In this chapter, we focused on the analysis of genomes, transcriptomes, and proteomes and considered important applications and findings from these endeavors. At the same time, we found many opportunities to consider the methods and reasoning by which much of this information was acquired. From the explanations given in the chapter, what answers would you propose to the following fundamental questions?

How can proteomics identify differences between the number of protein-coding genes predicted for a genome and the number of proteins expressed by a genome?

In Section 21.10 we briefly discussed the Human Proteome Map (HPM). An interactive Web site for the HPM is available at http://www.humanproteomemap.org. Visit this site, and then answer the questions in parts (a) and (b) and complete part (c).How many proteins were identified in this project?

Genomic sequencing has opened the door to numerous studies that help us understand the evolutionary forces shaping the genetic makeup of organisms. Using databases containing the sequences of 25 genomes, scientists examined the relationship between GC content and global amino acid composition [Kreil, D. P., and Ouzounis, C. A. (2001) Nucl. Acids Res. 29:1608–1615]. They found that it is possible to identify thermophilic species on the basis of their amino acid composition alone, which suggests that evolution in a hot environment selects for a certain whole organism amino acid composition. In what way might evolution in extreme environments influence genome and amino acid composition? How might evolution in extreme environments influence the interpretation of genome sequence data?

Based on the tree of life in Figure 16.12, would you expect human proteins to be more similar to fungal proteins or to plant proteins? Would you expect plant proteins to be more similar to fungal proteins or to human proteins?

The CBF genes of Arabidopsis are induced by exposure of the plants to low temperature.Can you design a method that would reveal these changes in gene expression in a way that a farmer could recognize them by observing plants growing in the field?

The CBF genes of Arabidopsis are induced by exposure of the plants to low temperature.How would you examine the temporal and spatial patterns of expression after induction by low temperature?