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HOW GENES AND GENOMES EVOLVE

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Can you answer the two attachments quizzes?;Attachments Preview;Chapter 9.doc Download Attachment;CHAPTER 9;HOW GENES AND GENOMES EVOLVE;2009 Garland Science Publishing;Generating Genetic Variation;9-1;Which of the following statements is false?;(a);A mutation that arises in a mothers somatic cell often causes a disease in;her daughter.;(b);All mutations in an asexually reproducing single-celled organism are;passed on to progeny.;(c);In an evolutionary sense, somatic cells exist only to help propagate germline cells.;(d);A mutation is passed on to offspring only if it is present in the germ line.;9-2;Your friend works in a lab that is studying why a particular mutant strain of;Drosophila grows an eye on its wing. Your friend discovers that this mutant strain;of Drosophila is expressing a transcription factor incorrectly. In the mutant;Drosophila, this transcription factor, which is normally expressed in the;primordial eye tissue, is now misexpressed in the wing primordial wing tissue;thus turning on transcription of the set of genes required to produce an eye in the;wing primordial tissue. If this hypothesis is true, which of the following types of;genetic change would most likely lead to this situation?;(a);a mutation within the transcription factor gene that leads to a premature;stop codon after the third amino acid;(b);a mutation within the transcription factor gene that leads to a substitution;of a positively charged amino acid for a negatively charged amino acid;(c);a mutation within an upstream enhancer of the gene;(d);a mutation in the TATA box of the gene;9-3;Match the type of phenotypic change below with the type of genetic change most;likely to cause it. Each type of genetic change may be used more than once, or;may not be used at all.;Phenotypic changes;1.;A protein normally localized in the nucleus is now localized in the;cytoplasm.;2.;A protein acquires a DNA binding domain.;3.;Tandem copies of a gene are found in the genome.;4.;A copy of a bacterial gene is now found integrated on a human;chromosome.;5.;A protein becomes much more unstable.;6.;A protein normally expressed only in the liver is now expressed in blood;cells.;Types of genetic change;A.;mutation within a gene;B.;gene duplication;C.;mutation in a regulatory region;D.;exon shuffling;E.;horizontal gene transfer;9-4;For each of the following sentences, fill in the blanks with the best word or phrase;in the list below. Not all words or phrases will be used, use each word or phrase;only once.;Sexual reproduction in a multicellular organism involves;specialized reproductive cells, called __________________s;which come together to form a __________________ that will;divide to produce both reproductive and;cells. A point mutation in the DNA is considered a;mutation if it changes a nucleotide that;leads to no phenotypic consequence, a point mutation is considered;if it changes a nucleotide within a gene and;causes the protein to be non-functional.;common;gamete;homologous;deleterious;unequal;somatic;neutral;intron;cellulose;zygote;9-5;Transposable elements litter the genomes of primates, and a few of them are still;capable of moving to new regions of the genome. If a transposable element;jumped into an important gene in one of your cells when you were a baby and;caused a disease, is it likely that your child would also have the disease? Explain.;9-6;What is the most likely explanation of why the overall mutation rates in bacteria;and in humans are roughly similar?;(a);Cell division needs to be fast.;(b);Most mutations are silent.;(c);There is a narrow range of mutation rates that offers an optimal balance;between keeping the genome stable and generating sufficient diversity in a;population.;(d);It benefits a multicellular organism to have some variability among its;cells.;9-7;For each statement below, indicate whether it is true or false and explain why.;A.;B.;C.;D.;E.;9-8;To meet a challenge or develop a new function, evolution essentially;builds from first principles, designing from scratch, to find the best;possible solution.;Nearly every instance of DNA duplication leads to a new functional gene.;A pseudogene is very similar to a functional gene but cannot be expressed;because of mutations.;Most genes in vertebrates are unique, and only a few genes are members;of multigene families.;Horizontal transfer is very rare and thus has had little influence on the;genomes of bacteria.;Two individuals are represented in each choice in Figure Q9-8, individual 1 is one;of the parents of individual 2. The asterisk seen in each choice indicates the;occurrence of a single mutation during the cell division. Which of the choices in;Figure Q9-8 will lead to a mutation in every cell of the individual in which the;original mutation occurred?;Figure Q9-8;9-9;Two individuals are represented in Figure Q9-9, individual 1 is one of the parents;of individual 2. The asterisk indicates the occurrence of a single mutation.;Figure Q9-9;What is the chance that individual 2 will inherit the mutation in individual 1?;(a);100%;(b);50%;(c);1 