AP Biology Study Guide: Enzyme Structure, Enzyme Catalysis,

Environmental Impact on Enzyme Function, Cellular Energy, Cell

Communication, Signal Transduction, Changes in Signal Transduction
Pathways, Feedback, Cell Cycle, and Regulation of Cell Cycle

(I) Enzyme Structure:

Enzymes are proteins that catalyze chemical reactions in the body.
Enzyme structure consists of an active site, which is the specific location where the substrate
binds, and the enzyme catalyzes the reaction.
Enzyme function can be affected by factors such as temperature, pH, and the presence of
inhibitors or activators.

Comprehension Questions:
1. What is the function of enzymes?

2. What is the structure of an enzyme?

3. What is the active site of an enzyme?

4. How can temperature affect enzyme function?

5. How can pH affect enzyme function?

1 Enzymes are biological molecules that catalyze (speed up) chemical reactions in living
organisms. They work by lowering the activation energy needed for a reaction to occur, thereby
increasing the rate of the reaction. Enzymes are essential for many biological processes,
including metabolism, DNA replication, and protein synthesis.

2 Enzymes are typically proteins, although some RNA molecules can also have enzymatic
activity. The structure of an enzyme can vary widely, but all enzymes have a specific
three-dimensional shape that allows them to interact with their substrate(s) in a very specific
way. Enzymes can have multiple subunits, and each subunit may have its own unique structure.

3 The active site of an enzyme is the region of the enzyme where the substrate(s) bind and the
chemical reaction takes place. The active site is typically a pocket or crevice on the surface of
the enzyme that is complementary in shape and charge to the substrate(s). The active site may
also contain amino acid residues that participate in the chemical reaction by donating or
accepting protons, or by stabilizing the transition state of the reaction.
4 Temperature can affect enzyme function in several ways. At low temperatures, enzyme activity
may be reduced because the molecules have less kinetic energy, which can make it more
difficult for the enzyme and substrate to interact. At higher temperatures, enzymes can become
denatured (unfolded) due to the increased thermal energy, which can cause the enzyme to lose
its specific shape and therefore its activity. There is typically an optimal temperature range for
each enzyme, where its activity is highest, and beyond which its activity will decrease.

5 pH can also affect enzyme function. Enzymes typically have an optimal pH range at which
they function best, depending on their specific amino acid composition and the chemical nature
of the substrate(s). Changes in pH can affect the ionization state of amino acid residues in the
active site, which can alter the shape and charge distribution of the enzyme, and therefore its
ability to interact with the substrate(s). Extreme changes in pH can also cause denaturation of
the enzyme, as with temperature.

6. Open Response Problem:

Explain the lock and key model of enzyme function and provide an example of an
enzyme-substrate complex.

The lock and key model is a simple way to visualize how enzymes work. According to this
model, the active site of an enzyme is a specific shape, like a lock, and the substrate is a
complementary shape, like a key. When the substrate fits into the active site, like a key in a lock,
the enzyme can catalyze a chemical reaction.

For example, let's consider the enzyme lactase and its substrate lactose. Lactase is an enzyme
produced in the small intestine that breaks down lactose, a disaccharide found in milk, into its
component monosaccharides, glucose, and galactose. The active site of lactase is a specific
shape that perfectly fits the lactose molecule, which has a specific arrangement of chemical
groups that complements the active site. When lactose enters the active site of lactase, the
enzyme changes shape slightly to better accommodate the substrate, and a chemical reaction
occurs that breaks the bond between glucose and galactose, releasing the two
monosaccharides.

In the lock and key model, the enzyme and substrate are like a key and lock that only fit
together in a specific way. Other molecules that do not have the correct shape and chemical
arrangement cannot fit into the active site of the enzyme, and so the enzyme does not catalyze
a reaction with them. This selectivity is one of the reasons why enzymes are so important in
biological systems, where many different molecules are present and need to be processed in
specific ways.
Multiple Choice Practice Problems:

7. Which of the following is a protein that catalyzes chemical reactions?

A. Carbohydrate
B. Lipid
C. Nucleic Acid
D. Enzyme
Answer: D

8. Which of the following is the specific location on an enzyme where the substrate binds?
A. Substrate site
B. Catalyst site
C. Active site
D. Inactive site
Answer: C

(II) Enzyme Catalysis:

Enzymes lower the activation energy required for a chemical reaction to occur, thereby
increasing the rate of the reaction.
Enzyme-substrate specificity is determined by the shape of the active site and the chemical
properties of the substrate.

Comprehension Questions:
9. How do enzymes increase the rate of chemical reactions?

