Chapter 5 Flashcards
(26 cards)
Describe protein-ligand interactions
- reversible, transient process of chemical equilibrium
- ligands bind via same noncovalent forces that dictate protein structure
- kinetics are described by the ka or kd
- after some time the process will reach the equilibrium where the association and dissociation rates are equal
- equilibrium composition is characterized by the equilibrium constant Ka
What is analysis in terms of the bound fraction?
-can determine the fraction of occupied binding sites (theta) from [PL]/([PL] + [P]) or [L]/([L] +[Kd])
What is P50 or P1/2 or Kd?
it is the ligand concentration when half of all available binding sited are bound
What is fractional saturation ?
the fraction of protein molecules that are staurated with ligand
What is the relationship between Kd and Ka?
Kd is 1/Ka so the higher the Ka, the lowers the Kd and thus the higher the affinity
When ligand concentration equals the Kd what is true regarding the fractional saturation?
the fractional saturation is 1/2
describe strong and weak binding strength
strong binding: Kd < 10 nM
weak binding: Kd > 10 uM
Describe the lock and key model
- only certain ligands can bind
- determined by the size, shape, charger, or hydrophobic/philic character of the binding site
Describe the induced fit model
- conformational changes may occur upon ligand binding
- allows for tighter binding of the ligand
- allows for high affinity for different ligands
Describe myoglobin
- main oxygen storage protein
- has a histidine residue and a plane of porphyrin ring system
Why is myoglobin a poor O2 transporter?
- it has a very strong affinity for oxygen
- the pO2 in lungs is about 13 kPa: it binds to oxygen well
- the pO2 in tissues is about 4 pKa: it will not release it
What is cooperitivity? Positive? Negative?
- binding sites being able to interact with each other
- positive: 1st binding event increases affinity at remaining site; recongized by sigmoidal binding curves
- negative: 1st binding event reduces affinity at remaining sites
What does the hill coefficient measure? What does it mean if it is equal to, greater than, or less than 1?
- the degree of co-operativity
- when greater than 1 there is positive co-operativity
- when less than 1 there is negative co-operativity
- when equal to 1 no co-operativity exists
What does allosteric mean?
binding of a ligand to one site affects the binding properties of a different site, on the same protein
What is homotropic regulation?
normal ligand of the protein is the allosteric regulator
What is heterotropic regulation?
different ligand affects the binding of the normal ligand
Why are specific amino acids highly conserved between the sequences of hemoglobin and myoglobin?
because those specific amino acids code for specific functions that the two share
What is the T/ Tense state of hemoglobin?
- more interactions, more stable
- lower affinity for O2
What is the R/ relaxed state of hemoglobin?
fewer interactions, more flexible
- higher affinity for O2
What triggers the conformational changes that lead to the T to R transition?
an O2 binding
involves breaking ion pairs between the alpha beta interface
What is the Bohr effect?
the pH difference between lungs and metabolic tissues increases efficiency of the O2 transport and delivery
-H+ binds to Hb and stabilizes the T state and leads to the release of O2 in the tissues
Between which subunits are ion pairs disrupted, and to where does the Histidine (HC3) relocate after oxygen binding?
the alpha and beta subunit are disrupted
How does CO2 contribute to the Bohr effect?
- CO2 is produced by metabolism in tissues and must be exported
- CO2 is exported in the form of a carbamate on the amino terminal residues of the polypeptide subunits
- the formation of a carbamate yields a proton which can contribute to the Bohr effect
- the carbamate forms additional salt bridges stabilizing the T state
describe the function/mechanism of 2,3 bis-phosphoglycerate (DPG)
- negative heterotropic regulator of Hb function
- small negatively charged molecule binds to the positively charged central cavity of Hb which stabilizes the T states
- allows for O2 releases in the tissues and adaptation to changes in altitude
