13 Protein function and molecular recognition Flashcards
What is a ligand?
A molecule that binds reversibly to a protein
Where does a ligand bind?
a binding site on a protein
What are the characteristics of a bidning site?
it is complementary to the ligand in size, shape, charge, and hydrophilic/phobic character
Why are protein-ligand interactions critical to life?
they allow rapid and reversible response to changing environmental and metabolic circumstances
How is the binding of a protein and ligand like an induced fit?
the binding is often coupled to a conformational change in the protein that makes the binding site more complementary to the ligand
How can protein-ligand interactions be described in letters?
What is Kd?
dissociation constant = used to express the addinity of a protein for a ligand (how strong they’re binding)
smaller kd = higher affinity
What is theta θ?
fraction of binding sites on the protein that are occupied by ligand
[PL]/ ([PL] + [P]
What is theta and L representing?
theta = fraction of binding sites on the protein that are occcupied by ligand
L= Kd, where half of the lingand binding sites are occupied, can be used to express the affinity of a protein for a ligand
which binds with higher affinity (i.e. binds tighter)
Avidin
smaller kd = higher affinity
the earlier half of ligand binding sites are occupied = stronger binding
which binds with higher affinity (i.e. binds tighter)?
X because it reaches theta (when half the binding sites are occupied) faster = kd is lower
X is half-saturated at a lower ligand concentration
if it needs less ligand to be saturated = it binds more strongly with ligand
when saturated at a lower kd = needs very little to be 50% saturated
if need a lot to be saturated = the ligand is not binding very strongly (binding then coming off) - low affinity
what is an oxygen-binding protein?
haemoglobin
What is the haemoglobin composed of?
4 subunits, 4 heme with iron atom (one each)
When does a haemoglobin undergo structural change?
when binding to O2
What is the T and R state of haemoglobin?
T and R state - 2 main changes
T state - bind with lower affinity w oxygen
R state - bind with higher affinity to oxygen
Why do we have 2 different states of haemoglobin?
High affinity is good for in the lungs to bind efficiently to O2, and Low affinity is good for tissues where O2 can be released
But low affinity in lungs is bad because it cant pick up oxygen, and high affinity in tissues is bad because it wouldnt release them
so haemoglobin transitions between T state (low affinity) to R state (high affinity) as more and more oxygen molecules are bound
What is happening here?
first O2 molecule binds weakly to a subunit in T state, its binding, leads to other subunits transition to R state and further O2 molecules binds tighter
what is positive cooperativity in haemoglobin?
the last O2 binds more strongly than the first
what is the inverse relationship that causes haemoglobin to release O2?
inverse relationship between binding of O2 and the binding of H+ and CO2
How does very low pH and high CO2 conc of peripheral tissues affect haemoglobin?
low Ph = High H+
the affinity of haemoglobin for O2 decreases and are released, then H+ and CO2 can be bound to haemoglobin
What happens to haemoglobin when the environment becomes less acidic?
haemoglobin have higher affinity for oxygen again
What is the Bohr effect?
how the pH and Co2 affect the O2 affinity
tissue: low pH, high Co2, affinity is low so oxygen is released and H+ and Co2 binds
lungs: Co2 is excreted so pH rises and affinity increases. then binds more O2 to be transported back to the peripheral tissues
What is O2 binding to haemoglobin regulated by?
2,3 - bisphosphoglycerate (BPG)