10. How is enzyme-substrate specificity determined?

11. Open Response Problem:

Explain how enzymes lower the activation energy required for a chemical reaction to occur.

Enzymes increase the rate of chemical reactions by lowering the activation energy required for
the reaction to occur. Activation energy is the energy required for a reaction to proceed, and
enzymes reduce this energy barrier by bringing the reactants (substrates) into close proximity
and in the proper orientation to allow them to react with each other. Additionally, the active site
of the enzyme can provide an environment that is favorable for the reaction to occur, such as by
stabilizing charged intermediates or by donating or accepting protons to facilitate the reaction.

Enzyme-substrate specificity is determined by the specific shape and chemical properties of the
active site of the enzyme. The active site of an enzyme is complementary in shape and charge
to its specific substrate(s), meaning that it has a unique three-dimensional structure that allows
it to interact with only certain molecules. This specificity is determined by the amino acid
sequence of the protein that makes up the enzyme, as well as the chemical nature of the
substrate(s). The active site can undergo conformational changes to better fit the substrate,
resulting in an enzyme-substrate complex that is more stable than the substrate alone.

Enzymes lower the activation energy required for a chemical reaction to occur by stabilizing the
transition state of the reaction. The transition state is the high-energy intermediate that forms
when the reactants are in the process of being transformed into the products of the reaction.
Enzymes can stabilize this transition state by binding to the substrate(s) in a way that distorts
the chemical bonds and makes it easier for the reaction to proceed. Additionally, the active site
of the enzyme can provide an environment that is conducive to the reaction, such as by
providing a hydrophobic or hydrophilic microenvironment or by participating in the reaction itself
through the use of covalently attached cofactors or prosthetic groups. By lowering the activation
energy required for the reaction to occur, enzymes make it possible for biological processes to
occur at rates that are necessary for life.

Multiple Choice Practice Problems:

12 Enzymes increase the rate of chemical reactions by:

A. Increasing the activation energy required
B. Decreasing the activation energy required
C. Changing the chemical properties of the substrate
D. Decreasing the concentration of the substrate
Answer: B

13 Enzyme-substrate specificity is determined by:

A. The shape of the enzyme
B. The shape of the substrate
C. The chemical properties of the enzyme
D. The chemical properties of the substrate
Answer: A

(III) Environmental Impact on Enzyme Function:

Environmental factors such as temperature and pH can affect enzyme function by altering the
shape of the enzyme and the active site.
Denaturation occurs when an enzyme loses its shape and therefore its ability to function.
Comprehension Questions:

15 How can temperature affect enzyme function?

16 How can pH affect enzyme function?
17 What is denaturation?
18 Open Response Problem:
Explain how changes in temperature or pH can impact enzyme function.
Temperature can affect enzyme function in several ways. At low temperatures, enzyme activity
is generally slow due to the lack of kinetic energy required for the enzyme-substrate complex to
form. As temperature increases, enzyme activity also increases until it reaches an optimal
temperature, at which point the enzyme activity is at its maximum. Above the optimal
temperature, however, the enzyme can become denatured and lose its three-dimensional
shape, which can result in a loss of enzyme activity.

pH can also affect enzyme function. Each enzyme has an optimal pH range at which it is most
active, and changes in pH outside this range can result in a loss of enzyme activity. This is
because enzymes have specific amino acid side chains that can be ionized at certain pH
values, and changes in pH can alter the overall charge of the enzyme or substrate, which can
disrupt the formation of the enzyme-substrate complex.

Denaturation is the process by which a protein loses its three-dimensional shape and its
biological activity. Denaturation can be caused by various factors such as heat, pH, or chemical
denaturants. In the case of enzymes, denaturation can lead to a loss of enzyme activity and a
decrease in the rate of catalysis.

Changes in temperature or pH can impact enzyme function by altering the three-dimensional

shape of the enzyme. Enzymes are sensitive to changes in their environment, and even small
changes in temperature or pH can cause the enzyme to change shape or lose its stability. This
can disrupt the formation of the enzyme-substrate complex and reduce enzyme activity. At high
temperatures, enzymes can become denatured and lose their biological activity altogether.
Similarly, at extreme pH values, enzymes can become ionized or lose their stability, leading to a
loss of activity. Therefore, it is important to maintain appropriate temperature and pH conditions
for enzymatic reactions to occur efficiently.

How do cells communicate with each other?

