Molecular Interaction pt 2

Question 1

What are the properties that binding sites for proteins have?

Answer 1

1. Affinity
2. Competition
3. Saturation

Question 2

Ligand

Answer 2

Any molecule or ion that binds to another molecules

Question 3

Substrates

Answer 3

Ligands that bind to enzymes & membrane transporters

Question 4

Protein signal molecules & protein transcription factors are ___________

Answer 4

Ligands

Question 5

__________ are selective about the molecules that they bind to

Answer 5

Proteins

Question 6

Specificity

Answer 6

The ability of a protein to bind to a certain ligand or group of related ligands

Question 7

Protein’s binding reaction are ___________

Answer 7

Reversible

Question 8

Affinity

Answer 8

The degree to which a protein is attached to a ligand

Question 9

If a protein has a _______ affinity for a ligand, then the protein is more than likely to bind to that ligand than to a ligand with a _______ affinity for

Answer 9

High, low

Question 10

The notation for protein ligand binding is what?

Answer 10

P + L (reversible arrows) PL

Question 11

Reversible bind reaction goes to a state of equilibrium where they forward & backward reactions are _________

Answer 11

Equal

Question 12

Binding reaction obey __________

Answer 12

Law of mass action

Question 13

Law of mass

Answer 13

When a reaction is at equilibrium the ratio of the products to the substrates is always the same & if it’s distributed by adding or removing the protein or ligand then the reaction will shift in the direction to restore it

Question 14

The dissociation constant indicates ___________

Answer 14

affinity

Question 15

K_eq = [PL]/[P][L]

Answer 15

= [PL]/[P][L]

Question 16

In protein binding reaction the equilibrium constant is a quantitative representation of the proteins’s affinity for the ligand where the ________ the affinity for the ligand the larger K_eq is

Answer 16

Higher

Question 17

The reciprocal of the equilibrium constant is the ______________

Answer 17

Dissociation constant (K_d)

Question 18

K_d

Answer 18

K_d = [P][L]/ [PL]

Question 19

A __________ K_d means low binding affinity of the protein to a ligand

Answer 19

Large

Question 20

A _______ K_d indicates higher affinity of the protein for the ligand

Answer 20

Low

Question 21

If a protein bind to several related ligands than can compare their _______ values to see which ligand is more likely to bind to the protein

Question 22

The related ligands that compete for the binding sites are called what?

Answer 22

Competitors

Question 23

Agonist

Answer 23

Competing ligands that mimic each other’s actions (ex. nicotine mimic a neurotransmitter)

Question 24

Isoforms

Answer 24

Closely related proteins whose function is similar but affinity for ligands differ

Question 25

Some proteins are inactive when synthesized in the cell where the activation of some proteins require what?

Answer 25

Cofactors

Question 26

Cofactors

Answer 26

Is an ion or small organic functional group

Question 27

Ionic cofactors are what?

Answer 27

Ca²⁺, Mg²⁺, & Fe²⁺

Question 28

Modulator

Answer 28

A factor that influences either protein binding or protein activity

Question 29

The two basic mechanism a modulator does is what?

Answer 29

1. The modular changes the proteins’ ability to bind to the ligand or it
2. The modular changes the protein’s activity or its ability to create a response

Question 30

Chemical modulars

Answer 30

Are molecules that bind covantely or noncovalently to proteins & alter their binding ability to their activity

Question 31

Antagonist (inhibitors)

Answer 31

Are chemical modulators that bind to a protein & decrease its activity

Question 32

Competitive inhibitors

Answer 32

Are reversible antagonist that compete with customary ligand for the binding site

Question 33

The binding of competitive inhibitors is ___________ where increasing the concentration of the customary ligand can displace the competitive inhibitor & decrease the inhibition

Answer 33

Reversible

Question 34

Irreversible antagonist

Answer 34

Bind tightly to the protein & can’t be displaced by competition

Question 35

______________ & _____________ modulators may be either antagonist or activators

Answer 35

Allosteric & covalent bonds

Question 36

Allosteric modulators

Answer 36

Bind reversibly to a protein at a regulatory site away from the binding site & by doing so change the shape of the binding site

Question 37

Allosteric inhibitors

Answer 37

Are antagonist that decrease the affinity of the binding site for the ligand & inhibit protein activation

Question 38

Allosteric Activators

Answer 38

Increase the probability of protein-ligand binding & enhance protein activity

Question 39

Covalent modulators

Answer 39

Are atoms or functional groups that bind covalently to proteins & alter the protein’s properties (They can either increase or decrease a protein’s binding ability or activity)

Question 40

Small changes in pH or temp. act as modulators to __________ or ____________ activity

Answer 40

Increase or decrease

Question 41

A denatured protein

Answer 41

Protein that lost its shape

Question 42

The body regulates the amount of ___________ in the body

Answer 42

Proteins

Question 43

Up regulation

Answer 43

The production of new proteins such as receptors, enzymes, & membrane transporters

Question 44

Down regulation

Answer 44

The removal of proteins

Question 45

Saturation in proteins

Answer 45

When a protein is fully occupied & rate reaches its maximum value

Question 46

__________ applies to enzymes, membrane transporters, receptors, binding proteins & immunoglobulins

Answer 46

Saturation