PROTEINS

A protein is a naturally occurring,

unbranched polymer in which the monomer
units are amino acids.
WHAT ARE
AMINO ACIDS?
 Anamino acid is an organic compound that
contains both an amino (-NH2) group and a
carboxyl (- COOH) group.
 Theamino acids found in proteins are always a-
amino acids.

 An -amino acid is an amino acid in which the

amino group and the carboxyl group are attached
to the -carbon atom.
 Over700 different naturally occurring
amino acids are known, but only 20 of
them, called standard amino acids, are
normally present in proteins.
 Amino acids are grouped according to side-chain
polarity. In this system there are four categories:
(1) nonpolar amino acids
(2) polar neutral amino acids
(3) polar acidic amino acid
(4) polar basic amino acids.

 This classification system gives insights into how

various types of amino acid side chains help determine
the properties of proteins
A nonpolar amino acid is an amino acid that contains one amino group, one
carboxyl group, and a nonpolar side chain. When incorporated into a protein, such
amino acids are hydrophobic (“water-fearing”); that is, they are not attracted to
water molecules.

They are generally found in the interior of proteins, where there is limited contact
with water.
A polar neutral amino acid is an amino acid that contains one amino group,
one carboxyl group, and a side chain that is polar but neutral. In solution at
physiological pH, the side chain of a polar neutral amino acid is neither acidic
nor basic.
A 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.

In solution at physiological pH, the side chain of a polar acidic amino acid bears
a negative charge; the side-chain carboxyl group has lost its acidic hydrogen
atom.
A 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.

In solution 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.
ESSENTIAL AMINO ACIDS
 An essential amino acid is an amino acid needed in the
human body that must be obtained from dietary sources
because it cannot be synthesized within the body from
other substances in adequate amounts.
 A peptide is an unbranched chain of amino acids, each
joined to the next by a peptide bond.

 Peptides are further classified by the number of amino

acids present in the chain.

 The bonds that link amino acids together in a peptide

chain are called peptide bonds.
 A peptidebond is a covalent bond
between the carboxyl group of one amino
acid and the amino group of another
amino acid.
Gly–Ala–Ser
IUPAC RULES FOR NAMING SMALL PEPTIDES ARE AS
FOLLOWS:

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 (cysteinyl), glutamine (glutaminyl),
and asparagine (asparaginyl).

Rule 3: The amino acid naming sequence begins at the N-

terminal amino acid residue.
ASSIGN IUPAC NAMES TO EACH OF THE
FOLLOWING SMALL PEPTIDES.
 Glu–Ser–Ala glutamylserylalanine

 Gly–Tyr–Leu–Val glycyltyrosylleucylvaline

 Gly–Ala–Leu Glycylalanylleucine

 Gly–Tyr–Ser–Ser Glycyltyrosylserylserine
BIOCHEMICALLY
IMPORTANT SMALL
PEPTIDES
Many relatively small peptides have been
shown to be biochemically active. Functions
for them include hormonal action,
neurotransmission, and antioxidant activity.
SMALL PEPTIDE HORMONES
 Oxytocin regulates uterine contractions and lactation.

 Vasopressin regulates the excretion of water by the

kidneys; it also affects blood pressure.
SMALL PEPTIDE NEUROTRANSMITTERS
 Enkephalins are pentapeptide neurotransmitters
produced by the brain itself that bind at receptor sites in
the brain to reduce pain.

 The two best-known enkephalins are Metenkephalin and

Leu-enkephalin, whose structures are

Met-enkephalin: Tyr–Gly–Gly–Phe–Met
Leu-enkephalin: Tyr–Gly–Gly–Phe–Leu
SMALL PEPTIDE ANTIOXIDANTS
 The tripeptide glutathione (Glu–Cys–Gly) is present in
significant concentrations in most cells and is of
considerable physiological importance as a regulator of
oxidation–reduction reactions.

 Specifically, glutathione functions as an antioxidant,

protecting cellular contents from oxidizing agents such
as peroxides and superoxides (highly reactive forms of
oxygen often generated within the cell in response to
bacterial invasion)
PRIMARY STRUCTURE OF
PROTEINS
 Primary protein structure is the order in which amino
acids are linked together in a protein.

 The primary structure of a specific protein is always the

same regardless of where the protein is found within an
organism.
SECONDARY
STRUCTURE OF
PROTEINS
SECONDARY PROTEIN STRUCTURE
 Secondary protein structure is the arrangement in space
adopted by the backbone portion of a protein.

