BIOCHEMISTRY

LECTURE / PROTEINS

AMINO ACIDS
• Organic compound
• Building blocks of proteins
• All proteins are made up from 20
standard amino acids
• Essential to life > proteins form is
involved in virtually all cell functions
• Colorless, crystalline solid

GENERAL STRUCTURE
CLASSIFICATION OF AMINO ACIDS
I. Classification on the basis of R-group

II. Classification on the basis of Catabolism

III. Classification on the basis of Nutrition

I. CLASSIFICATION ON THE BASIS OF R-GROUP

• Carboxyl group (-COOH)

• Amino group (-NH2)
• Carbon (alpha carbon)
• Hydrogen atom (H)
• “Variable” group or “R” group
• Side chain > vary in size, shape,
charge, acidity, functional groups
present hydrogen bonding ability and
chemical reactivity
NON-POLAR AMINO ACIDS
• Amino acids with nonpolar side
chains
• Contains unchanged hydrocarbon
groups or benzene rings as side
chains
• Does not gain or lose protons or
participate in hydrogen or ionic bonds

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• Oily or Lipid-like > a property that

promotes hydrophobic interactions

NON-POLAR

➢ Glycine
➢ Alanine
➢ Valine
➢ Leucine
➢ Isoleucine
➢ Phenylalanine
➢ Tryptophan
➢ Methionine
➢ Proline

POLAR ACIDIC AMINO ACID

• Contain a side chain that functions as
an acid and is capable of becoming
ionized by donating a hydrogen atom
to the surrounding environment
• Second carboxyl group being part of
the side chain

POLAR NEUTRAL AMINO ACIDS

• Polar amino acids have side chains
with either a net positive or a net
negative
➢ Serine
➢ Asparagine
➢ Threonine ➢ Aspartic acid
➢ Glutamine ➢ Glutamic acid
➢ Tyrosine
➢ Cysteine

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• Amino group tend to accept protons,

producing a positive charged amino
acid

II. CLASSIFICATION OF AMINO ACIDS ON

THE BASIS OF CATABOLISM
➢ Glucogenic amino acids:
• Carboxyl group tend to lose • These amino acids serve as
protons, producing a negative precursors gluconeogenesis for
charged amino acid glucose formation
• GAMD (Glycine, Alanine, Methionine,
POLAR BASIC AMINO ACIDS
Aspartic acid).
• Each of their side chains contains an
➢ Ketogenic amino acids:
additional amino group beyond what
• These amino acids breakdown to
is found in the core structure of the
form ketone bodies
amino acid it can accept a hydrogen
• Leucine and Lysine
atom from the existing environment.
➢ Both glucogenic and ketogenic amino
• Second amino group being part of the
acids:
side chain
• These amino acids breakdown
to form precursors for both
ketone bodies and glucose
• Isoleucine, Phenylalanine,
Tryptophan and Tyrosine
➢ Essential & Nonessential Amino acids
• Essential - must be consumed
➢ Histidine in the diet, cannot be
➢ Lysine synthesized by the body
➢ Arginine • Nonessential – can be
synthesized by the body

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• The amino acids in living systems exist

primarily in the L form

CHIRALITY
• Four different groups attached to the
α-carbon atom in all of the standard
amino acid except glycine

• Complete dietary protein FISHER PROJECTION FORMULAS FOR

• Incomplete dietary protein AMINO ACID:

• Limiting amino acid

• Complementary dietary proteins

STEREOCHEMISTRY OF AMINO ACIDS

• Since the amino acids (except for
glycine) contain four different groups
connected to the α-carbon, they are
ZWITTERIONS
chiral, and exist in two enantiomeric
• Double ions
forms:
• A molecule that has a positive charge
on one atom and a negative charge
on another atom, but which has no
net charge

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ISOELECTRIC POINT
• pH at which an amino acid solution
has no net charge because an equal
number of positive and negative
charges are present.
• In solution, the structure of an amino
acid can change with the pH of the
solution:
• Lowering the pH of the solution causes
the zwitterion to pick up a proton
CYSTEINE: A CHEMICALLY UNIQUE AMINO ACID
• Only standard amino acid that
contains a sulfhydryl group (-SH)
• Dimerizes > reacts with another
cysteine molecule tom form cystine
• Increasing the pH of the solution molecule
causes the zwitterion to lose proton: • Cystine > contains 2 cysteine residues
linked by a disulfide bond

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OXIDATION - REDUCTION (COOH) and amine group of two

different amino acids join and
releases a molecule of water

PEPTIDE
• A chain of amino acids AMINO ACID RESIDUE
• Each joined or linked to the next by a • Portion of an amino acid structure
peptide bond that remains after the release of
• Amide linkage formed by the reaction water
between α-carboxyl group of one
HYDROLYTIC REACTION
amino acid and α-amino group of
• When peptide bonds are broken by
another amino acid with the
hydrolysis, the hydroxyl group (OH)
elimination of water molecule
and hydrogen (H) from water are
added.

