AP Biology 3.1 Enzyme Structure Study Notes - New Syllabus Effective 2025
AP Biology 3.1 Enzyme Structure Study Notes- New syllabus
AP Biology 3.1 Enzyme Structure Study Notes – AP Biology – per latest AP Biology Syllabus.
LEARNING OBJECTIVE
Explain how enzymes affect the rate of biological reactions.
Key Concepts:
- Structure and functions of enzymes
3.1.A.1 – Functions of enzymes
Enzymes are specialized proteins (and in some cases RNA molecules) that act as catalysts in living organisms. They speed up the chemical reactions required for life by lowering the activation energy, all without being consumed in the process. Enzymes play a crucial role in everything from digestion and metabolism to DNA replication and cell communication.
Almost all known enzymes are proteins. Previously it was believed that all enzymes are chemically protein in nature. Then, certain nucleic acids known as ribozymes are also found to have catalytic properties. Students study protein-based enzymes when they learn about this group of organic biomolecules. The reason is that very little is known about ribozymes.
➢ Enzyme Specificity
- Each enzyme catalyzes only one kind of reactions
- Enzyme are usually named after the molecules they target
■ Replace suffix of substrate with -ase
● Ex. maltose catalyzed by maltase - Substrates are the targeted molecules (reactant)
➢ Enzyme-Substrate Complex
- Enzyme brings about transition state by helping the substrate(s) get into position
- Accomplished through active site
Enzymes perform a wide variety of essential tasks in the body. Their main role is catalysis—making reactions happen faster and more efficiently. They also serve highly specialized roles in regulating and controlling biological pathways. The most important functions of enzymes include:
- Catalysis of metabolic reactions such as glycolysis, fermentation, and the citric acid cycle.
- Digestion of nutrients, including proteins, fats, and carbohydrates.
- DNA replication and repair, ensuring genetic information is accurately copied and maintained.
- Cell signaling, where enzymes help transmit messages inside and between cells.
- Detoxification of harmful substances (e.g., hydrogen peroxide breakdown by catalase).
- Energy production through aerobic and anaerobic respiration.
- Macromolecule synthesis, including the production of proteins and nucleic acids.
Induced fit
■ Enzyme slightly changes shape to accommodate the shape of substrates
■ Sometimes certain factors are necessary for this process
■ Cofactors sometimes aid induced fit and also help catalyze reactions
● Nonprotein helpers of enzymes
● Ex. vitamins
➢ Factors affecting reaction rates
○ Temperature
■ Although the rate of reaction increases with temperature, it only does so up to a point, because too much heat can denature an enzyme
■ $Q_10$
● Measure of sensitivity of a physiological process of enzymatic reaction rate
$Q_{10}=\left(\frac{R_2}{R_1}\right)^{\left(\frac{10}{T_2-T_1}\right)}$
- Temp must be celsius or kelvin
■ Same unit for $T_1 and T_2$ - Two reaction rates $(k_1 and k_2) $must have same unit
- Reaction rates with$ Q_10=1$ are temperature independent
- pH
■ Most enzyme’s ideal $\text pH$ is 7
➢ Enzyme Regulation
- Cell can control enzymatic reactions by regulating the conditions that change the shape of the enzyme
- Can be turned off/on by things that bind to them
■ Some bind at active site
■ Some bin at allosteric sites (non-active sites) - Competitive inhibition
■ If a substance has the exact complementary shape to the active site, it can compete with the substrate and block it from getting into the active site
■ If there is enough substrate available, it will out-compete the inhibitor and the reaction will occur
■ As substrate is used up, inhibitor out-competes the substrate and less reaction will occur - Allosteric inhibitors/Non Competitive inhibition
■ Binds to an allosteric site
■ Distorts shape of enzyme so it cannot function until the inhibitor is removed
■ Substrate can still bind if active site is intact, but the enzyme will not be able to catalyze the reaction
■ Activators can also be used to stabilize the enzyme’s active state
■ Inhibitors stabilize the inactive state - Enzymes can also be controlled by negative feedback mechanisms
■ Product of reaction the enzyme is helping is also an allosteric inhibitor
■ Prevents a cell from wasting resources by synthesizing more of a product than is needed
3.1.A.2 – Enzyme-substrate complex model
A German scientist, Emil Fischer postulated the lock and key model in 1894 to explain the enzyme’s mode of action. Fischer’s theory hypothesized that enzymes exhibit a high degree of specificity towards the substrate. This model assumes that the active site of the enzyme and the substrate fit perfectly into one another such that each possesses specific predetermined complementary geometric shapes and sizes. Thus, the shape of the enzyme and substrate do not influence each other. This specificity is analog to the lock and key model, where the lock is the enzyme, and the key is the substrate. In certain circumstances, if a second substrate similar in shape and size to the primary substrate is made to bind to the enzyme, this second substrate also fits in the active site too.
How does it work?
- Binding of the substrate(s) to the enzyme at their active site takes place, thereby forming an enzyme-substrate complex.
- Enzymes catalyze the chemical reaction to take place, which can either be a synthesis reaction (favors bond formation) or a decomposition reaction (favors bond breakage).
- As a result, the formation of one or more products takes place, and the enzymes are released for their reuse in the next reaction.
Limitations: –
- It doesn’t explain how the enzyme-substrate complex is stabilized in the transition state.
- This model supposes the enzyme is a rigid structure whose shape does not change upon binding with a suitable substrate. However, this is not supported by recent research, which states that there is a change in conformation of the active site of the enzyme upon binding of substrate.
- It does not describe the condition for binding multiple substrates to the enzyme.
Later, it was found that enzyme specificity toward one substrate is not always true. Although there are enzymes that specifically bind with only one substrate, there are also enzymes that exhibit broad specificity towards different but similarly structured substrates, such as lipase that can bind to different types of lipids. Similarly, proteases such as trypsin and chymotrypsin can degrade multiple types of proteins. Thus, the lock and key model is flawed, and the induced fit model was introduced to give a more refined view of the mode of enzymatic action.