What are the three types of cell signaling?
What is the difference between endocrine and paracrine signaling?
Explain how the endocrine, paracrine, and autocrine signaling pathways differ.
Cells communicate with each other through a variety of mechanisms. One way is through direct
contact, such as through gap junctions that allow molecules to pass

Multiple Choice Practice Problems:

19 Which of the following is a possible result of denaturation?

A. Increased enzyme activity
B. Decreased enzyme activity
C. No effect on enzyme activity
D. Increased substrate concentration
Answer: B
20 At what temperature do enzymes typically denature?
A. 0°C
B. 25°C
C. 50°C
D. 100°C
Answer: C
Cell Communication:

Cells communicate with each other through chemical signals such as hormones and
neurotransmitters.
Cell signaling can be classified as endocrine, paracrine, or autocrine.
Comprehension Questions:

21 How do cells communicate with each other?

22 What are the three types of cell signaling?
23 What is the difference between endocrine and paracrine signaling?
24 Open Response Problem:
Explain how the endocrine, paracrine, and autocrine signaling pathways differ.

Cells communicate with each other through a variety of mechanisms. One way is through direct
contact, such as through gap junctions that allow molecules to pass between adjacent cells.
Another way is through the secretion of signaling molecules, which can diffuse through the
extracellular space and bind to receptors on nearby or distant cells.

The three types of cell signaling are endocrine, paracrine, and autocrine signaling.

Endocrine signaling involves the release of hormones into the bloodstream, which can then
travel to target cells throughout the body. Examples of hormones include insulin, thyroid
hormone, and growth hormone.
Paracrine signaling involves the release of signaling molecules that diffuse locally and bind to
receptors on nearby cells. Examples of paracrine signaling molecules include cytokines, growth
factors, and neurotransmitters.
Autocrine signaling involves the release of signaling molecules that bind to receptors on the
same cell that produced them. This type of signaling is important for regulating cellular growth
and differentiation, as well as for maintaining homeostasis.
The main difference between endocrine and paracrine signaling is the distance over which the
signaling molecules can travel. Endocrine signaling involves the release of hormones into the
bloodstream, which can travel long distances to reach their target cells. Paracrine signaling, on
the other hand, involves the release of signaling molecules that only diffuse locally and are
generally limited to acting on cells in the immediate vicinity of the signaling cell. Autocrine
signaling is a special case of paracrine signaling in which the signaling molecule binds to
receptors on the same cell that produced it.
The endocrine, paracrine, and autocrine signaling pathways differ in terms of the distance over
which signaling molecules can travel and the specificity of the signaling. Endocrine signaling is
generally more diffuse and less specific than paracrine signaling, as hormones can travel
throughout the body and bind to receptors on a wide variety of cells. Paracrine signaling is more
specific, as the signaling molecules are limited to acting on cells in the immediate vicinity of the
signaling cell. Autocrine signaling is even more specific, as the signaling molecule only acts on
receptors on the same cell that produced it. Additionally, these signaling pathways can have
different temporal dynamics, with endocrine signaling often slower and longer-lasting than
paracrine or autocrine signaling, which can act more quickly and have shorter durations.

Multiple Choice Practice Problems:

25 Which of the following is a type of chemical signal used in cell communication?

A. Protein
B. Lipid
C. Hormone
D. All of the above
Answer: D

26 Which of the following types of signaling involves a signal released by a cell that affects
neighboring cells?
A. Endocrine signaling
B. Paracrine signaling
C. Autocrine signaling
D. Both A and C
Answer: B

Signal Transduction:

Signal transduction is the process by which a signal is transmitted from the cell surface to the
interior of the cell.
Signaling pathways often involve the activation of proteins such as kinases and phosphatases.
Comprehension Questions:

27 What is signal transduction?

28 What proteins are commonly involved in signaling pathways?
29 Open Response Problem:
30 Explain how a signal is transmitted from the cell surface to the interior of the cell during
signal transduction.

Signal transduction is the process by which cells convert signals from their environment into
specific cellular responses. This process involves a series of molecular interactions, which allow
cells to detect and respond to extracellular stimuli, such as hormones, growth factors, and
neurotransmitters.
Proteins play a central role in signal transduction pathways. There are several classes of
proteins commonly involved in signaling, including receptors, enzymes, and transcription
factors. Receptors are typically located on the cell surface and bind to specific ligands, such as
hormones or growth factors. Once bound, receptors undergo a conformational change, which
triggers a cascade of intracellular signaling events.

Enzymes are also critical components of signaling pathways. These proteins catalyze the
transfer of phosphate groups from ATP to other proteins, a process known as phosphorylation.
Phosphorylation can activate or inhibit proteins, and it is a key mechanism by which cells
regulate their responses to extracellular signals.

