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52 Cards in this Set

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What are ligands?
molecules which attach non-covalently to a protein binding site.
What is the ligand for hemoglobin and myoglobin?
Oxygen
In what way does oxygen bind to myoglobin?
hyperbolic
What are the typical curves for protein-ligand interactions?
hyperbolic
How can the hyperbolic curves be derived?
The equilibrium constant for the dissociation reaction.
What os the equation for hyperbolic bunding cureves?
fractional binding=Y=[Mb * O2] = {[mbtot]*[O2]}/Kd+[O2]
What is Kd?
Kd is the quantititative expression of the affinity of the binding site for the oxygen and is where the oxygen concentration that gives half-maximal binding.
What is the equation for Kd?
Y = [O2]/ Kd + [O2] = Kd / 2 Kd = .5
Why is oxygen binding to myoglobin reversible?
heme oxidation invloves a sandwhich intermediate.
What does the myoglobin binding site contain?
heme as a prosthetic group.
What does myoglobin do?
transport O2 from the blood to the cells.
What does the heme bind to?
4 nitrogens, a histidine (proximal histidine), and a O2 with histidine attached (proximal histidine).
Why does myoglobin behave fidderentyl than free heme?
It is the distal histidine.
Myoglobines tertiarry sttructure consists of?
75% alpha helix
How does the simulating ligand binding site interact with an organic moleculer system?
It forms a 'Picket Fence" heme.
How can you get oxygen binding without inactinvating the heme?
By forming a "sandwhich" intermediate.
Oxygen cannot oxidize the heme because?
In free solution oxygen binds to the heme, but then the oxygn oxidizes the heme and inacitvates it by preventing it from binding with oxygen and allowing it to bind with water.
Does oxygen bind reversibly?
Yes
What does a picket heme fence do?
By mimicing the effects of a polypeptide chain of myoglobin and oxygen, we use bug bulky groups to show that the oxygen is not free, but buried, as a result it binds reversibly.
What is a competitive inhibitor ro myoglobin?
Carbon monoxide
How Much tighter does Co bing to oxygen?
20,000x
What id the Kd for CO/ Kd?
1/20,000
Why is it a fraction?
Kd measures dissaciation. we want affinity so we flip the numbers.
Why is this a problem?
CO is synthesized in small amounts in metabolism which couls interfere with myoglobin in vivo.
How is this overcome?
CO binding to myoglobin is only 25x stronger than oxygen and the concentration of oxygen is hihg enough to outcompete the tissue CO.
What is hemoglobin?
A regulatory protein.
What is the structure of hemoglobin?
A tetramer?
What at the subunits of hemoglobin?
2 alpha subunits, and 2 beta subunits
What molecule does hemoglobin subunits resemble?
Myoglobin
How does oxygen bind to hemoglobin?
Sigmodial
What is the physiological significance of the sigmodial curve?
a sigmodial curve reflects a cooperativity in ligand binding.
How can coopertivity hills be measured?
a hill plot
How can cooperativity be measured ina hill plot?
We take the log of both sides. log {Y - (1-Y)} = n log [O2] - log Kd.
What is n in the hill plot formula?
n is the straight line of slope n where n if the hill coefficeient.
How does oxygen binding aafect the structure hemoglobin?
beOXYHb to OXYhb. alters the tertiary and quaternary structures.
How does oxygen binding to the hemoglobin affect the iron of the heme?
iron lies below the plane of the heme in deoxyhemoglobin. oxygen binding pulls the iron into the heme plate which pulls on the histidine attached to the iron. moving the histidine produces a teriary strucutre change in the subunit. changing the tertiary strucutre changes the quaternary strucutre since the subunts shift relative to each other.
How does the change in structure reailt in the cooperitivity in oxygen binding?
subunit interfaces have hydrophobic amino acids plus slat bridges. oxygen binding requires some of these slat bridges which require energy, making the first oxygen difficult to bind. binding subsequent oxygen is easier.
When does the shift in the strucutre occurr?
When the oxygen binds to each alpha and beta pair allows the quaternary strucuture to change from deoxy to oxy.
What other molecules affest hemoglobin bninding to oxygen?
protein, carbon dioxide, and 2,3-biphosphoglycerate.
Do protein, carbon dioxide, and 2,3-biphosphoglycerate. bind ot the heme?
No.
What are protein, carbon dioxide, and 2,3-biphosphoglycerate termed.
allosteric regulators
What are formed in tissue metabolism?
protons
What do protons do?
stabalize the deoxy form of hemoglobin. bohr effect.
What does the stabalization of the deoxy form of hemoglobin do?
promotes oxygen release in actively metablozing tissues, lowers the pH environment which promote the formation of additional salt bridges between subunits which increses the energy cost of binding the first oxygen.
What does 2,3-biphosphoglycerate do for the whole organism?
modulates oxygen affinity
What does 2,3-biphosphoglycerate do?
BPG stabalizes the deoxyhemoglobin, binds in the cavity between subunits which forms additional salt bridges between subunts that stabalize the deoxy conoformation and makes oxygen binding more difficult. E.G, accilimation to altitude change, fetal hemoglobin.
What is the basic idea behind enzyme catalysis?
enzymes increase the rate of reaction by deacreasing the energy of activation.
How do we study the active sites of aminoa cise and their chemical porperties that are repsonsicle ofr that?
kinectic studies, x-ray cystallography of es or el complexes, site directed mutagenesis.
What kind of kinetic studies exists?
substrate specifity, pH dependence, inhibotor studies.
How does substrate specifity work?
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
How does inhibotor studies work?
side chains-specific reagents: ligand enters the active site and affects the side chain specifically.
What does x-ray cystallography of es or el complexes reveal?
the contacts between substrate and active site amino acids