Page 69 - Genetics_From_Genes_to_Genomes_6th_FULL_Part3

Problems 363

b. Why would you want to define the consensus se- to the proper window.) At the top of this window are
quence? How would you decide whether the four se- control buttons that allow you to move your view to the
quences were worth comparing to define a consensus? left or right, zoom in (even to the level of the nucleo-
c. How could you use this general strategy for defining tide sequence), zoom out, or (on the second row) jump
a consensus sequence to determine which amino to a different chromosomal position. Below these but-
acids of a protein are most crucial for its function? tons is a diagram, called an idiogram, of the chromo-
20. In the human immune system, so-called B cells can some you are viewing, with a region in red indicating
the particular region of the chromosome you are look-
make more than a billion different types of antibody ing at. (You can also click on the idiogram to move
molecules that protect us from infection. However, our around.)
genomes have only three genes that encode the polypep-
tides found in antibodies. What experiments could you a. How many exons are in the CFTR gene?
perform to determine what kind of combinatorial events b. Is the CFTR gene located on the short arm (the
occur at the DNA level (V-D-J joining) and RNA level p arm) or the long arm (the q arm) of human
(alternative splicing) for any of these genes? chromosome 7?
21. Chimpanzees have a set of hemoglobin genes very sim- c. In which direction is the CFTR gene transcribed: to-
ilar to the set in humans that was shown in Fig. 10.11. ward the centromere, or away from the centromere?
For example, the genomes of both species have α1, Now zoom out the view by 10×.
α2, β, Gγ, Aγ, δ, ε, and ζ genes.
a. Of the human and chimpanzee hemoglobin genes, d. What are the names of the genes that flank CFTR
on either side? Are these genes transcribed from
which would be considered homologous? Which the same strand of chromosome 7 as CFTR, or
paralogous? Which orthologous? from the other strand?
b. When comparing genomes, geneticists would usu- Now zoom out 100× until the entirety of chromosome
ally like to know which genes are the most likely to 7 is visible.
perform similar if not identical functions in differ-
ent species. This determination can be somewhat e. What is the approximate size of chromosome 7 in
complicated in the case of gene families. Would Mb?
paralogous genes or orthologous genes be more f. What is the approximate location of the centromere
likely to be functionally equivalent? Explain. on human chromosome 7?
c. Which gene would have the greatest degree of nu- g. What is the significance of the RefSeq genes’ ap-
cleotide similarity to the human β gene: the chim- pearing to pile up when you are viewing the whole
panzee β gene, or the human γ gene? Explain. chromosome?
d. Rationalize the pattern of hemoglobin genes in the 24. On your computer’s browser, view the page
two species with the existence of duplication and accessed by the URL: http://blast.ncbi.nlm.nih.gov/
divergence events among the hemoglobin genes Blast.cgi
depicted in Fig. 10.12. The heading “Basic BLAST” lists various pro-
22. Complete genome sequences indicate that the human grams that allow you to search for DNA or protein se-
genome has roughly 27,000 genes, while the worm quences related to any DNA or protein sequence
(nematode) genome has about 22,000 genes. Explain query. For this problem, choose “nucleotide blast.”
how the human genome with only about 20% more On the window that comes up, make sure that the da-
genes can encode a creature enormously more com- tabase “Human genomic + transcript” is selected (so
plex than the worm. that you will search through the RefSeq for humans
and not any other species). Now, in the large box un-
der “Enter Query Sequence” you should type in the
nucleotide sequence from Fig. 9.7f. Then hit the blue
Section 10.3 “BLAST” button at the bottom and wait for the re-
23. On your computer’s browser, view the page accessed by sponse from the NCBI computer, which may take up
the URL: http://genome.ucsc.edu/cgi-bin/hgGateway to a few minutes.
In the Search Term box at the top, type CFTR (for The response will come in several sections; you
the CFTR gene responsible for cystic fibrosis), then hit should migrate to the Descriptions. The “E value”
“GO.” You will be directed to a window showing the column in the list is a statistical measure of the prob-
organization of the CFTR gene on human chromosome ability that a given sequence is related to your query
7. (If a list appears instead of a picture, click on the by chance in the RefSeq database you are searching.
first link at the top of the list, and you will be directed The lower the E value (the closer to zero), the more