Lecture 10

Question 1

Explain the function of Oxidoreductases

Answer 1

Oxidoreductases move electrons via redox reactions

Question 2

Explain the function of Transferases

Answer 2

Transferases move a functional group via “group transfer”

Question 3

Explain the function of Hydrolases

Answer 3

Hydrolases break a chemical bond by adding water across it (hydrolysis)

Question 4

Explain the function of Isomerases

Answer 4

Isomerases Rearrange the order of atoms in a molecule (isomerization)

Question 5

Explain the function of Lysases

Answer 5

Lysases break a chemical bond without using water

Question 6

Explain the function of Ligases

Answer 6

Ligases use ATP to paste 2 pieces together (make a chemical bond)

Question 7

For the following metabolic chemistry reactions, state the general result that occurs:

Nucleophilic substitution:

Nucleophilic Addition:

Carbonyl Condensation:

Elimination:

Oxidation-Reduction:

Answer 7

Nucleophilic substitution: Swaps functional groups

Nucleophilic Addition: Adds functional groups

Carbonyl Condensation: Changes the # of carbons

Elimination: Increases the bond order

Oxidation-Reduction: Moves electrons

Question 8

State the type of chemical interaction that would occur between molecules with the following characteristics:

Non-Polar & Polar:

+ & - :

H-bond donor & H-bond acceptor:

Answer 8

Non-Polar & Polar: Van der Waals interaction

+ & - : Charge-Charge interaction

H-bond donor & H-bond acceptor: Hydrogen-bonding interaction

Question 9

Describe the active site of an enzyme in terms of the amount of residues involved, it’s environment, what determines it’s specificity, and what type of interactions occur there.

Answer 9

The active site is composed of only a few residues out of the entire protein

It is a 3D cleft/crevice/pocket that creates a unique microenvironment

it determines its substrate specificity by the size and charge complementarity

It’s interactions with the substrate are noncovalent interactions

Question 10

Define Allosteric binding. does this type of binding behave differently than active site interactions?

Answer 10

Allosteric binding: Does NOT occur at the active site of an enzyme, but it involves a 2nd substrate that binds to a “secondary site”

No, interactions that occur in the allosteric binding site follow the same rules as interactions that occur in the active site

Question 11

Describe what occurs when a competitive inhibitor binds to an enzyme. How does this compare to allosteric inhibition?

Answer 11

competitive inhibitors bind to the active site of the enzyme and “box out” the normal substrate from the active site

Allosteric inhibitors bind to a secondary site of an enzyme and change the conformation of the active site so that the normal substrate is no longer favored in the microenvironment of the active site

Question 12

Define allosteric activation

Answer 12

Allosteric activators bind to a secondary site on an enzyme and cause a change in the active site that creates a more favorable microenvironment for the substrate

(basically the exact opposite of allosteric inhibitors)

Question 13

Compare Apoenzymes with Holoenzymes

Answer 13

Apoenzymes: are an incomplete enzyme that will remain inactive until a cofactor and/or coenzyme interacts with it to activate it

Holoenzymes: whole and completely enzymatically active enzymes that already contain the necessary cofactor/coenzyme

(Apoenzyme + cofactor/coenzyme = Holoenzyme)

Question 14

give the name, equation, and a general description of the following constants:

KA

KD

Answer 14

KA: Affinity/Association constant

KA = [E*S] / [E][S]
coming together

KD: Dissociation constant

KD = [E][S] / [E*S]
breaking apart

Question 15

What is equal to the concentration of ligand where there is 1/2 of the available binding sites that are full? (basically, what value describes when the receptor is half-saturated)

Answer 15

KD (dissociation constant)

Question 16

Define Cooperativity as it pertains to ligands and active sites

Answer 16

Cooperativity: binding of each subsequent ligand influences the affinity (strength of interaction) of the next ligand to bind to an active site

Question 17

In terms of cooperativity, interpret the following hill coefficients:

nH = 1:

nH > 1:

0 < nH < 1:

Answer 17

nH = 1: no cooperativity (sites are independent)

nH > 1: positive cooperativity (affinity increases)

0 < nH < 1: negative cooperativity (affinity decreases)

Question 18

State the function of the following transferases:

ATP and pyridoxal phosphate

Answer 18

transfer a phosphate group

Question 19

State the function of the following transferases:

SAM, Tetrahydrofolate, and 5’-deoxyadenosylcobalamin

Answer 19

transfer a methyl group

Question 20

State the function of the following ligase:

TPP

Answer 20

links structures together via a +/- Aldehyde group (-COH)

Question 21

State the function of the following ligases:

CoASH and Lipoamide

Answer 21

links structures together via a +/- Acyl group (-COR)

Question 22

State the function of the following ligase:

Biotin

Answer 22

links structures together via a +/- CO2 group

Question 23

Describe what it means when:

Y = 1:

Y = 0:

Y = 0.5:

Answer 23

Y = 1: the enzyme is fully saturated

Y = 0: there are no ligands bound to an enzyme

Y = 0.5: half of the enzymes are bound to ligands (half saturation)

Question 24

Plotting Y vs [S] yields what type of a curve? what type of plot must you use if you wish to have a linear curve?

Answer 24

a hyperbolic curve

scatchard plots will produce a linear plot

Question 25

Define an enzyme-ligand situation where Theta will be needed to describe the level of saturation. Define what Theta represents.

Answer 25

when n > 1 (basically the enzyme is already fully saturated and there is still more ligand in the solution), then Theta will represent the “fractional saturation”

Theta describes the fraction of protein molecules that contain ligand BUT we will need multiple species of E*S AND our binding sites may or may not be identical or equivalent

Question 26

What is nH, and how does it fit into the hill equation used to plot the ligand reaction?

Answer 26

nH is the hill coefficient that describes where n = the exact number of binding sites present

nH represents the slope of a hill plot

Question 27

what represents the Y-intercept of the hill equation (used to create a hill plot)

Answer 27

Y-intercept = log (1/KD)

Question 28

State the “Toward the Hill Equation” and be sure to include what each of the variables represents

Answer 28

Toward the Hill Equation: E + nS = E * Sn

E: enzyme/protein

S: substrate

n: number of binding sites