a rapid negative feedback loop dampens the response to input signals; a delayed negative feedback loop creates a biochemical oscillator; positive feedback yields a models to accurately describe the systems that generate transient signal pulses or respond only to sustained inputs. enormous complexity of cellular The dynamic behavior of these network motifs can be dissected in detail with deter-networks and to predict undiscovered ministic and stochastic mathematical modeling. components and mechanisms?
Which statements are true? explain why or why not. Discuss the following problems.
8–1 Because a monoclonal antibody recognizes a spe-8–7 A common step in the isolation of cells from a cific antigenic site (epitope), it binds only to the specific sample of animal tissue is to treat the tissue with trypsin, protein against which it was made. collagenase, and EDTA. Why is such a treatment nece ssary, and what does each component accomplish? And 8–2 Given the inexorable march of technology, it why does this treatment not kill the cells?
seems inevitable that the sensitivity of detection of molecules will ultimately be pushed beyond the yoctomole 8–8 Tropomyosin, at 93 kd, sediments at 2.6S, whereas level (10–24 mole). the 65-kd protein, hemoglobin, sediments at 4.3S. (The sedimentation coefficient S is a linear measure of the rate 8–3 If each cycle of PCR doubles the amount of DNA of sedimentation.) These two proteins are drawn to scale synthesized in the previous cycle, then 10 cycles will give a in Figure Q8–1. How is it that the bigger protein sediments 103-fold amplification, 20 cycles will give a 106-fold amplimore slowly than the smaller one? Can you think of an fication, and 30 cycles will give a 109-fold amplification.
analogy from everyday experience that might help you 8–4 To judge the biological importance of an interac-with this problem? tion between protein A and protein B, we need to know quantitative details about their concentrations, affinities, and kinetic behaviors.
8–5 The rate of change in the concentration of any molecular species X is given by the balance between its rate of appearance and its rate of disappearance.
8–6 After a sudden increase in transcription, a protein with a slow rate of degradation will reach a new steady state level more quickly than a protein with a rapid rate of degradation.
tropomyosinhemoglobinFigure Q8–1 Scale models of tropomyosin and hemoglobin (Problem 8–8).
8–9 Hybridoma technology allows one to generate monoclonal antibodies to virtually any protein. Why is it, then, that genetically tagging proteins with epitopes is such a commonly used technique, especially since an epitope tag has the potential to interfere with the function of the protein?
8–10 How many copies of a protein need to be present in a cell in order for it to be visible as a band on an SDS gel? Assume that you can load 100 μg of cell extract onto a gel and that you can detect 10 ng in a single band by silver staining the gel. The concentration of protein in cells is about 200 mg/mL, and a typical mammalian cell has a volume of about 1000 μm3 and a typical bacterium a volume of about 1 μm3. Given these parameters, calculate the number of copies of a 120-kd protein that would need to be present in a mammalian cell and in a bacterium in order to give a detectable band on a gel. You might try an order-of-magnitude guess before you make the calculations.