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AMINO ACIDS
Structures and Properties
Essential Amino Acids
Molecular Handedness
Peptide Bond Formation and Characteristics
Biochemically Important Small Peptides
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Amino acid
• the building blocks of protein
• molecule contains both an amino
group and a carboxylic acid
functional group and a side chain all
attached to an ɑ-carbon
• nature of this side chain
distinguishes ɑ-amino acids from
each other
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Standard Amino Acid

• is one of the 20 amino acids normally
found in proteins building blocks of
protein
• There are four categories:
• nonpolar amino acids
• polar neutral amino acids
• polar acidic amino acids, and
• polar basic amino acids.
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Nonpolar, Neutral Side Chains

• is an amino acid that contains one
amino group, one carboxyl group,
and a nonpolar side chain
• are hydrophobic
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Nonpolar, Neutral Side Chains

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Nonpolar, Neutral Side Chains

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Nonpolar, Neutral Side Chains

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Polar, Neutral Side Chains

• is an amino acid that contains one
amino group, one carboxyl group
and a side chain that is polar but
neutral
• in physiological pH, the side chain
of a polar neutral amino acid is
neither acidic nor basic
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Polar, Neutral Side Chains

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Polar Acidic Amino Acid

• is an amino acid that contains one
amino group and two carboxyl
groups, the second carboxyl group
being part of the side chain
• physiological pH, the side chain of a
polar acidic amino acid bears a
negative charge the side-chain
carboxyl group
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Polar Acidic Amino Acid

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Polar Basic Amino Acid

• is an amino acid that contains two
amino groups and one carboxyl group,
the second amino group being part of
the side chain
• at physiological pH, the side chain of a
polar basic amino acid bears a positive
charge, the nitrogen atom of the amino
group has accepted a proton
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Polar Basic Amino Acid

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Number of
State in Hydrophobic
Classification of
Carboxyl Physiological or
Amino Acids Amino Group pH Hydrophilic
Group

nonpolar amino acids 1 1 ---

Hydrophobic

polar neutral amino 1 1 Neutral Hydrophilic

acids
polar acidic amino 1 2 Acidic Hydrophilic
acids,
polar basic amino 2 1 Basic Hydrophilic
acids.
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Names of the Standard Amino Acids

• often abbreviated using three-letter
codes except in four cases, these
abbreviations are the first three letters
of the amino acid's name
• one-letter code for amino acid names
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Names of the Standard Amino Acids

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Three-Letter One-Letter
Amino Acid
Abbreviation Abbreviation

Alanine Ala A

Cysteine Cys C

Valine Val V
Serine Ser S

Tryptophan Trp W
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THE ESSENTIAL AMINO

ACIDS
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Essential Amino Acid

• is an amino acid needed by the
human body that must be
obtained from dietary source
because it cannot be
synthesized within the body
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*
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Phenylalanine
• Function/s: precursor for the
neurotransmitters tyrosine,
dopamine, epinephrine and
norepinephrine
• Sources: milk, cheese, and
yogurt
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Valine
• Function/s: helps stimulate muscle
growth and regeneration and is
involved in energy production
• Sources: beef, chicken, pork, fish,
tofu, yogurt, beans, podded peas,
seeds, nuts, and whole grains like
oatmeal
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Threonine
• Function/s: part of structural
proteins such as collagen and
elastin, which are important
components of the skin and
connective tissue
• Sources: lean beef, soy, pork,
chicken, liver, cheese, shellfish,
nuts, seeds, and beans
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Tryptophan
• Function/s: is precursor to
serotonin, a neurotransmitter
that regulates your appetite,
sleep and mood
• Sources: chicken, eggs,
cheese, fish, peanuts, pumpkin
and sesame seeds.
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Methionine
• Function/s: necessary for tissue
growth and the absorption of
zinc and selenium
• Sources: beef, fish, pork, tofu,
milk, cheese, nuts, beans, and
whole grains
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Leucine
• Function/s: helps regulate blood
sugar levels, stimulates wound
healing and produces growth
hormones
• Sources: chicken, beef, pork,
fish (tuna), tofu, milk, cheese,
squash seeds, and eggs
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Isoleucine
• Function/s: immune function,
hemoglobin production and
energy regulation
• Sources: eggs, soy, seaweed,
turkey, chicken, cheese, and
fish
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Lysine
• Function/s: protein synthesis,
hormone and enzyme production and
the absorption of calcium, production
of collagen and elastin
• Meat, specifically red meat, pork, and
poultry.
• Sources: cheese, sardines, eggs, tofu,
isolated soy protein, and Spirulina.
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Histidine
• Function/s: used to produce
histamine, a neurotransmitter that is
vital to immune response, digestion,
sexual function and sleep-wake
cycles
• Sources: meat, eggs, dairy protein
(casein), cereal grains, and legumes
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Arginine
• is an essential amino acid in
children required for growth but not
an essential amino acid for adults
• Sources: milk, cheese, and yogurt
• Functions: wound healing,
removing ammonia from the body,
immune function
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Complete Dietary Protein

