phenylalanine For
Tryptophan Wellness

9
 Hydrophobic Amino Acids
Methionine, Proline, Phenylalanine, and Tryptophan
Mnemonic
Glycine Go
GAVLI MPFW
Alanine And
Valine Vote
Leucine Like
Isoleucine It
Methionine Matters
Proline Please
Phenylalanine For
Tryptophan Wellness

10
 Polar Amino Acids Have Side Chains That
Contain an Electronegative Atom
Polar amino acids are neutral overall, yet they are polar because the R
group contains an electronegative atom that hoards electrons.

Mnemonic:
Stand Tall You Can Never Quit 11
 Polar Amino Acids
Serine, Threonine, and Tyrosine
STY CNQ

Mnemonic:
Stand Tall You
Can Never Quit 12
 Polar Amino Acids
Cysteine, Asparagine, and Glutamine
STY CNQ

Mnemonic:
Stand Tall You
Can Never Quit 13
 Applications of Biochemistry

Glutamine plays a number of important

roles in rapidly dividing cells, including
cancer cells. In addition to being used in
protein synthesis, glutamine enhances fuel
metabolism by providing components for
the TCA cycle, which oxidizes carbon
fuels. Glutamine also provides nitrogens
for the synthesis of nucleotides, which are
required for RNA and DNA synthesis.

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 Positively Charged Amino Acids Are Hydrophilic
• Amino acids having positively charged side chains are very hydrophilic.

• The R group of lysine is topped with an amino group, whereas that of

arginine is topped with a guanidinium group.

Mnemonic
Kitties
R
Hairy
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 Applications of Biochemistry

DID YOU KNOW?

Lysine is an essential amino acid, which
means that human beings cannot
synthesize lysine and must obtain it in the
diet. In experimental animals kept on a
cereal-based diet, inadequate dietary
lysine increased stress-induced anxiety.
Recent studies suggest that this response
to lysine deprivation may be true for
human beings, too.

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Positively Charged Amino Acids Are Hydrophilic:
Histidine (H)
• Histidine has an imidazole side chain
that can be uncharged or positively
charged at neutral pH.

Figure 3.6 Histidine ionization. Histidine can

bind or release protons near physiological pH.

• Histidine is found at the active sites of many enzymes

that require a proton donor or proton acceptor.
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 Negatively Charged Amino Acids Have
Acidic Side Chains
• The two amino acids in
this group, aspartic acid
and glutamic acid, have
acidic side chains that are
usually negatively
charged under
intracellular conditions.

• These amino acids are

often called aspartate and
glutamate to emphasize
the presence of the
negative charge on their
side chains.

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 Applications of Biochemistry

DID YOU KNOW?

Monosodium glutamate (MSG), which
is glutamate with sodium bound to an
acid group, is commonly used as a
taste enhancer. In fact, the taste of
glutamate and aspartate (called
umami, from the Japanese word for
“deliciousness”) is one of the five
primary tastes, the others being sweet,
sour, bitter, and salty.

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 The Ionizable Side Chains Enhance Reactivity
and Bonding
Typical pKa Values of Ionizable Groups in Proteins
• Seven of the 20 amino
acids—tyrosine, cysteine,
arginine, lysine, histidine, and
aspartic and glutamic acids—
have readily ionizable side
chains.

• These seven amino acids are

able to form ionic bonds as
well as to donate or accept
protons (called acid–base
catalysis) to facilitate
reactions.

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 LAP time

Getting to know our AMINO ACIDS!

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 Section 3.3 Essential Amino Acids Must be
Obtained from the Diet
Table 3.2 Basic set of 20 Amino acids
• Most microorganisms Nonessential Essential
can synthesize the
entire basic set of 20 Alanine Histidine
amino acids, whereas Arginine Isoleucine
human beings can
make only 11 of them. Asparagine Leucine
• Amino acids that cannot
Aspartate Lysine
be generated in the Cysteine Methionine
body must be supplied
by the diet and are Glutamate Phenylalanine
termed essential amino Glutamine Threonine
acids. The others are
called nonessential Glycine Tryptophan
amino acids. Proline Valine
Serine
Tyrosine 22
 Applications of Biochemistry
Pathological Conditions
Result If Protein Intake Is
Inadequate

Kwashiorkor is a form of malnutrition

resulting from inadequate consumption of
amino acids usually ingested as proteins.

A Child Suffering from Kwashiorkor: Note the swollen belly and limbs. This
swelling (edema) is due to fluid collecting in the tissues because there is not
enough protein in the blood. 23