Welcome to the World of Proteins!

Hello future Biologists! This chapter is all about proteins—the workhorse molecules of life. Everything you see, from the enzymes that digest your food to the structures that make up your hair and muscles, is built or controlled by proteins.

Understanding their structure is absolutely essential in A Level Biology because it directly dictates their function. Don't worry if the vocabulary seems complex; we will break down the process step-by-step, starting with the simplest building blocks.

1. Amino Acids: The Fundamental Monomers

1.1 The General Structure of an Amino Acid

Proteins are large polymers (macromolecules) built from smaller units called amino acids. There are 20 different common amino acids used in living organisms.

Every amino acid shares a common, core structure, often represented by the following diagram (you must be able to describe and draw this general structure):

\(H\)
\(\mid\)
\(N-C-C\)
\(\mid\quad\mid\quad\parallel\)
\(H\quad R\quad O\)
\(\mid\)
\(H\)

This structure contains four main parts, all attached to a central carbon atom (the alpha carbon):

  • A Carboxyl group (\(-\text{COOH}\))
  • An Amino group (\(-\text{NH}_2\))
  • A single Hydrogen atom (H)
  • A variable R group (or side chain)

Did you know? The R group is what makes each of the 20 amino acids unique. It determines the chemical properties of the amino acid (e.g., whether it is polar, non-polar, charged, etc.), which is vital for the final protein shape.

1.2 Forming and Breaking the Peptide Bond

Amino acids join together to form chains called polypeptides. The bond that holds them together is called a peptide bond.

Formation (Condensation)

When two amino acids join, the reaction is called condensation (or dehydration synthesis).

  1. The carboxyl group of one amino acid reacts with the amino group of another amino acid.
  2. A molecule of water is removed (\(H_2O\)).
  3. A peptide bond is formed between the carbon of the carboxyl group and the nitrogen of the amino group.

Two amino acids joined together form a dipeptide. Many amino acids joined together form a polypeptide.

Breakage (Hydrolysis)

The peptide bond can be broken by the reverse reaction, called hydrolysis.

  1. A molecule of water is added.
  2. The water molecule splits the peptide bond, returning the carboxyl and amino groups to their original structure.

Key Takeaway: Amino acids are linked by peptide bonds formed via condensation, resulting in a polypeptide chain.

2. The Hierarchy of Protein Structure

A polypeptide chain must fold into a very specific 3D shape to become a functional protein. This folding process is described in four structural levels. Remember, structure dictates function!

2.1 Primary Structure (1°)

The primary structure is simply the specific, linear sequence of amino acids in the polypeptide chain.

  • It is determined by the genetic code (DNA/mRNA).
  • It is held together exclusively by strong peptide bonds.
  • Analogy: If a protein is a book, the primary structure is the exact order of letters in every word. A change here (like in sickle cell anaemia) changes everything.

2.2 Secondary Structure (2°)

The secondary structure is the folding of the polypeptide chain into regular, repeating patterns, formed through interactions between the atoms of the peptide backbone (not the R groups).

The two main types are:

  • Alpha-helix (\(\alpha\)-helix): A coiled, spiral structure.
  • Beta-pleated sheet (\(\beta\)-pleated sheet): A structure folded like a concertina.

These structures are held in place by Hydrogen bonds forming between the C=O group of one peptide bond and the N-H group of another, further along the chain. Hydrogen bonds are individually weak, but collectively strong and numerous.

2.3 Tertiary Structure (3°)

The tertiary structure is the complex, final, three-dimensional shape of a single polypeptide chain. This structure determines the protein's function (e.g., creating the active site of an enzyme).

