Chapter 3: Section C: Interactions of proteins and ligands

Question 1

ligand

Answer 1

• any molecule bound to the surface of a protein
• electrical attractions
• hydrophobic interactions

Question 2

binding site

Answer 2

• region of a protein to which a ligand binds

Question 3

4 characteristics of protein binding sites

Answer 3

• chemical specificity
• affinity
• saturation
• competition

Question 4

chemical specificity of protein binding sites

Answer 4

• protein binding sites are ligand specific
• based on binding site shape (protein tertiary structure)
• different binding sites have different degrees of chemical specificity

Question 5

affinity of protein binding sites

Answer 5

• the strength of binding between the ligand and binding-site
• depends on true strength of attraction between the protein and ligand
• different proteins may have the same chemical specificity, but different affinities

Question 6

saturation of protein binding sites

Answer 6

• the fraction of total binding sites that are occupied at any given time
• for a population of binding sites
• 100% saturated = all available binding sites are occupied
• 50% saturated = half of available binding sites are occupied
• for a single binding site, 50% saturated means that it is occupied by a ligand 50% of the time

Question 7

saturation depends on what

Answer 7

• concentration of the unbound ligand in solution (% saturation increases ligand concentration until 100% reached)
• affinity of binding site for ligand…the greater the affinity f the binding site, the lower the ligand concentration required to achieve a certain degree of saturation
• affinity measured according to the ligand concentration necessary to produce 50% saturation)

Question 8

competition of protein binding sites

Answer 8

• ligands that bind to same binding site compete with each other for that site

Question 9

Regulation of the binding site characteristics

Answer 9

• mechanisms for controlling cellular functions often involve regulating protein activity
• change protein shape and therefore change binding sites
• regulate protein synthesis and degredation

Question 10

protein shape is altered by what

Answer 10

• allosteric modulation

- covalent modulation

Question 11

2 binding sites of allosteric modulation

Answer 11

• function (active) site

- regulatory site

Question 12

functional (active) allosteric site

Answer 12

• binds the ligand that generates the physiologic function of the protein

Question 13

regulatory allosteric site

Answer 13

• binds a modulator molecule alters the shape of the functional site
• turn on functional site
• turn off functional site
• increase or decrease binding - affinity

Question 14

cooperativity

Answer 14

• interactions between functional binding sites of multimeric proteins
• binding of a ligand to one functional binding site increases the affinity of the binding sites on the other polypeptide chains –> progressive increase in affinity for the ligand as more and more binding sites are occupied

Question 15

Covalent modulation

Answer 15

• covalent bonding of charged chemical groups to one or more of the protein’s side chains
• usually occurs through the addition of a phosphate group by phosphorylation
• -> protein kinase
• -> introduces a negative charge that changes protein conformation, altering the functional binding sites
• dephosphorylation removes the phosphate group