Proteins

  • Proteins are biological polymers composed of amino acids.
  • Amino acids linked together by peptide bond to form a polypeptide chain.
  • One or more polypeptide chain twisted into 3D shape to form protein.
  • Protein complex shapes includes various folds, loops and curves.
  • It is an essential constituent of all cells.
  • It is in every part of body, skin, muscles, hair, blood, organs, eyes, finger nails and bones.
  • These are macromolecular polymers composed of amino acid as basic unit.
  • Protein molecules: fibrous: elongated and insoluble. And Globular: compact, soluble, spherical.
                  Globular protein                           Fibrous protein
Polypeptide chains are compactly folded to form spherical or globular shapePolypeptide chains are extended along one axis and are spherically wound to form fibers
4 types of bonds: H-bonds, ionic bonds, disulphide bonds and hydrophobic bonds, which maintains a tertiary structure.H-bonds between amino acids residue, so usually have high degree of secondary structure.
Soluble in waterInsoluble in water
Non-contractileContractile
Ex. Egg albumin, globulins, Hb, all enzymes, etc.Ex. Alpha-keratin of hair, nails, claws, horns, etc. Elastin, Collagen
 Long, parallel chains form fibres
  
 

Types of protein:

Simple protein:

Gives only amino acid on hydrolysis. Ex. Ribonuclease

Composed of only alpha-amino acids.

Albumins: soluble in water and dilute in salt solution. It is present in egg white portion and in blood. It is neutral.

Globulins: insoluble in water but soluble in dilute salt solution. It is present in antibodies in blood serum and as blood fibrinogen. It is neutral.

Histones: soluble in water and insoluble in dilute ammonium hydroxide. It is basic in nature. Ex. Chromatin.

Conjugated protein:

Gives amino acid and non- amino acids components on hydrolysis.

Conjugated proteins:

Class  Prosthetic groupExamples  
Lipoprotein  Lipids  Beta1- lipoprotein of blood, yolk, serum, milk, and cell membranes
Glycoprotein  Carbohydrate  Immunoglobulin G
Phosphoprotein  Phosphate groupCasein of milk
Hemoprotein  Heme (Fe porphyrin)Haemoglobin  
Flavoprotein  Flavin nucleotideSuccinate dehydrogenase
Metalloprotein  Fe Zn Ca   Mo Cu  Ferritin Alcohol dehydrogenase Calmodulin (any Ca-bindingg protein) Dinitrogenase Plastocyanin  

Conjugated protein

  • Prosthetic group: an inorganic/organic component (non amino acid) that is covalently bound to a protein and essential for its activity.
  • Cofactor: an inorganic/organic component is not covalently bound to a protein.

Functional diversity of proteins:

  • Enzymes: Hexokinase, kinase, etc.
  • Transport proteins: haemoglobin, lipoprotein, membrane transport proteins.
  • Nutrient and storage proteins: albumin, casein.
  • Contractile protein: actin, myosin, tubulin, etc.
  • Structural protein: collagen, desmosine, elastin, keratin, spider web protein.
  • Defense protein: immunoglobulin, fibrinogen, thrombin, snake venom, bacterial toxins, rcin, abrin, etc.
  • Regulatory protein: hormones, GTP – binding protein.
  • Other proteins – antifreeze protein, monellin, etc.

Homologous proteins

Group of protein perform same function in all organism but are evolutionary related (structural resemble)

Example: Hb – oxygen transport

                  Mb – tissues O2  – transport

                 Cytochrome – C

Conservative substitution:

When one amino acid of one part is changed by another. Ex: 1 polar acid changed by 1 another polar amino acid.

Ubiquitin

With help of ubiquitin, protein degrade after the completion of its function, if ubiquitin do not function then a cell gets block.

Protein conformation

It is stabilized by weak interactions and the stability of unfold state of protein is maintained by high degree of entropy and H-bonding interaction of many group in polypeptide chain.

Conformation:

Spatial arrangement of atoms in a protein and a change in conformation could occur by rotation about single bond.

Levels of architecture of proteins:

  • Primary structure: it refers to amino acid sequence and all covalent bond between amino acids and location of disulphide bonds.
  • Secondary structure: refers to regular recurring arrangement.
  • Tertiary structure: refers to spatial relationship between all amino acids.
  • Quaternary structure: refers too spatial relationship between different polypeptides.

