Chapter 5 Protein Function (R) Flashcards
Ligand
A molecule bound reversibly by its binding site
Transient
Momentary, Brief
Induced Fit
conformational changes in a protein that makes the binding site more receptive to a ligand.
Q # 1 Why is it important that iron is incorporated into the heme group, rather than free in the cell?
Iron promotes the formation ROS’ (reactive oxygen species) such as hydroxyl molecules, that damage DNA and macromolecules
Prosthetic group
a compound permanently associated with a protein that contributes to the protein’s function
Heme
protein bound prosthetic group associated with iron
Q # 2 What is the shape of a heme group?
A heme group consists of a complex organic ring structure (Protoporphyrin) to which is bound a single iron atom (Fe2+). Fe2+ is buried deep within the heme molecule as well as being associated with four nitrogen molecules that donate electrons This prevents Fe2+ from going to Fe3+ which irreversibly binds O2. One of the two free groups is bound by His, the other allows binding of oxygen
Globins
widespread function of proteins whose functions include; oxygen transport and storage, sensing oxygen, nitric oxide or carbon monoxide
Q # 4 How is the heme group attached to and positioned within the myoglobin molecule?
The heme group is at the center of the myoglobin, and it is surrounded by 8 alpha helical segments
Ka
Ka is an association constant that describes the equilibrium between the complex and the unbound components of the complex ;For P + L PL; Ka = [PL]/[P][L]; Where P=protein, L = ligand
;The larger the Ka, association constant, the higher the affinity there is of the ligand for a protein; Units M^-1
;also equal to ka/kd
Ka[L] = [PL]/[P]
Shows that the proportion of bound protein to free ligand is directly proportional
Theta (ø) of Ka
Where theta equals the fraction of binding sites occupied divided by total binding sites
ø = [L]/([L] + 1/Ka)
ø = 0.5?
The [L] at which half of the available ligand-binding sites are occupied corresponds to 1/Ka
Dissociation constant (Kd) is simply equal to:
1/Ka
Kd
the equilibrium constant for the release of a ligand ;For PL -> P + L;
Kd = [P][L]/[PL]= kd/ka
Theta (ø) of Kd
1) Where theta equals the fraction of binding sites occupied divided by total binding sites 2) When [L] equals Kd, half of the ligand binding sites are occupied. 3) A lower value of Kd results in a higher affinity of ligand for a protein 4) Units (M)
ø = [L]/([L] + Kd
What exactly is Theta ø?
Theta ø is the amount, specifically the percentage, of protein bound to its ligand.
What exactly is Kd?
Kd, the equilibrium dissociation constant is the concentration of a ligand [Lx] at which 50% of the ligand binding sites are bound
Q # 6 In an oxygen -binding curve for myoglobin, why is the term pO2 used rather than [O2]?
pO2 is used because measuring the amount of oxygen in fluid, specifically the circulatory system is tough. In laboratory settings, the partial pressure of O2 is easier to measure than the concentration of oxygen dissolved in solution. Recall, that O2 is not readily soluble in blood
Q # 7 What does the term [PL] mean in terms of specific molecules?
[PL] is the amount of ligand bound to a protein
Q#9 What is the relationship between Kd and the ability of a protein such as myoglobin to bind to its ligand?
Kd is the point at which 50% of the protein is bound by its ligand. Specifically in this problem, Kd means that 50% of the ligand, oxygen, is bound to the protein, Myoglobin
Q # 8 Why are the total number of oxygen binding sites in a solution of myoglobin equal to [PL] + [P]?
The total number is such, because [PL] is the amount of protein already bound, and [P] are the available sites that have not been bound, but have the potential to be bound..
Q # 10 Given that free heme binds CO 20,000 times better than it binds O2, why don’t we all succumb to carbon monoxide poisoning?
Because carbon monoxide is not a prevalent gas in the atmosphere. Also, His E7 sterically hinders the binding of CO to myoglobin
Hemocytoblasts
precursor stem cell that generates hemoglobin
Does hemoglobin reproduce? Why or why not?
It does not. As hemoglobin cell undergo differentiation, they lose organelles and nucleus. They only survive for about 120 days
Q # 11 Why is it important that erythrocytes are so small?
It is important that erythrocytes are so small, because the body needs a substantial amount of transporters of oxygen throughout. Small cells, more oxygen transport.
Q # 12 Could myoglobin substitute for hemoglobin in Red Blood Cells?
No. hemoglobin functions better as a storage molecule, because it does not respond to changes in the concentration of dissolved oxygen.
What are some of the physical features associated with hemoglobin?
1) it is spherical 2) tetramer (two alpha chains and two beta chains) 3) contains four heme groups
Q #14 Why do you think the histidine residues E7 and F8 are invariant between myoglobin and the alpha and beta chains of hemoglobin?
They may be invariant, because they both have the same function, to bind oxygen. Subtle differences in overall structure give difference in affinity, but they still have the same goal. Recall, that the E7 residue is also important to sterically hinder the ability of CO to bind to hemoglobin
Q # 15 What weak bonds or interactions, other than ion pairs are important to hemoglobin’s quaternary contacts?
1) Hydrophobic interactions predominate at all interfaces. 2) hydrogen bonding is also important.
What is the R state, and how does it relate to the affinity in binding of hemoglobin and oxygen?
The R state, oxyhemoglobin, is the conformation of hemoglobin that has a higher affinity for oxygen. The R state is brought about when the T state binds an oxygen molecule, which breaks some of the ion pairs which stabilize the T structure. Amino acid changes involved are the proximal His F8. Heme becomes more planar.
What is the T state, and how does it relate to the affinity in the binding of hemoglobin and oxygen?
deoxyhemoglobin. more stable when oxygen is absent. stabilized by ion pairs that lie at the a1b2 and a2b1 interface.
What happens as subsequent oxygen molecules bind to hemoglobin?
As hemoglobin adds more oxygen from the T state to the R state, it increases affinity for the addition for another oxygen molecule
Allosteric protein
The binding of a ligand to one site affects the binding properties of another site on the same protein
modulators
ligands that change the conformation of a protein
homotrophic interaction
Occurs when the modulator and the ligand are the same.
