Chapter 14

11.  Because bacteria have small genomes (roughly 3-Mb pairs) and essentially no repeating sequences, the whole-genome shotgun approach would be used.

13.  A scaffold is also called a supercontig. A contig is a sequence of overlapping reads assembled into a unit, and a scaffold is a collection of joined-together contigs.

18.  Yes. The operator is the location at which repressor functionally binds through interactions between the DNA sequence and the repressor protein.

23.  You can determine whether the cDNA clone is a monster or not by the alignment of the cDNA sequence against the genomic sequence. (Computer programs for doing such alignments are available.) Is the sequence derived from two different sites? Does the cDNA map within one (gene-size) region in the genome or to two different regions? Introns may complicate the matter.

27. 

  1. Because the triplet code is redundant, changes in the DNA nucleotide sequence (especially at those nucleotides encoding the third position of a codon) can occur without changing its encoded protein.

  2. Protein sequences can be expected to evolve and diverge more slowly than do the genes that encode them.

33.  The correct assembly of large and nearly identical regions is problematic with either method of genomic sequencing. However, the whole-genome shotgun method is less effective at finding these regions than the clone-based method. This method also has the added advantage of easy access to the suspect clone(s) for further analysis.

36.  15 percent are essential gene functions (such as enzymes required for DNA replication or protein synthesis).

25 percent are auxotrophs (enzymes required for the synthesis of amino acids or the metabolism of sugars, etc.).

60 percent are redundant or pathways not tested (genes for histones, tubulin, ribosomal RNAs, etc., are present in multiple copies; the yeast may require many genes under only unique or special situations or in other ways that are not necessary for life in the laboratory).