PROTEINS

PRESENTED BY:DEEPIKA KAITHALM.Sc. SEMESTER IVDEPARTMENT OF APPLIED PHYSICS

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

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:

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.

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.

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.

CLASSIFICATION OF AMINO ACIDS BY R GROUP

The amino acids are classified into five main classes based on the properties oftheir 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.

NON-POLAR ALIPHATIC R GROUP

AROMATIC R GROUP

POLAR, UNCHARGED R GROUP

POSITIVELY CHARGED R GROUP (BASIC)

NEGATIVELY CHARGED R GROUP (ACIDIC)

STRUCTURAL ORGANIZATION OF PROTEINS

The structural and functional features of proteins and protein complexes areaddressed 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)

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.

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 Ci-C’i - Ni+1 - C

i+1.Side chain dihedral:• ci (χ1) is defined as Ni- C

i-C - O

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.

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.

α-HELIX & β-SHEET

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.

STRUCTURE OF HEME GROUP

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.