ASSIGNMENT

ANALYTICAL CHEMISTRY
M.Sc. III SEM
(2023-25)
TOPIC:

TOPIC:
PRIMARY, SECONDARY , TERTIARY
AND QUATERNARY STRUCTURES OF
PROTEIN

SUBMITTED TO :
Dr. NEHA GUPTA

SUBMITTED BY:
Aditi Verma
INTRODUCTION:
 The 20 amino acids commonly found in proteins are joined together by peptide
bonds.
 The linear sequence of the linked amino acids contains the information necessary
to generate a protein molecule with a unique three-dimensional shape.
 The complexity of protein structure is best analyzed by considering the molecule
in terms of four organizational levels, namely: Primary, Secondary, Tertiary &
Quaternary.
o Why knowing protein structure is important?
o A protein’s function depends on its specific conformation. In almost every
case, the function depends on its ability to recognize and bind to some
other molecule. For example, antibodies bind to particular foreign
substances that fit their binding sites. Enzyme recognize and bind to
specific substrates, facilitating a chemical reaction.

Note:

o A functional protein consists of one or more polypeptides that have been

precisely twisted, folded, and coiled into a unique shape.
o It is the order of amino acids that determines what the three-dimensional
conformation will be.
o Levels of Protein Structure

 Primary Structure of Protein:

 The simplest level of protein structure, primary structure, is simply the sequence
of amino acids in a polypeptide chain.
 For example, the hormone insulin has two polypeptide chains, A and B, Each
chain has its own set of amino acids, assembled in a particular order. For
instance, the sequence of the A chain starts with glycine at the N-terminus and
ends with asparagine at the C-terminus and is different from the sequence of the
B chain.
 The primary structure of proteins involves the sequence of amino acids in a
polypeptide chain.
 Understanding the primary structure of proteins is important because many
genetic diseases result in proteins with abnormal amino acid sequences, which
cause improper folding and loss or impairment of normal function.Thus, studying
the poly peptide chain means studying the primary structure of protein
 Peptide bond
o In proteins, amino acids are joined covalently by peptide bonds. Peptide
bond are amide linkages between the α-carboxyl group of one amino acid
and the α-amino group of another. For example, valine and alanine can
form the dipeptide valine through the formation of a peptide bond.

o
 Characteristics of the peptide bond:

 The peptide bond has a partial double-bond character, that is, it is shorter than a
single bond, and is rigid and planar.
 The peptide bond is generally a trans bond (instead of cis) in large part because
of steric interference of the R-groups when in the cis position.

 Peptide bonds are not broken by conditions that denature proteins, such as
heating & high concentrations of urea.

 Prolonged exposure to a strong acid or base at elevated temperatures is required

to hydrolyze these bonds non enzymically. C. 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. For
example, in the previous figure 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.
 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.
 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 an N-terminal valine, a glycine, and a C-
terminal leucine is called vinyl glycine, leucine.
2.Secondary Structure of Proteins:

o The secondary structure of the polypeptide is a three-dimensional

structure.
o It results from hydrogen bond formation between hydrogen of –NH group
of peptide bond and the carbonyl oxygen –C=O of another peptide bond.
o According to H-bonding there are two main forms of secondary structure:

 α-helix:
 α-helix is a spiral structure, consisting of a tightly packed, coiled polypeptide
backbone core, with the side chains of the component amino acids extending
outward from the central axis to avoid interfering sterically with each other.
 Formed by a H-bond between every 4th peptide bond – C=O to N-H Usually
found in proteins that span a membrane
 The helix can either coil to the right or the left.
 Each turn of an α-helix contains 3.6 amino acids.
 Proline disrupts an α-helix because its secondary amino group is not
geometrically compatible with the right-handed spiral of the α-helix.
 Example of proteins contains α-helices: keratins are a fibrous protein. They are
a major component of tissues such as hair and skin.
 Myoglobin, a globular, flexible protein molecule

 β-sheets:
 It is another form of secondary structure in which two or more polypeptides (or
segments of the same peptide chain) are linked together by hydrogen bond
 between H- of NH- of one chain and carbonyl oxygen of adjacent chain (or
segment).
 In β-sheet all of the peptide bond components are involved in hydrogen bonding.
 Unlike the α-helix, β-sheets are composed of two or more peptide chains (β-
strands), or segments of polypeptide chains, which are almost fully extended.
 The surfaces of β-sheets appear “pleated,” and these structures are, therefore,
often called “β-pleated sheets.”