 The two most common types of secondary structure are

the alpha helix (-helix) and the beta pleated sheet (β-
pleated sheet)
ALPHA HELIX STRUCTURE
 An alpha helix structure is a protein secondary structure
in which a single protein chain adopts a shape that
resembles a coiled spring (helix), with the coil
configuration maintained by hydrogen bonds.

 The hydrogen bonds are between groups of every

fourth amino acid
BETA PLEATED SHEET
 A beta pleated sheet structure is a protein secondary
structure in which two fully extended protein chain
segments in the same or different molecules are held
together by hydrogen bonds.
TERTIARY STRUCTURE OF PROTEINS
 Tertiary protein structure is the overall three-dimensional
shape of a protein that results from the interactions
between amino acid side chains (R groups) that are
widely separated from each other within a peptide chain.
QUATERNARY STRUCTURE OF
PROTEINS
 Quaternary protein structure is the organization among
the various peptide chains in a multimeric protein.

 Most multimeric proteins contain an even number of

subunits (two subunits = a dimer, four subunits = a
tetramer, and so on). The subunits are held together
mainly by hydrophobic interactions between amino acid
R groups.
PROTEIN CLASSIFICATION BASED ON
SHAPE
 A fibrous protein is a protein whose molecules have an
elongated shape with one dimension much longer than
the others.

 Fibrous proteins tend to have simple, regular, linear

structures. There is a tendency for such proteins to
aggregate together to form macromolecular structures.
 A globular protein is a protein whose molecules have
peptide chains that are folded into spherical or globular
shapes.

 The folding in such proteins is such that most of the

amino acids with hydrophobic side chains (nonpolar R
groups) are in the interior of the molecule and most of
the hydrophilic side chains (polar R groups) are on the
outside of the molecule.

 Generally, globular proteins are water-soluble

substances.
 A membrane protein is a protein that is found associated
with a membrane system of a cell.

 Membrane protein structure is somewhat opposite that of

globular proteins, with most of the hydrophobic amino
acid side chains oriented outward.

 Thus, such proteins tend to be water insoluble and they

usually have fewer hydrophobic amino acids than
globular proteins.
 KERATIN
 The fibrous protein  keratin is particularly abundant in
nature, where it is found in protective coatings for organisms.
It is the major protein constituent of hair, feathers, wool,
fingernails and toenails, claws, scales, horns, turtle shells,
quills, and hooves.
COLLAGEN
 Collagen, the most abundant of all
proteins in humans (30% of total
body protein), is a major structural
material in tendons, ligaments, blood
vessels, and skin; it is also the
organic component of bones and
teeth.
PROTEIN CLASSIFICATION
BASED ON FUNCTION
1. Catalytic proteins. Proteins are probably best known
for their role as catalysts. Proteins with the role of
biochemical catalyst are called enzymes. Enzymes
participate in almost all of the metabolic reactions that
occur in cells.

2. Defense proteins. These proteins, also called

immunoglobulins or antibodies, are central to the
functioning of the body’s immune system. They bind to
foreign substances, such as bacteria and viruses, to help
combat invasion of the body by foreign particles.
 Transport proteins. These proteins bind to particular
small biomolecules and transport them to other locations
in the body and then release the small molecules as
needed at the destination location.

 Messenger proteins. These proteins transmit signals to

coordinate biochemical processes between different
cells, tissues, and organs. A number of hormones that
regulate body processes are messenger proteins,
including insulin and glucagon.
 Contractile proteins. These proteins are necessary for
all forms of movement. Actin and myosin are examples
of such proteins. Human reproduction depends on the
movement of sperm. Sperm can “swim” because of long
flagella made up of contractile proteins.

 Structural proteins. These proteins confer stiffness and

rigidity to otherwise fluidlike biochemical systems.
 Transmembrane proteins. These proteins, which span a
cell membrane help control the movement of small
molecules and ions through the cell membrane.

 Storage proteins. These proteins bind (and store) small

molecules for future use.
 Regulatory proteins. These proteins are often found
“embedded” in the exterior surface of cell membranes.
They act as sites at which messenger molecules,
including messenger proteins such as insulin, can bind
and thereby initiate the effect that the messenger
“carries.”

 Nutrient proteins. These proteins are particularly

important in the early stages of life, from embryo to
infant. Casein, found in milk, and ovalbumin, found in
egg white, are two examples of such proteins.
PROTEIN DENATURATION
Protein denaturation is the partial or complete
disorganization of a protein’s characteristic three-
dimensional shape as a result of disruption of its
secondary, tertiary, and quaternary structural
interactions