Proteins and Nucleic Acids (OCR A-Level Biology A): Revision Notes

Proteins

Introduction

Proteins are large biological molecules with diverse and vital roles in living organisms. They account for approximately $60\%$ of the organic molecules in cells (excluding water).

Functions of proteins:

• Structural: Components of cytoplasm, muscle fibres, collagen in skin and bone, keratin in hair, elastin in connective tissue
• Catalytic: All enzymes are proteins
• Transport: Carrier molecules in cell membranes, haemoglobin for oxygen transport
• Communication: Many hormones (e.g. insulin)
• Defence: Antibodies in the immune system
• Growth and repair: Building blocks for new cells and tissues

Amino acids: the building blocks

Proteins are polymers composed of smaller subunits called amino acids. These amino acids act as monomers that link together to form protein chains.

General structure of amino acids

All amino acids share a common basic structure containing four groups attached to a central carbon atom:

1. Amino group (–NH₂): Basic functional group (shown in purple in diagrams)
2. Carboxyl group (–COOH): Acidic functional group (shown in pink/red in diagrams)
3. Hydrogen atom (H)
4. R group (residual group): Variable side chain (shown in green in diagrams)

The R group determines amino acid identity

There are 20 different amino acids that make up proteins in living organisms. The R group is the only part that differs between amino acids, giving each its unique properties.

R group characteristics:

• Size: Ranges from a single hydrogen atom (glycine) to large complex groups
• Polarity: Can be polar (hydrophilic) or non-polar (hydrophobic)
• Charge: May be acidic, basic, or neutral

Examples of amino acids:

• Glycine: Smallest amino acid with H as its R group
• Alanine: Contains a methyl group (–CH₃) as its R group
• Leucine: Has a larger branched hydrocarbon R group

Types of R groups

Polar/charged R groups (hydrophilic):

• Acidic polar amino acids: e.g. aspartic acid with –CH₂–COOH
• Basic polar amino acids: e.g. arginine with (–CH₂)₃–HN–CNH–NH₂
• Polar uncharged amino acids: e.g. serine with –CH₂OH

Non-polar R groups (hydrophobic):

• e.g. valine with –CH(CH₃)₂

Peptide bond formation

Condensation reaction

Two amino acids join together through a condensation reaction (also called dehydration synthesis):

• The hydroxyl group (–OH) from the carboxyl group of one amino acid combines with a hydrogen atom (H) from the amino group of another
• One molecule of water (H₂O) is released
• A covalent bond called a peptide bond forms between the carbon of one amino acid and the nitrogen of the next

The resulting molecule is called a dipeptide.

Hydrolysis reaction

The peptide bond can be broken by hydrolysis:

• One molecule of water (H₂O) is added
• The peptide bond breaks
• Two separate amino acids are reformed

Polypeptides

A polypeptide is a chain of many amino acids joined by peptide bonds.

Key features:

• Each polypeptide has an N-terminal (amino end) and a C-terminal (carboxyl end)
• Polypeptides vary in:
  • Number of amino acids (from tens to hundreds)
  • Types of amino acids present
  • Sequence (order) of amino acids

The specific sequence, number and type of amino acids determine the properties and function of the resulting protein.

Levels of protein structure

Protein molecules are organized at different structural levels. Understanding these levels is essential for understanding how proteins function.

Primary structure

The primary structure is the specific sequence of amino acids in the polypeptide chain, including:

• The exact order of amino acids
• The number of amino acids
• The position of any disulfide bonds

Secondary structure

The secondary structure forms when the polypeptide chain folds or coils due to hydrogen bonding between amino acids at different positions along the chain.

Two main types of secondary structure exist:

Alpha helix (α-helix):

• The polypeptide chain coils into a right-handed spiral (like a spring)
• Stabilized by hydrogen bonds between the C=O of one amino acid and the N–H of an amino acid further along the chain
• Creates a rod-like structure

Beta pleated sheet (β-sheet):

• The polypeptide chain folds back and forth like a concertina
• Adjacent parallel or antiparallel strands are held together by hydrogen bonds
• Creates a sheet-like structure with a pleated appearance

Tertiary structure

The tertiary structure is the complex three-dimensional shape that forms when the secondary structure folds and coils further.

