Proteins | MiM

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.

Learn Classification of Proteins in 2 minutes.

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 shape	Polypeptide 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 water	Insoluble in water
Non-contractile	Contractile
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 group	Examples
Lipoprotein	Lipids	Beta1- lipoprotein of blood, yolk, serum, milk, and cell membranes
Glycoprotein	Carbohydrate	Immunoglobulin G
Phosphoprotein	Phosphate group	Casein of milk
Hemoprotein	Heme (Fe porphyrin)	Haemoglobin
Flavoprotein	Flavin nucleotide	Succinate dehydrogenase
Metalloprotein	Fe Zn Ca Mo Cu	Ferritin Alcohol dehydrogenase Calmodulin (any Ca-bindingg protein) Dinitrogenase Plastocyanin

Prosthetic group: an inorganic/organic component (non amino acid) that is covalently bound to a protein and essential for its activity.
Co–factor: 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.

Biology Notes for A level: #13. Protein - Primary, Secondary, Tertiary and Quaternary structure

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
-NH₂group
-COOH group
Variable or R group

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 – fibrin

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 conformation	Zig-Zag conformation
Interchain	Inter and Intra- chain
R-group project outside	R-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 –NH₃group of different amino group residues.