Protein- Structure and

Function

“It’s all in the shape”

KEY CONCEPT

 Proteins are made of amino acids. Amino acids vary in

structure and function because their side chains vary in
composition. As a result, proteins vary widely in structure
and function.
 polymers of L-D-amino acids
 Protein Function

• Proteins play a key role in biological processes. They can fulfill a vast variety of
tasks.
• Enzymes catalyze the complex set of chemical reactions that are collectively
referred to as life. These chemical reactions are on the other hand regulated by
proteins, which act either directly as components of enzymes or indirectly in the
form of chemical messengers, or their receptors.
• Proteins are engaged in the transport and storage of biologically important
substances such as metal ions, oxygene, glucose, lipids, and many other molecules.
• In the form of muscle fibers and other contractile assemblies, proteins generate the
coordinated mechanical motion of numerous biological processes, including the
separation of chromosomes during cell division and the movement of your eyes
as you read this text.
• Proteins such as rhodopsin in the retina of your eye, acquire sensory information that
is processed through the action of nerve cell proteins.
• The proteins of the immune system, such as the immunoglobulins, form an
essential biological defense system in higher animals.
• Proteins carry out a wide range of functions in the cell. This variety in capability is
the result of the range of structures found in proteins and the wide variety of
molecules proteins can bind with high specificity.
• All of this results from the peculiar structure of proteins
1. Structural proteins : Keratin of hair and nails, collagen of bone.
2. Enzymes or catalytic proteins : Hexokinase, pepsin.
3. Transport proteins : Hemoglobin, serum albumin.
4. Hormonal proteins : Insulin, growth hormone.
5. Contractile proteins : Actin, myosin.
6. Storage proteins : Ovalbumin, glutelin.
7. Genetic proteins : Nucleoproteins.
8. Defense proteins : Snake venoms, Immunoglobulins.
9. Receptor proteins for hormones, viruses
 Protein Structure and Function

The four steps of chemical evolution (each

requiring energy-input) are:
• (1) production of small molecules containing
reduced carbon…
• …(2) creation of a prebiotic soup of amino
acids, sugars, and nitrogenous bases…
• …(3) linkage of these organic subunits to make
the large organic molecules important in cells
today…
• … and (4) evolution of a self-replicating
molecule.
 The Nature of Side Chains

• The 20 major amino acids differ only in the

variable side chain or R-group attached to the
central carbon. R-groups differ in their size, shape,
reactivity, and interactions with water.
• Nonpolar hydrophobic R-groups cannot form
hydrogen bonds with water and tend to group
together, whereas polar hydrophilic R-groups
interact readily with water (Table 3.1).
• All amino acids except glycine have optical
isomers, but only ―left-handed‖ forms are found in
cells.
 How Do Amino Acids Link
to Form Proteins?

• Amino acids polymerize to form proteins

(Figure 3.7). Polymerization reactions require
energy and are not spontaneous.
 The Peptide Bond

• Condensation reactions bond the carboxyl

group of one amino acid to the amino group of
another to form a peptide bond (Figure 3.9).
•A polypeptide is flexible and has directionality (the N-terminus has
a free amino group, the C-terminus a free carboxyl group),
and its side chains extend out from the backbone (Figure 3.10).
 STRUCTURE OF PROTEINS

• Primary structure is the linear sequence of amino acids in the polypeptide chain(s)
of a protein.

• Secondary structure- the local spatial arrangement of a polypeptides backbone

atoms without regard to the conformations of its side chains.

Secondary Structure consists of local regions of poly peptide chains that have a
regular conformation (- helices, - sheets etc) which is stabilized by H-bonds.

• Tertiary structure - the overall arrangement of secondary structure elements.

• Tertiary Structure refers to the 3-D configuration of an entire polypeptide chain
.This includes - helices & - sheets and regions that are globular or spherical

• Quaternary structure- the arrangement of several polypeptide chains

• Quaternary Structure consists of number of polypeptide chains or subunits joined
by noncovalent interactions.
 Primary Structure