A covalent bond between the carboxyl group

of one amino acid and the amino group of
another amino acid
PEPTIDE NOMENCLATURE
• RULE 1: C-terminal amino acid residue
keeps its full amino acid name
• RULE 2: All of the other amino acid
residue have names that end in -yl.
The -yl suffix replaces the -ine or -ic
acid ending of the amino acid
Except for tryptophan (tryptophyl),
cysteine (cysteinyl), glutamine
(glutaminyl), and asparagrine
CONDENSATION REACTION
• A peptide bond forms by (asparaginyl),

condensation when the acid group

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• Rule 3: The amino acid naming • Nonapeptide

sequence begins at the N-terminal • Differ in the amino acid present in
amino acid residue position 3 and 8

ISOMERIC PEPTIDES
• Peptides that contain the same
amino acids but in different order
with different properties
SMALL PEPTIDE NEUROTRANSMITTERS
• Enkephalins
• Met-enkephalin (Try-Gly-Gly-Phe-
Met)
• Leu-enkephalin (Try-Gly-Gly-Phe-
Leu)

SMALL PEPTIDE ANTIOXIDANTS

• Glutathione

Biochemically Important Small Peptides

• Hormones
• Neurotransmitters • Tripeptide
• Antioxidants • (glutamic acid, cysteine, and glycine)

SMALL PEPTIDE HORMONES

• OXYTOCIN
• VASOPRESSIN

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PROTEINS
• Most abundant bioorganic substance
• Next to water, protein is the most
abundant substances in all cell
• Greek word “PROTEIOS”- first
importance
• Macromolecules composed
polymers of covalently linked amino
acids that involved in every cellular
processes
• Plasma proteins are synthesized in
the Liver (Secreted by hepatocyte into
the circulation except
Immunoglobulins)
• Provides 12-20% of the total daily
body energy requirement
• 50% - 70% of the cell’s dry weight
• Can bear positive and negative
➢ Enzymes
CLASSIFICATIONS OF PROTEINS
Based on:
• Monomeric or Multimeric
• Protein Structure
of • Chemical Composition
• Shape
• Functions
PROTEIN CLASSIFICATION BASED ON
MONOMERIC OR MULTIMERIC
Monomeric protein
• Protein in which only one peptide
chain is present
Multimeric protein
• Protein in which more than one

(Amphoteric) peptide chain is present

• Can be both a weak base or weak

acid
• Their solubility is due to high dielectric
property
• Involved in most of the body functions
and life processes
• The sequence of amino acids is
determined by DNA

FUNCTIONS:
➢ Energy production
➢ Water distribution
➢ Buffer
➢ Transporter
➢ Antibodies
➢ Cellular proteins
➢ Structural proteins

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➢ Alpha helix
➢ Beta-pleated sheet
PROTEIN CLASSIFICATION BASED ON
PROTEIN STRUCTURE
• More complex than that of simple
organic molecules
• 4 levels of organization in protein
structure:
➢ Primary
➢ Secondary
➢ Tertiary
• Alpha Helix
➢ Quaternary
➢ Single protein chain twisted
I. PRIMARY STRUCTURE to resemble a coiled helical
➢ Linear sequence of the side chains spring
that are connected to the protein ➢ Hydrogen bonds > between
backbone N-H and C=O groups of every
➢ AA are linked to each other through fourth amino acid
covalent peptide bonding in a specific
sequence to form a polypeptide chain

II. SECONDARY STRUCTURE

• Regular folding f=of regions of
polypeptide chain
• Hydrogen bonding causes proteins
chains to fold and align to produce
orderly patterns

2 most common types:

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• Beta Pleated Sheet

➢ Severa protein chains lie side
by side, held by hydrogen
bonds between adjacent
chains
➢ Two fully extended protein
chain segments in the same or
different molecules are held
together by hydrogen bonds
COVALENT DISULFIDE BONDS
• Strongest interaction
• Can form between the -SH groups of
two cysteine residues that are close to
each other in the same chain, or
between cysteine residues in different
chains
• These bridges hold the protein chin in
a loop or some other 3D shape

III. TERTIARY STRUCTURE

• Three-dimensional arrangement of all
the amino acids in the polypeptide
chain ELECTROSTATIC ATTRACTIONS (SALT BRIDGES)
• Biologically active, native • Attractions between ions that result
conformation is maintained by from the interactions of the ionized
multiple noncovalent bonds side chains of acidic amino acids
(interactions of the R groups of the (-COO-) and the side chains of basic
amino acid) amino acids (-NH3+)

Interaction responsible:

➢ Disulfide bonds
➢ Electrostatic interactions
➢ Hydrogen bonds
➢ Hydrophobic interaction

