This document discusses proteins and their structure. It begins by introducing proteins and their composition of amino acids linked into peptide chains. It then describes the 20 main amino acids and how they are classified. The four levels of protein structural organization - primary, secondary, tertiary, and quaternary structure - are outlined. Common secondary structures like the alpha helix and beta sheet are also defined. Specific proteins like hemoglobin and myoglobin are then examined in more detail, including their subunit composition and role in oxygen transport.

1. PROTEINS
PRESENTED BY:
DEEPIKA KAITHAL
M.Sc. SEMESTER IV
DEPARTMENT OF
APPLIED PHYSICS

2. CONTENTS
 INTRODUCTION
 TYPES OF PROTEINS
 AMINO ACIDS
 CLASSIFICATION OF AMINO ACIDS
 STRUCTURAL ORGANIZATION OF PROTEINS
 AMINO ACIDS AND BASES
 PEPTIDE BONDS
 DIHEDRAL ANGLES
 HEMOGLOBIN AND MYOGLOBIN

3. INTRODUCTION OF PROTEINS
 Proteins are molecular machines, building blocks, and arms of a living cell.
Their major and almost sole function is enzymatic catalysis of chemical
conversions in and around the cell.
 Proteins are polymers: they are built up by amino acids that are linked into
a peptide chain.
 The chain consists of a chemically regular backbone (“main chain”) from
which various side chains (R1, R2, . . . ,RM) project:

4. PROTEINS
 There are twenty main species of amino acid residues. Their position in
the protein chain is gene-encoded.
 The peptide bond allows for rotation of protein and therefore protein can
fold and orient the R group in favorable positions.
 Protein shape is determined by the sequence of amino acids.

5. TYPES OF PROTEINS
According to their “environmental conditions” and general structure, proteins can
be roughly divided into three classes:
1) FIBROUS PROTEIN: It is usually water-deficient aggregates; their structure is
usually highly hydrogen bonded; highly regular and maintained mainly by
interactions between various chains.
2) MEMBRANE PROTEINS: It reside in a water-deficient membrane environment
(although they partly project into water). The intra-membrane portions are
highly regular and highly hydrogen-bonded; but restricted in size by the
membrane thickness.
3) GLOBULAR PROTEINS: They are less regular and their structure is maintained
by interactions of chain with itself and sometimes by chain interactions with
cofactors.

6. AMINO ACIDS
• Amino acids are the basic structural constituents of naturally occurring
proteins. They all consists of amino group (NH+
3), a carboxylate group (COO-), a
hydrogen atom and a substituent group, R, called side chain, bounded to a
central carbon atom (C atom). There are 20 standard amino acid.

7. CLASSIFICATION OF AMINO
ACIDS BY R GROUP
The amino acids are classified into five main classes based on the properties of
their R groups. These are:
 Non-polar, Aliphatic R Group
 Aromatic R Group
 Polar, Uncharged R Group
 Positively Charged R Group
 Negatively Charged R group
There are 20 different types of amino acids.

8. NON-POLAR ALIPHATIC R
GROUP

9. AROMATIC R GROUP

10. POLAR, UNCHARGED R
GROUP

11. POSITIVELY CHARGED R
GROUP (BASIC)

12. NEGATIVELY CHARGED R
GROUP (ACIDIC)

13. STRUCTURAL ORGANIZATION
OF PROTEINS
The structural and functional features of proteins and protein complexes are
addressed at four levels of hierarchal organization. These are:
1. Primary structure (1o-Structure)
2. Secondary structure (2o-Structure)
3. Tertiary structure (3o-Structure)
4. Quaternary structure (4o-Structure)

14. Continued………
1. PRIMARY STRUCTURE: A description of all covalent bonds (mainly
peptide bonds and disulfide bonds) linking amino acid residues in a
polypeptide chain is its primary structure. The most important element
of primary structure is the sequence of amino acid residues.
2. SECONDARY STRUCTURE: Secondary structure refers to particularly
stable arrangements of amino acid residues giving rise to recurring
structural patterns.
3. TERTIARY STRUCTURE: Tertiary structure describes all aspects of the
three-dimensional folding of a polypeptide.
4. QUATERNARY STRUCTURE: When a protein has two or more polypeptide
subunits, their arrangement in space is referred to as quaternary
structure.

15. DIHEDRAL ANGLES
• Diagram showing a polypeptide chain with a
side group.
Main chain angle/ Backbone dihedral
• phi (φ) is defines as C’i-1- Ni- C
i-C’i.
• psi (ψ) is defined as Ni- C
i-C’i - Ni+1.
• omega (ω) is defined as C
i-C’i - Ni+1 - C
i+1.
Side chain dihedral:
• ci (χ1) is defined as Ni- C
i-C - O

16. α-HELIX
• The α-helix is a stable right-handed helical structure and is also called a 3.613 –
helix. It is a rod-like structure.

17. β-SHEET
• The β-sheet structure is pleated sheet and results from inter-molecular
hydrogen bonds (between N-H and C=O group of neighbouring strands)
perpendicular the strand axis.

18. α-HELIX & β-SHEET

19. HEMOGLOBIN
• Hemoglobin is a tetramer composed of two each of two types of closely
related subunits, alpha and beta.
• Hemoglobin transport O₂ from lungs to tissues.
• Hemoglobin is hydrophilic.

20. STRUCTURE OF HEME
GROUP

21. MYOGLOBIN
• Myoglobin is a monomer (so it doesn't have a quaternary structure at all).
• Myoglobin binds oxygen more tightly than does hemoglobin. This difference in
binding energy reflects the movement of oxygen from the bloodstream to the
cells, from hemoglobin to myoglobin.
• Myoglobin is hydrophilic in outside
and hydrophobic in inside.