• A protein’s primary structure is its unique sequence of

amino acids.
• Because the amino acid R-groups affect a polypeptide’s size,
shape, chemical reactivity, and interactions with water, just a
single amino acid change can radically alter protein function
(Figure 3.13).
The particular sequence of amino acids in a peptide
or protein is referred to as the primary structure.
For example, a hormone that stimulates the thyroid
to release thyroxine consists of a tripeptide Glu-
His-Pro.
 Although other sequences are possible for these three amino acids, only the
tripeptide with the Glu-His-Pro sequence of amino acids has hormonal activity.
Sequences such as His-Pro-Glu or Pro-His-Glu do not produce hormonal activity.
Thus the biological function of peptides as well as proteins depends on the order of
the amino acids.
When cells are damaged, a polypeptide called bradykinin is released at the site,
which stimulates the release of prostaglandins. The presence of bradykinin, which
contains nine amino acids, regulates blood pressure.
• Primary structure - the amino acid sequence of the proteins polypeptide
chains.
• Proteins are linear polymers of 20 different amino acids linked by covalent
amide bonds, called peptide bonds in a specific sequence of its constituent
amino acids.
• The sequence of amino acids that make up a protein is called its primary
structure.
• The Primary structure defines the linear sequence of amino acids and is due
to the peptide bond . The order of the amino acids is called the amino acid
sequence. The sequences of all polypeptide chains of a protein is defined as
the primary structure.
• The primary structure of a protein determines the three-dimensional
structure and the function of the protein.
• Peptide bonds are formed between the carbon atom (C) of the carboxyl
group and the nitrogen atom (N) of the amino group of an amino acid.
• Another way of saying this is that peptide bonds are formed by a
condensation reaction between the amine group of one amino acid and
the carboxyl group of another resulting in an amide group. The
elements of water are removed as a by product of this reaction. Water
(HOH) forms from the -OH of the carboxyl group of one amino acid and a
hydrogen from the -NH2 group of the other amino acid. The product is
called a peptide. Thus both peptides and proteins have amino and carboxyl
ends.
• The amino acids can be linked in any order, but the order of amino acids is
unique to a given protein and is referred to as that protein's "primary
structure."
• The repeating sequence of “C-N-C-C-" resulting from amide bond formation is
called the "polypeptide backbone."
• The directionality of the linkage results in directionality in the resulting polypeptide
chain. The amino group on the first amino acid is referred to as the protein's "N-
terminus" and the carboxyl group on the last amino acid is the "C-terminus."
• Remember:
• Primary structure COVALENT PEPTIDE BONDS
• The protein backbone is represented as "C-N-C-C-".
• Peptide bonds are formed between the carbon atom (C) of the carboxyl group and
the nitrogen atom (N) of the amino group of an amino acid
• The structure of a protein determines its biochemical function
• The amino acids can be linked in any order but the order of amino acids is unique to
a given protein and is referred to as that protein's "primary structure."
 Determination of primary structure
1. Determination of amino acid composition.
The hydrolysis may be carried out either by acid or alkali treatment
or by enzyme (Pronase) hydrolysis. Treatment with enzymes,
however results in smaller peptides rather than amino acids.
2. Degradation of protein or polypeptide into smaller fragments.
Liberation of polypeptides : Treatment with urea or guanidine
hydrochloride. For cleaving the disulfide linkages between the
polypeptide units, treatment with performic acid is necessary.
Number of polypeptides : The number of polypeptide chains
can be identified by treatment of protein with dansyl chloride.
Breakdown of polypeptides into fragments : Polypeptides are
degraded into smaller peptides by enzymatic (trypsin,
chymotrypsin, pepsin and elastase) or chemical methods –CNBr
3. Determination of the amino acid sequence.
 Secondary Structure
• Secondary structure results from hydrogen
bonding between the carboxyl oxygen of one
amino acid residue and the amino hydrogen of
another. A polypeptide must bend to allow this
hydrogen bonding and usually forms an -helix or
-pleated sheet (Figure 3.14).

•A protein’s secondary structure increases its

stability—although each hydrogen bond is very
weak relative to a covalent bond, the large number
of hydrogen bonds makes these structures stable.
 α-Helix
[Link] α -helix is a tightly packed coiled structure with amino acid side chains extending
outward from the central axis.
2. The α -helix is stabilized by extensive hydrogen bonding. It is formed between H atom
attached to peptide N, and O atom attached to peptide C. The hydrogen bonds are
individually weak but collectively, they are strong enough to stabilize the helix.
3. All the peptide bonds, except the first and last in a polypeptide chain, participate in
hydrogen bonding.
4. Each turn of α -helix contains 3.6 amino acids and travels a distance of 0.54 nm. The
spacing of each amino acid is 0.15 nm.
5. α -Helix is a stable conformation formed spontaneously with the lowest energy.
6. The right handed α -helix is more stable than left handed helix (a right handed helix
turns in the direction that the fingers of right hand curl when its thumb points in the
direction the helix rises).
7. Certain amino acids (particularly proline) disrupt the D-helix. Large number of acidic
(Asp, Glu) or basic (Lys, Arg, His) amino acids also interfere with α -helix structure.
α-Helix is found in
Keratins – almost completely helical; major component of hair, skin
· Rigidity determined by no. of –S-S- bonds
· Hb – 80% helical so globular, flexible molecule
 β-Pleated sheet

