JEARNIE LOU M.

ARROYO BSMT – M14 IOCHEM14B

AMINO ACIDS
• Amino acids differ from one
another by the chemical
• Amino acids are the building
composition of their R group
blocks of proteins.
(side chains).
• The sequence of the (bases) in
the gene that encodes the protein
determines the precise amino
acid content, and the sequence
of those amino acids, of a
specific protein.
• The chemical properties of the
amino acids of proteins
determine the biologic activity of
the protein.
• An amino acid contains at least
one of both amino and carboxylic
acid functional groups.

AMINO ACIDS WITH

ELECTRICALLY CHARGED
SIDE CHAINS

• A chain of amino acids is known

as a polypeptide, and a large
polypeptide constitutes a
protein.
• In human serum, proteins
average about 100 to 150 amino
acids in the polypeptide chains.

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 JEARNIE LOU M. ARROYO BSMT – M14 IOCHEM14B
maintenance of energy levels by
regulating glucose

AMINO ACIDS WITH

HYDROPHOBIC SIDE CHAINS LEUCINE
• A branched-chain amino acid;
second most common amino
acid found in protein; necessary
for the optimal growth of infants
and for nitrogen balance in
adults

LYSINE
ESSENTIAL AMINO ACIDS
• Has a net positive charge, which
makes it one of the basic amino
acids by charge; plays a role in
ARGININE
the production of antibodies
• A complex amino acid that is and lowers triglyceride levels.
often found at the catalytic site
in proteins and enzymes due to
its amine-containing side chain METHIONINE
• A sulfur-containing amino acid;
helps to initiate translation of
HISTIDINE
messenger RNA by being the
• 0ne of the basic (by pH) amino first amino acid incorporated
acids due to its imidazole side into the N-terminal position of
chain; it is the direct precursor all proteins
of histamine

PHENYLALANINE
ISOLEUCINE
• A nonpolar amino acid because
• A branched-chain amino acid; of the hydrophobic nature of its
needed to help maintain, heal, benzyl side chain; plays a key
and repair muscle tissue, skin, role in the biosynthesis of other
and bones; it is also needed for amino acids; component of
hemoglobin formation and aspartame

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 JEARNIE LOU M. ARROYO BSMT – M14 IOCHEM14B

THREONINE
• An alcohol-containing amino ASPARAGINE
acid that is an important
• The first amino acid to be
component in the formation of
isolated; it is the ß-amide of
collagen, elastin and tooth
aspartic acid synthesized from
enamel
aspartic acid and ATP; its main
function is converting one
amino acid into another via
TRYPTOPHAN
amination or transamination
• Precursor for serotonin and
melatonin, a neurohormone and
powerful antioxidant; a natural ASPARTIC ACID
relaxant, it helps alleviate
• Derived from alanine with one
insomnia by inducing sleep,
of the B-hydrogens replaced by
soothes anxiety, and reduces
a carboxylic acid group;
depression
precursor of asparagine,
arginine, lysine, methionine,
threonine, isoleucine, and
VALINE
several nucleotides
• A branched-chain amino acid
that is a constituent of fibrous
protein in the body; needed for CYSTEINE
muscle metabolism and
• Classified as a nonessential
coordination, tissue repair, and
amino acid, but it may be
maintenance of nitrogen
essential for infants, the elderly,
balance
and individuals with certain
metabolic diseases or
malabsorption syndromes;
ALANINE
named after cystine, its oxidized
• One of the simplest of the amino dimer.
acids; involved in the
breakdown of glucose; product
of the breakdown of DNA and
dipeptides (anserine and
GLUTAMIC ACID
carnosine), and the conversion
of pyruvate • A very polar amino acid due to
its net negative charge; present
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 JEARNIE LOU M. ARROYO BSMT – M14 IOCHEM14B
in a wide variety of foods and is
responsible for one of the five
TYROSINE
basic tastes of the human sense
of taste (umami). • Synthesized from
phenylalanine; precursor of the
adrenal hormones epinephrine,
GLUTAMINE norepinephrine, and dopamine
and the thyroid hormones,
• The most abundant amino acid
including thyroxine.
in the body, being involved in
more metabolic processes than
any other amino acid
TWO NEW AMINO ACIDS

GLYCINE
SELENOCYSTEINE
• The simplest amino acid
synthesized in the body; the • Was named as an amino acid in
only amino acid that is not 2002
optically active because it has • Encoded by a UGA codon, which
no stereoisomers; has a sweet is normally a stop codon
taste and is used as a • Selenium analogue of cysteine,
sweetener/taste enhancer in which a selenium atom
replaces sulfur

