Proteins and enzymes

Introduction to Proteins and Enzymes

Welcome! In this chapter, we are diving into the world of proteins and enzymes. These molecules are the "workhorses" of the body. Whether it's building muscle, transporting oxygen in your blood, or speeding up chemical reactions so you can stay alive, proteins are at the heart of it all.

In the context of Topic 2: Genes and Health, understanding proteins is vital because genes are essentially the "instruction manuals" for building them. If a gene is mutated (like in Cystic Fibrosis), the protein it builds might not work correctly. Let’s break down how these amazing molecules are built and how they function.

1. The Building Blocks: Amino Acids

Proteins are polymers made up of smaller units called amino acids. While there are many different amino acids, they all share a basic common structure.

Basic Structure of an Amino Acid

Every amino acid has a central carbon atom bonded to four partners:

• An amino group (\(-NH_{2}\))
• A carboxyl group (\(-COOH\))
• A hydrogen atom (\(-H\))
• A residual group (represented as the R group)

Note: You do not need to learn the specific chemical structures of different R groups, but you must know that the R group is what makes each amino acid unique! Some R groups are attracted to water (hydrophilic), while others repel it (hydrophobic).

The Peptide Bond

When two amino acids join together, they do so via a condensation reaction. This means a molecule of water (\(H_{2}O\)) is released. The bond formed between the amino acids is called a peptide bond.

• Two amino acids joined = a dipeptide.
• Many amino acids joined in a long chain = a polypeptide.

Quick Review: Think of amino acids as individual Lego bricks. The peptide bond is the "click" that holds them together. The sequence of these bricks determines what you are building!

2. Protein Structure: From Chains to 3D Shapes

A protein isn't just a long string; it has to fold into a very specific 3D shape to do its job. We describe this folding in four levels:

Primary Structure

This is the simple sequence of amino acids in the polypeptide chain. This sequence is determined by the DNA. Even changing one single amino acid in a chain of hundreds can completely change the protein's final shape.

Secondary Structure

The chain doesn't stay straight. Parts of the polypeptide chain fold or coil due to hydrogen bonds forming between the amino acids. The two most common shapes are:

• Alpha (\(\alpha\)) helix: A delicate coil like a telephone wire.
• Beta (\(\beta\)) pleated sheet: Folded like a paper fan.

Tertiary Structure

This is the overall three-dimensional shape of the protein. The protein folds further into a complex shape held together by bonds between the R groups. These bonds include:

• Ionic bonds (between charged R groups).
• Disulfide bridges (strong covalent bonds between R groups containing sulfur).
• Hydrogen bonds.
• Hydrophobic and hydrophilic interactions.

Crucial Point: The primary structure (the sequence) determines exactly where these bonds form, which determines the final 3D shape!

Quaternary Structure

Some proteins are made of more than one polypeptide chain joined together. For example, haemoglobin is made of four chains working as one unit.

3. Globular vs. Fibrous Proteins

Proteins generally fall into two categories based on their shape and function.

Globular Proteins

These are spherical and "compact." Their hydrophobic R groups are tucked inside, while hydrophilic R groups are on the outside, making them soluble in water. This makes them great for transport.

Example: Haemoglobin. It is a globular protein designed to carry oxygen around the body in the blood.

Fibrous Proteins

These consist of long, thin strands. They are insoluble in water and very strong, making them perfect for structural roles.

Example: Collagen. This protein provides strength to our skin, tendons, and bones. It is made of three polypeptide chains wrapped around each other like a rope.

Key Takeaway: Shape = Function. Globular proteins "do" things (like enzymes or transport), while fibrous proteins "build" things (like structure).

4. Enzymes: Biological Catalysts

Enzymes are globular proteins that act as biological catalysts. This means they speed up chemical reactions without being used up themselves.

How do they work?

Every reaction needs a certain amount of energy to get started—this is called activation energy. Enzymes work by reducing the activation energy, allowing reactions to happen at lower temperatures (like body temperature!).

Specificity and the Active Site

Enzymes are highly specific. This is because they have a uniquely shaped active site that only fits one specific molecule, called the substrate.

• Lock and Key Theory: The substrate fits the active site perfectly, like a key in a lock.
• Induced Fit Theory: The active site changes shape slightly as the substrate binds to it, creating an even tighter fit (like a glove stretching to fit a hand).

Intracellular vs. Extracellular

• Intracellular enzymes: Work inside cells (e.g., enzymes involved in DNA replication).
• Extracellular enzymes: Work outside cells (e.g., digestive enzymes in your gut).

5. Factors Affecting Enzyme Action

Because enzymes are proteins, their shape is sensitive to their environment. If the shape of the active site changes, the substrate can no longer bind. This is called denaturation.

Temperature and \(Q_{10}\)

As temperature increases, molecules move faster (more kinetic energy). This leads to more successful collisions between enzymes and substrates. However, if it gets too hot, the bonds holding the protein together break, and the enzyme denatures.

We can calculate the temperature coefficient (\(Q_{10}\)) to see how much the rate of reaction increases when the temperature is raised by \(10^\circ\text{C}\):

\(Q_{10} = \frac{\text{Rate at } (T + 10)^\circ\text{C}}{\text{Rate at } T^\circ\text{C}}\)

For most biological reactions between \(0^\circ\text{C}\) and \(40^\circ\text{C}\), the \(Q_{10}\) value is approximately 2 (meaning the rate doubles for every \(10^\circ\text{C}\) rise).

Enzyme and Substrate Concentration

• Substrate Concentration: Increasing substrate concentration increases the rate of reaction because there are more molecules to collide with the enzymes. However, eventually, all active sites become "saturated" (busy), and the rate levels off.
• Enzyme Concentration: Increasing enzyme concentration increases the rate because there are more active sites available. The rate will only level off if there isn't enough substrate to keep the enzymes busy.

6. Core Practicals (Skills Focus)

In your exams, you might be asked about the following practical investigations:

Core Practical 4: Effect of enzyme/substrate concentration

To measure the initial rate of reaction, you measure how much product is formed (or substrate used) in the first few seconds of the reaction. This is important because as the reaction continues, the substrate runs out, which slows the rate down.

Core Practical 12: Effect of temperature on enzyme rate

You would measure the rate at different temperatures and use the results to calculate \(Q_{10}\) or identify the "optimum" temperature (where the enzyme works fastest).

Common Mistake to Avoid: Don't say an enzyme "dies" at high temperatures. Enzymes are molecules, not living things! Always use the term denatured.

Summary: The "Big Picture"

In Topic 2: Genes and Health, we look at how a mutation in the DNA sequence (Primary Structure) leads to a misfolded protein (Tertiary Structure). In Cystic Fibrosis, a faulty transport protein in the cell membrane doesn't work correctly because its 3D shape is wrong. This is why understanding the link between the amino acid sequence and the final protein shape is the key to understanding genetic diseases!