in 100,000;(d);none;9-10;Consider a gene with a particular function. Mutation X and mutation Y each cause;defects in the function of the encoded protein, yet a gene containing both;mutations X and Y encodes a protein that works even better than the original;protein. The odds are exceedingly small that a single mutational event will;generate both mutations X and Y. Explain a simple way that an organism with a;mutant gene containing both mutations X and Y could arise during evolution.;9-11;For each of the following sentences, fill in the blanks with the best word or phrase;in the list below. Not all words or phrases will be used, use each word or phrase;only once.;Most variation between individual humans is in the form of;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 __________________ then the herbicides could;become useless. Families of related genes can arise from a single;ancestral copy by __________________ and subsequent;divergence;exon shuffling;gene duplication;horizontal gene transfer;9-12;purifying selection;single-nucleotide polymorphisms;synteny;unequal crossing-over;Figure Q9-12 shows an experiment used to determine the spontaneous mutation;rate in E. coli. If the spontaneous mutation rate in E. coli is 1 mistake in every 109;nucleotides copied, about how many colonies would you expect to see on the;plates lacking histidine if you were to assay 1011 cells from the culture for their;ability to form colonies?;Figure Q9-12;(a);(b);(c);(d);9-13;1;2;10;100;The spontaneous mutation rate in E. coli was determined by performing assays to;test for the frequency of an AT to GC change. These assays were performed using;E. coli that started out unable to produce histidine (His) because of an inserted;UGA stop codon that disrupted the region coding for an enzyme required to;produce histidine. When a spontaneous mutation arose that enabled the UGA stop;codon to code for tryptophan, the E. coli cells were then able to produce the;enzyme required for histidine production. Would you expect a change in the;spontaneous mutation rate of 1 mistake every 109 nucleotides copied if reversion;of the stop codon to cysteine (instead of tryptophan) could cause the bacteria to;produce histidine? Explain. (The codon table is shown in Figure Q9-13 to help;you answer this question.);Figure Q9-13;9-14;Which of the following changes is least likely to arise from a point mutation in a;regulatory region of a gene?;(a);a mutation that changes the time in an organisms life during which a;protein is expressed;(b);a mutation that eliminates the production of a protein in a specific cell;type;(c);a mutation that changes the subcellular localization of a protein;(d);a mutation that increases the level of protein production in a cell;9-15;Which of the following statements about gene families is false?;(a);Because gene duplication can occur when crossover events occur, genes;are always duplicated onto homologous chromosomes.;(b);Not all duplicated genes will become functional members of gene;families.;(c);Whole genome duplication can contribute to the formation of gene;families.;(d);Duplicated genes can diverge in both their regulatory regions and their;coding regions.;9-16;Figure Q9-16 shows the evolutionary history of the globin gene family members.;Figure Q9-16;Given this information, which of;the following;statements is true?;(a);The ancestral globin gene;arose 500;million years ago.;(b);The -globin gene is more closely related to the -globin gene than to the;-globin gene.;(c);The nucleotide sequences of the two -globins will be most similar;because they are the closest together on the chromosome.;(d);The fetal -globins arose from a gene duplication that occurred 200;million years ago, which gave rise to a -globin expressed in the fetus and;a -globin expressed in the adult.;9-17;Panels (A) and (B) of Figure Q9-17 show substrates of exon shuffling and the;outcome of exon shuffling after recombination. Horizontal lines and small filled;circles represent chromosomes and centromeres, respectively. Exons are labeled;A, B, C, and D. Homologous recombination or shuffling may take place at short;repeated homologous DNA sequences in introns, because DNA sequences have a;polarity, the repeated sequences can be considered to have a head and a tail and;thus are drawn as arrows. A large X represents a recombinational crossover. Panel;(A) shows that recombination between two direct repeats located on opposite;sides of the centromere yields one circular product that contains a centromere and;a second product that lacks a centromere and will therefore be lost when the cell;divides. Panel (B) shows that recombination between inverted repeats flanking the;centromere will keep the rearranged chromosome intact. Draw the products of;recombination when the repeated sequences are located on different;chromosomes, as shown in panels (C) and (D). Will these products be faithfully;transmitted during cell division?;Figure Q9-17;9-18;Which of the following would contribute most to successful exon shuffling?;(a);shorter introns;(b);a haploid genome;(c);exons that code for more than one protein domain;(d);introns that contain regions of similarity