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Biochemistry > Structures and Function Receptors and Ligands > Flashcards

Structures and Function Receptors and Ligands Flashcards

1
Q

Small molecules that binds a protein at a binding site

A

Ligands

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2
Q

Binds at the binding site and results in a response. Not a normal ligand. Ex: Opiates binding in the place of normal endorphins

A

Agonist

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3
Q

Something that binds and block the binding site

A

Antagonist

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4
Q

Proteins bind ligand by slightly _ their _

A

adjusting, conformations

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5
Q

Why must ligand binding be a reversible process?

A

The receptors need to be reused

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6
Q

O2 binding to myoglobin and hemoglobin. ATP binding to myosin. Actin binding

A

Protein-ligand interaction examples

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7
Q

With protein and ligand binding, when there is a high concentration of ligand there is more of what form

A

More of the complex state (PL)

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8
Q

The dissociation constant measures what?

A

Kd measures binding affinity

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9
Q

when kd = [L] what is theta

A

1/2. Kd is the [L] where 1/2 of the binding sites are occupied

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10
Q

Smaller Kd is weaker or stronger affinity for the ligand?

A

Stronger

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11
Q

A monomeric protein in the Globin family. Hemoglobin has 4 of these

A

Myoglobin (Mb)

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12
Q

Myoglobin is what kind of storehouse?

A

O2 storehouse. Binds and releases oxygen

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13
Q

Structural adaptation that occurs between protein and ligand

A

induced fit

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14
Q

Why do we need a delivery system for a gas like oxygen?

A

Oxygen is not very soluble in liquid and water. Needs to be bound to something like myoglobin

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15
Q

Myoglobin’s center contains iron. Why is that important?

A

Fe and Cu have a strong tendency to bind to O2. They reversibly bind to O2.

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16
Q

Iron is often incorporated into a protein bound prosthetic group called _

A

heme

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17
Q

Iron atom has 6 coordinated bonds, 4 nitrogen atoms that are part of a flat _ ring system. Nitrogens are a part of histidines

A

Porphyrin

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18
Q

Can any amino acids reversibly bind to O2

A

No

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19
Q

What does heme do when it is coordinated with a protein?

A

It controls the reactivity of the Fe (Iron)

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20
Q

Histidine coordinates the Fe and allows how many sides of Fe to bind to O2?

A

One

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21
Q

The specific structure of the binding pocket will affect…

A

ligand binding

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22
Q

Myoglobin slightly “breathes” between what states

A

bound and unbound

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23
Q

CO and NO bind with a higher affinity to the heme iron than O2. Why is that bad?

A

When CO or NO bind to the heme group, oxygen is excluded and cannot be transported through the body.

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24
Q

Mb follows what kind of binding pattern

A

hyperbolic

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25
Q

Carries O2 from lungs to tissues. 4 subunits (2 alpha + 2 beta, each with one Heme Fe). Subunits are similar to Mb

A

Hemoglobin (Hb)

26
Q

What forces hold the hemoglobin subunits together?

A

Hydrogen bonds, hydrophobic interactions, covalent, ionic, and van der Waals.

27
Q

Hb subunits change conformation slightly when O2 is bound. What are the two conformations?

A

T state and R state

28
Q

Which conformation has a low affinity to oxygen?

A

T state

29
Q

Which conformation has a high affinity to oxygen?

A

R state

30
Q

The transition from T state to R state is called what?

A

Cooperative Binding

31
Q

Where the binding of one ligand affects the structure and the binding affinity of the other ligand

A

Cooperative binding

32
Q

Cooperative binding of T and R states allows what to occur?

A

Allows Hb to pick up and deliver its cargo

33
Q

Sigmoid binding curves suggest what kind of binding?

A

Cooperative binding

34
Q

What do sigmoid binding curves show?

A

The transition from low to high-affinity conformation

35
Q

Sigmoid curves are an example of allostery. What does that mean?

A

Binding at one site affects the shape of another site

36
Q

What 4 things contribute to the binding affinity of O2 in Hb (thus the stabilization of the R and T states)?

A

pO2 (how much O2 is around), pH, CO2 concentration, and binding of 2,3-Bishosphoglycerate (BPG)

37
Q

Which state occurs when the histidine residues are in the center of hemoglobin?

A

The R state. Histidine’s are deprotonated and neutral, so they can be next to each other

38
Q

What part of the body is the R state commonly found?

A

The lungs

39
Q

Which state is associated with a high pH (more basic)?

A

The R state

40
Q

Which state is associated with a low pH (more acidic)?

A

The T state

41
Q

Which part of the body is the T state commonly found?

A

The muscles

42
Q

In the T state, the histidine residues are on opposite sides of hemoglobin. Why?

A

Because the T state has a lower pH, the histidine residues are protonated and charged. When they are next to each other, they repel each other so they have to be farther away.

43
Q

In the T state, what other amino acid do the histidine residues have electrostatic interactions with?

A

Asp

44
Q

Step 1 of Hb process

A

In lungs, pO2 is high, CO2 is low, and pH of blood is about 7.6. Hb arrives in T state with no O2 and with BPG bound.

45
Q

Step 2 of Hb process

A

Hb recognizes that there is oxygen to deliver. BPG unbinds so that oxygen can bind

46
Q

Step 3 of Hb process

A

Because the first O2 molecules bound, the other O2 molecules binding is easy. There is cooperative binding so a transition into the R state occurs.

47
Q

Step 4 of Hb process

A

Heme group is taken to the muscle tissue. A working muscle needs O2. The pO2 is low, the CO2 is high, and the pH is about 7.2 (lower than before)

48
Q

Step 5 of Hb process

A

H+ binds to specific residues on Hb (Ex: HisHc3) which causes Hb to return to the T state. O2 falls off Hb to participate in cellular respiration

49
Q

Why is the pH lower in deep tissues?

A

Enzyme carbonic anhydrase turns CO2 into bicarbonate, which diffuses out in the blood and lowers pH. Indirect effect of CO2 on the T-state

50
Q

Step 6 of Hb process

A

CO2 binds to the N-term of each globin chain which stabilizes the T state. H+ binds to other amino acids (like HisHc3 which binds to Asp94)

51
Q

How many carbon dioxides can each hemoglobin pick up and take to blood

A

4

52
Q

H+ and CO2 binding to different sites on the Hb _ the T-state. This is a _ effect

A

Stabilizes, Direct

53
Q

Step 7 of Hb process

A

BPG returns and binds to Hb which further stabilizes the T-state. Makes sure that the O2 stays out

54
Q

When is BPG produced?

A

During regular metabolism

55
Q

How many BPG molecules binds the Hb tetramer between the beta subunits in the T-state?

A

1

56
Q

What is predominate charge on BPG?

A

Negative

57
Q

What kind of amino acids are responsible for BPG binding to the beta subunits?

A

Positively charged amino acids like Lysine, Arginine, Histidine

58
Q

At high concentrations, should BPG be bound or unbound?

A

Bound

59
Q

Bohr effect for hemoglobin

A

The Bohr effect describes hemoglobin’s lower affinity for oxygen secondary to increases in the partial pressure of carbon dioxide and/or decreased blood pH. This lower affinity, in turn, enhances the unloading of oxygen into tissues to meet the oxygen demand of the tissue.

60
Q

Does all of the O2 that is carried around in the blood diffuse out?

A

No, much of the O2 carried does not diffuse out.

Biochemistry (8 decks)

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