β -Pleated sheets (or simply β -sheets) are composed of two or more

segments of fully extended peptide chains (Fig.4.10). In the
β -sheets, the hydrogen bonds are formed between the neighbouring
segments of polypeptide chain(s).

As such, the D-helix and E-sheet are commonly found in the same protein structure
(Fig.4.11). In the globular proteins, E-sheets form the core structure.
 Tertiary Structure

• Amino acid R-groups are largely responsible for a

polypeptide’s three-dimensional shape or tertiary structure. R-
groups can interact with other side chains or with the peptide-
bonded backbone, causing the polypeptide to bend and fold into
a precise shape (Figure 3.15).

•R-group interactions include (in order of strength): covalent

disulfide bonds, ionic bonds, hydrogen bonds, and hydrophilic
or hydrophobic interactions stabilized by van der Waals
interactions.
Domains : The term domain is used to represent the basic units
of protein structure (tertiary) and function. A polypeptide with
200 amino acids normally consists of two or more domains.
 Quaternary Structure
• A great majority of the proteins are composed of single polypeptide
chains. Some of the proteins, however, consist of two or more
polypeptides which may be identical or unrelated. Such proteins are
termed as oligomers and possess quaternary structure. The individual
polypeptide chains are known as monomers, protomers or subunits.
A dimer consits of two polypeptides while a tetramer has four.
 Quaternary Structure

• Some proteins contain several polypeptide

subunits; the bonding of two or more subunits
produces quaternary structure (Figure 3.16).
• The combined effects of primary, secondary,
tertiary, and sometimes quaternary structure
(Table 3.2) allow for amazing diversity in protein
form and function.
 Folding and Function

• Protein folding is often spontaneous, because the

hydrogen bonds and van der Waals interactions
make the folded molecule more stable
energetically than the unfolded molecule.

•A denatured (unfolded) protein is unable to

function normally.

•Proteins called molecular chaperones help

proteins fold correctly in cells.
Classification
1. Simple proteins
(a) Globular proteins : These are spherical or oval in shape, soluble in water or other
solvents and digestible.
(i) Albumins : Soluble in water and dilute salt solutions and coagulated by heat. e.g.
serum albumin, ovalbumin (egg), lactalbumin (milk).
(ii) Globulins : Soluble in neutral and dilute salt solutions e.g. serum globulins, vitelline
(egg yolk).
(iii) Glutelins : Soluble in dilute acids and alkalies and mostly found in plants e.g. glutelin
(wheat), oryzenin (rice).
(iv) Prolamines : Soluble in 70% alcohole.g. gliadin (wheat), zein (maize).
(v) Histones : Strongly basic proteins, soluble in water and dilute acids but insoluble in
dilute ammonium hydroxide e.g. thymus histones.
(vi) Globins : These are generally considered along with histones. However, globins are
not basic proteins and are not precipitated by NH4OH.
(vii) Protamines : They are strongly basic and resemble histones but smaller in size and
soluble in NH 4OH. Protamines are also found in association with nucleic acids e.g. sperm
proteins.
(viii) Lectins are carbohydrate-binding proteins, and are involved in the interaction
between cells and proteins. They help to maintain tissue and organ structures. In the
laboratory, lectins are useful for the purification of carbohydrates by affinity
chromatography e.g. concanavalin A, agglutinin.
(b) Fibrous proteins : These are fiber like in shape,
insoluble in water and resistant to digestion. Albuminoids or
scleroproteins are predominant group of fibrous proteins.
(i) Collagens are connective tissue proteins lacking
tryptophan. Collagens, on boiling with water or dilute acids,
yield gelatin which is soluble and digestible
(ii) Elastins : These proteins are found in elastic tissues
such as tendons and arteries.
(iii) Keratins : These are present in exoskeletal structures
e.g. hair, nails, horns. Human hair keratin contains as much
as 14% cysteine