Proteins - Structure And Function Binding Interactions Flashcards
Definition of a ligand
A ligand is a molecule which binds to a protein at a specific site, often triggering a conformational change that affects the activity of the protein.
Receptor definition
A receptor is the binding partner of a ligand, and is usually involved in signal transduction across membranes
Specific binding definition
Occurs when the binding partner/receptor only interact with specific ligands (biological systems)
Non-specific binding
When the binding partner will interact with a wide range of different ligands, not distinguishing between them
Complex definition
A complex is the combination of a ligand and its binding partner/receptor
Strength of binding definition
Definition of dissociation constant
Definition of equilibrium constant
1) Determined by how much energy is required to separate the binding partner and ligand in the complex.
2)
-A measure of the extent to which a substance is dissociated into ions
-Equal to the product of the concentrations of dissociated ions divided by the concentration of the undissociated substance
3)
-Equilibrium constant expresses the ratio of products to reactants at equilibrium and the extent to which reactants have been converted to products.
-Equal to the product of the product concentrations divided by the concentration of the reactant
Explain the 2 enzyme binding models
1) Lock and Key binding model - the shape of the active site is exactly complementary to the substrate
2) The induced fit binding model - the shape of the active site changes on binding the substrate to give exact complementarity, implying the protein to be flexible and dynamic in shape (more accurate model)
1) Considering the equation A + B <—> C, and using the equilibrium constant, dissociation constant, and your brain, simplify to put in a form of fractional saturation (Y) = a function of [B].
2) By putting the equation in the form Y against a single variable, plot the graph of Y against B
3) State the concentration of B that causes half-saturation
4) Explain mathematically whether a lower or higher dissociation constant would lead to stronger binding
5) Draw Y against log[B]
1) Y = [B] / {Kd + [B]}
2) Hyperbola with asymptote at Y = 1
3) When [B] = Kd = 1/Ke
4) A lower dissociation constant since Y is greater at all concentrations of B
5) sigmoidal curve
Analyse the binding of oxygen to the myoglobin using: Mb + O2 <—> MbO2, Ke, Kd, and Y (fraction of myoglobin saturation). And give the fractional saturation when Kd = [O2]
Plot a graph of fractional myoglobin saturation against Partial Pressure of Oxygen (essentially the concentration but for gases)
1) Y[Mb] = [O2] / Kd + [O2], with Kd = [O2] at half saturation, Y = 0.5
2) hyperbola as usual
What does Kd represent
1) Kd represents the binding affinity of a specific site
2) A higher value of Kd represents more dissociated ions, so lower binding affinity
3) A lower value of Kd represents more undissociated molecules so higher binding affinity
1) How does fractional saturation equation change when there are multiple, q, identical binding sites that do not interact with each other (have the same Kd/binding affinities)
2) draw the hyperbola of Y against [B] and log[B] respectively
1) The equation becomes q[B] / {Kd + [B]}
2) This gives a similar hyperbola with higher values of Y, but a sigmoidal curve for log[B]
Draw diagrams for when there are multiple binding sites, q, that are not identical and do not interact (different Kd and binding affinities)
1) we get a superposition of binding curves with almost 2 sigmoid curves ajdacent to each other
Explain Positive and Negative Cooperativity between different binding sites that interact
1) Positive cooperativity is an allosteric process which occurs when the binding of one ligand increases the affinity of the other binding site to the other ligand (Decreases Kd2, increases affinity and thus increases Y)
2) Negative cooperativity is an allosteric process which occurs when the binding of one ligand decreases the affinity of the other binding site to the other ligand
How does cooperativity and allostery affect the free energy of the products of the 2 step reaction.
Explain the differences between direct and indirect cooperativity
Positive cooperativity lowers the free energy of the product, and therefore favours indirect or direct positive cooperative processes between two ligands which lead to this lower energy
Direct cooperativity usually involves a ligand binding, giving the intermediate a higher affinity to the second ligand
Indirect cooperativity involves a ligand binding, stimulating a separate molecule to stimulate the increase in affinity for the second ligand.
How can positive or negative cooperativity be determined experimentally of a A+B <—> C and C+D <—> E. Given the ligands for this reaction are B and D.
The hill equation can be used to determine this. Y = [L]^n / Kd + [L]^n where n is the minimum number of ligand binding sites. By plotting the Y against [L], if n is larger than 1, then we assume that ligand cooperativity has lead to the increase in affinity of a receptor to the ligand, and has thus lead to higher fractional saturation, Y (still less than or equal to 1)
