15. Genomes and Genomics

Proteomics

Multiple Choice
SDS-PAGE is a method used to separate proteins by which of the following characteristics?
Multiple Choice
Which of the following methods would be best to identify an amino acid sequence of a protein?
Open Question
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?
Open Question
How do high-throughput techniques such as computer-automated, next-generation sequencing, and mass spectrometry facilitate research in genomics and proteomics? Explain.
Open Question
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?
Open Question
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?
Open Question
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?
Open Question
The two-hybrid method facilitates the discovery of protein–protein interactions. How does this technique work? Can you think of reasons for obtaining a false-positive result, that is, where the proteins encoded by two clones interact in the two-hybrid system but do not interact in the organism in which they naturally occur? Can you think of reasons you might obtain a false-negative result, in which the two proteins interact in vivo but fail to interact in the two-hybrid system?
Open Question
Annotation of the human genome sequence reveals a discrepancy between the number of protein-coding genes and the number of predicted proteins actually expressed by the genome. Proteomic analysis indicates that human cells are capable of synthesizing more than 100,000 different proteins and perhaps three times this number. What is the discrepancy, and how can it be reconciled?
Open Question
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).Use the 'Query' tab and select the 'Gene family' dropdown menu to do a search on the distribution of proteins encoded by a pathway of interest to you. Search in fetal tissues, adult tissues, or both.
Open Question
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 fetal tissues were analyzed?
Open Question
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?
Open Question
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?