Glossary Biology Protein

Protein

Proteins are physically and functionally complex macromolecules that are heteropolymers of amino acids. Their very name, derived from the Greek word proteios, literally means “holding the first place” and signifies the importance of these molecules.

Role of Protein

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Proteins play diverse roles in the biological world; for example, the spider-web protein is many times stronger than the toughest steel. Hair, feathers, and hooves are composed of keratin. Crystalin constitutes the transparent lens material found in our eyes and is required for vision. Very small quantities of certain proteins missing from the blood can signify that one’s metabolic processes are going out of control.

Similarly, juvenile-onset diabetes mellitus occurs due to a lack of insulin. Dwarfism can be due to deficiency of the growth hormone, which is again a protein. A unique “antifreeze” blood protein allows Antarctic fish to survive at body temperatures below freezing. You can clearly see why proteins are considered to be so important in the field of biochemistry.

Amino acids

Amino acids contain amino (–NH2) and carboxyl (–COOH) groups and, depending upon the relative position of amino group with respect to the carboxyl group, can be classified as α, β, γ, δ, and so on. We only obtain α-amino acids after the hydrolysis of proteins. They may also contain other functional groups.

All α-amino acids have trivial names that usually reflect the property of that compound or its source. For example, glycine gets its name from the fact that it is sweet in taste (Greek: glykos, meaning “sweet”) and tyrosine because it was first obtained from cheese (Greek: tyros, meaning “cheese”). Amino acids are generally represented by a three-letter symbol, though a one-letter symbol is also used at times.

Amino acids may be acidic, basic or neutral depending on the relative number of amino and carboxyl groups in their structure. For example, amino acids that have an equal number of amino and carboxyl groups are neutral in nature. While those with more amino than carboxyl groups are basic and those with more carboxyl groups than amino groups are acidic.

The amino acids that can be synthesized in the body are known as nonessential amino acids. On the other hand, those which cannot be synthesized in our body and must be obtained through diet are known as essential amino acids.

Properties of amino acids

Physically, amino acids are generally colorless, crystalline solids. They are water-soluble, have high melting points, and and behave like salts rather than simple amines or carboxylic acids. This behavior is because of the presence of both acidic (carboxyl group) and basic (amino group) groups in the same molecule. Amino acids are amphoteric (or amphiprotic) in nature; that is, they can react either as an acid or as a base.

In an aqueous solution, the carboxyl group can lose a proton (H+) and the amino group can accept a proton, producing a dipolar ion known as the Zwitter ion. Although the Zwitter ion itself is overall neutral, it contains both positive and negative charges. In Zwitter ionic form, amino acids demonstrate amphoteric behavior because they react both with acids and bases.

When there are equal positive and negative charges on an amino acid in solution, it is electrically neutral and does not migrate either towards the positive or the negative electrode when placed in an electrolytic cell. The pH at which this phenomenon takes place is known as the isoelectric point.

Except for glycine, all other naturally occurring α-amino acids are optically active because the α-carbon atom is asymmetric. Optically active amino acids exist both in ‘D’ and ‘L’ forms. Most naturally occurring amino acids are observed to possess the L-configuration. L-amino acids are represented by writing the –NH2 group on left hand side while drawing their structure.

Polypeptides

We’ve already discussed that proteins are polymers of α-amino acids that are connected to each other by peptide bonds/linkages. Chemically, a peptide bond is an amide formed between a –COOH group and an –NH2 group. The reaction between two molecules of similar or different amino acids takes place by the combination of the amino group of one molecule with the carboxyl group of the other.

This reaction results in the elimination of a water molecule and the formation of a peptide bond (–CO–NH–). The product of the reaction is known as a dipeptide because it is composed of two amino acids. For example, when the carboxyl group of glycine combines with the amino group of alanine, it yields a dipeptide known as glycylalanine.

Similarly, if a third amino acid combines with a dipeptide, the resulting product is known as a tripeptide. It contains three amino acids linked by two peptide bonds. Likewise, when four, five or six amino acids are linked together, their respective products are known as tetrapeptides, pentapeptides or hexapeptides respectively.

When the number of the reacting amino acids is more than ten, then the products are known as polypeptides. A polypeptide having more than a hundred amino acid residues and a molecular mass higher than 10,000u is known as a protein. However, keep in mind that the difference between a polypeptide and a protein is not very clear.