to one another;Reconstructing Lifes Family Tree;9-19;Which of the following statements is true?;(a);The intron structure of most genes is conserved among vertebrates.;(b);The more nucleotides there are in an organisms genome, the more genes;there will be in its genome.;(c);(d);9-20;Because the fly Drosophila melanogaster and humans diverged from a;common ancestor so long ago, a gene in the fly will show more similarity;to another gene from the same species than it will to a human gene.;An organism from the same Order will be more likely to have genomes of;the same size than will a more evolutionarily diverged animal.;Given the evolutionary relationship between higher primates shown in Figure Q920, which of the following statements is false?;Figure Q9-20;(a);(b);(c);(d);The last common ancestor of humans, chimpanzees, gorillas, and;orangutans lived about 14 million years ago.;Chimpanzees are more closely related to gorillas than to humans.;Humans and chimpanzees diverged about 6 million years ago.;Orangutans are the most divergent of the four species shown in Fig. Q920.;9-21;In humans and in chimpanzees, 99% of the Alu retrotransposons are in;corresponding positions. Which of the following statements below is the most;likely explanation for this similarity?;(a);The Alu retrotransposon is not capable of transposition in humans.;(b);Most of the Alu sequences in the chimpanzee genome underwent;duplication and divergence before humans and chimpanzees diverged.;(c);The Alu retrotransposons are in the most beneficial position in the genome;for primates.;(d);The Alu retrotransposons must also be in the same position in flies.;9-22;You are interested in finding out how the budding yeast Saccharomyces;cerevisiae is so good at making bread and have collected five new related species;from the wild. You sequence the genomes of all of these new species and also;consult with a fungal biologist to help you construct the phylogenetic tree shown;in Figure Q9-22. You find that species V, W, and X make pretty good bread;whereas species Y and Z do not, suggesting that the last common ancestor of;species X and S. cerevisiae may have the genes necessary for making good bread.;You compare the gene sequences of species X and S. cerevisiae and find many;identical coding sequences, but you also identify nucleotides that differ between;the two species. Which species would be the best to examine to determine what;the sequence was in the last common ancestor of species X and S. cerevisiae?;Figure Q9-22;(a);(b);(c);(d);species V;species W;species Y;species Z;9-23;Which of the following statements is false?;(a);The human genome is more similar to the orangutan genome than it is to;the mouse genome.;(b);A comparison of genomes shows that 90% of the human genome shares;regions of conserved synteny with the mouse genome.;(c);Primates, dogs, mice, and chickens all have about the same number of;genes.;(d);Genes that code for ribosomal RNA share significant similarity in all;eucaryotes but are much more difficult to recognize in archaea.;9-24;The puffer fish, Fugu rubripes, has a genome that is one-tenth the size of;mammalian genomes. Which of the following statements is not a possible reason;for this size difference?;(a);Intron sequences in Fugu are shorter than those in mammals.;(b);Fugu lacks the repetitive DNA found in mammals.;(c);The Fugu genome seems to have lost sequences faster than it has gained;sequences over evolutionary time.;(d);Fugu has lost many genes that are part of gene families.;9-25;Which of the following regions of the genome is the least likely to be conserved;over evolutionary time?;(a);the upstream regulatory region of a gene that encodes the region;conferring tissue specificity;(b);the upstream regulatory region of a gene that binds to RNA polymerase;(c);the portion of the genome that codes for proteins;(d);the portion of the genome that codes for RNAs that are not translated into;protein;9-26;The evolutionary relationships between seven different species, G, H, J, K, L, M;and N are diagrammed in Figure Q9-26.;Figure Q9-26;Given this information, which of the following statements is false?;(a);These are all highly related species, because the sequence divergence;between the most divergent species is 3%.;(b);Species M is just as related to species G as it is to species J.;(c);Species N is more closely related to the last common ancestor of all of;these species than to any of the other species shown in the diagram.;(d);Species G and H are as closely related to each other as species J and K are;to each other.;9-27;You are working in a human genetics laboratory that studies causes and;treatments for eye cataracts in newborns. This disease is thought to be;caused by a deficiency in the enzyme galactokinase, but the human gene;that encodes this enzyme has not yet been identified. At a talk by a visiting;scientist, you learn about a strain of bakers yeast that contains a mutation;called gal1 in its galactokinase gene. Because this gene is needed to;metabolize galactose, the mutant strain cannot grow in galactose medium.;Knowing that all living things evolved from a common ancestor and that;distantly related organisms