Since introns are largely genetic junk, they do not have to be removed precisely from

How Cells Read the Genome: From DNA to Protein

Since introns are largely genetic junk, they do not have to be removed precisely from the primary transcript during RNA splicing.

Wobble pairing occurs between the first position in the codon and the third position in the anticodon.

During protein synthesis, the thermodynamics of base-pairing between tRNAs and mRNAs sets the upper limit for the accuracy with which protein molecules are made.

Protein enzymes are thought to greatly outnumber ribozymes in modern cells because they can catalyze a much greater variety of reactions and all of them have faster rates than any ribozyme.

In which direction along the template must the RNA polymerase in Figure Q61 be moving to have generated the supercoiled structures that are shown? Would you expect supercoils to be generated if the RNA polymerase were free to rotate about the axis of the DNA as it progressed along the template?

You have attached an RNA polymerase molecule to a glass slide and have allowed it to initiate transcription on a template DNA that is tethered to a magnetic bead as shown in Figure Q62. If the DNA with its attached magnetic bead moves relative to the RNA polymerase as indicated in the figure, in which direction will the bead rotate?

The human -tropomyosin gene is alternatively spliced to produce different forms of -tropomyosin mRNA in different cell types (Figure Q63). 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).

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 Q64). 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 Q64). 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?

Which of the following mutational changes would you predict to be the most deleterious to gene function? Explain your answers. 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. Substitution of one nucleotide for another in the middle of the coding sequence.

Prokaryotes and eukaryotes both protect against the dangers of translating broken mRNAs. What dangers do partial mRNAs pose for the cell?

Both hsp60-like and hsp70 molecular chaperones share an affinity for exposed hydrophobic patches on proteins, using them as indicators of incomplete folding. Why do you suppose hydrophobic patches serve as critical signals for the folding status of a protein?

Most proteins require molecular chaperones to assist in their correct folding. How do you suppose the chaperones themselves manage to fold correctly?

What is so special about RNA that it is hypothesized to be an evolutionary precursor to DNA and protein? What is it about DNA that makes it a better material than RNA for storage of genetic information?

If an RNA molecule could form a hairpin with a symmetric internal loop, as shown in Figure Q65, could the complement of this RNA form a similar structure? If so, would there be any regions of the two structures that are identical? Which ones?

Imagine a warm pond on the primordial Earth. Chance processes have just assembled a single copy of an RNA molecule with a catalytic site that can carry out RNA replication. This RNA molecule folds into a structure that is capable of linking nucleotides according to instructions in an RNA template. Given an adequate supply of nucleotides, will this single RNA molecule be able to use itself as a template to catalyze its own replication? Why or why not?