Proteins

Protein
•  Next to water, PROTEINS are the most
abundant substances in most cells.

•  They are particularly important class of

food molecules because they provide an
organism not only with C and H, but also
with N and S, elements which are
unavailable from fats and carbohydrates.
 Protein
•  PROTEINS are high molar mass
compounds consisting largely or entirely of
chains of amino acids.

•  They are utilized in the building of new

tissues and in the maintenance of tissues
already developed.
 Some functions of proteins

•  The light produced by fireflies is the result of a reaction involving the

protein luciferin and ATP, catalyzed by the enzyme luciferase.
•  Erythrocytes contain large amounts of the oxygen-transporting
protein hemoglobin.

•  The protein keratin, formed by all vertebrates, is the chief structural

component of hair, scales, horn, wool, nails, and feathers.
 PEPTIDES and PROTEINS
-  Amino acids can assemble into chains (peptides,
polypeptides, proteins)

§  Can be very short to very long

Dipeptide = two amino acids linked
Tripeptide = three amino acids linked

§  Amino acids sometimes called RESIDUES

§  Identity and function of a protein or peptide is
determined by
o  Amino acid composition
o  Order of amino acids in the chain
§  Amino acids are linked by COVALENT BONDS =
PEPTIDE BONDS
§  Peptide bond is an amide linkage formed by a
condensation reaction (loss of water)
§  Brings together the alpha-carboxyl of one amino acid
with the alpha-amino of another
§  Portion of the AA left in the peptide is termed the
amino acid RESIDUE

o  Amino acids sometimes called RESIDUES

o  R groups remain UNCHANGED – remain active
o  N-terminal amino and C-terminal carboxyl are also
available for further reaction
§  peptide bonds are amide bonds that occur between
the carboxyl group of one amino acid and the amino
group of the next with the loss of water.

§  Peptides are always written in the N è C direction

§  Each peptide has ONLY ONE free amino group and
ONE free carboxyl group; others are neutralized by
formation of the peptide bond.
The Peptide bond
•  holds amino acids together in chains
•  peptides are formed through the union of 2 or more α-­‐amino acids
via the peptide bond formation
•  A peptide bond joining 2 amino acids produces a dipeptide
•  may be termed di- ; tri- ; tetra- and so on based on the number of
amino acids they contain
•  Almost all of the peptide bonds in proteins are planar
and have a trans configuration.

•  This is quite important physiologically because it

makes protein structure relatively rigid.

•  the peptide bonds are covalent and quite stable – can

be disrupted by chemical or enzymatic hydrolysis but
are not directly influenced by salt concentration,
change in pH, or solvent
 Naming the Peptide
•  By convention, the free amino end (N-terminal) of the
peptide chain is written to the left and the free carboxyl
end (C-terminal) to the right.

•  Therefore, all amino acid sequences are read from the

N- to the C-terminal end of the peptide.

Ø For example, the order of the amino acids is “valine,

alanine.”
•  Linkage of many amino acids through peptide bonds
results in an unbranched chain called a polypeptide.
 Naming the Peptide
Ø Each component amino acid in a polypeptide is
called a “residue” because it is the portion of the
amino acid remaining after the atoms of water
are lost in the formation of the peptide bond.

Ø When a polypeptide is named, all amino acid

residues have their suffixes (-ine, -an, -ic, or -
ate) changed to -yl, with the exception of the C-
terminal amino acid.

For example, a tripeptide composed of:

N-terminal valine, a glycine, and a C-terminal
leucine is called valyl glycyl leucine.
 Naming peptides:

Ø  The pentapeptide serylglycyltyrosylalanylleucine, or

Ser–Gly–Tyr–Ala–Leu.
§  Peptides are named beginning with the amino terminal residue,
which by convention is placed at the left. The peptide bonds are
shaded in yellow; the R groups are in red.
Small Peptides with Physiological Activity
1.  Aspartame (Asp-Phe)
•  Sold under the trade names Nutrasweet and Equal.
•  aspartame is the artificial sweetener used in almost every
diet food on the market today. Its caloric content is the
same as sucrose but is ~ 180 times as sweet .
 Small Peptides with Physiological Activity

2.  Glutathione, GSH (Glu-Cys-Gly)

•  The tripeptide, produced by the body itself, is present in
significant concentrations in most cells and is of considerable
physiological importance as a regulator of oxidation-reduction
reactions.
 Small Peptides with Physiological Activity