often have homologous genes that perform;similar functions, you wonder whether the human galactokinase gene can;function in yeast. Because you have an optimistic temperament, you;decide to pursue this line of experimentation. You isolate mRNA gene;transcripts from human cells, use reverse transcriptase to make;complementary DNA (cDNA) copies of the mRNA molecules, and ligate;the cDNAs into circular plasmid DNA molecules that can be stably;propagated in yeast cells. You then transform the pool of plasmids into;gal1 yeast cells so that each cell receives a single plasmid. What will;happen when you spread the plasmid-containing cells on Petri dishes that;contain galactose as a carbon source? How can this approach help you find;the human gene encoding galactokinase?;9-28;A.;B.;When a mutation arises, it can have three possible consequences;beneficial to the individual, selectively neutral, or detrimental. Order these;from most likely to least likely.;The spread of a mutation in subsequent generations will, of course, depend;on its consequences to individuals that inherit it. Order the three;possibilities in part A to indicate which is most likely to spread and;become over-represented in subsequent generations, and which is most;likely to become under-represented or disappear from the population.;9-29;Some types of gene are more highly conserved than others. For each of the;following pairs of gene functions, choose the one that is more likely to be highly;conserved.;A.;genes involved in sexual reproduction / genes involved in sugar;metabolism;B.;DNA replication / developmental pathways;C.;hormone production / lipid synthesis;9-30;Figure Q9-30 shows a hypothetical phylogenetic tree. Use this tree to answer the;following questions.;Figure Q9-30;A.;How many years ago did species M and N diverge from their last common;ancestor?;B.;C.;D.;How much nucleotide divergence is there on average between species M;and N?;Are species M and N more or less closely related to each other than;species P and S are?;In looking for functionally important nucleotide sequences, is it more;informative to compare the genome sequences of species M and N or;those of species M and Q?;9-31;For each statement below, indicate whether it is true or false and explain why.;A.;All highly conserved stretches of DNA in the genome are transcribed into;RNA.;B.;To find functionally important regions of the genome, it is more useful to;compare species whose last common ancestor lived 100 million years ago;rather than 5 million years ago.;C.;Most mutations and genome alterations have neutral consequences.;D.;Proteins required for growth, metabolism, and cell division are more;highly conserved than those involved in development and in response to;the environment.;E.;Introns and transposons tend to slow the evolution of new genes.;9-32;Your friend has sequenced the genome of her favorite experimental organism, a;kind of yeast. She wants to identify the locations of all the genes in this genome.;To aid her search, she collaborates with another researcher, one who has;sequenced the genome of a distantly related yeast species. Luckily, the absence of;introns simplifies the effort. She and her collaborator use a computer program to;align similar stretches of DNA sequence from the two genomes. The program;yields the graphical output shown in Figure Q9-32, where the horizontal lines;represent a portion of the two genomic sequences and vertical lines indicate where;the sequences differ. (No vertical line means that the sequence is identical in the;two yeasts.) Label both the functionally conserved regions and the divergent;(nonconserved) sequences. Are all of the functionally conserved regions likely to;be transcribed into RNA? If not, what might be the function of the nontranscribed;conserved regions?;Figure Q9-32;9-33;The genomes of some vertebrates are much smaller than those of others. For;example, the genome of the puffer fish Fugu is much smaller than the human;genome, and even much smaller than those of other fish, primarily because of the;small size of its introns.;A.;Describe a mechanism that might drive evolution toward small introns or;loss of introns and could therefore account for the evolutionary loss of;introns according to the introns early hypothesis.;B.;Describe a mechanism that might drive evolution toward more or larger;introns and could thereby account for the evolutionary appearance of;introns according to the introns late hypothesis.;9-34;It is thought that all eucaryotes all have about 300 genes in common. Would you;predict that these genes would be used at different times during the life cycle of;multicellular animals? Explain your answer.;9-35;Which of the following functions do you not expect to find in the set of genes;found in all organisms on Earth?;(a);DNA replication;(b);DNA repair;(c);protein production;(d);RNA splicing;9-36;Which of the following generalities about genomes is true?;(a);All vertebrate genomes contain roughly the same number of genes.;(b);All unicellular organisms contain roughly the same number of genes.;(c);The larger an organism, the more genes it has.;(d);The more types of cell an organism has, the more genes