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Proteins Structures and Molecular Properties

In this Proteins Structures and Molecular Properties post we have briefly explained about proteins structure, classifications, functions and importance.

Proteins are large, complex molecules that play many critical roles in the body. They do most of the work in cells and are required for the structure, function, and regulation of the body’s tissues and organs

Peptide bond

The amino acids are held together in a protein by covalent peptide bonds or linkages. These bonds are rather strong and serve as the cementing material between the individual amino acids.

Formation

When the amino group of an amino acid combines with the carboxyl group of another amino acid, a peptide bond is formed. Note that a dipeptide will have two amino acids and one peptide (not two) bond. Peptides containing more than 10 amino acids (decapeptide) are referred to as polypeptides.

proteins

Formation of a peptide bond

Characteristics

The peptide bond is rigid and planar with partial double bond in character. It generally exists in Trans configuration. Both C=O and NH groups of peptide bonds are polar and are involved in hydrogen bond formation.

Writing

Conventionally, the peptide chains are written with the free amino end (N-terminal residue) at the left, and the free carboxyl end (C-terminal residue) at the right. The amino acid sequence is read from N-terminal end to C-terminal end. Incidentally, the protein biosynthesis also starts from the N-terminal amino acid.

Proteins Structure

The three dimensional configuration of is determined by the linear sequence of amino acid residues in a polypeptide chain, and the proteins structure determines its function.

Carbon, hydrogen, oxygen, nitrogen, and sulphur are all elements found in proteins.  Some of these may also contain phosphorus, iodine, and metal traces such as ion, copper, zinc, and manganese.

It can have up to 20 different types of amino acids.  Each amino acid has an amine group on one end and an acid group on the other, as well as a distinct side chain. The backbone of all amino acids is the same, but the side chain varies from one amino acid to the next.

proteins

Proteins Structures and Molecular Properties

Proteins Structures and Molecular Properties

1. Primary Structure

The primary proteins structure is the precise arrangement of amino acids that form their chains. The precise sequence is critical because it determines the final fold and thus the function of the protein.

Proteins are made up of a number of polypeptide chains linked together. These chains contain amino acids arranged in a specific sequence that is unique to the protein. Any change in the sequence has an effect on the entire protein.

2. Secondary Structure

Proteins are not made up of simple polypeptide chains. The interaction between the amine and carboxyl groups of the peptide link causes these polypeptide chains to fold. The proteins structure is the shape that a long polypeptide chain can take.

They have been discovered to exist in two different types of proteins structure: α-helix and β-pleated sheet proteins structure. This structure results from the regular folding of the polypeptide chain’s backbone caused by hydrogen bonding between the peptide bond’s -CO and -NH groups.

α-Helix

α-Helix is one of the most common ways in which a polypeptide chain forms all possible hydrogen bonds by twisting into a right-handed screw with the -NH group of each amino acid residue hydrogen-bonded to the -CO of the adjacent turn of the helix. The polypeptide chains twisted into a right-handed screw.

β-pleated sheet

In this arrangement, the polypeptide chains are stretched out beside one another and then bonded by intermolecular H-bonds. In this proteins structure, all peptide chains are stretched out to nearly maximum extension and then laid side by side which is held together by intermolecular hydrogen bonds. The proteins structure resembles the pleated folds of drapery and therefore is known as β-pleated sheet

3. Tertiary Structure

This proteins structure results from further folding of the secondary proteins structure. This structure is held together by H-bonds, electrostatic forces, disulphide linkages, and Vander Waals forces. The tertiary structure represents the overall folding of the polypeptide chains, as well as additional folding of the secondary structure.

It produces two major molecular shapes: fibrous and globular. Hydrogen bonds, disulphide linkages, van der Waals forces, and electrostatic forces of attraction are the primary forces that stabilise the secondary and tertiary proteins structure.

4. Quaternary Structure

The spatial arrangement of various tertiary proteins structure gives rise to the quaternary proteins structure. Some of it are composed of two or more polypeptide chains referred to as sub-units. The spatial arrangement of these subunits with respect to each other is known as quaternary proteins structure.

Classification

They are classified in several ways. Three major types of classification based on their function, chemical nature and solubility properties and nutritional importance are discussed here.

A. Functional classification

Based on the functions proteins perform, They are classified into the following nine different groups (with examples)

Structural protein: Keratin of hair and nails, collagen of bone.