2.  Glutathione, GSH (Glu-Cys-Gly)

•  It functions as an antioxidant, protecting cellular contents from
oxidizing agents such as peroxides and superoxides.
•  In GSH, Glu is bonded to Cys through the side-chain carboxyl
group rather than through the α-carbon carboxyl group
Small Peptides with Physiological Activity
3.  Enkephalins
•  Two pentapeptides found in the brain are known as enkephalins,
naturally occurring analgesics (pain relievers)
•  The two enkephalins differ only in the amino acid at the
carboxyl end of the peptide chain.
Small Peptides with Physiological Activity

3.  Enkephalins
•  It is thought that the aromatic side chains of tyrosine and
phenylalanine in these peptides play a role in their activities.
•  It is also thought that there are similarities between the three-
dimensional structures of opiates, such as morphine, and those of
the enkephalins.
•  As a result of these structural similarities, opiates bind to the
receptors in the brain intended for the enkephalins and thus
produce their physiological activities.
 Small Peptides with Physiological Activity
4.  Oxytocin and Vasopressin
•  The difference between these two peptides is that oxytocin has an
isoleucine residue at position 3 and a leucine residue at position
8.
•  Vasopressin has a phenylalanine residue at position 3 and an
arginine residue at position 8.
•  Both of these peptides have considerable physiological
importance as hormones.
Ø  The complexity of protein
structure is best analyzed
by considering the
molecule in terms of four
organizational levels:

§  Primary
§  Secondary
§  Tertiary
§  Quaternary
BONDING and PROTEIN STRUCTURE

•  the important properties and functions of proteins can

be more easily understood if we know something about
their structures and the bonding accounting for their
structures.

•  the structure of proteins is subdivided into 1o ; 2o ; 3o ;

4o according to the type of interactions of the amino
acid
BONDING and PROTEIN STRUCTURE

A. PRIMARY STRUCTURE

•  The 1o structure of a protein is the sequence of amino

acid residues in a protein chain – i.e., the order in
which the amino acids are connected to each other

•  frequently referred to as the backbone of the protein

molecule

Ø  the 1o structure of proteins are translations of

information contained in genes; Defined, non-random
sequence of amino acids along the peptide backbone.
PRIMARY STRUCTURE (1°)
Ø  Described in two ways:
§  Amino acid composition
§  Amino acid sequence

e.g. M-L-D-G-C-G Peptide A

M-L-C-D-G-G Peptide B

Composition is IDENTICAL; Sequence is DIFFERENT!

Ø  How to determine the COMPOSITION:

o  Purify the protein of interest – separate away from all other
types of proteins and biomolecules
o  Estimate the molecular weight of the protein
o  Establish the composition by complete hydrolysis of the protein
under acidic conditions ( Treat with 6M HCl at 110°C; 12-36
hours)
BONDING and PROTEIN STRUCTURE

B. SECONDARY STRUCTURE

•  Secondary structure is the arrangement in space of the

atoms in the peptide backbone.
•  when the primary sequence of the polypeptide folds
into regularly repeating structures, secondary structure
is formed; tells something about shape/conformation of
protein molecule
•  the only bond responsible for the 2o structure of
proteins is H-bonding between peptide bonds, the
– C = O of one peptide group and the – N – H of
another peptide linkage farther along the backbone.
TYPES OF 20 STRUCTURE

1.  Helix Structure

•  governed by intramolecular H-bonding ; the α-helix is

the most stable helical arrangement
•  in an α helix, all of the amino acid side chains (R
groups) lie outside the helix; there is not enough room
for them in the interior; the helix is so tightly wound
that the space in the center is too small for solvent
molecules to enter
•  the H-bonds of the α-helix are parallel to the long axis
of the helix; these bonds lock the α-helix into place
Ø  the polypeptide chain in an α-helix is right-handed
TYPES OF 20 STRUCTURE
1.  Helix Structure

certain amino acids do not foster α-helix formation:

•  strong electrostatic repulsion owing to the proximity of

several charged groups of the same sign, such as
groups of positively charged lysine and arginine
residues or groups of negatively charged glutamate and
aspartate residues.

