to a glass slide and have allowed it to initiate transcription on a template DNA that is tethered to a magnetic bead as 6–4 During protein synthesis, the thermodynamics of shown in Figure Q6–2. If the DNA with its attached mag-base-pairing between tRNAs and mRNAs sets the upper netic bead moves relative to the RNA polymerase as indilimit for the accuracy with which protein molecules are cated in the figure, in which direction will the bead rotate?
made.
6–5 Protein enzymes are thought to greatly outnum-Figure Q6–2 System for measuring the rotation of DNA ber ribozymes in modern cells because they can catalyze magnet a much greater variety of reactions and all of them have (Problem 6–7). The magnet faster rates than any ribozyme. holds the bead upright (but doesn’t interfere with its Discuss the following problems. bead rotation), and the attached tiny fluorescent beads allow 6–6 In which direction along the template must the the direction of motion to DNA be visualized under the
RNA polymerase in Figure Q6–1 be moving to have gen- microscope. RNA polymerase is erated the supercoiled structures that are shown? Would you expect supercoils to be generated if the RNA poly-RNA the glass slide.
merase were free to rotate about the axis of the DNA as it progressed along the template? glass slide
Figure Q6–3 Alternatively spliced mRNAs from the human α-tropomyosin gene (Problem 6–8). (A) Exons in the human α-tropomyosin gene. The locations and relative sizes of exons are shown by the blue and red rectangles, with alternative exons in red.
(B) Splicing patterns for four α-tropomyosin mRNAs. Splicing is indicated by lines connecting the exons that are included in the mRNA.
6–8 The human α-tropomyosin gene is alternatively spliced to produce different forms of α-tropomyosin mRNA in different cell types (Figure Q6–3). For all forms of the mRNA, the protein sequences encoded by exon 1 are the same, as are the protein sequences encoded by exon 10. Exons 2 and 3 are alternative exons used in different mRNAs, as are exons 7 and 8. Which of the following statements about exons 2 and 3 is the most accurate? Is that statement also the most accurate one for exons 7 and 8? Explain your answers.
A. Exons 2 and 3 must have the same number of nucleotides.
b.
Exons 2 and 3 must each contain an integral number of codons (that is, the number of nucleotides divided by 3 must be an integer).
C.
Exons 2 and 3 must each contain a number of nucleotides that when divided by 3 leaves the same remainder (that is, 0, 1, or 2).
6–9 After treating cells with a chemical mutagen, you isolate two mutants. One carries alanine and the other carries methionine at a site in the protein that normally contains valine (Figure Q6–4). After treating these two mutants again with the mutagen, you isolate mutants from each that now carry threonine at the site of the original valine (Figure Q6–4). Assuming that all mutations involve single-nucleotide changes, deduce the codons that are used for valine, methionine, threonine, and alanine at the affected site. Would you expect to be able to isolate valineto-threonine mutants in one step?
6–10 Which of the following mutational changes would you predict to be the most deleterious to gene function? Explain your answers.
frst Ala second Figure Q6–4 Two rounds of treatment treatment mutagenesis and the altered amino acids at a single position in Val Thr a protein (Problem 6–9).
1.
Insertion of a single nucleotide near the end of the coding sequence.
2.
Removal of a single nucleotide near the beginning of the coding sequence.
3.
Deletion of three consecutive nucleotides in the middle of the coding sequence.
4.