MYP Integrated Sciences Biochemistry and Enzymes Notes

What Is a Chemical Reaction?

1. Every chemical reaction involves breaking old bonds and forming new bonds between atoms.
2. Breaking bonds requires energy, forming bonds releases energy.
3. A reaction only happens if the reactant molecules have enough energy to reach a temporary high-energy arrangement called the transition state.
4. Once reactants pass this point, they can form products much more easily.
5. Cells depend on thousands of reactions every second to stay alive.

How Do Reactions Reach the Transition State?

1. Reactant molecules cannot simply turn into products instantly.
2. They must first collide with enough energy to break their existing bonds.
3. This required energy is called the activation energy barrier.
4. When molecules reach this energy level, they enter the transition state.
5. The transition state is unstable and lasts a fraction of a second before collapsing into products.

Why Do Some Reactions Happen Quickly While Others Are Very Slow?

1. A high activation energy makes a reaction slow because few molecules have enough energy to react.
2. A low activation energy makes a reaction fast.
3. Temperature increases particle movement, creating more high-energy collisions.
4. Concentration affects how often molecules collide in the first place.
5. Orientation matters. Molecules must hit each other in the correct alignment for bonds to break and form.

Why Are Chemical Reactions Essential in Living Cells?

1. Cells rely on chemical reactions to:
   1. Release energy from food (respiration).
   2. Build essential molecules such as proteins, lipids, and nucleic acids.
   3. Break down toxins and waste products.
   4. Copy DNA before cell division.
   5. Send signals using neurotransmitters and hormones.

What Are Some Examples of Biochemical Transformations Inside Cells?

Below is a more specific look into some key biochemical transformations you'll run into in later topics.

1. Converting One Amino Acid into Another (Phenylalanine → Tyrosine)

1. Amino acids are the building blocks of proteins.
2. Humans use 20 amino acids.
3. Some come from food, others can be made inside cells.
4. In this reaction, the enzyme phenylalanine hydroxylase adds an OH group to phenylalanine.
5. This produces tyrosine, which cells use to make important signalling molecules.

2. Breaking Down Lactose (Lactose → Glucose + Galactose)

1. Lactose is a disaccharide, meaning it is made of two linked sugars.
2. These sugars are glucose and galactose.
3. The enzyme lactase breaks lactose into glucose and galactose.
4. These simpler sugars can then be absorbed into the bloodstream.

3. Detoxifying Ethanol in the Liver

1. Ethanol is a toxic organic compound found in alcoholic drinks.
2. The liver converts ethanol into ethanal, then into ethanoic acid.
3. Each step makes the molecule less harmful and easier for the body to remove.

4. Converting Extra Glucose Into Fat

1. When glucose levels are high, cells convert glucose into fatty acids.
2. Fatty acids are attached to glycerol to form triglycerides, the main storage form of fat.
3. This process stores excess energy so it can be used later.

How Do Cells Control All These Reactions?

1. Cells control reactions using enzymes, which lower the activation energy needed for molecules to react.
2. Without enzymes, most reactions inside cells would happen far too slowly for life to function.
3. Enzymes allow cells to decide when, where, and how fast specific reactions occur.

How Do Enzymes Work?

1. Enzymes are proteins folded into a very specific three-dimensional shape.
2. A small part of the enzyme forms the active site, where the substrate binds.
3. Only substrates with the correct shape and chemical properties can bind, this feature is known as specificity.
4. When the substrate enters the active site, they form an enzyme–substrate complex.
5. Inside the active site, the enzyme weakens certain bonds or positions molecules so they react more easily.
6. The reaction reaches the transition state with much less energy than normal.
7. Products leave the active site, and the enzyme remains unchanged and ready to catalyze the next reaction.

What Makes the Active Site So Effective?

1. When the substrate binds, the enzyme tightens around it to improve contact.
2. This tightening is called induced fit, and it positions key chemical groups exactly where they need to be.
3. Better alignment reduces the activation energy and makes it easier for bonds to break or form.
4. Once products are released, the active site returns to its original shape.

How Do Enzymes Lower Activation Energy?

1. Enzymes speed reactions by:
   1. Bringing reactants together so they collide in the correct orientation.
   2. Applying strain to bonds, making them easier to break.
   3. Stabilizing the transition state, so less energy is required to reach it.
   4. Creating a helpful microenvironment, such as acidic or charged conditions inside the active site.
   5. Providing an alternative reaction pathway with a lower activation energy.

Why Do Enzymes Only Work With Certain Substrates?

1. The shape of the active site is determined by the enzyme’s tertiary structure.
2. Even small changes in amino acid sequence can alter the active site shape.
3. If the substrate doesn't fit, it can't bind, and no reaction occurs.
4. This prevents unwanted reactions and keeps cell chemistry under control.