PROLINE
PYRROLYSINE
• Precursor of hydroxyproline,
which is manufactured into • 22nd naturally occurring
collagen, tendons, ligaments, genetically encoded amino
and heart muscle by the body; acid used by some Archaea
works with vitamin C to promote • Encoded by the UAG codon,
healthy connective tissues normally a stop codon
• A lysine derivative

SERINE
• An alcohol-containing amino
acid because of its methyl side
chain, which contains a hydroxy
group; was first isolated from a
silk protein
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 JEARNIE LOU M. ARROYO BSMT – M14 IOCHEM14B

Acid-Base Properties of • Aspartic and glutamic acids have

Amino Acids two carboxyl groups and one
amino group.
• Amino acids with one amino • In strong acid (low pH), all three
group and one carboxyl group of these groups are in their acidic
are better represented by a form (protonated). As the pH is
dipolar ion structure. raised and the solution becomes
more basic, each group in
succession gives up a proton.

• The amino group is protonated

and present as an ammonium
ion, whereas the carboxyl group • Electrophoresis
has lost its proton and is present • Electrophoresis is an important
as a carboxylate anion method for separating amino
• This dipolar structure is acids that takes advantage of
consistent with the salt-like these charge differences.
properties of amino acids, which • In a typical electrophoresis
have rather high melting points experiment, a mixture of amino
(even the simplest, glycine, melts acids is placed on a solid support
at 233°C) and relatively low (e.g., paper), and the support is
solubilities in organic solvents. bathed in an aqueous solution at
• Amino acids are amphoteric. a controlled pH.
They can behave as acids and • An electrical field is then applied
donate a proton to a strong base, across the paper.
or they can behave as bases and • Amino acids that are positively
accept a proton from a strong charged at that pH migrate
acid. toward the negatively charged
cathode. Amino acids that are
negatively charged migrate
toward the positively charged
anode.

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 JEARNIE LOU M. ARROYO BSMT – M14 IOCHEM14B

• Migration ceases when the Ninhydrin Reaction

electrical field is turned off.
• Ninhydrin is a useful reagent for
detecting amino acids and
determining the concentrations
of their solutions.
• It is the hydrate of a cyclic
triketone, and when it reacts
with an amino acid, a violet dye
is produced.
• Because most amino acids do
not have exactly the same
charge at a given pH, mixtures
of amino acids can be
separated by electrophoresis
because the components
migrate toward the anode or
cathode at different rates.
• Electrophoresis is also used to
separate peptides and
proteins because they behave
much like their building
blocks, the amino acids, at a
given pH.

Reactions of Amino Acids

• In addition to their acidic and
basic behavior, amino acids
undergo other reactions typical
of carboxylic acids or amines
• Carboxyl group can be
esterified
• Amino group can be
acetylated to an amide

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 JEARNIE LOU M. ARROYO BSMT – M14 IOCHEM14B

bond. It links two cysteine

PROTEINS units
• If the two cysteine units are in
different parts of the same chain
• Proteins are naturally occurring
of a peptide or protein, a
polymers composed of amino
disulfide bond between them will
acid units joined one to another
form a "loop," or large ring.
by peptide bonds.
• If the two units are on different
chains, the disulfide bond will
cross-link the two chains.

Proteins play numerous roles in

biological systems
• Peptides are oligomers of amino
acids that play important roles in
many biological processes.
• Insulin: controls our blood
sugar levels
• Bradykinin: controls our blood
pressure
• Oxytocin: regulates uterine
contraction and lactation

Disulfide Bond
• Aside from the peptide bond, the
only other type of covalent bond
between amino acids in peptides
and proteins is the disulfide

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 JEARNIE LOU M. ARROYO BSMT – M14 IOCHEM14B

Primary Structure of • Linus Pauling proposed that the

polypeptide chain coils about
Proteins itself in a spiral manner to form
a helix, held rigid by intra-chain
hydrogen bonds. The a-helix, as
• The backbone of proteins is a
it is called, is right-handed and
repeating sequence of one
has a pitch of 5.4 A, or 3.6 amino
nitrogen and two carbon atoms.
acid units.

Secondary Structure of
Proteins
• Regularly repeating structures
stabilized by hydrogen bonds
between the amino acids within
the protein.
• Common secondary structures
are the a-helix and B-pleated
sheet with most serum proteins
forming a helix.
• Secondary structures add new
properties to a protein such as
strength and flexibility

a-Helix
• X-ray crystallographic studies of
a-keratin, a structural protein
present in hair, wool, horns, and
nails, showed that some feature
of the structure repeats itself
every 5.4 Å.