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HYDROGEN BONDS
• Hydrogen bonding is between R
groups
• While in secondary structure it is
between the C=O and NH portions of
the backbone
HYDROPHOBIC ATTRACTION
• Result from the attraction of
nonpolar groups
• These interactions are particularly
important between the benzene
rings in phenylalanine or tryptophan
• This type of interaction is relatively
weak, but since it acts over large
surface areas, the net effect is a
strong interaction.
TERTIARY STRUCTURE INTERACTIONS
QUATERNARY STRUCTURE
• Arrangement of the subunits to form
a larger protein
• Each of the polypeptide subunits has
its own primary, secondary, and
tertiary structure
• The three-dimensional shape of a
protein consisting of two or more
independent peptide chains which
results from non-covalent interaction
between R group.
➢ Electrostatic interaction
➢ Hydrogen bonds
➢ Hydrophobic interaction
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PROTEIN HYDROLYSIS TYPES OF CONJUGATED PROTEINS

Classes Prosthetic Specific Example Function

Group of Ex
Hemoprotein Heme Hemoglobin Carrier
unit of
Oxygen
in blood
Lipoprotein Lipid LDL, HDL Lipid
carrier
PROTEIN DENATURATION
Glycoprotein Carbohy Gammaglobulin Antibody
drate
Nucleoprotei Nucleic Ribosomes Protein
n acid synthesis
Metalloprote Metal ion Ferritin -Fe Storage
in Ceruloplasma - of certain
Cu metals

PROTEIN CLASSIFICATION BASED ON PROTEIN CLASSIFICATION BASED ON

CHEMICAL COMPOSITION SHAPE
• Simple protein > A protein which only Fibrous Protein
amino acid residues are present ➢ Elongated shape with one dimension
• Conjugated protein > A protein that much longer than the others
has one or more non-amino acid ➢ Water insoluble
entities present in its structure in ➢ usually have a single type of
addition to one or more peptide secondary structure
chains ➢ Provide support and external
➢ Prosthetic group - non amino protection
acid components of ➢ major in components of
conjugated protein, which connective tissue, elastic
may be organic or inorganic tissue, hair, and skin

Ex: keratin, collagen, elastins, myosins, fibrins

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KERATIN ➢ Water Soluble – enable to travel

➢ soft or hard fibrous protein
➢ highly insoluble in water
➢ composed of multiple
twisted into thicker filaments
through the blood and other body
fluids
α-helices ➢ Contain several types of secondary
structure
➢ Involved in metabolic chemistry-
performing functions like catalysis,
transport, regulation

Ex: Hemoglobin, Myoglobin, insulin,

transferrin, immunoglobulins

COLLAGEN
➢ Most abundant protein in your body
➢ Major component of connective
tissues that make up several body
parts, including tendons, ligaments, HEMOGLOBIN
skin, and muscles • Tetramer with each subunit contains
HEME group > binds oxygen

MYOGLOBIN
• Monomer
• Single peptide chain and a heme unit

GLOBULAR PROTEIN
➢ Folded into Spherical or Globular
shapes

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PROTEIN CLASSIFICATION BASED ON • Messenger Protein

FUNCTIONS ➢ Transmit signals to coordinate
• Catalytic Protein biochemical processes
➢ Nearly all reactions in living ➢ Example is HORMONES
organisms are catalyzed by ➢ Body processes regulated by
proteins proteins include growth (growth
➢ Biochemical catalyst are hormone) and thyroid functions
called ENZYMES (thyrotropin)
➢ Without these catalysts • Structural Protein
• Defense Protein ➢ Confer stiffness and rigidity to
➢ Immunoglobulins or otherwise fluid like biochemical
antibodies are central to systems.
functioning of the body’s Ex: Collagen, Keratin
immune system
➢ Another protective function
is blood clotting, carried out
by thrombin and fibrinogen
• Transport Protein
➢ Binds to particular small
biomolecules and
transport them to other
location in the body
➢ Some proteins bind small
• Contractile Protein
molecules or ions and
➢ Necessary for all forms of
transport them through
movement
the body
Ex: Actin and Myosin
- Serum albumin is a blood
protein that carries fatty acids
between fat (adipose) tissue
and other organs

- Hemoglobin carries oxygen

from the lungs to other body
tissues

- Transferrin is a carrier of iron

in blood plasma

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• Storage Protein
➢ Bind (and store) small molecules
for future use
➢ Some proteins provide a way to
store small molecules or ions, e.g.,
ovalbumin (used by embryos
developing in bird eggs), casein (a
milk protein) and gliadin (wheat
seeds), and ferritin (a liver protein
TYPES AND CHARACTERISTICS OF ANTIBODIES
which complexes with iron ions)
• Transmembrane Protein
➢ Help control the movement of
small molecules and ions
through the cell membrane

GLYCOPROTEINS
• A conjugated protein that contains
carbohydrates or carbohydrate
derivatives in addition to amino acids

Example:

- Collagen

- Immunoglobulins

- Blood group markers LIPOPROTEINS

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