Question 1 A polypeptide ligand binds its receptor protein with 1:...

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Question 1
A polypeptide ligand binds its receptor protein with 1:1 stoichiometry. The ligand and receptor are mixed in a closed system, and binding is allowed to equilibrate.
If the free concentration of ligand is equal to the Ko of binding, what fraction of the receptor molecules are bound at steady state?

Question 2
Rank the following forms of cell-cell communication from most localized to most systemic.

Question 3
1. Drow a sketch of the dose response curve for hGH-stimulated proliferation (with [hGH] on a log scale). Label the values of [hGH] corresponding to the EC50 and the self-inhibitory IC50.
2. Explain why formation of the dimeric complex is inhibited at high [hGH].
3. Why don't hGH mutants with lower site 1 off-rate show lower EC50 values?

Question 4
Which of the following is NOT true of the Thiele Modulus?
Select one:
a. It compares the time scale of reaction to the time scale of diffusion.
b. All of these are true of the Thiele Modulus.
c. lt compares the rate of diffusion to the rate of convection.
d. It appears in both chemical engineering and tissue patterning problems.
e. It compares the length scale of a tissue to the dynamic length scale of the morphogen.

Question 5
Which of the following is NOT true of models of transcription factors (TFs) binding to DNA as discussed in class?
Select one:
a. All of the other answers are true of TF/DNA binding models discussed in class.
b. The total number of binding sites is conserved.
c. In the simple case of one TF and one binding site, transcription, as a function of TF concentration, linearly rises at low concentrations, and flattens out at high concentrations.
d. They are conceptually similar to Michaelis-Menten enzyme kinetics.
e. The probability of transcription is related to a term describing the bound state that results in transcription, divided by the sum of terms for all possible states.

Question 6
Which of the following are valid engineering principles discussed in relation to biology? You can choose more than one answer. Each right answer chosen gives partial credit, and each wrong answer chosen gives a partial penalty. Therefore, you must choose all of the right answers, and avoid all of the wrong answers, to receive full credit.
Select one or more:
a. Feedback loops must be finely-tuned to result in oscillator behavior.
b. Anticipation of future events is a design feature of evolution.
c. The Thiele Modulus must be tuned to be roughly 3-5.
d. Systems are always designed such that multiple performance objectives can be easily decoupled, and thus do not compete with each other.
e. The difference in morphogen concentration between two cells that must be different from one another must be less or equal to the error with which nuclei read morphogen concentration.
f. Each layer of regulation comes with a price. That is, trade-offs are a fact of life.
g. Regulation should be designed to anticipate even rare disturbances, just in case they are encountered.
h. Layers of regulation are necessary to correct for disturbances encountered in the wild.

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