9-18 Explain how ESTs are identified and how they aid in finding the genes within an organism’s genome.
Answers
9-1 C, D, E. A is false because it is sexual reproduction that requires the production of germ-line cells. B is false because mutations are carried in the genetic material and the only genetic material passed along to the offspring of a sexually-reproducing organism comes from a germ-line cell (not a somatic cell).
9-2 It is not likely that child would have the disease, because it is unlikely that the mutation is carried in the germ line. Probably the mutation occurred in a cell that gave rise to
somatic cells and not germ cells. Only mutations in germ cells are passed onto progeny.
9-3 Choice (d) is the correct answer. Choices (a), (b), and (e) are probably false. Choice (c) is true but cannot explain the similar mutation rate.
9-4 (a) False. Evolution can work only by tinkering with the tools and materials on hand, not by starting from scratch to make completely new genes or pathways. New functions arise from the ancestral functions by a process of gradual mutational change, and thus may not represent the best possible solution to a problem.
(b) False. Many duplications are subsequently lost or become pseudogenes, and only a few evolve into new genes.
(c) True. Pseudogenes look very similar to normal genes but cannot produce a full-length protein due to one or more disabling mutations.
(d) False. A large proportion of the genes in vertebrates (and many other species) are members of multigene families.
(e) False. By some estimates, 20% of the genomic DNA in some bacterial species arose by horizontal gene transfer.
9-5 The simplest way to evolve the new gene is by duplication and divergence. If the gene is duplicated, then the cell or lineage can maintain one functional, intact old copy of the original gene and can thus tolerate the disabling mutations in the other copy. The second copy can first be modified by the X or Y mutation that impairs its function; second, at some later time, the gene with the single mutation can acquire the additional mutation to yield the doubly mutant X+Y gene with the new or improved function.
9-6 Most variation between individual humans is in the form of single nucleotide
polymorphisms. Exon shuffling may arise by recombination within introns and can create proteins with novel combinations of domains. Scientists and government regulators must be very careful when introducing herbicide-resistant transgenic corn plants into the environment, because if resistant weeds arise from horizontal gene transfer then the herbicides could become useless. Families of related genes can arise from a single ancestral copy by gene duplication and subsequent divergence.
9-7 See Figure A9-7. The products of panel (C) will be segregated to progeny cells reliably.
In contrast, one product in panel (D) will have two centromeres and the other will lack a centromere. The chromosome without a centromere will be rapidly lost as cells divide.
The chromosome containing two centromeres probably will be broken during mitosis (see Chapter 19), and subsequently lost or severely damaged.
Figure A9-7
9-8 Choice (d) is the correct answer. Exon shuffling is facilitated by long introns (thus choice (a) is incorrect) and by short exons that each code for one protein domain (thus choice (c) is incorrect). Since exon shuffling can occur via recombination between introns, introns with regions of similarity to one another will facilitate shuffling. A haploid genome will probably be less prone to exon shuffling than a diploid genome (thus choice (b) is incorrect) because having two copies of each gene allows an organism to keep one copy of the gene as a backup while it shuffles the other copy. Exon shuffling is possible only because many proteins are modular, composed of short, folded domains that have discrete functional properties (thus choice (e) is incorrect).
9-9 On galactose medium, the original gal1– yeast cells cannot grow, nor can cells that received plasmids containing most human cDNA sequences. However, yeast cells that received a plasmid with the human galactokinase gene will probably be able to grow on galactose medium and produce many progeny. This kind of “selection” procedure is very powerful, because even if only 1 in 100,000 cells has the ability to grow under particular conditions it will be easy to find it. The other 99,999 cells will die in the petri plate and will therefore be invisible to the investigator. Indeed, scientists have found that the human galactokinase gene can function perfectly well in yeast and thus can “rescue” the defect of the gal1– mutant. It was initially astonishing that genes from humans can function properly in yeast, but this phenomenon has now been observed for many genes.
9-10 A. Selectively neutral, detrimental, beneficial. Most nucleotide changes in the genome, or mutations, will have little to no effect on the fitness of the individual because many changes are not located in regions that encode a protein or regulate expression of a gene. Even changes within a coding region may not change the amino acid encoded or may cause a conservative amino acid change, for example from one small nonpolar amino acid to another. Most changes that have a
functional consequence will interfere with the regulation of a gene or the behavior of the encoded protein, usually rendering it useless and occasionally making it harmful or yielding a new function. Only very rarely will a mutation improve the performance of the gene or its encoded protein.
B. Beneficial, selectively neutral, detrimental. Individuals bearing beneficial mutations will be more likely to have more offspring than others in the
population, and thus the beneficial mutations will become over-represented in the population in subsequent generations. Individuals bearing detrimental mutations will be likely to have fewer children and grandchildren, and thus these mutations will be culled from the population, though perhaps not eliminated.