it has.;Examining The Human Genome;9-37;The human genome has 3.2 109 nucleotide pairs. At its peak, the Human;Genome Project was generating raw nucleotide sequences at a rate of 1000;nucleotides per second. At the rate of 1000 nucleotides per second, how long;would it take to generate 3.2 109 nucleotides of sequence?;9-38;The average size of a protein in a human cell is about 430 amino acids, yet the;average gene in the human genome is 27,000 nucleotide pairs long. Explain.;9-39;Which of the following statement about pseudogenes is false?;(a);Pseudogenes code for microRNAs.;(b);Pseudogenes share significant nucleotide similarity with functional genes.;(c);Pseudogenes are no longer expressed in the cell.;(d);There are estimated to be approximately 20,000 pseudogenes in the human;genome.;9-40;Which of the following statements about the human genome is false?;(a);More than 40% of the human genome is made up of mobile genetic;elements.;(b);More of the human genome codes for intron sequences than for exon;sequences.;(c);About 1.5% of the human genome codes for exons.;(d);The exons are mainly what is conserved between the genomes of humans;and other mammals.;9-41;The nucleotide sequences between individuals differ by 0.1%, yet the human;genome is made up of about 3 109 nucleotide pairs. Which of the following;statements is false?;(a);In most human cells, the homologous autosomes differ from each other by;0.1%.;(b);All changes between human individuals are single-nucleotide;polymorphisms.;(c);Any two individuals (other than identical twins) will generally have more;than 3 million genetic differences in their genomes.;(d);Much of the variation between human individuals was present 100,000;years ago, when the human population was small.;9-42;Propose a reason to explain why highly repetitive regions of the genome are;particularly susceptible to expansions and contractions in number.;9-43;Which of the following processes is not thought to contribute to diversity in the;genome of human individuals?;(a);exon shuffling;(b);single-nucleotide polymorphisms;(c);CA repeats;(d);duplication and deletion of large blocks of sequence;9-44;For each statement below, indicate whether it is true or false and explain why.;A.;The increased complexity of humans compared with flies and worms is;largely due to the vastly larger number of genes in humans.;B.;Repeats of the CA dinucleotide are useful for crime investigations and;other forensic applications.;C.;Most single-nucleotide polymorphisms cause no observable functional;differences between individual humans.;D.;There is little conserved synteny between human and mouse genes.;E.;The differences between multicellular organisms are largely explained by;the different kinds of genes carried on their chromosomes.;9-45;The number of distinct protein species found in humans and other organisms can;vastly exceed the number of genes. This is largely due to ______________.;(a);protein degradation;(b);alternative splicing;(c);homologous genes;(d);mutation;9-46;You are studying a gene that has four exons and can undergo alternative splicing.;Exon 1 has two alternatives, exon 2 has five alternatives, exon 3 has three;alternatives, and exon 4 has four alternatives. If all possible splicing combinations;were used, how many different splice isoforms could be produced for this gene?;(a);22;(b);(c);(d);9-47;30;60;120;Alternative exons can arise through the duplication and divergence of existing;exons. What type of mutation below would be least tolerated during the evolution;of a new exon?;(a);a nucleotide change of A to G;(b);a deletion of three consecutive bases.;(c);mutation of the first nucleotide in the intron;(d);a nucleotide change that alters a TT dinucleotide to AA;How We Know: Counting Genes;9-48;Explain how ESTs are identified and how they aid in finding the genes within an;organisms genome.;9-49;Your friend discovered a new multicellular organism living under the polar ice;caps, and brought it back to the laboratory, where it seems to be growing well.;Your friend is particularly interested in the proteins that allow this organism to;survive in extreme cold. Because he is interested in proteins and because he has;learned that most of the human genome does not code for exons, he is considering;sequencing expressed sequence tags from this organism. What do you think the;pitfalls of this approach might be? Explain.;9-50;The yeast genome was sequenced more than 10 years ago, yet the total number of;genes continues to be refined. The sequencing of closely related yeast species was;important for validating the identity of short (less than 100 nucleotides long) open;reading frames (ORFs) that were otherwise difficult to predict. What is the main;reason that these short ORFs are hard to find?;(a);The human genome does not have short ORFs.;(b);The short ORFs code for RNAs.;(c);Many short stretches of DNA may, by random chance, not have a stop;codon, making it difficult to distinguish those that code for proteins from;those that do not.;(d);Short ORFs occur mainly in gene-rich regions, making them difficult to;identify by computer programs.

 

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