•  crowding (steric repulsion) caused by the proximity of

several bulky side chains: as is the case with valine,
isoleucine, and threonine.
TYPES OF 20 STRUCTURE

1.  Helix Structure

TYPES OF 20 STRUCTURE

2.  Pleated-sheet structure or β-conformation

•  governed by intermolecular H-bonds between protein

chains to form a zigzag, sheet-like arrangement
•  all of the carbonyl oxygen and amide hydrogen are
involved in H-bonds, and the polypeptide chain is
nearly completely extended
•  R groups are located above and below the plane of the
sheet.
•  proteins with this structure are crystalline and quite
insoluble in aqueous solvents
TYPES OF 20 STRUCTURE

2.  Pleated-sheet structure

or β-conformation
TYPES OF 20 STRUCTURE

2.  Pleated-sheet structure or β-conformation

a)  parallel structure

Ø  chains are running in

the same direction;

Ø  the –COOH and -

NH2 ends of the
proteins lying all at
the top or all at the
bottom of the sheet.
TYPES OF 20 STRUCTURE

2.  Pleated-sheet structure or β-conformation

b)  antiparallel structure

Ø  protein chains alternate in such a way that the - COOH

end of one chain is next to the –NH2 end of the
other.
Ø  chains are running in opposite directions
o more stable than parallel because of fully collinear
H-bonds form.
TYPES OF 20 STRUCTURE

2.  Pleated-sheet structure or β-conformation

b)  antiparallel structure

TYPES OF 20 STRUCTURE

2.  Pleated-sheet structure or β-conformation

C. TERTIARY STRUCTURE

•  the overall three-dimensional shape that results from

the interaction of groups in the side chain (-R) of the
amino acids widely separated from each other within the
chain;

•  defines the biological function of proteins

•  proteins may have, in general, either of the two forms

of tertiary structure:

(a) fibrous and (b) globular

C. TERTIARY STRUCTURE

•  fibrous proteins (insoluble): having polypeptide chains

arranged in long strands or sheets

-structures that provide support, shape, and external

protection to vertebrates are made of fibrous proteins

•  globular proteins (soluble): having polypeptide chains

folded into a spherical or globular shape.

-most enzymes and regulatory proteins are globular

proteins.
C. TERTIARY STRUCTURE
Ø  Fibrous proteins are adapted for a structural function.

a.  α-Keratin

•  The α-keratins have evolved

for strength
•  Found in mammals, these
proteins constitute almost the
entire dry weight of hair, wool,
nails, claws, quills, horns,
hooves, and much of the outer
layer of skin.
•  The α-keratin is a right-handed
helix.
C. TERTIARY STRUCTURE

b.  Collagen

•  Like the -keratins, collagen has

evolved to provide strength.
•  It is found in connective tissue
such as tendons, cartilage, the
organic matrix of bone, and the
cornea of the eye.

•  It is left-handed and has three

amino acid residues per turn.
•  consists of three polypeptide
chains wrapped around each
other in a rope-like twist, or
triple helix
C. TERTIARY STRUCTURE

c.  Silk Fibroin

•  Fibroin, the protein of silk, is produced by insects and

spiders.
•  Its polypeptide chains are predominantly in the β-­‐
conformation.

•  The overall structure is stabilized by extensive

hydrogen bonding between all peptide linkages in the
polypeptides of each β-­‐sheet and by the optimization
of van der Waals interactions between sheets.
C. TERTIARY STRUCTURE

c.  Silk Fibroin

C. TERTIARY STRUCTURE

Globular Proteins

a.  Myoglobin

•  a relatively small oxygen-binding protein of muscle cells.

•  It functions both to store oxygen and to facilitate oxygen
diffusion in rapidly contracting muscle tissue.
•  particularly abundant in the muscles of diving mammals such
as the whale, seal, and porpoise, whose muscles are so rich in
this protein that they are brown.
•  Storage and distribution of oxygen by muscle myoglobin
permit these animals to remain submerged for long periods of
time.
C. TERTIARY STRUCTURE

Globular Protein
a.  Myoglobin
INTERACTIONS/LINKAGES Responsible
for 3o Structure

Ø  these linkages aid in holding the protein in a

rather rigid structure
1. salt linkages / ionic interaction/ electrostatic
attraction
2. H-bonds
3. disulfide bonds
4. hydrophobic bond
5. van der Waals forces
6. polar group interactions with water
Summary of the weak interactions that help maintain the tertiary structure of a protein.
D. QUATERNARY STRUCTURE

•  the final level of protein structure and pertains to those

proteins that consist of multiple polypeptide chains.
•  Each chain is called a subunit: a polypeptide chain
having primary, secondary, and tertiary structural
features that is a part of a larger protein

•  myoglobin has no 4o structure; it has only 1 chain

•  hemoglobin has 4o structure; it consists of 4
separate chains called protein subunits: 2αand 2β
chains – each chain is bound to a separate heme
group
D. QUATERNARY STRUCTURE

•  collagen has 4o structure; composed of 3 strands of the

same protein twisted together in a helical fashion like
a piece of a rope.
Ø  The forces that hold the quaternary structure of a protein are
the same as those that hold the tertiary structure.