 3. Tertiary structure of globular proteins

 The three-dimensional arrangement of protein structure is referred to as tertiary
structure. It is a compact structure with hydrophobic side chains held interior
while the hydrophilic groups are on the surface of the protein molecule. This type
of arrangement ensures stability of the molecule.
 Bonds of tertiary structure: Besides the hydrogen bonds, disulfide bonds (S-S-),
ionic interactions (electrostatic bonds), hydrophobic interactions and van der
Waals forces also contribute to the tertiary structure of proteins.
 Domain: a compact and self-folding component of the protein that usually
represents a discreet structural and functional unit. Polypeptide chains that are
greater than 200 amino acids in length generally consist of two or more domains.

 QUATERNARY STRUCTURE OF PROTEINS

 Many proteins consist of a single polypeptide chain, and are defined as

monomeric proteins. However, others may consist of two or more polypeptide
chains that may be structurally identical or totally unrelated.

 The arrangement of these polypeptide subunits is called the quaternary structure

of the protein. Subunits are held together by noncovalent interactions (for
example, hydrogen bonds, ionic bonds, and hydrophobic interactions).
 Collagen is a fibrous protein of three polypeptides that are supercoiled like a
rope.
 Hemoglobin is a globular protein with two copies of two kinds of polypeptides.
 Subunits may either function independently of each other, or may work
cooperatively, as in hemoglobin, in which the binding of oxygen to one subunit
of the tetramer increases the affinity of the other subunits for oxygen.
 

 Note:
 Any protein consisting of a single polypeptide chain is not in the quaternary
structure and, is defined as monomeric protein.

 If there are two subunits, the protein is quaternary and is called "dimeric", if three
subunits "trimeric", and, if several subunits, "multimeric."
o Denaturation and Misfolding of Proteins

 Protein denaturation results in the unfolding and disorganization of the protein’s

secondary and tertiary structures, which are not accompanied by hydrolysis of
peptide bonds.
 Denaturing agents include heat, organic solvents, mechanical mixing, strong
acids or bases, detergents, and ions of heavy metals such as lead and mercury.
 Denaturation may, under ideal conditions, be reversible, in which case the protein
refolds into its original native structure when the denaturing agent is removed.
However, most proteins, once denatured, remain permanently disordered.
 Denatured proteins are often insoluble and, therefore, precipitate from solution.
 o Protein Classification
 Fibrous Protein

o Polypeptides arranged in long strands or sheets

o Water insoluble (lots of hydrophobic AA’s)
o Strong but flexible
o Structural protein or contractile proteins (keratin, collagen, muscle,
microtubules, cytoskeleton, mitotic spindle, cilia, flagella)

 Globular Protein

o Polypeptide chains folded into spherical or globular form

o Water soluble
o Contain several types of secondary structure
o Diverse functions (enzymes, hemoglobin, immunoglobulins, membrane
receptor sites regulatory proteins)
CONCLUSION:

Proteins have a hierarchical structure with four distinct levels. The primary structure
is the linear sequence of amino acids, forming the basis for all higher levels. The
secondary structure involves local folding patterns like α-helices and β-sheets,
stabilized by hydrogen bonds. The tertiary structure is the three-dimensional
conformation driven by side-chain interactions such as hydrogen bonds, ionic bonds,
and hydrophobic effects. The quaternary structure emerges when multiple
polypeptide chains associate to form functional complexes, like hemoglobin.

Each level of structure is crucial for the protein's stability, shape, and function.
Alterations in any level can disrupt protein activity and lead to dysfunction. The
hierarchy highlights the intricate relationship between structure and function, enabling
proteins to perform diverse roles in biological systems. Understanding these levels is
essential for studying protein behavior and their role in life processes.