protein function pt.1

Question 1

what is Kd

Answer 1

it is the ligand concentration at 1/2 occupancy or .5 Y

Question 2

what does the occupancy rate Y depend on?

Answer 2

it depends on the concentration of the ligand

Question 3

hwo does the occupancy rate tell us about the affinity?

Answer 3

the Kd value at 0.5 occupancy tells you the affinity

a low kd tells you that the affinity is high

a high kd tells you that the affinity is low

Question 4

what is the proble with getting O2 into our bloodstream?

Answer 4

it is nonpolar and insoluble so it cannot be transported through membranes

Question 5

why can we not bind O2 to a free transition metla like iron to transport it?

Answer 5

when Fe2+ binds with O2, it will oxidize into Fe3+ irreversibly and covalently bind to the O2, rendering it unusable for transfer

Question 6

how do proteins aid in the problem with oxygen?

Answer 6

proteins can be used to transport o2 molecules through the incorporation of a heme group

Question 7

what is the purpose of a heme group

Answer 7

it is a heterocyclic ring protoporphryin structure that coordinates nitrogen atoms to the Fe2+ in a planar fashion in 4 of the 6 d orbitals

Question 8

how does myoglobin bind reversibly with O2?

Answer 8

the heme group coordinately binds with the d orbitals in the Fe2+ atom, which prevents it from oxidizing to Fe3+.

The proximal histidine binds to the 5th d orbital, further preventinf oxidation and also aiding in the geometry restriction of the Fe atom.

The histidines (proximal and distal) play roles in restricting the Fe2+ geometry so that the oxygen cannot form constructtive oribital overlap.
this prevents it from forming covalent bonds, and it instead allows the O2 to bind reversibly

Question 9

what are globins

Answer 9

they are a protein family that is comprised of 8 alpha helical segments that fold in aparticular way to facilitate the transport of O2

Question 10

why is carbon monoxide poisoning bad?

Answer 10

CO can bind better to the Fe2+ group than the O2 group can. This means that it can form more constructive orbital overlaps and form irreversible covalent bonds that prevent O2 molecules from binding

Question 11

how do you overcome carbon monoxide posioning

Answer 11

outcompeting the CO molecules with more O2

Question 12

why can myoglobin not transport o2 to tissues?

Answer 12

in the lungs, the Y=0.98 and PO2 is 13 kPa while in tissues the Y=0.95 and the PO2 is 4 kPa.

the occupancy is relatively the same at these two points, demonstrating that myoglobin holds onto the O2 molecules tightly even when it is supposed to release it

this makes it a better storage molecule