Question

Describe what is meant by each of the following terms, using specific examples where appropriate: (a) polypeptide; (b) protein; (c) N-terminal amino acid; (d) \(\alpha\) helix; (e) denaturation.

Short answer

Polypeptide is a single chain of amino acids, a protein is a complex molecule formed by polypeptides, N-terminal amino acid is the start of a polypeptide that has a free amine group, \(\alpha\) helix is a coiled configuration in protein secondary structure, and denaturation is a process where proteins lose their higher-order structure due to external stress.

Step-by-step solution

Defining Polypeptide

(a) A polypeptide is a single linear polymer chain of amino acids bonded together by peptide bonds. It is a crucial structure in proteins. For example, insulin is a protein that consists of two polypeptide chains.

Defining Protein

(b) A protein is a complex molecule formed by one or more polypeptides. They play numerous critical roles in the body, such as antibodies for defense, enzymes for metabolism, and hemoglobin for oxygen transport.

Defining N-terminal Amino Acid

(c) The N-terminal amino acid is the amino acid at the start of a polypeptide or protein that has a free amine group (-NH2). In a peptide sequence, the N-terminal is the end where the amino group is not involved in a peptide bond.

Defining Alpha Helix

(d) The \(\alpha\) helix refers to a specific configuration in the secondary structure of proteins, where the polypeptide backbone is twisted into a right-handed coiled structure. Each turn of the helix involves 3.6 residues (amino acids). An example can be provided from keratin, the protein found in hair and nails.

Defining Denaturation

(e) Denaturation is the process in which proteins lose their higher order structure (secondary, tertiary, quaternary) due to external stress like heat or acidity, while the primary structure remains intact. For instance, when an egg is boiled, the heat causes the proteins in the egg white to denature, changing it from a clear substance to white and solid.

Key concepts

Protein Structure

Proteins, often described as the building blocks of life, are large, complex molecules that play many critical roles within organisms. Essential to the structure and function of all living cells, proteins are composed of building units called amino acids. There are four levels of structure that define a protein's shape and functionality:

• The primary structure is the unique sequence of amino acids in a polypeptide chain.
• The secondary structure includes arrangements such as alpha helices and beta sheets, formed by hydrogen bonding.
• The tertiary structure is the three-dimensional shape resulting from attractions between the side chains of the amino acids in the polypeptide chain.
• Finally, the quaternary structure is the arrangement of multiple folded protein subunits in a multi-subunit complex.

A single protein's shape is crucial to its function, and any alterations can have significant impacts on how it performs its tasks within the body.

Alpha Helix

The alpha helix is a fundamental motif in the secondary structure of proteins. It resembles a coiled spring, a structure stabilized by hydrogen bonds between the backbone atoms in the polypeptide chain. Each turn of this right-handed helix includes 3.6 amino acid residues, and the tightness of the coil is maintained by the hydrogen bonds that form between the N-H group of one amino acid and the C=O group four residues earlier.

While exploring examples, keratin is a classic one where the alpha helix plays a structural role, providing strength and flexibility to hair, nails, and skin. This coiled structure allows for elongation and elasticity, attributes that are vital for the protein's function in our body's structures.

Amino Acids

Amino acids are the organic compounds that combine to form proteins. There are twenty standard amino acids, each with a basic amino group (-NH2), an acidic carboxyl group (-COOH), and a unique side chain or R group which determines the characteristics of that amino acid. They are linked together by peptide bonds to form polypeptide chains.

At one end of the polypeptide chain is the N-terminal amino acid, which has a free amino group, whereas the opposite end, known as the C-terminus, has a free carboxyl group. The sequence and properties of the amino acids in a protein dictate its final structure and function. For instance, the protein hemoglobin is made of chains of amino acids that fold into a specific shape, allowing it to carry oxygen throughout the body efficiently.

Denaturation Process

Denaturation is the process in which proteins lose their natural shape and, consequently, their function due to external factors such as changes in pH, temperature, or the presence of heavy metals. These factors disrupt the delicate balance of non-covalent bonds that maintain the protein's structure. Importantly, while the protein's primary structure, its amino acid sequence, remains unchanged, its secondary and tertiary structures unravel.

The classic example of denaturation is the white of an egg turning opaque and solid when heated. This process, while often irreversible in the kitchen, can sometimes be reversed in the laboratory, offering scientists valuable insights into protein folding and stability.