Chapter 5

Question 1

A ligand is a molecule that binds ____ and ____ to another larger molecule

Answer 1

Specifically and reversibly

Question 2

How is the induced fit analogy more accurate when describing the way a ligand binds as opposed to the lock and key method?

Answer 2

The enzyme/receptor that the ligand binds to is not the exact shape as the ligand. Instead, the receptor will change shape slightly to accept the ligand once they are within range of each other

Question 3

Kd represents the _____ constant, which can be expressed the same as Ka with the products on the top of the ratio and the reactants on the bottom

Answer 3

dissociation constant

Question 4

As the Kd decreases, the affinity of the ligand to bind with the protein _____

Answer 4

increases

Inverse relationship

Question 5

Why is it important for enzymes to have low affinity’s for binding with ligands?

Answer 5

Enzymes need to be able to let go of their ligands easily, so they need to prefer being in the dissociated state over the binded state

Question 6

A heme group is composed of pyrrole rings and methyl groups with one ____ in the middle

Answer 6

Iron

Question 7

When the Kd equals the concentration of the ligand, what is the fraction of ligands bound to enzymes?

Answer 7

1/2, because it implies that half of the binding sites are occupied

Question 8

What is the difference between myoglobin and hemoglobin?

Answer 8

Myoglobin is designed to hold onto oxygen. It is stored in the muscles and can be used to transport O2 around the muscles when supply is low. It is also monomeric. Hemoglobin is a tetrameric protein with 2 alpha and 2 beta chains. It is designed for the transport and delivery of O2 to the tissues and has two states: the R state for binding with O2 and the T state for dropping O2 off

Question 9

Myoglobin has ____ heme group while hemoglobin has ____

Answer 9

One
Four

Question 10

How does the structure of hemoglobin change when O2 binds?

Answer 10

The heme group is bent slightly before the O2 binds, but straightens out when the O2 binds with the Iron. This affects the rest of the molecule, bc the heme group is attached to a HIS that pulls on the rest of the molecule during the flattening of the heme group (when O2 binds)

Question 11

O2 binds to the _____ of the heme group

Answer 11

Iron

Question 12

Why are CO-, CN-, and SO deadly?

Answer 12

They bind to hemoglobin with a higher affinity than O2, so the hemoglobin will stay in the R state and not let go

Question 13

How does a ligand binding to one domain affect the others surrounding it?

Answer 13

The domain that was just bound will have its structure slightly altered. This will affect the other domains by altering their structure too and putting them in a conformation that makes them more likely to bind with their own ligands

Question 14

Hemoglobins binding occurs cyclically. The __ state picks up the O2 from the lungs, then the __ state brings it to the tissues and deposits it, turning back into the __ state

Answer 14

T

R

T

Question 15

The T state has a low affinity for O2 because _____ while the R state has a high affinity for O2 because _____

Answer 15

The T state is the one without O2, which means it must like to give it away. The R state is the one with O2, which means it must like to hold onto it

Question 16

The Hill equation expresses the level of cooperation in an allosteric protein. It looks like:

Answer 16

ln(theta/1-theta)= nh log[L]-log Kd

Where theta is the fraction of the enzyme and ligand bound together, and nh is the Hill coefficient

Question 17

In the Hill equation, nh ___ than 1 means the system is positively cooperative. nh __ to n means the system is completely cooperative. nh __ 1 means the system is non-cooperative, and nh __ than 1 means the system shows negative cooperation

Answer 17

greater than

equal to

equal to

less than

Question 18

What is the purpose of 2,3-BPG?

Where does it bind?

Answer 18

It’s an allosteric modulator that increases the amount of hemoglobin T states by lowering hemoglobins affinity for binding to O2. Without 2,3-BPG, hemoglobin would prefer not to let go of O2 and would always be in the R state

Binds to the donut hole of hemoglobin. This hole is open in the T state and closed in the R state, so 2,3-BPG forces it to stay open

Question 19

Allosteric means the binding of one ligand to one site affects _____

Answer 19

the binding properties of the another site on the same protein

Question 20

What negative allosteric modulator is associated with the Bohr effect? Where does this modulator bind?

Answer 20

H+, the proton. At higher levels of H+ (created through combustion/respiration), the amount of T state is increased.

At the HIS that’s attached as a side group. The protonated HIS then forms an ion pair with the ASP next to it, and this stabilizes the T state so much that it will stay in the T state until it reaches the lungs, where the pH is higher and the HIS will be deprotonated

Question 21

How does CO2 act as an allosteric modulator?

Answer 21

CO2 binds to the amino group, which then releases H+ and the Bohr effect starts. It stabilizes the T state so that more O2 is dropped off than with a lower pH alone

Question 22

Rank the three allosteric modulators in order of increased oxygen carrying capacity

Answer 22

BPG
H+ (Bohr effect)
CO2 and the Bohr effect

Question 23

What is the mutation present in sickle cell anemia

Answer 23

A mutation from Glu to Val changes the shape of hemoglobin so that it can’t transport O2 and gets stuck in the walls of capillaries. This is a modification that, when present as Rr, is favorable in populations with high rates of malaria

Question 24

What are the general uses for antibodies?

Answer 24

Monoclonal or polyclonal (depends on the number of regions they are designed to recognize on the molecule), and also in pharmaceuticals to be used for drugs and vaccines