Transcription factors are another important class of signaling proteins. These proteins can bind
to specific DNA sequences and regulate the transcription of target genes. In this way, signaling
pathways can alter gene expression and ultimately lead to changes in cellular behavior.

Signal transduction typically begins with the binding of a ligand to a cell surface receptor. This
binding event initiates a series of intracellular signaling events, which are often propagated by
the phosphorylation and dephosphorylation of specific proteins. These events can ultimately
lead to the activation of transcription factors and the regulation of gene expression. Some
signaling pathways are relatively simple, involving just a few proteins, while others are more
complex and involve numerous proteins and feedback loops. Regardless of their complexity,
signal transduction pathways are essential for cells to respond to their environment and carry
out their normal physiological functions.

Multiple Choice Practice Problems:

31 Which of the following is a protein commonly involved in signaling pathways?

A. Enzyme
B. Hormone
C. Receptor
D. All of the above
Answer: C

32 Signal transduction involves the transmission of a signal from:

A. The interior of the cell to the cell surface
B. The cytoplasm to the nucleus
C. The cell surface to the interior of the cell
D. The nucleus to the cytoplasm
Answer: C

Changes in Signal Transduction Pathways:

Signal transduction pathways can be modified by changes in the structure or activity of proteins
involved in the pathway.
Feedback mechanisms can also modulate signal transduction pathways.
Comprehension Questions:

33 How can signal transduction pathways be modified?

34 What is feedback?
35 Open Response Problem:
Explain how changes in the structure or activity of proteins involved in a signaling pathway can
alter the pathway.

Signal transduction pathways can be modified in several ways, including through the action of
extracellular regulators, the alteration of protein expression or activity, or the modification of
protein interactions. Feedback is an important mechanism by which cells can modulate their
responses to extracellular signals, and it involves the regulation of signaling pathway activity by
downstream products or signals.

Feedback can occur through negative or positive regulation. Negative feedback occurs when
downstream products or signals inhibit upstream components of the signaling pathway, resulting
in a decrease in pathway activity. Positive feedback occurs when downstream products or
signals activate or enhance the activity of upstream components of the signaling pathway,
leading to an increase in pathway activity.

Changes in the structure or activity of proteins involved in a signaling pathway can alter the
pathway in several ways. For example, mutations in the gene encoding a receptor or
downstream signaling protein can lead to alterations in ligand binding, signal transduction, or
protein-protein interactions, resulting in changes in pathway activity. Similarly, alterations in
protein expression levels or modifications, such as phosphorylation, acetylation, or
ubiquitination, can also affect signaling pathway activity. For instance, phosphorylation can
activate or deactivate a protein, change its conformation, or modulate its interaction with other
proteins.

Changes in protein structure or activity can have different effects on signaling pathways
depending on the context of the cell or tissue. For example, a mutation in a signaling protein
that causes constitutive activation of the pathway can lead to uncontrolled cell proliferation and
cancer in some contexts, while in other contexts, it may have no effect or even be beneficial.
Therefore, understanding the regulation and modification of signaling pathways is critical for
understanding how cells respond to their environment and for developing therapeutic strategies
to modulate cellular behavior.

Multiple Choice Practice Problems:

36 Changes in the structure or activity of proteins involved in a signaling pathway can result in:
A. Increased pathway activity
B. Decreased pathway activity
C. No effect on pathway activity
D. Increased protein degradation
Answer: A

37 Feedback mechanisms can modulate signaling pathways by:

A. Increasing pathway activity
B. Decreasing pathway activity
C. Preventing the activation of downstream targets
D. All of the above
Answer: D

Cell Cycle and Regulation of Cell Cycle:

The cell cycle consists of interphase, mitosis, and cytokinesis.

The cell cycle is regulated by checkpoints that ensure that the cell is ready to progress to the
next phase.
Comprehension Questions:

38 What are the phases of the cell cycle?

39 How is the cell cycle regulated?
40 Open Response Problem:
Explain the role of checkpoints in the regulation of the cell cycle.

The cell cycle is the series of events that occur in a cell leading to its division into two daughter
cells. There are four main phases of the cell cycle: G1 (Gap 1), S (Synthesis), G2 (Gap 2), and
M (Mitosis). During G1, the cell grows and prepares for DNA replication. In S phase, DNA is
replicated. In G2 phase, the cell grows and prepares for cell division. Finally, in M phase, the cell
divides into two daughter cells.

