Biology Exam #2

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Questions and Answers

What role does adenylyl cyclase play in the signaling pathway?

It transports calcium ions into the cell.

It functions as a transcription factor.

It converts ATP to $cAMP$. (correct)

It binds to the extracellular signal molecules.

Which of the following statements accurately describes extracellular signal molecules?

They bind to receptors without entering the cell. (correct)

They directly activate protein kinase A.

They are called second messengers within the cell.

They enter the cell to initiate a response.

In what way do second messengers such as $cAMP$ primarily function in the cell?

By binding to extracellular ligands.

By spreading through the cytoplasm to activate enzymes. (correct)

By transporting proteins across the cell membrane.

By directly entering the nucleus to regulate gene expression.

Where do most responses to extracellular signals occur when they involve transcription factors?

In the nucleus. Signup and view all the answers

Which of the following is a likely effect of signaling pathways that regulate enzymes in the cytoplasm?

Modification of existing enzyme activities. Signup and view all the answers

What type of signaling involves the direct contact between adjacent cells?

Local signaling Signup and view all the answers

Which structures facilitate the direct transfer of substances between animal cells?

Gap junctions Signup and view all the answers

In which type of signaling do local regulators like growth factors function?

Local signaling Signup and view all the answers

What is the main purpose of hormone signaling in multicellular organisms?

To coordinate activities over long distances Signup and view all the answers

Which of the following is an example of paracrine signaling?

Neurotransmitters acting on neighboring nerve cells Signup and view all the answers

What is the primary role of an enzyme in a chemical reaction?

To lower the activation energy barrier Signup and view all the answers

Which statement accurately describes the relationship between enzymes and free energy?

Enzymes do not affect the change in free energy Signup and view all the answers

What is meant by activation energy (Ea) in the context of chemical reactions?

The minimum energy required to initiate a reaction Signup and view all the answers

How do enzymes differ from heat as a catalyst in biological reactions?

Enzymes can selectively speed up reactions without harming themselves Signup and view all the answers

Which statement is true regarding the enzyme sucrase?

It is a protein that catalyzes the hydrolysis of sucrose Signup and view all the answers

What term describes the molecule on which an enzyme acts?

Substrate Signup and view all the answers

What is the primary reason enzymes are specific for their substrates?

The shape of the active site complements the shape of the substrate. Signup and view all the answers

Which process in cell signaling involves the specific binding of a signal molecule to a receptor?

Reception Signup and view all the answers

Which of the following is NOT a way the active site contributes to catalysis?

Increasing substrate temperature Signup and view all the answers

What happens to the receptor when a ligand binds to it?

It undergoes a shape change. Signup and view all the answers

What type of molecule do G proteins bind to?

GTP Signup and view all the answers

What happens when all enzyme molecules in a solution are saturated with substrate?

Adding more enzyme can increase the reaction speed. Signup and view all the answers

Which statement about cofactors is correct?

Cofactors can be either inorganic or organic. Signup and view all the answers

How are GPCRs categorized in terms of their structure and function?

As transmembrane receptors Signup and view all the answers

Which of the following is NOT a type of membrane receptor?

Cytoplasmic receptors Signup and view all the answers

What is the main role of the signal transduction pathway?

To convert the signal to a cellular response Signup and view all the answers

What characteristic is common among G proteins?

They share a similar structure. Signup and view all the answers

Which cellular activity is a result of the final stage of cell signaling?

Synthesis of proteins Signup and view all the answers

What is the primary function of ligand-gated ion channels?

To facilitate the movement of ions into and out of cells Signup and view all the answers

Where are intracellular receptors primarily located?

In the cytoplasm or nucleus of target cells Signup and view all the answers

How does phosphorylation affect protein activity?

It can convert an inactive protein into an active form Signup and view all the answers

Which of the following best describes the role of protein kinases in signal transduction?

They transfer phosphate groups from ATP to proteins. Signup and view all the answers

What does signal transduction involve?

Multiple steps to amplify and regulate cellular responses Signup and view all the answers

What happens during dephosphorylation?

Phosphates are removed from proteins, turning off the signal pathway. Signup and view all the answers

Which statement is true about the amplification in signal transduction?

It generates a large cellular response from a small number of molecules. Signup and view all the answers

What is a phosphorylation cascade?

