easy and quick notes on proteins, for UG and PG students

1. PROTEINS
PRESENTED BY:
DEEPIKA KAITHAL
M.Sc. SEMESTER IV
DEPARTMENT OF
APPLIED PHYSICS
Archana Soni archi22ss@gmail.com

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.