Enzymes or catalytic protein: Hexokinase, pepsin.

Transport protein: Hemoglobin, serum albumin.

Hormonal protein: Insulin, growth hormone.

Contractile protein: Actin, myosin.

Storage protein: Ovalbumin, glutelin.

Genetic protein: Nucleoproteins.

Defense protein: Snake venoms, Immunoglobulins.

 Receptor protein: Hormones, viruses

B. Chemical nature and solubility

This is a more comprehensive and popular classification of proteins. It is based on the amino acid composition, proteins structure, shape and solubility properties. Proteins are broadly classified into 3 major groups.

1. Simple proteins

They are composed of only amino acid residue. On hydrolysis these proteins yield only constituent amino acids. It is further divided into: Fibrous protein: Keratin, Elastin, Collagen, Globular protein: Albumin, Globulin, Glutelin, Histones

2. Conjugated proteins

Nucleoproteins: Nucleic acid (DNA or RNA) is the prosthetic group e.g. nucleohistones, nucleoprotamines. Glycoproteins: The prosthetic group is carbohydrate, which is less than 4% of protein. The term mucoprotein is used if the carbohydrate content is more than 4%. e.g. mucin (saliva), ovomucoid (egg white).

Lipoproteins: Protein found in combination with lipids as the prosthetic group e.g. serum lipoproteins. Phosphoproteins: Phosphoric acid is the prosthetic group e.g. casein (milk), vitelline (egg yolk). Chromo proteins: The prosthetic group is coloured in nature e.g. hemoglobins, cytochromes. Metalloproteins: These proteins contain metal ions such as Fe, Co, Zn, Cu, Mg etc., e.g. ceruloplasmin (Cu), carbonic anhydrase (Zn).

3. Derived proteins

The derived proteins are of two types. The primary derived are the denatured or coagulated or first hydrolysed products of proteins. The secondary derivatives are the degraded (due to breakdown of peptide bonds) products of proteins

a. Primary derived

Coagulated proteins: These are the denatured proteins produced by agents such as heat, acids, alkalies etc. e.g. cooked proteins, coagulated albumin (egg white). Proteans: These are the earliest products of protein hydrolysis by enzymes, dilute acids, alkalies etc. which are insoluble in water. e.g. fibrin formed from fibrinogen. Metaproteins: These are the second stage products of protein hydrolysis obtained by treatment with slightly stronger acids and alkalies e.g. acid and alkali metaproteins.

b. Secondary derived

These are the progressive hydrolytic products of protein hydrolysis. These include proteoses, peptones, polypeptides and peptides.

Properties

1. Solubility: Proteins form colloidal solutions instead of true solutions in water. This is due to the huge size of protein molecules.

2. Molecular weight: The proteins vary in their molecular weights, which, in turn, is dependent on the number of amino acid residues. Each amino acid on an average contributes to a molecular weight of about 110. Majority of proteins/polypeptides may be composed of 40 to 4,000 amino acids with a molecular weight ranging from 4,000 to 440,000.

3. Shape: There is a wide variation in the protein shape. It may be globular (insulin), oval (albumin) fibrous or elongated (fibrinogen).

4. Isoelectric pH: Isoelectric pH (pI) as a property of amino acids has been described. The nature of the amino acids (particularly their ionizable groups) determines the pI of a protein. The acidic amino acids (Asp, Glu) and basic amino acids (His, Lys, Arg) strongly influence the pI. At isoelectric pH, the proteins exist as zwitterions or dipolar ions. They are electrically neutral (do not migrate in the electric field) with minimum solubility, maximum perceptibility and least buffering capacity.

5. Acidic and basic: Proteins in which the ratio (H Lys + H Arg)/(H Glu + H Asp) is greater than 1 are referred to as basic proteins. For acidic proteins, the ratio is less than 1

6. Precipitation: Proteins exist in colloidal solution due to hydration of polar groups (COO–, NH3+, OH). Proteins can be precipitated by dehydration or neutralization of polar groups.

7. Colour reactions: The proteins give several colour reactions which are often useful to identify the nature of the amino acids present in them

Further Readings

Reference

  1. https://www.britannica.com/science/protein
  2. https://www.biologyexams4u.com/2011/10/protein-structure.html
  3. https://open.umn.edu/opentextbooks/textbooks/biochemistry-free-for-all-ahern

Proteins Structures and Molecular Properties