Module 2

What are the general functions of proteins in cells?

Enzymes, structural support, transport, motor activity, storage, signaling, receptors, regulation.

What is the role of ligands in protein binding?

Ligands bind to proteins selectively through weak noncovalent interactions.

What creates binding sites on proteins?

Protein folding creates crevices or cavities on the protein surface.

What is the role of an active site in enzymes?

It is where substrate molecules bind to form an enzyme-substrate complex.

How do enzymes facilitate chemical reactions?

By holding substrates in precise orientation, rearranging charge distribution, and straining substrate bonds.

What effect do competitive inhibitors have on enzymes?

They reduce enzyme activity by competing with substrate for the active site.

What are hydrolases?

A class of enzymes that catalyze hydrolysis reactions.

What is feedback inhibition?

A regulatory mechanism where the end product inhibits an early enzyme in the pathway.

How do allosteric enzymes function?

They have multiple binding sites, and binding at allosteric sites alters enzyme activity.

What is an example of positive regulation in enzymes?

Rising ADP levels promote enzyme activity involved in ATP production.

What is protein phosphorylation?

The addition of a phosphate group to an amino acid side chain to regulate protein activity.

How do GTP-binding proteins act as molecular switches?

They switch between active (GTP-bound) and inactive (GDP-bound) states.

What is the purpose of ATP in motor proteins?

ATP provides energy for directional movement and conformational changes in motor proteins.

How does kinesin move along microtubules?

It binds ATP, undergoes a conformational change, and moves forward using ATP hydrolysis.

What are protein machines?

Large complexes of proteins that collaborate to perform specific cellular tasks.

What is the significance of covalent modifications of proteins?

They regulate protein behavior, activity, stability, and degradation.

What is the role of scaffold proteins?

They organize cellular processes by bringing interacting proteins together.

What drives the formation of intracellular condensates?

Phase separation driven by weak interactions between macromolecules.

What is an example of an intracellular condensate?

The nucleolus or centrosome.

What type of interactions are crucial for protein-ligand binding?

Hydrogen bonds, electrostatic interactions, and van der Waals forces.

What is the enzyme-substrate complex?

The intermediate formed when a substrate binds to an enzyme's active site.

How can enzymes catalyze the same reaction multiple times?

The enzyme remains unchanged after releasing the product and can bind to new substrates.

What happens when an inhibitor binds to an enzyme?

The enzyme is rendered inactive and cannot catalyze the reaction.

What type of enzyme is a kinase?

Enzymes that add phosphate groups.

What role do motor proteins play in cells?

They facilitate movement by changing shape and moving along filamentous structures.

What occurs during ATP hydrolysis in motor proteins?

It drives directional movement by powering conformational changes.

What are unstructured regions in scaffold proteins for?

They act as flexible tethers to enhance protein-protein interactions.

How does phosphorylation generally affect proteins?

It can either activate or deactivate them, depending on the context.

What is the significance of shape complementarity in binding?

It ensures specific interactions between the protein and the ligand.

What is an example of allosteric regulation?

CTP binding to aspartate transcarbamoylase turns the enzyme off.

What does ATP hydrolysis provide for protein complexes?

It coordinates conformational changes allowing controlled activity.

What are synaptic protein assemblies involved in?

Memory formation.

What is the function of storage proteins?

They store essential molecules for later use.

Describe the role of transport proteins.

They move molecules across cell membranes or within cells.

What is the function of motor proteins in cellular movement?

They generate movement by leveraging ATP energy.

How do feedback mechanisms help regulate cellular processes?

They prevent overproduction of substances by inhibiting pathways.

What occurs to the enzyme when a substrate binds?

It forms an enzyme-substrate complex, leading to product formation.

What is the effect of rising levels of certain ligands on enzyme activity?

They can promote increased enzyme activity when energy is low.

What is the purpose of scaffolding in cellular processes?

To organize interactions and enhance the efficiency of cellular functions.

What are the key components of protein machines?

Multiple proteins working together in a synchronized manner.

What is the molecular basis of allosteric regulation?

Binding at the allosteric site changes the enzyme's conformation and activity.

What is the role of protein phosphatases?

They remove phosphate groups from proteins, reversing phosphorylation.

What is the main driver of intracellular condensate formation?

Weak intermolecular interactions leading to phase separation.

How do enzymes achieve specificity in catalysis?

Through precise interactions at the active site tailored to specific substrates.

What role do regulatory proteins play in cellular processes?

They control various cellular functions and activities.