Primary structure

It is sequence of amino acids in polypeptide chain.

Unique order in which amino acids are linked together to form a protein.

There is the peptide linkage in the form of bonding.

Structure of peptides are: amino acids whose amino group is free and group called N-terminal end, and other whose carboxyl group is free and group called C-terminal end.

Proteins are constructed from a set of 20 amino acids. Generally, amino acids have following structural properties:

C (alpha-C) bonded to 4 group below:-

  • H – atom
  • -NH2 group
  • -COOH group
  • Variable or R group
The Astrophysics & Astrochemistry Laboratory: Amino Acids and Their  Production during the Photolysis of Astrophysically Relevant Ices
  • Amino acids sequence of a protein is determined by information found in a cellular genetic code.

Secondary structure

Formed by folding of primary structure.

2 polypeptide are held together by H-bonds.

The coiling or folding of a polypeptide chain that gives proteins its 3D structure.

It is the arrangement od amino acids chain due to the H-bonds between atoms at different parts of the chain.

Ex: collagen and silk – fibroin

Proteins can assume 2 conformational structure: α-helix and β-pleated sheet

α-helix:

  • Resembles a coiling spring
  • Secured by H-bonding in polypeptide chain.
  • Constraints which affect the stability of α-helix:
  • Electrostatic repulsions (or attraction) between amino acid residues with charged R-group.
  • The bulkiness of adjacent R-group.
  • The interaction between amino acid side chain spaced 3 or 4 residues apart.
  • Occurrence of proline structure.
  • Interaction between amino acid at ends of helix and electric dipole inherent to this structure.
  • There is intrachain H-bonding.

Β-pleated sheet:

  • Appears to be folded or pleated and is held together by H-bonding between polypeptide units of the folded chain that lie adjacent to one another.
  • 2 types:
  •  Parallel beta sheets:-chains of polypeptides, which run in the same direction.
  •  Anti-parallel beta sheets:-chains of polypeptides, which run in the opposite direction to eachother.
  •  These are both intra and inter- chain H bonding, it is extended or zig-zag conformations.
     Α-helix     Β– helix
Helical conformationZig-Zag conformation
InterchainInter and Intra- chain
R-group project outsideR-group is projected alternately
  

Tertiary structure

  • Refers to the 3D-structure of polypeptide chains of a protein.
  • There are several types of bonds and forces that hold a protein in its tertiary structure.
  • Hydrophobic interactions: Greatly contribute to folding and shaping of a protein. ‘R’ group – amino acid: hydrophobic or hydrophilic.
  • Hydrophilic R-group: seek contact with aqueous environment
  • Hydrophobic R-group: seek to avoid water and position themselves towards the center of protein.
  • Hydrogen bonding: In the polypeptide chain and between amino acid R group helps to stabilize protein structure by holding the protein in shape established by hydrophobic interactions.
  • Due to protein folding, Ionic bonding can occur between positively and negatively charged R group that come in close contact with one another.
  • Folding also results in Covalent bonding between R group of cysteine amino acid. This type of bonding forms: disulfide bridge.
  • Interactions called Vander wall forces also assist in stabilization. These contribute to bonding that occurs between molecules.

Quaternary  structure

  • Proteins are formed by more than one polypeptide chain and joined together by covalent bond.
  • Each polypeptide is called as a subunit.
  • Quaternary structure formed by interachain.
  • When protein formed by similar subunit : homogenous quaternary structure, and when protein formed by dissimilar subunit: heterogenous quaternary structure. It is consists of 2 identical α-chain and 2- identical β-promoter.
  • Most stable structure.

Stability

Less stable to more stable:

Primary to secondary to tertiary to quaternary

Chemical bonds involved in protein structure

Strong bonds

Peptide bonds: covalent bonds formed by dehydration synthesis between alpha-carboxyl group of one amino acid and alpha-amino group of adjacent amino acid.

Disulphide bonds: covalent bonds formed between the S-containing cysteine residue of polypeptide chain.

Weak bonds

Hydrogen bonds: sharing of H-atoms between the –N and –C=O of different peptide bond.

Hydrophobic bonds: when two chains of amino acids come together, no true bonds are formed.

Ionic, electrostatic or salt linkages: formed between closely lying –COO and –NH3 group of different amino group residues.