Structures and Function Receptors and Ligands Flashcards
Small molecules that binds a protein at a binding site
Ligands
Binds at the binding site and results in a response. Not a normal ligand. Ex: Opiates binding in the place of normal endorphins
Agonist
Something that binds and block the binding site
Antagonist
Proteins bind ligand by slightly _ their _
adjusting, conformations
Why must ligand binding be a reversible process?
The receptors need to be reused
O2 binding to myoglobin and hemoglobin. ATP binding to myosin. Actin binding
Protein-ligand interaction examples
With protein and ligand binding, when there is a high concentration of ligand there is more of what form
More of the complex state (PL)
The dissociation constant measures what?
Kd measures binding affinity
when kd = [L] what is theta
1/2. Kd is the [L] where 1/2 of the binding sites are occupied
Smaller Kd is weaker or stronger affinity for the ligand?
Stronger
A monomeric protein in the Globin family. Hemoglobin has 4 of these
Myoglobin (Mb)
Myoglobin is what kind of storehouse?
O2 storehouse. Binds and releases oxygen
Structural adaptation that occurs between protein and ligand
induced fit
Why do we need a delivery system for a gas like oxygen?
Oxygen is not very soluble in liquid and water. Needs to be bound to something like myoglobin
Myoglobin’s center contains iron. Why is that important?
Fe and Cu have a strong tendency to bind to O2. They reversibly bind to O2.
Iron is often incorporated into a protein bound prosthetic group called _
heme
Iron atom has 6 coordinated bonds, 4 nitrogen atoms that are part of a flat _ ring system. Nitrogens are a part of histidines
Porphyrin
Can any amino acids reversibly bind to O2
No
What does heme do when it is coordinated with a protein?
It controls the reactivity of the Fe (Iron)
Histidine coordinates the Fe and allows how many sides of Fe to bind to O2?
One
The specific structure of the binding pocket will affect…
ligand binding
Myoglobin slightly “breathes” between what states
bound and unbound
CO and NO bind with a higher affinity to the heme iron than O2. Why is that bad?
When CO or NO bind to the heme group, oxygen is excluded and cannot be transported through the body.
Mb follows what kind of binding pattern
hyperbolic
Carries O2 from lungs to tissues. 4 subunits (2 alpha + 2 beta, each with one Heme Fe). Subunits are similar to Mb
Hemoglobin (Hb)
What forces hold the hemoglobin subunits together?
Hydrogen bonds, hydrophobic interactions, covalent, ionic, and van der Waals.
Hb subunits change conformation slightly when O2 is bound. What are the two conformations?
T state and R state
Which conformation has a low affinity to oxygen?
T state
Which conformation has a high affinity to oxygen?
R state
The transition from T state to R state is called what?
Cooperative Binding
Where the binding of one ligand affects the structure and the binding affinity of the other ligand
Cooperative binding
Cooperative binding of T and R states allows what to occur?
Allows Hb to pick up and deliver its cargo
Sigmoid binding curves suggest what kind of binding?
Cooperative binding
What do sigmoid binding curves show?
The transition from low to high-affinity conformation
Sigmoid curves are an example of allostery. What does that mean?
Binding at one site affects the shape of another site
What 4 things contribute to the binding affinity of O2 in Hb (thus the stabilization of the R and T states)?
pO2 (how much O2 is around), pH, CO2 concentration, and binding of 2,3-Bishosphoglycerate (BPG)
Which state occurs when the histidine residues are in the center of hemoglobin?
The R state. Histidine’s are deprotonated and neutral, so they can be next to each other
What part of the body is the R state commonly found?
The lungs
Which state is associated with a high pH (more basic)?
The R state
Which state is associated with a low pH (more acidic)?
The T state
Which part of the body is the T state commonly found?
The muscles
In the T state, the histidine residues are on opposite sides of hemoglobin. Why?
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.
In the T state, what other amino acid do the histidine residues have electrostatic interactions with?
Asp
Step 1 of Hb process
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.
Step 2 of Hb process
Hb recognizes that there is oxygen to deliver. BPG unbinds so that oxygen can bind
Step 3 of Hb process
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.
Step 4 of Hb process
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)
Step 5 of Hb process
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
Why is the pH lower in deep tissues?
Enzyme carbonic anhydrase turns CO2 into bicarbonate, which diffuses out in the blood and lowers pH. Indirect effect of CO2 on the T-state
Step 6 of Hb process
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)
How many carbon dioxides can each hemoglobin pick up and take to blood
4
H+ and CO2 binding to different sites on the Hb _ the T-state. This is a _ effect
Stabilizes, Direct
Step 7 of Hb process
BPG returns and binds to Hb which further stabilizes the T-state. Makes sure that the O2 stays out
When is BPG produced?
During regular metabolism
How many BPG molecules binds the Hb tetramer between the beta subunits in the T-state?
1
What is predominate charge on BPG?
Negative
What kind of amino acids are responsible for BPG binding to the beta subunits?
Positively charged amino acids like Lysine, Arginine, Histidine
At high concentrations, should BPG be bound or unbound?
Bound
Bohr effect for hemoglobin
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.
Does all of the O2 that is carried around in the blood diffuse out?
No, much of the O2 carried does not diffuse out.