This 3D shape is critical for protein function and is maintained by several types of bonds and interactions:

Types of bonds in tertiary structure:

1. Hydrogen bonds: Weak attractions between slightly charged groups (δ⁺ and δ⁻) on different amino acids
2. Ionic bonds: Attractions between oppositely charged R groups (positive and negative)
3. Hydrophobic interactions: Association of non-polar R groups that exclude water
4. Disulfide bonds: Strong covalent bonds between sulfur atoms in cysteine residues (–S–S–)

Two main tertiary structure types:

Globular proteins:

• Fold into compact, roughly spherical shapes
• Generally soluble in water
• Examples: enzymes, antibodies, hormones (insulin), haemoglobin
• Function: metabolic roles requiring 3D shape (e.g. enzyme active sites)

Fibrous proteins:

• Form long, rope-like or strand-like structures
• Generally insoluble in water
• Examples: collagen, keratin, elastin, fibrin
• Function: structural support and strength

Quaternary structure

Some proteins consist of more than one polypeptide chain. The quaternary structure describes how these multiple chains (subunits) associate to form a functional protein.

Key features:

• Two or more polypeptide chains held together by hydrogen bonds, ionic bonds, and disulfide bonds
• The protein only functions when all subunits are correctly assembled
• Subunits may be identical or different
• Some quaternary proteins include non-protein components (prosthetic groups)

Examples of proteins

Globular protein: haemoglobin

Structure:

• Contains four polypeptide chains: two α-chains and two β-chains
• Each chain associates with a haem group (prosthetic group)
• The haem group contains an iron ion (Fe²⁺ or Fe³⁺) within a porphyrin ring
• The four chains are held together by hydrogen bonds, ionic bonds, and hydrophobic interactions
• Forms a compact, roughly spherical (globular) shape

Function: Oxygen transport in red blood cells. Each iron ion can bind one oxygen molecule, allowing each haemoglobin molecule to carry four oxygen molecules.

Solubility: Soluble in water/blood plasma

Fibrous protein: collagen

Structure:

• Contains three polypeptide chains twisted around each other like a rope or plait
• Each chain consists of a repeating sequence of three amino acids
• One of these amino acids is always glycine (the smallest amino acid)
• The chains are held together by numerous hydrogen bonds and covalent bonds
• Multiple collagen molecules associate to form collagen fibrils, which combine to form collagen fibres

Function: Provides strength and structural support in:

• Artery walls (withstands blood pressure)
• Tendons (connects muscle to bone)
• Bone and cartilage (structural framework)
• Skin (provides elasticity and strength)

Solubility: Insoluble in water

Comparison of haemoglobin and collagen

Feature	Haemoglobin	Collagen
Protein type	Globular	Fibrous
Number of polypeptides	4 (two α, two β chains)	3
3D structure	Compact, ball-like shape	Long, twisted fibrous structure
Helical structure	Right-handed α-helix	Left-handed helix
Solubility	Soluble in water	Insoluble in water
Amino acid variety	Contains most of the 20 amino acids	Limited variety; high glycine content with repeating triplet sequence
Prosthetic group	Contains haem group with iron	No prosthetic group
Biological role	Oxygen transport	Structural support in arteries, tendons, cartilage, bone, and skin elasticity

Other important proteins

Insulin:

• Globular protein and hormone
• Composed of two polypeptide chains: chain A (21 amino acids) and chain B (30 amino acids)
• Chains held together by three disulfide bridges
• First protein to have its amino acid sequence determined (Fred Sanger, 1955)
• Function: regulates blood glucose levels

Enzymes:

• All enzymes are globular proteins
• Examples: amylase, catalase, trypsin
• Require specific 3D shape to form active sites
• Active site is complementary to specific substrate molecules
• Function: catalyse (speed up) biochemical reactions

Keratin:

• Fibrous protein found in hair and nails
• Provides structural strength

Elastin:

• Fibrous protein in connective tissue, skin, tendons, and bone
• Can stretch and return to original shape
• Provides elasticity

Testing for proteins: the biuret test

The biuret test is a qualitative biochemical test that detects the presence of proteins.

Principle: Copper ions (Cu²⁺) in alkaline solution react with peptide bonds to form a coloured complex.

Procedure:

1. Add equal volumes of protein solution and sodium hydroxide (NaOH)
2. Shake to mix thoroughly
3. Add a small amount of copper sulfate solution drop by drop
4. Shake between each addition
5. Observe colour change

Results:

Test solution	Colour before reagents	Colour after reagents	Interpretation
Protein present	Cloudy suspension	Mauve/purple	Positive result
No protein (control)	Cloudy suspension	Blue (copper sulfate colour)	Negative result