PROTEIN BIOCHEMISTRY

1. PROTEIN
Presented by INSHA UR RAHMAN
Presented to MISS ASIA FAZAL
Sub: Biochemistry
DPT BATCH-I (SEM-III)
KIHST
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2. Introduction
• Protein derived from the Greek word “proteios” meaning “of the first rank”.
• Protein is a polymer consist of repeating units of Amino acid (monomers).
• Amino acids act as a building block of proteins.
• Every protein synthesised in accordance with instructions contained in DNA.
• They act as biological catalyst (enzyme).
• Participate cell signal and recognition factor.
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3. Basic Structure of Protein
• Amino acid is building block of protein.
• More than 20 amino acids combine thru peptide bond form a polypeptide chain
(protein).
• Carboxyl group of one amino acid and amino group of other amino acid combine
thru peptide bond by releasing water molecule.. This process is called as
“Condensation”.
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6. Structure of Protein
The structure of protein depends upon the special arrangement of
polypeptide present in a molecule.
I. Primary structure
II. Secondary structure
III. Tertiary structure
IV. Quaternary structure.
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7. Primary structure
• The sequence of amino acids in a protein is called primary structure of protein.
• Amino acids combine thru peptide bond.
• Each component Amino acid in a polypeptide chain is called a “residue” or
“moiety”
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8. Diagrammatic representation of primary
structure
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• The end of the peptide with a free carboxyl group is called the carboxy-
terminus or C-terminus.
• The terms amino-terminus or N-terminus describe the end of the sequence with a
free α-amino group
• Chain always start with N-terminus
• A specific sequence of nucleotides in DNA is transcribed into mRNA
(Transcription) which is read by the ribosome in a process called translation
• proteins have unique amino acid sequences, which defines the structure and
function of that protein
• The sequence of a protein can be determined by methods called Edman
degradation
• For example, insulin is composed of 51 amino acids in 2 chains. One chain has 31
amino acids, and the other has 20 amino acids.

10. Characteristics of Peptide bond.
• Peptide bond has partial double bond feature that is shorter than single bond.
• Bond is rigid and planar & prevent free rotation around bond b/w carbonyl
carbon and nitrogen of peptide bond.
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11. Secondary structure
• Peptide chains may acquire spiral shape or may be present in a zig zag manner.
This zig-zagging of chain is called secondary structure.
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It consists of
α-helix
β-sheet (composed of β-
strands)
β-bends ( reverse, β-turns)
Nonrepetitive secondary
structure
Supersecondary structures
(motifs)

12. Contd…….
α-Helix
• It is rigid & right handed spiral structure.
• A very diverse & most common group.
• 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.
• stabilized by extensive hydrogen bonding.
• Amino acids 3 or 4 residues apart in primary sequence.
• The H-bond form b/w the O of C=O and Of each peptide bond in
the strand and the H of the N-H group of the peptide bond four
amino acid below it in the helix.
• Each turn of helix contains 3.6 amino acids.
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13. Contd…
• Some amino acids disrupts an α-helix like:
1. Proline
• its secondary amino group is not geometrically compatible with the
α-helix
• inserts a kink in the chain
2. charged amino acids (glu, arg, asp, his, lys)
• disrupt the helix by forming ionic bonds, or by electrostatically
repelling each other. 13