Polypeptides with fewer amino acids are often referred to as proteins if they tend to have a well-defined conformation like a protein. A good example is insulin, which contains 51 amino acids.

Structure of proteins

Depending on their molecular shape, proteins can be classified into two types:

Fibrous proteins

A fiber-like structure is formed when the polypeptide chains run parallel to each other and are held together by hydrogen bonds and disulfide bonds. Fibrous proteins are usually insoluble in water. Some common examples of such proteins are keratin (found in hair, wool, and silk) and myosin (found in muscles).

Globular proteins

The structure of a globular protein is produced when the chains of polypeptides coil around to give rise to a spherical shape. These proteins are generally soluble in water. Insulin and albumin are common examples of globular proteins.

Structure and Shape of Proteins

We may study the structure and shape of proteins at four different levels – the primary, secondary, tertiary and quaternary levels. Each of these levels is more complex than the one preceding it.

Primary structure

Proteins may possess one or more polypeptide chains. Every polypeptide in a protein features amino acids linked to each other in a specific sequence; it is this sequence of amino acids that constitutes the primary structure of that protein. Any change in the primary structure leads to the formation of a different protein.

Scientists imagine the primary structure of a protein as a line, with the left end represented by the first amino acid and the right end represented by the last amino acid. The first amino acid is also known as the N-terminal amino acid, whereas the last amino acid is known as the C-terminal amino acid.

Secondary structure

The protein thread does not exist throughout its length as an extended rigid rod. It is folded in the form of a helix, very similar to a revolving staircase. The secondary structure of proteins refers to the different shapes in which a long polypeptide chain can exist.

These chains are found to exist in two different kinds of structures: the α-helix structure and the β-pleated sheet structure. These structures arise due to the regular folding of the backbone of the polypeptide chain by virtue of hydrogen bonding between the C=O and the –NH– groups of the peptide bond.

In an α-Helix, the polypeptide chain is often found to form all possible hydrogen bonds by twisting into a right handed screw (helix) with the –NH– group of each amino acid residue that is hydrogen bonded to the C=O of an adjacent turn of the helix.

In the β-pleated sheet structure, all the peptide chains are stretched out to more or less the upper limit of extension and subsequently laid side by side and held together by intermolecular hydrogen bonds. The structure appears very much like pleated folds of drapery, and thus earns its characteristic name.

In natural proteins, we only get to observe right-handed helices.

Tertiary structure

The tertiary structure of proteins represents overall folding of the polypeptide chains arising due to the further folding of the secondary structure. Here, the long protein chain is folded upon itself like a hollow woollen ball, giving us a three-dimensional view of the protein.

It leads to the development of the two major molecular shapes we’ve already discussed above – fibrous and globular. The main forces that stabilize the secondary and tertiary structures of proteins are hydrogen bonds, disulphide linkages, van der Waals forces and electrostatic forces of attraction.

The tertiary structure has been found to be absolutely essential for the numerous biological activities of proteins.

Quaternary structure

Some proteins are composed of two or more individually folded polypeptide chains known as subunits. The spatial arrangement of these subunits with respect to each other (for example, a linear string of spheres, spheres stacked upon each other in the form of a cube or a plate, and so on) is known as the quaternary structure of the protein.

Adult human haemoglobin consists of four subunits, two of which are identical to each other. Thus, two subunits of α-type and two subunits of β-type together constitute the human haemoglobin (Hb) molecule.

Denaturation of proteins

Proteins found in a natural biological system, possessing a unique three-dimensional structure and biological activity, are known as native proteins. When a protein in its native form is subjected to physical change such as a change in temperature, or chemical change such as a change in pH, the hydrogen bonds in its structure are disturbed.

Due to disruption, the protein globules unfold, the helix gets uncoiled, and protein subsequently loses its biological activity. This phenomenon is known as the denaturation of the protein. During denaturation, the secondary and tertiary structures of the protein are destroyed but its primary structure remains intact.A common example of denaturation is the coagulation of egg white on boiling. Another commonly seen example is curdling of milk that is caused due to the formation of lactic acid by the Lactobacilli present in the milk.

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