The cell cycle is regulated by a complex network of molecular pathways, which ensure that the
events of each phase occur in the correct order and at the appropriate time. Cyclin-dependent
kinases (CDKs) and cyclins are key regulators of the cell cycle, and their levels and activities
fluctuate throughout the cycle.

Checkpoints are key regulators of the cell cycle that ensure that each phase occurs correctly
before proceeding to the next phase. There are three main checkpoints in the cell cycle: the G1
checkpoint, the G2 checkpoint, and the M checkpoint. The G1 checkpoint ensures that the cell
has grown sufficiently before entering S phase, and it is also a point of decision for the cell to
enter a quiescent state called G0. The G2 checkpoint ensures that DNA replication has
occurred correctly before the cell enters M phase. The M checkpoint ensures that chromosomes
are properly attached to the spindle fibers before the cell divides.
Checkpoints are regulated by various cellular pathways and signaling molecules, which monitor
the status of the cell and trigger appropriate responses if abnormalities are detected. For
example, DNA damage can activate checkpoint pathways, leading to cell cycle arrest and DNA
repair. Failure of checkpoints can lead to genomic instability and contribute to the development
of cancer.

In summary, the cell cycle is regulated by a complex network of molecular pathways, including
cyclins and CDKs, and is monitored by checkpoints, which ensure that each phase occurs
correctly before the cell proceeds to the next phase. Checkpoints are regulated by various
signaling pathways and help maintain genomic stability.

Multiple Choice Practice Problems:

41 Which of the following is not a phase of the cell cycle?

A. Interphase
B. Mitosis
C. Cytokinesis
D. Apoptosis
Answer: D

Vocab
Phosphorylation: Phosphorylation is the process of adding a phosphate group (PO4) to a
molecule, typically a protein or enzyme, which can change its activity or function. This
modification is carried out by enzymes called kinases and can affect a wide range of cellular
processes, such as gene expression, metabolism, and cell signaling.

Scaffolding Proteins: Scaffolding proteins are large, multi-domain proteins that serve as
structural platforms for organizing and regulating the activity of signaling pathways within cells.
They interact with other signaling molecules, such as enzymes and receptors, to form complex
signaling networks and can help to localize signaling components to specific subcellular
compartments.

Competitive Inhibition: Competitive inhibition is a type of enzyme inhibition in which a molecule

competes with the substrate for binding to the active site of an enzyme, reducing the enzyme's
activity. This type of inhibition can be overcome by increasing the substrate concentration.

Non-Competitive Inhibition: Non-competitive inhibition is a type of enzyme inhibition in which a

molecule binds to an allosteric site on an enzyme, changing the shape of the enzyme and
reducing its activity. This type of inhibition cannot be overcome by increasing the substrate
concentration.

Cooperativity: Cooperativity refers to the phenomenon where the binding of a ligand (such as a
substrate or inhibitor) to one site on a protein or enzyme affects the binding or activity of another
site on the same protein or enzyme. This can lead to sigmoidal (S-shaped) curves in enzyme
activity or ligand binding.

Phospholipase C: Phospholipase C (PLC) is an enzyme that cleaves phospholipids in the

plasma membrane, producing two important second messengers, inositol triphosphate (IP3)
and diacylglycerol (DAG). The release of IP3 triggers the release of calcium ions from the
endoplasmic reticulum, which is a calcium storage organelle within cells.

Synaptic Signaling: Synaptic signaling is the process by which neurons communicate with each
other through specialized structures called synapses. During synaptic signaling,
neurotransmitters are released from the presynaptic neuron and bind to receptors on the
postsynaptic neuron, leading to changes in the electrical or chemical activity of the postsynaptic
neuron.

Endergonic: Endergonic refers to a chemical reaction or process that requires energy input to
occur. This type of reaction or process has a positive Gibbs free energy change (∆G>0),
indicating that energy is absorbed or stored during the reaction.

Exergonic: Exergonic refers to a chemical reaction or process that releases energy during the
reaction. This type of reaction or process has a negative Gibbs free energy change (∆G<0),
indicating that energy is released or transferred during the reaction.

Hydrolysis: Hydrolysis is a chemical reaction in which a molecule is broken down into smaller
components through the addition of water. This type of reaction is commonly used to break
down polymers, such as proteins or carbohydrates, into their constituent monomers.

Non-Polar Particle Diffusion: Non-polar particle diffusion refers to the movement of non-polar
molecules, such as oxygen or carbon dioxide, through a biological membrane from an area of
higher concentration to an area of lower concentration, driven by the concentration gradient.
This type of diffusion occurs passively and does not require the input of energy.