A sequence of protein activations resulting from multiple phosphorylations. Signup and view all the answers

What characterizes competitive inhibitors in enzyme activity?

They bind to an active site of an enzyme, blocking substrate access. Signup and view all the answers

Which statement best describes noncompetitive inhibitors?

They alter the enzyme's shape without blocking the active site. Signup and view all the answers

What is a significant aspect of irreversible enzyme inhibitors?

They form covalent bonds with the enzyme, permanently disabling it. Signup and view all the answers

How does allosteric regulation affect enzyme activity?

It can either inhibit or stimulate an enzyme's function. Signup and view all the answers

What role does cooperativity play in enzyme activity?

It amplifies the response of enzymes to substrate binding. Signup and view all the answers

What is the purpose of feedback inhibition in metabolic pathways?

It prevents the pathway from producing excess final products. Signup and view all the answers

What can mutations in genes result in regarding enzyme function?

Changes in the amino acid composition leading to altered enzyme activity. Signup and view all the answers

What is a common characteristic of allosterically regulated enzymes?

They are generally composed of multiple polypeptide subunits. Signup and view all the answers

Study Notes

Enzyme Inhibitors

Competitive inhibitors bind to the active site of an enzyme, preventing substrate binding.
Noncompetitive inhibitors bind to a different site on the enzyme, changing the active site's shape and reducing its effectiveness.
Reversible enzyme inhibitors bind through weak interactions.
Irreversible inhibitors form covalent bonds; toxins and poisons are often irreversible inhibitors.

Evolution of Enzymes

Changes in genes (mutations) can alter the amino acid composition of an enzyme.
Altered enzymes may have a new activity or bind to a different substrate.
Under specific environmental conditions, a modified enzyme form might be favored due to its function.

Regulation of Enzyme Activity

Cells regulate metabolic pathways by:
- Controlling the expression of genes encoding enzymes.
- Regulating enzyme activity after they're formed.
Allosteric regulation: A regulatory molecule binds to a protein at a site distinct from the active site, affecting its function.
Allosterically regulated enzymes often have multiple polypeptide subunits.
The enzyme complex can transition between active and inactive forms.
Binding of an activator stabilizes the active form, while an inhibitor stabilizes the inactive form.
Cooperativity: Binding of one substrate molecule to one active site affects the other subunits, promoting activity. This amplifies the enzyme's response.
Feedback inhibition: The end product of a metabolic pathway inhibits the pathway's initial steps, preventing overproduction.

Extracellular Signal Molecules (Ligands)

Ligands (first messengers) bind to receptors without entering the cell.
Second messengers are small, non-protein, water-soluble molecules or ions that spread throughout the cell. Examples include:
- cyclic AMP (cAMP)
- calcium ions (Ca²⁺)
cAMP is a widely used second messenger.
Adenylyl cyclase converts ATP to cAMP in response to extracellular signals, activating protein kinase A.

Cellular Responses to Signals

Responses to signals may occur in the cytoplasm or the nucleus:
- In the nucleus: Signaling pathways often regulate the synthesis of proteins by turning genes on or off. The activated molecule may act as a transcription factor.
- In the cytoplasm: Other pathways regulate the activity of existing enzymes.

Three Stages of Cell Signaling

Cells receiving signals undergo three processes:
- Reception: Detection of the signal.
- Transduction: Conversion of the signal into a cellular response through a signal transduction pathway.
- Response: A cellular activity in response to the signal.

Three Stages of Signal Transduction

Reception: The signal molecule (ligand) binds specifically to a receptor.
- Binding often causes a shape change in the receptor, directly activating it.
- Many receptors are plasma membrane proteins.
- Water-soluble signal molecules bind to receptor proteins spanning the plasma membrane.
- There are three main types of membrane receptors:
  - G protein-coupled receptors (GPCRs)
  - Ligand-gated ion channels
  - Receptor enzymes

G Protein-Coupled Receptors (GPCRs)

GPCRs are plasma membrane receptors that work with G proteins.
G proteins bind to GTP, an energy-rich molecule.
Many G proteins have similar structures.
GPCR pathways are diverse in their functions.

