8–11 You have isolated the proteins from two adjacent spots after two-dimensional polyacrylamide-gel electrophoresis and digested them with trypsin. When the masses of the peptides were measured by MALDI-TOF mass spectrometry, the peptides from the two proteins were found to be identical except for one (Figure Q8–2). For this peptide, the mass-to-charge (m/z) values differed by 80, a value that does not correspond to a difference in amino acid sequence. (For example, glutamic acid instead of valine at one position would give an m/z difference of around 30.) Can you suggest a possible difference between the two peptides that might account for the observed m/z difference?
Masses of peptides measured by MALDI-TOF mass spectrometry (Problem 8–11).  Only the numbered peaks differ between the two protein samples.
8–12 You want to amplify the DNA between the two stretches of sequence shown in Figure Q8–3. Of the listed primers, choose the pair that will allow you to amplify the DNA by PCR.
8–13 In the very first round of PCR using genomic DNA, the DNA primers prime synthesis that terminates only when the cycle ends (or when a random end of DNA is encountered). Yet, by the end of 20 to 30 cycles—a typical amplification—the only visible product is defined precisely by the ends of the DNA primers. In what cycle is a double-stranded fragment of the correct size first generated?
DNA to be amplifed
Figure Q8–3 DNA to be amplified and potential PCR primers (Problem 8–12).
8–14 Explain the difference between a gain-of-function mutation and a dominant-negative mutation. Why are both these types of mutation usually dominant?
8–15 Discuss the following statement: “We would have no idea today of the importance of insulin as a regulatory hormone if its absence were not associated with the human disease diabetes. It is the dramatic consequences of its absence that focused early efforts on the identification of insulin and the study of its normal role in physiology.” 8–16 You have just gotten back the results from an RNA-seq analysis of mRNAs from liver. You had anticipated counting the number of reads of each mRNA to determine the relative abundance of different mRNAs. But you are puzzled because many of the mRNAs have given you results like those shown in Figure Q8–4. How is it that different parts of an mRNA can be represented at different levels?
8–17 Examine the network motifs in Figure Q8–5. Decide which ones are negative feedback loops and which are positive. Explain your reasoning.
8–18 Imagine that a random perturbation positions a bistable system precisely at the boundary between two stable states (at the orange dot in Figure Q8–6). How would the system respond?
Figure Q8–4 RNA-seq reads for a liver mRNA (Problem 8–16). The exon structure of the mRNA is indicated, with protein-coding segments indicated in light blue and untranslated regions in dark blue. The numbers of sequencing reads are indicated by the heights of the vertical lines above the mRNA.
Figure Q8–5 Network motifs composed of transcription activators and repressors (Problem 8–17).