The tertiary structure is maintained by interactions between the variable R groups. These interactions include:

Interactions Holding Tertiary Structure
  1. Hydrophobic Interactions:
    • Non-polar (water-hating) R groups are pushed together towards the centre of the protein, shielded from the surrounding water (aqueous environment).
    • This is one of the most important forces driving the initial folding.
  2. Hydrogen Bonding:
    • Occurs between polar R groups (those with slight charges).
    • These bonds are relatively weak but occur frequently throughout the structure.
  3. Ionic Bonding:
    • Occurs between R groups that have opposite full electrical charges (e.g., an amino group that has accepted a proton, \(\text{NH}_3^+\), and a carboxyl group that has lost a proton, \(\text{COO}^-\)).
    • These are stronger than H bonds but are easily broken by changes in pH.
  4. Covalent Bonding (Disulfide Bonds):
    • Formed between the sulfur atoms of two cysteine amino acids.
    • This is a very strong, permanent bond (often called a sulfur bridge or disulfide bridge).

2.4 Quaternary Structure (4°)

The quaternary structure is only present if the final functional protein consists of more than one polypeptide chain joined together.

For example, a protein might be made of two, three, or even dozens of different polypeptides that must combine to form the complete molecule. These polypeptides are often referred to as subunits.

Encouragement: The key difference between 2° and 3° structure is *where* the bonds occur. 2° involves the backbone; 3° involves the R groups. Master the four types of R-group interactions!

Quick Review: Levels of Structure

1° (Primary): Sequence. Held by Peptide Bonds.
2° (Secondary): Folding (\(\alpha\)-helix, \(\beta\)-sheet). Held by Hydrogen Bonds (Backbone).
3° (Tertiary): Final 3D shape. Held by 4 R-group interactions (H, Ionic, Hydrophobic, Disulfide).
4° (Quaternary): Multiple polypeptides (subunits).

3. Functional Classes of Proteins

Proteins are broadly categorised based on their solubility and overall role: Globular or Fibrous.

3.1 Globular Proteins (The Physiological Workers)

Globular proteins are compact, roughly spherical (ball-shaped), and are generally soluble in water.

  • They have polar, hydrophilic R groups on the outside, allowing them to interact with water.
  • They usually have physiological roles (carrying out reactions and transport).
  • Examples: Enzymes (like Catalase), hormones (like Insulin), and Transport proteins (like Haemoglobin).

Case Study: Haemoglobin (Syllabus 2.3.5, 2.3.6)

Haemoglobin is the protein responsible for oxygen transport in your red blood cells. It is a classic example of a complex, soluble globular protein.

  • Structure (Quaternary): It consists of four polypeptide subunits—two identical alpha (\(\alpha\)) chains (or $\alpha$-globin) and two identical beta (\(\beta\)) chains ($\beta$-globin).
  • Prosthetic Group: Each of the four chains is associated with a non-protein molecule called a haem group.
  • Function: Each haem group contains one iron ion (\(\text{Fe}^{2+}\)). This iron ion is the binding site for one oxygen molecule (\(\text{O}_2\)). Therefore, one haemoglobin molecule can carry up to four oxygen molecules.
  • Key Role of Iron: The iron allows for the reversible binding of oxygen, picking it up in the lungs and releasing it in respiring tissues.

3.2 Fibrous Proteins (The Structural Builders)

Fibrous proteins are long, rope-like molecules, often forming long parallel chains. They are generally insoluble in water.

  • They have R groups that are largely hydrophobic, making them useful for strong, structural roles.
  • Examples: Keratin (in hair and nails), actin/myosin (in muscle), and Collagen.

Case Study: Collagen (Syllabus 2.3.7, 2.3.8)

Collagen is the most abundant protein in the human body, providing strength to connective tissues like tendons, cartilage, and bone.

  • Structure: A collagen molecule consists of three polypeptide chains coiled tightly around each other to form a triple helix.
  • Arrangement: Individual collagen molecules are arranged side-by-side, linking with each other to form much larger structures called collagen fibres. They are often held together by covalent cross-links.
  • Relationship to Function:
    • The triple helix shape provides immense tensile strength (resistance to stretching).
    • The arrangement of collagen molecules in long fibres means they are staggered, preventing weak spots and increasing structural integrity, making them excellent for binding tissues together (e.g., tendons connecting muscle to bone).

Key Takeaway: Globular proteins (like Haemoglobin) are soluble and perform dynamic physiological roles, while fibrous proteins (like Collagen) are insoluble and provide structural support and strength.