Ligand-Gated Ion Channels

These receptors act as gates for ions.
Ligand binding opens the gate, allowing specific ions (Na⁺ or Ca²⁺) to pass through.
These channels are crucial in the nervous system, triggering electrical signals.

Intracellular Receptors

Located in the cytoplasm or nucleus of target cells.
Bind to small or hydrophobic chemical messengers (steroid or thyroid hormones, NO in plants and animals).
The activated receptor enters the nucleus and acts as a transcription factor, turning on specific genes.

Transduction

Involves multiple steps to amplify the signal.
Signal amplification allows a few external molecules to trigger a large cellular response.
This amplification offers more coordination and regulation of the response.
Relay molecules involved in signal transduction are often proteins.
At each step, the signal is transformed into a different form, often through protein shape changes.

Phosphorylation and Dephosphorylation

These processes are common mechanisms for regulating protein activity.
Protein kinases transfer phosphate groups from ATP to a protein, often activating it.
When multiple kinases participate in a pathway, they form a phosphorylation cascade.
Protein phosphatases remove phosphates from proteins, turning off the signal transduction pathway.
Dephosphorylation makes the kinases available for reuse.

Week 3: Introduction to Metabolism Part 1 - Enzyme Activity

Catalysts speed up reactions without being consumed.
Enzymes are macromolecular catalysts, most of which are proteins.
Example: Sucrase catalyzes the hydrolysis of sucrose.
- Sucrose → Glucose + Fructose

Activation Energy Barrier

Chemical reactions involve bond breaking and forming.
Activation energy (Ea) is the energy required to start a reaction by breaking bonds in reactants.
Heat can provide this energy but is a non-selective catalyst and can denature proteins.

How Enzymes Speed Up Reactions

Organisms use catalysis to selectively speed up reactions.
Enzymes lower the activation energy barrier without being consumed.
Enzymes do not affect the change in free energy (ΔG); they only speed up reactions that would occur eventually.

Substrate Specificity of Enzymes

Enzymes are specific for the reactions they catalyze.
Substrate is the reactant molecule that the enzyme acts on.
The enzyme-substrate complex is formed when the enzyme binds to the substrate.
Active site is the region on the enzyme where the substrate binds.
Specificity is determined by the shape of the active site and substrate.
Enzymes undergo a shape change (induced fit) when interacting with the substrate.

Catalysis in the Enzyme's Active Site

Substrates are held in the active site by weak interactions (hydrogen bonds).
The active site lowers the activation energy (Ea) and converts substrates to products.
After product release, the active site is available for another substrate.
The active site can lower Ea by:
- Orienting substrates correctly.
- Straining substrate bonds.
- Providing a favorable microenvironment.
- Covalently bonding to the substrate.
Increasing substrate concentration can speed up the reaction rate until the enzyme is saturated.
At saturation, adding more enzyme is needed to increase reaction speed.

Cofactors

Non-protein molecules that help carry out processes difficult for amino acids.
May be inorganic (metal ions) or organic.
Coenzymes are organic cofactors.
Most vitamins act as coenzymes or the raw materials for coenzyme synthesis.

Cell Signaling

Multicellular organisms use cell-to-cell communication to coordinate activities.
Communication is also essential for unicellular organisms.
The process typically involves cell plasma membranes.

Local Signaling

Eukaryotic cells can communicate through direct contact.
Animal and plant cells have junctions connecting the cytoplasm of adjacent cells:
- Gap junctions (animal cells)
- Plasmodesmata (plant cells)
Free passage of substances between cells is a form of local signaling.

Paracrine Signaling

Communication between nearby cells.
Local regulators are secreted by signaling cells and travel short distances.
Examples:
- Growth factors stimulate nearby cells to grow and divide.
- Neurotransmitters are a specialized type of local signaling in the nervous system.

Long-Distance Signaling

Plants and animals use hormones for long-distance signaling.
In endocrine signaling (animals), hormones are released by specialized cells and travel through the circulatory system.
- Hormones vary in size and shape.

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Description

This quiz explores the intricate mechanisms of enzyme inhibitors, including competitive and noncompetitive inhibitors, and the distinctions between reversible and irreversible inhibitors. Additionally, it delves into the evolution of enzymes through genetic changes and the regulation of enzyme activity in metabolic pathways.