Proteins and enzymes

Welcome to Proteins and Enzymes!

Hi there! Welcome to one of the most "active" chapters in your Biology B course. In this section, we are diving into the world of proteins—the molecular machines that do almost everything in your body—and enzymes, the specialized proteins that keep your metabolism running at lightning speed. We’ll also look at how these molecules help your blood clot to save your life and how doctors use them to diagnose diseases. Don't worry if some of the names of the chemicals seem like a mouthful at first; we will break them down step-by-step!

1. The Building Blocks: Amino Acids

Before we can build a massive protein, we need the basic units. These are called amino acids. Think of them like individual Lego bricks that can be snapped together to build anything from a tiny car to a huge castle.

The Structure of an Amino Acid

Every amino acid has the same basic "backbone" structure. It consists of:
1. An amine group (\(-NH_2\))
2. A carboxyl group (\(-COOH\))
3. A central carbon atom
4. A variable R group (this is the "side chain" that makes each of the 20 amino acids different).

Making the Chain: Peptide Bonds

When two amino acids join together, they do so via a condensation reaction. This means a molecule of water is released. The bond that forms between them is called a peptide bond.
• Two amino acids joined = a dipeptide.
• Many amino acids joined = a polypeptide.

Quick Review: The Basics

Prerequisite Check: Remember that a condensation reaction removes water to bond molecules, while hydrolysis adds water to break them apart. You'll see these terms constantly in Biology!

2. Identifying Amino Acids: Chromatography

Sometimes scientists need to figure out which amino acids are in a mixture. They use a technique called paper chromatography.

How it works: A drop of the mixture is placed on paper, and a solvent moves up the paper, carrying the amino acids with it. Different amino acids travel at different speeds because of their size and solubility.

The \(Rf\) Value: To identify the amino acids, we calculate the Retention Value (\(Rf\)). This is a simple ratio:
\( Rf = \frac{\text{distance moved by the solute (amino acid)}}{\text{distance moved by the solvent (the liquid)}} \)

Common Mistake to Avoid: The \(Rf\) value is always less than 1. If you get a number higher than 1, you’ve probably put the solvent distance on the top of the fraction by mistake! Also, amino acids are colorless, so we spray them with a chemical called ninhydrin to turn them purple/brown so we can see them.

Key Takeaway

Amino acids join by peptide bonds via condensation. We use chromatography and \(Rf\) values to identify them in the lab.

3. Protein Structure: From String to Shape

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

1. Primary Structure: The simple sequence (order) of amino acids in the polypeptide chain. If you change even one amino acid, the whole protein might fail!
2. Secondary Structure: The chain folds or coils into an alpha-helix or beta-pleated sheet, held together by hydrogen bonds.
3. Tertiary Structure: The chain folds further into a complex 3D shape. This is held by several bonds: disulfide bridges, ionic bonds, and hydrogen bonds. For globular proteins (like enzymes), this shape is everything.
4. Quaternary Structure: Some proteins are made of more than one polypeptide chain joined together. Haemoglobin is a classic example.

Haemoglobin: A Special Case

Haemoglobin is a globular protein with a quaternary structure (4 chains). It also contains a prosthetic group called haem, which contains an iron ion (\(Fe^{2+}\)). This "non-protein" part is essential because it’s where the oxygen actually binds.

Key Takeaway

The tertiary structure creates the specific 3D shape. Prosthetic groups (like haem) are extra bits that help a protein do its job.

4. Enzymes: The Biological Catalysts

Enzymes are globular proteins that speed up chemical reactions without being used up. They are incredibly picky (specific) about which molecules they work with.

How They Work

Every enzyme has an active site. Because of the specific tertiary structure, only one type of substrate molecule will fit into it.
1. The substrate fits into the active site to form an enzyme-substrate complex (ESC).
2. The enzyme lowers the activation energy (the energy needed to start the reaction).
3. The reaction happens, and products are released.

Factors Affecting Enzyme Rate

• Temperature: As it gets warmer, molecules move faster and collide more, increasing the rate. However, if it gets too hot, the bonds in the tertiary structure break, the active site changes shape, and the enzyme is denatured.
• pH: Each enzyme has an optimum pH. If the pH moves too far away from this, the ionic bonds are disrupted, leading to denaturation.
• Substrate/Enzyme Concentration: Increasing these will increase the rate, but only up to a point where all active sites are busy (the saturation point).

Did you know?

Without enzymes, it would take weeks to digest a single meal. Your body simply couldn't function fast enough to stay alive!

5. Blood Clotting: An Enzyme-Controlled Process

When you cut yourself, your body needs to plug the hole fast. This is a cascade of reactions where one enzyme activates the next.

The Step-by-Step Process

1. Damage: When a blood vessel is damaged, platelets and the damaged tissue release a substance called thromboplastin.
2. Activation: In the presence of calcium ions (\(Ca^{2+}\)), thromboplastin acts as an enzyme to trigger the conversion of prothrombin (inactive) into thrombin (active).
3. The Mesh: Thrombin then acts as an enzyme to turn fibrinogen (a soluble protein) into fibrin (insoluble fibers).
4. The Clot: These fibrin fibers form a mesh that traps red blood cells, creating a blood clot.

First Aid for Blood Loss

If the body can't stop the bleeding alone, we can help by:
• Applying direct pressure to the wound (helps the physical plugging).
• Using dressings to provide a surface for platelets to adhere to.

Memory Aid: "Pro" means "Before"

If you see a protein ending in "-ogen" (Fibrinogen) or starting with "Pro-" (Prothrombin), it usually means it is the inactive version. Think of it as being "Pro-active"—it's waiting to be turned on!

6. Enzymes in Medicine

Doctors use our knowledge of enzymes and inhibitors (substances that stop enzymes) to treat and diagnose patients.

Diagnostic Enzymes

If certain enzymes are found in high levels in the blood, it can signal organ damage:
• Blood Amylase: High levels can suggest inflammation of the pancreas.
• LDH (Lactate Dehydrogenase): Can be used to help identify tissue damage or certain types of anemia.

Treatments and Inhibitors

• Streptokinase: An enzyme used as a "clot-buster" drug to dissolve dangerous blood clots in patients having a heart attack.
• Aspirin: Acts as an inhibitor for enzymes that lead to inflammation and blood clotting.
• Warfarin: An inhibitor used to prevent blood from clotting too easily in high-risk patients.

Key Takeaway

Enzymes are tools. We can measure them to see if someone is sick (diagnosis) or use them/stop them to make someone better (treatment).

Final Summary Review

• Proteins are made of amino acids joined by peptide bonds.
• Tertiary structure determines the shape of the active site in enzymes.
• Enzymes lower activation energy.
• Blood clotting is a cascade: Thromboplastin \(\rightarrow\) Thrombin \(\rightarrow\) Fibrin.
• Medical treatments often involve using enzymes like streptokinase or inhibitors like warfarin.