• contains all of the essential amino acids
the same relative amount in which the
body needs them
• animal sources is usually complete
dietary protein such as casein from milk
and proteins found in meat, fish, and
eggs
• soy is the only common plant protein that
is a complete dietary protein
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Incomplete Dietary Protein

• is a protein that does not contain
adequate amounts, relative to
the body’s needs of one or more
of the essential amino acids
• Gelatin from animal sources
(tryptophan is the limiting amino
acid)
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Incomplete Dietary Protein

limiting amino acids in plants
• lysine (wheat, rice, oats, and
corn)
• methionine (beans and peas),
and
• tryptophan (corn and beans).
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Limiting Amino Acid

• is an essential amino acid that
is missing or present but
inadequate amounts, in an
incomplete dietary protein
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Complementary Dietary Proteins

• are two or more incomplete
dietary proteins that when
combined, provide an adequate
amount of all essential amino
acids
• Rice and Beans
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CHIRALITY AND
MOLECULAR
HANDEDNESS
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Alpha (ɑ-) amino acid

• An amino acid in
which the amino
group is bonded
to the carbon
atom next to the
-COOH group.
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Fischer Projection Formulas

1. The -COOH group is put at the top of the
projection formula, the R group at the bottom.
This positions the carbon chain vertically.
2. The -NH3, group is in a horizontal position.
Positioning it on the left denotes the L isomer,
and positioning it on the right denotes the D
isomer.
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BIOCHEMICALLY
IMPORTANT SMALL
PEPTIDES
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Peptide bond
• is an amide bond that links two
amino acids together.
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Polypeptide
• is a long
unbranched
chain of
amino
acids.
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Peptide bond
• The end with the free H3N+ group
is called the N-terminal end and
the end with the free COO- group
is called the C-terminal end. The
individual amino acids within a
peptide chain are called amino
acid residues.
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Amino Acid Residues

• residue is the portion of an
amino acid structure that
remains, after the release of
H2O, when an amino acid
participates in peptide bond
formation becomes part of a
peptide chain.
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Peptide Nomenclature
• Rule 1: The C-terminal amino acid residue (located
at the far right of the structure) keeps its full amino
acid name
• Rule 2: All of the other amino acid residues have
names that end in -yl. The -yl suffix replaces the
-ine or -ic acid ending of the amino acid name,
except for tryptophan (tryptophyl), cysteine
(cystenyl), glutamine (glutaminyl), and asparagine
(asparaginyl)
• Rule 3: The amino acid naming sequence begins
at the N-terminal amino acid residue
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Peptide Nomenclature
• Glu-Ser-Ala
• Glutamyl-seryl-alanine
• Gly-Tyr-Val
• Glycyl-tyrosyl-valine
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Isomeric Peptides
• contain the same amino acids but in
different order are different molecules
(constitutional isomers) with different
properties.
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Small Peptide Hormones

• produced by the pituitary gland, are
oxytocin and vasopressin
• nonapeptide (nine amino acid
residues) with six of the residues
held in the form of a loop by a
disulfide bond formed from the
interaction of two cysteine residues.
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Small Peptide Hormones

• Oxytocin regulates
uterine contractions
and lactation.
• Vasopressin regulates
the excretion of water
by the kidneys; it also
affects blood pressure.
Another name for
vasopressin is
antidiuretic hormone
(ADH)
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Small Peptide Neurotransmitters

• Enkephalins are pentapeptide
neurotransmitters
• produced by the brain itself that bind at
receptor sites in the brain to reduce pain
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Small Peptide Neurotransmitters

• Met-enkephalin is involved in phenomena
associated with modulated pain perception,
regulation of memory and emotional
conditions
• Leu-enkephalin controls gonadal function.
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Small Peptide Antioxidant

• Glutathione is a tripeptide (Glu-
Cys-Gly) that functions as
antioxidant protecting cellular
contents from oxidizing agents
such as peroxides and
superoxides
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Small Peptide Antioxidant

• an acidic amino acid, is bonded to Cys
through the side-chain carboxyl group
rather than through its a-carbon
carboxyl group