9-11 (a) Sugar metabolism (b) DNA replication (c) Lipid synthesis.
These pathways or phenomena are fundamental to the growth and proliferation of all cells, including bacteria, and thus are likely to be highly conserved from species to species.
9-12 A. M and N diverged 10 million years ago.
B. There is an average of 2.0% nucleotide substitution in M compared to N (follow the path connecting the two species, which is twice the distance between each one and their common ancestor).
C. Neither more nor less. They show roughly the same degree of relatedness. The sequence divergence between M and N is about 2.0%, the same as that between P and S. Both pairs of species diverged 10 million years ago.
D. It is more informative to compare species that are separated by a greater
evolutionary distance, thus comparing M and Q which diverged 20 million years ago will be better able to identify sequences likely to be important for function.
Closely related species share many sequences by chance because insufficient time has been allowed for neutral mutations to accumulate.
9-13 (a) False. Many highly conserved stretches of DNA are not transcribed but instead contain information critical for regulating where and when genes are expressed.
(b) True. Species that diverged recently have many identical stretches of DNA sequence by chance, whereas sequence similarity between species that diverged long ago is probably due to functional constraints.
(c) True. Most genomic changes do not alter the amino acid sequence of proteins or the regulatory properties of genes. Even some mutations that cause minor alterations have little functional consequence.
(d) True. All organisms need to perform a similar basic set of fundamental functions, such as those for metabolism, protein synthesis, and DNA replication. Proteins involved in these functions are shared by descent, and their evolution is
constrained. Different species and cells are likely to require different
developmental paths and to encounter different environmental challenges, so the proteins involved in these processes will tend to be more variable. For example, bacteria do not undergo elaborate developmental programs and so lack many of the regulators of development found in animals.
(e) False. Introns and transposons can act as sites where recombinational crossovers occur. Transposons can also catalyze genetic rearrangements. Rearrangements occurring within these sequences are less likely to be detrimental than those occurring elsewhere in the genome. In general only the short intron sequences required for splicing are important to intron function; alterations in sequences outside the splicing sites may have no consequences for intron function and thus will not be subject to purifying selection.
9-14 See Figure A9-14. Not all of the functionally conserved regions will be transcribed into RNA. Some of the functionally conserved regions are likely to encode RNA and others are likely to be critical for regulating when the gene is transcribed and when it is turned off. These nontranscribed regulatory regions may be conserved nearly as much as the coding regions.
Figure A9-14
9-15 A. Loss of introns may be caused by spontaneous deletions or selection pressure to decrease the time or cost of DNA replication.
B. Acquisition of intron sequences provides a selective advantage in the face of transposon insertions. According to this idea, introns became sinks for transposon and virus insertion to protect the rest of the genome. Alternatively, introns may provide another advantage to the host genome: by providing ample sites for crossing over, larger introns could facilitate exon shuffling and thus the generation of new genes with novel functions.
9-16 (a) False. The number of genes differs only by about a factor of two. It is thought that the increased complexity of humans is due largely to differences in when and where the genes are expressed. Differential splicing may also be a major
contributor to the relative complexity of humans.
(b) True. There are CA repeats in many locations throughout the genome. Because the number repeats at a given location varies greatly between individuals and families, it can be used as an identifying characteristic to match two samples (e.g., blood samples) from the same or related individuals.
(c) True. Nearly all single-nucleotide polymorphisms have no effect on the
appearance or behavior of the individual, but a few cause important differences.
(d) False. Human and mouse chromosomes show extensive synteny, with blocks of chromosomal DNA exhibiting homologous genes arranged in the same order between the two species.
(e) False. Multicellular organisms are built from essentially the same toolbox of gene building blocks, but the parts are put together differently due to regulatory
differences that dictate when and where and how much of each protein is made.
Alternative splicing can also have an important role, as it can generate several proteins from a single gene in some species, yet the homologous gene in other species may produce only one protein.
9-17 Choice (b) is the correct answer. Alternative splicing can produce several different mRNA transcripts from a single gene, and these transcripts can be translated into several different but related proteins. Choices (c), (d), and (e) do not yield more protein species than genes. Protein degradation (choice (a)) can produce several proteins from a single gene, but this mechanism is used sparingly.
9-18 To identify expressed sequence tags, or ESTs, mRNA must first be isolated from cells.
This mRNA is converted into complementary DNA (cDNA) using specialized nucleic acid polymerases. The nucleotide sequence of a short region of each cDNA is then determined. Each short sequence (or EST) corresponds to a portion of a gene that was expressed in the cells from which the mRNA was isolated; each sequence can be used as a tag to identify or manipulate the gene from which it came. A collection of ESTs can be fed into a computer to search for matches to the total genome sequence and thereby identify the sequences and chromosomal locations of many genes.