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 JEARNIE LOU M. ARROYO BSMT – M14 IOCHEM14B

B-Pleated Sheet Tertiary Structure of

• The structural protein b-keratin, Proteins
obtained from silk fibroin, shows • Refers to the three-dimensional
a different repeating pattern (7 overall shape/conformation as a
Å) in its x-ray crystal structure. result of the folding or the
• To explain the data, Pauling spatial relationship of the
suggested a pleated-sheet secondary structures to one
arrangement of the peptide another
chain. • Results from the interaction of
• In the pleated sheet, peptide side chains and is stabilized
chains lie side by side and are through the hydrophobic effect,
held together by inter-chain ionic attraction, hydrogen
hydrogen bonds. bonds, and disulfide bonds.
• The function and physical and
chemical properties of a protein
depend on its tertiary structure
of the protein molecule.
Proteins generally fall into one of
two main classes: fibrous or
globular

Fibrous proteins are animal

structural materials and hence are
water insoluble. They, in turn, fall
into three general categories:
▪ Keratins: make up
protective tissue (skin, hair,
feathers, claws, and nails)
▪ Collagens: form connective
tissue (cartilage, tendons,
and blood vessels)
▪ Silks: such as the fibroin of
Adjacent chains run in opposite spider webs and cocoons.
directions. The repeating unit in
each chain, which is stretched out
compared with the a-helix, is about ▪
7 Å.
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 JEARNIE LOU M. ARROYO BSMT – M14 IOCHEM14B

• Keratins and collagens have Globular proteins are very

helical structures, whereas silks different from fibrous proteins.
have pleated-sheet structures. They tend to be water soluble and
• A large fraction of the R groups have roughly spherical shapes.
attached to these frameworks are Instead of being structural,
nonpolar, accounting for the globular proteins perform various
insolubility of these proteins in other biological functions.
water.
▪ Enzymes: biological
• In hair, three a helices are catalysts
braided to form a rope, the ▪ Hormones: chemical
helices being held together by messengers that regulate
disulfide cross-links. The ropes biological processes
are further packed side by side in ▪ Transport proteins:
bundles that ultimately form the carriers of small molecules
hair fiber. from one part of the body to
• The a-keratin of more rigid another (albumin,
structures, such as nails and hemoglobin, ceruloplasmin,
claws, is similar to that of hair, transferrin)
except that there is a higher ▪ Storage proteins: act as
percentage of cysteine amino food stores (ovalbumin of
acid units in the polypeptide egg white)
chain. Therefore, there are more
disulfide cross-links, giving a
firmer, less flexible overall • Globular proteins have more
structure. amino acids with polar or ionic
• To summarize, nonpolar R side chains than the water-
groups and disulfide cross-links, insoluble fibrous proteins.
together with helical or sheet- • An enzyme or other globular
like backbones, tend to give protein that carries out its
fibrous proteins their rather function mainly in the aqueous
rigid, insoluble structures. medium of the cell will adopt a
structure in which the nonpolar,
hydrophobic groups point in
toward the center and the polar
or ionic R groups point out
toward the water.

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 JEARNIE LOU M. ARROYO BSMT – M14 IOCHEM14B

• Globular proteins are mainly • These perform a necessary

helical, but they have folds that function at the active site of the
permit the overall shape to be protein, where the nonprotein
globular. portion, a molecule of the
• One of the 20 amino acids, porphyrin heme, binds the
proline has a secondary amino oxygen.
group. Wherever a proline unit • The outer surface of the protein
occurs in the primary peptide includes many highly polar
structure, there will be no N-H amino acid residues (lysine,
group available for intra-chain arginine, glutamic acid)
hydrogen bonding.
• Myoglobin, the oxygen-transport
protein of muscle, is a good
example of a globular protein. It
contains 153 amino acid units,
yet is extremely compact, with
very little empty space in its
interior.
• Approximately 75% of the amino
acid units in myoglobin are part
of eight right-handed a-helical
sections. There are four proline
units, and each occurs at or near
"turns" in the structure. There
are also three other "turns" Quaternary Protein
caused by structural features of Structure
other R groups.
• Some high-molecular-weight
proteins exist as aggregates of
• The interior of myoglobin several subunits. These
consists almost entirely of aggregates are referred to as the
nonpolar R groups, such as those quaternary structure of the
of leucine, valine, phenylalanine, protein.
and methionine. The only • Aggregation helps to keep
interior polar groups are two nonpolar portions of the protein
histidines. surface from being exposed to
the aqueous cellular
environment.

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 JEARNIE LOU M. ARROYO BSMT – M14 IOCHEM14B

• Hemoglobin, the oxygen-

transport protein of red cells,
provides an example of such
aggregation. It consists of four
almost spherical units, two a
units with 141 amino acids and
two ß units with 146 amino
acids. The four units come
together in a tetrahedral array.

• Many other proteins form similar

aggregates. Some are active only
in their aggregate state, whereas
others are active only when the
aggregate dissociates into
subunits.
• Aggregation in quaternary
structures, then, provides an
additional control mechanism
over biological activity.

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