Chapter 21: Problem 7
Intron frequency varies considerably among eukaryotes. Provide a general comparison of intron frequencies in yeast and humans. What about intron size?
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Chapter 21: Problem 7
Intron frequency varies considerably among eukaryotes. Provide a general comparison of intron frequencies in yeast and humans. What about intron size?
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Archaea (formerly known as archaebacteria) is one of the three major divisions of living organisms; the other two are eubacteria and eukaryotes. Nanoarchaeum equitans is in the Archaea domain and has one of the smallest genomes known, about 0.5 Mb. How can an organism complete its life cycle with so little genetic material?
Comparisons between human and chimpanzee genomes indicate that a gene that may function as a wild type or normal gene in one primate may function as a disease-causing gene in another (The Chimpanzee Sequence and Analysis Consortium, Nature, \(437: 69-87,2005\) ). For instance, the \(P P A R G\) locus (regulator of adipocyte differentiation) is associated with type 2 diabetes in humans but functions as a wild-type gene in chimps. What factors might cause this apparent contradiction? Would you consider such apparent contradictions to be rare or common? What impact might such findings have on the use of comparative genomics to identify and design therapies for disease-causing genes in humans?
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: (a) How do we know which contigs are part of the same chromosome? (b) How do we know if a genomic DNA sequence contains a protein-coding gene? (c) What evidence supports the concept that humans share substantial sequence similarities and gene functional similarities with model organisms? (d) 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? (e) What evidence indicates that gene families result from gene duplication events? (f) How have microarrays demonstrated that, although all cells of an organism have the same genome, some genes are expressed in almost all cells, whereas other genes show celland tissue-specific expression?
Annotations of the human genome have shown that genes are not randomly distributed, but form clusters with gene "deserts" in between. These "deserts" correspond to the dark bands on G-banded chromosomes. Comparisons between the human transcriptome map and the genome sequence show that highly expressed genes are also clustered together. In terms of genome organization, how is this an advantage?
Review the Chapter Concepts list on page \(556 .\) All of these pertain to how genomics, bioinformatics, and proteomics approaches have changed how scientists study genes and proteins. Write a short essay that explains how recombinant DNA techniques were used to identify and study genes compared to how modern genomic techniques have revolutionized the cloning and analysis of genes.
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