14. Contd…..
β-Sheet
• Form of secondary structure in which all peptide bond components are involved in
hydrogen.
• Because beta-sheet appears “pleated” they are often called β-pleated sheet.
• Sheet is formed by two or more peptide chains (β-strands) aligned laterally &
stabilised by H-bonds b/w carboxyl & amino groups of amino acid.
• the H-bonds are perpendicular to the polypeptide back bone.
• H-bond found between the two strands, the O of C=O in one strand with the H of
the Amino group of the adjacent strand (Interchain bond)
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16. Parallel and antiparallel sheets:
• polypeptide chains of β-sheets are arranged either
Parallel
• Adjacent polypeptide chains running in the same direction.
• formed by a single polypeptide chain
folding back on itself.
Antiparallel
• when the adjacent polypeptide chains
run in opposite direction
• More stable due to well-aligned H-bond
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18. Contd…..
β-bends (reserve turn,β-turn)
• composed of four amino acids, one of which may be proline—the amino acid that
causes a “kink” in the polypeptide chain. Glycine (simplest amino acid).
• Reverse the direction of a polypeptide chain to get folded structure, helping it form a
compact, globular shape
• often include charged amino acids
• usually found on the surface of protein molecules
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19.  Nonrepetitive secondary structure
• Approximately one half of an average globular protein is
organized into repetitive structures, such as the α-helix and/or β-
sheet
• the remainder of the polypeptide chain is described as having a
loop or coil conformation
• They may be irregular or unique.
• 50% of globular proteins are nonrepetitive
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20.  Supersecondary structures (motifs)
• Globular proteins are constructed by combining secondary structural elements (α-
helices, β-sheets, nonrepetitive sequences).
• These form primarily the core region—that is, the interior of the molecule.
• They are connected by loop regions (for example, β-bends) at the surface of the protein.
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22. Tertiary Structure
• Twisting or folding polypeptide chains, three dimensional structure represents
tertiary structure of protein.
• Tertiary refers to both folding of domain & to final arrangement of domains in
polypetide.
• Bondings that stabilize the structure are disulphide bonds (-s-s-) covalent
linkage, hydrophobic interaction, hydrogen bonds & ionic interaction.
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23. Contd…
The three-dimensional & stabilized structure of globular protein is due to
the:
• Hydrophobic interactions (Interior of the chain b/w uncharged Amino acids)
• Hydrophilic Interaction (at the surface of chain b/w Charged Amino acids)
• Hydrogen bonds (b/w polar groups of amino acids on the surface of proteins)
• Ionic interactions (b/w charged amino acid)
• Disulfide bonds (formed from the sulfhydryl group (–SH) of each of two cysteine
residues (separated from each other by many amino acids) to produce a cystine
residue.
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25. Contd…
• fundamental functional and three-dimensional structural units of
polypeptides
• Form by Folding of the peptide chain
• Polypeptide chain have >200 amino acids in length generally consist of
two or more domains.
• The core of a domain is built from combinations of supersecondary
structural elements (motifs)
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26. Quaternary structure
• Quaternary means four.
• Quaternary protein is the arrangement of multiple folded protein or coiling
protein molecule in a multi subunit complex.
• A variety of bonding interaction include H-bonding, salt bridges, & disulphide
bonds.
• E.g Hemoglobin
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29.  Classification of Protein
• Globular proteins
• Fibrous proteins
According to
structure
• Simple protein
• Conjugated protein
According to
composition
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According to
function

30. Classification according to Structure
a) Globular Protein
• Globular proteins or spheroproteins are spherical ("globe-like") proteins and
are one of the common protein .
• Globular proteins are somewhat water-soluble (forming colloids in water),
unlike the fibrous or membrane proteins.
• There are multiple fold classes of globular proteins, since there are many
different architectures that can fold into a roughly spherical shape.
EXAMPLES
Hemoglobin, myoglobin
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31. Structure of hemoglobin
• Hemoglobin is composed of four polypeptide chains: two α chains and
two β chains—held together by noncovalent interactions
• Quaternary structure of hemoglobin is composed of two identical dimers,
(αβ)1 and (αβ)2.
• The two polypeptide chains within each dimer are held tightly together
by hydrophobic interactions (both in the interior & on the surface).
• Ionic and hydrogen bonds also occur between the members of the dimer.
• Weak ionic interaction b/w dimers—position of dimers different in
deoxyhemoglobin & oxyhemoglobin
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32. T.form:
• The deoxy form of hemoglobin is
called the “T,” or taut
• the two αβ dimers interact through
a network of ionic bonds & H-
bonds
R.Form
• The oxygenated form of hemoglobin
is called the R.form (Relaxed form).
• The binding of oxygen to
hemoglobin causes the rupture of
some of the ionic bonds and H-
bonds b/w the αβ dimers
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33. Function of Hemoglobin
• Hemoglobin is found exclusively in red blood cells (RBCs), where
its main function is to transport oxygen (O2) from the lungs to the
capillaries of the tissues.
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34. b) Fibrous protein
• A Fibrous protein is a protein with an elongated shape. Fibrous
proteins provide structural support for cells and tissues.
• There are special types of helices present in two fibrous proteins α-
keratin and collagen.
• These proteins form long fibres that serve a structural role in the
human body.
Examples are,
I. Collagen
II. Elastin 34

35. Collagen
• Collagen is the most abundant protein in the human body
• A typical collagen molecule is a long, rigid structure in which three polypeptides (referred
to as “α chains”) are wound around one another in a rope-like triple helix.
• The three polypeptide α chains are held together by hydrogen bonds between the
chains.
• Each helix contain approximately 1,000 amino acids.
• Per turn contains 3 amino acid.
• α chains are combined to form the various types of collagen found in the tissues.
• Collagen is rich in proline and glycine.
• Collagen contains hydroxy - proline (hyp) and hydroxylysine (hyl), which are not present
in most other proteins
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36.  Structure of collagen
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37.  Types of Collagen
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38.  Formation of Collagen
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39. Elastin
• Elastin is a highly elastic protein in connective tissue that can stretch and bend
in any direction, giving connective tissue elasticity. .
• composed of elastin and glycoprotein microfibrils are found in the lungs, the
walls of large arteries, and elastic ligaments
• Elastin helps skin to return to its original position when it is poked or pinched.
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40.  Structure of Elastin
• linear polypeptide composed of about 700 amino acids (primarily nonpolar).
• rich in proline & lysine but little number of hydroxyproline and hydroxy lysine.
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43. Classification a/c to Composition
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44. Functional Classification of Protein.
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45. Any Questions ?
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