Ø  These include hydrogen bonds between polar amino acids,

ionic bridges between oppositely charged amino acids, Van
der Waals forces between nonpolar amino acids, and
disulfide bridges.
D. QUATERNARY STRUCTURE

The structure of hemoglobin.

 Hemoglobin
Myoglobin

Ø  The heme group has an Fe atom to

The structure of hemoglobin.
which oxygen binds.
PROTEIN DENATURATION

Ø  refers to the breaking of any bond in protein except

the 1o bond (peptide bond).
Ø  when protein is in the cell, it is in its natural
conformation, in its native state. If this native state
is changed in any way, the protein is said to be
denatured.

•  denaturation often radically changes both the

physical and chemical properties of the protein;

•  proteins lose their activity, although under certain

conditions this loss may be reversible (renaturation)
PROTEIN DENATURATION

Ø  Protein denaturation results in the unfolding and

disorganization of the protein's secondary, tertiary and
quaternary structures, which are not accompanied by
hydrolysis of peptide bonds.
Some selected physical and chemical denaturing
agents

1. heat – disrupts H-bonds and hydrophobic attractions

by making molecules vibrate too violently; produces
coagulation, as in the frying of an egg
2. microwave radiation – causes violent vibrations of
molecules that disrupt H-bonds
3. ultraviolet radiation – operates very similarly to the
action of heat (e.g., sunburn)
4. acids and bases – disrupts salt linkages
5. violent whipping or shaking – causes molecules in
globular shapes to extend to longer lengths, which then
entangle
Some selected physical and chemical denaturing
agents

6. detergent – affects H-bonds and salt linkages

7. organic solvents (e.g., ethanol, 2-propanol, acetone) –
interfere with H-bonds, because these solvents also can
form H-bonds; quickly denatures protein in bacteria,
killing them (the disinfectant action of 70% ethanol)
8. strong acids and bases – disrupt H-bonds and salt
bridges; prolonged action leads to actual hydrolysis of
peptide bonds
9. salts of heavy metals (e.g., salts of Hg2+, Ag+, Pb2+) –
metal ions combine with – SH groups and form
poisonous salts; precipitates proteins
Some selected physical and chemical denaturing
agents

10. reducing agents – oxidize disulfide linkages to

produce – SH groups
The denaturation of proteins by heat.
(a) The -helical proteins are in solution. (b) As heat is applied, the
hydrogen bonds maintaining the secondary structure are disrupted,
and the protein structure becomes disorganized. The protein is
denatured. (c) The denatured proteins clump together, or coagulate,
and are now in an insoluble form.
 The effect of pH
on proteins. (a)
This
protein has an
overall charge
of 2. When a
base is added,
some of the
protonated
amino groups
lose their
protons. Now
the protein is
isoelectric;
it has an equal
number of
positive and
n e g a t i v e
(b) This protein has an overall charge of 2. As acid is
charges.
added, some of the carboxylate groups are protonated. The
result is that the protein becomes isoelectric.
Some practical aspects of protein denaturation

Ø  Organic compounds such as soap, detergents,

phenol, and aliphatic alcohol

§  The hydrophobic portions of these compounds interact

with the hydrophobic core of the protein, while the
hydrophilic portion is H-bonded with the aqueous
environment.

§  This causes swelling and concomitant unfolding of the

protein molecules.
Some practical aspects of protein denaturation

Ø  Permanent hair waving

§  keratin has a high proportion of S-containing amino

acids; the –S – S – linkages give shape to the hair

§  process involves the breaking of these linkages by

reducing agent →brings disorderliness of linkages

o  placed on curlers and set in the desired pattern  

o  finally neutralized with an oxidizing agent to reform –
S –S – linkages this time between different amino
acids