Peptide Bonds & Protein Basics

How is a peptide bond formed between amino acids, and what type of reaction is it?

A peptide bond forms when the carboxyl group (–COOH) of one amino acid reacts with the amino group (–NH₂) of another, producing a condensation (dehydration) reaction — meaning a molecule of water (H₂O) is released.

Reaction steps:

1. The hydroxyl group (–OH) from the carboxyl of one amino acid and a hydrogen atom (–H) from the amino group of another combine to form water.

2. A covalent bond forms between the carbon atom of the carboxyl group and the nitrogen atom of the amino group.

3. This C–N bond is the peptide bond (also called an amide bond).

What is a polypeptide, and how does it relate to proteins?

A polypeptide is a long chain of amino acids linked by peptide bonds.
Each polypeptide is formed by repeated condensation reactions between amino acids.
When one or more polypeptides fold into a specific 3D shape, they form a functional protein.

Details:

• A dipeptide = 2 amino acids linked by one peptide bond.

• A polypeptide may contain hundreds or even thousands of amino acids.

• The sequence of amino acids (the order of R groups) determines the protein’s structure and function.

What is the directionality of a polypeptide chain, and why is it important?

Polypeptides have two distinct ends:

• N-terminus (Amino end): The end with a free amino group (–NH₂ or –NH₃⁺).

• C-terminus (Carboxyl end): The end with a free carboxyl group (–COOH or –COO⁻).

During protein synthesis, amino acids are always added to the C-terminus, giving the chain a directionality from N → C.
This orientation is critical for:

• Reading genetic information correctly.

• Determining how proteins fold and interact.

• Enzymatic recognition (many enzymes read or act in the N→C direction).

Describe the Primary Structure of a protein.

The primary structure is the sequence of amino acids in the polypeptide chain, held together by peptide bonds.
It is determined by the gene’s DNA sequence and dictates the higher-level structures of the protein (secondary, tertiary, and quaternary).

What is meant by Secondary Structure in proteins, and what types exist?

The secondary structure refers to the regular coiling or folding of parts of the polypeptide chain due to hydrogen bonding between atoms in the peptide backbone (not the R groups).

What are the two types of Secondary structure 

1. α-Helix (Alpha helix):

   • Formed when the chain coils into a spiral held together by hydrogen bonds between every 4th amino acid.

   • Each N–H group forms a hydrogen bond with the C=O group of the amino acid 4 residues earlier.

   • Found commonly in fibrous proteins (e.g., keratin in hair, nails).

2. β-Pleated Sheet (Beta sheet):

   • Formed when two or more parts of the polypeptide chain run alongside each other, linked by hydrogen bonds.

   • Can be parallel (same direction) or antiparallel (opposite directions).

   • Found in silk fibroin and other fibrous structures.

What is the Tertiary Structure of a protein, and what forces maintain it?

The tertiary structure is the overall 3D shape of a single polypeptide chain, resulting from interactions between R groups of the amino acids.
This determines the protein’s specific function.

What types of bonds are included?

1. Hydrogen bonds – between polar R groups.

2. Ionic bonds – between oppositely charged R groups (acidic & basic side chains).

3. Disulfide bridges – covalent bonds between sulfur atoms of cysteine residues (–S–S–).

4. Hydrophobic interactions – nonpolar R groups cluster inwards to avoid water, stabilizing structure.

5. Van der Waals forces – weak attractions between nonpolar groups in close proximity.

What is the Quaternary Structure of a protein, and how does it differ from tertiary structure?

The quaternary structure refers to the association of two or more polypeptide chains into a functional protein complex.
Each individual chain is called a subunit.

What is the difference between fibrous and globular proteins?

Feature	Fibrous Proteins	Globular Proteins
Shape	Long, strand-like	Compact, spherical
Solubility	Insoluble in water	Soluble in water
Function	Structural (support, protection)	Functional (enzymes, transport, hormones)
Example	Collagen, keratin, elastin	Haemoglobin, insulin, enzymes