Chapter 1-6 Review: Binding, Affinity, Modulation, and Signaling

Flashcards cover binding sites, affinity, capacity/saturation, competition, environmental and covalent/allosteric modulation, phosphorylation, regulatory units (PKA), and GPCR signaling concepts discussed in the notes.

Can binding sites be located internal in a molecule as long as there's surface access?

Yes. Binding sites are on surfaces; they can be internal if accessible from the exterior.

What does affinity describe in ligand–binding?

The strength of attraction between a binding site and its ligand; high affinity means the complex is stable and dissociates slowly.

What does the term saturation mean in a binding curve?

All binding sites are occupied; percent saturation reaches 100%.

Why is carbon monoxide a problem for hemoglobin?

CO has a higher affinity for hemoglobin than oxygen; it occupies binding sites preferentially, reducing O2 transport.

What does the 'lock and key' concept illustrate in this context?

A good fit between ligand and binding site leading to high affinity and a low probability of the ligand dissociating.

What does capacity refer to in binding scenarios?

The total number of available binding sites in a system.

What does saturation describe in a binding system with many sites?

The fraction of binding sites that are occupied by ligands; at 100% saturation, all sites are filled.

How can affinity be modulated by environmental factors?

Environmental changes such as temperature, pH, and osmolarity can alter protein conformation and binding affinity.

What effect does increasing temperature have on Brownian motion and binding?

Higher temperature increases Brownian motion, which can influence binding dynamics and affinity.

What is phosphorylation and which enzyme mediates it?

Covalent addition of a phosphate group to a molecule, typically mediated by a kinase.

Differentiate covalent modulation from allosteric modulation.

Covalent modulation involves covalent bonds (e.g., phosphorylation) to alter activity; allosteric modulation involves noncovalent binding at a regulatory site to change activity.

Describe the regulatory unit of cyclic AMP–dependent protein kinase (PKA) and its activation.

PKA has catalytic and regulatory subunits; the regulatory subunit inhibits the catalytic subunit; binding of cAMP to the regulatory subunit causes dissociation and activation of the catalytic subunit.

What happens when cyclic AMP binds to the regulatory subunit of PKA?

The regulatory subunit dissociates from the catalytic subunit, activating the kinase.

What signaling sequence is described as a 'sandwich' involving a messenger, receptor, and G protein?

A chemical messenger binds a receptor, the receptor then interacts with a G protein to propagate the signal.

What is the common second messenger produced from ATP in these signaling pathways?

Cyclic AMP (cAMP) is produced from ATP and acts as a second messenger.

What does the term 'binding site accessibility' imply?

Binding sites must be accessible on or from the surface; if not accessible, ligands cannot bind.

Why is the saturation curve's plateau important?

It indicates that all binding sites are full and adding more ligand cannot increase occupancy.