Deck 14: Regulation of Gene Expression in Eukaryotes

Question 1

Identifying an autosomal recessive mutation in a mutagenic screen in Drosophila requires identification of a mutant in the F3 generation. If testing for a sex- linked recessive lethal mutation (e.g., cn l + using a balancer chromosome such as cnCyO), in which generation can lines with mutations be identified?

Answer 1

F2

Question 2

A researcher is interested in testing the role for a highly- conserved amino acid in the function of a mouse protein. She has been unable to locate any pre- existing variants in this codon among a large number of available mouse strains. What might be her approach to generating such mutants?

A) Use RNAi to knockdown the expression of the target gene.
B) Use RNAi to interfere with translation of the gene.
C) Use transposons to generate insertion alleles in the gene.
D) Measure the expression of this gene in mice as they develop.
E) Use CRISPR- cas to cause DNA cleavage at the codon encoding this amino acid.

Answer 2

E

Question 3

In order to identify genes that function together in genetic pathways researchers can perform modifier screens, looking for second site enhancers or suppressors of a mutant. Which of the following is the most reasonable strategy for carrying out a suppressor screen in particular?

A) screen for enhancer- trap strains that show gene expression differences in the original mutant.
B) mutagenize the original mutant and look for new mutations that reduce the severity of the original mutant phenotype
C) isolate mutants with phenotypes similar to the original mutant phenotype and then cross the mutants to identify the affected gene(s)
D) identify mutations that, when crossed with the original mutant, result in synthetic lethality
E) analyze the DNA sequence near the mutation of interest, looking for sequences that may act as silencers

Answer 3

B

Question 4

A mutagenesis screen provides 24 alleles shown by complementation analysis to be in the same gene, which of the following is true?

A) The gene, in whole or in part, must be involved in transformation.
B) These mutants can be used to identify the function of this gene.
C) The gene being studied must be present in more than one copy per haploid genome.
D) The gene must be highly conserved in evolution.
E) The gene must be involved in regulating a signal pathway.

Question 5

If you wish to use RNAi to reduce the expression of a gene in an organism. What would you inject into the organism?

A) Dicer with double- stranded (ds) DNA
B) dsRNA including transposase
C) ssRNA complementary to cDNA
D) dsRNA homologous to the gene
E) ssRNA complementary to introns of the target gene

Question 6

Genes for regulatory elements, such as creb, were found to be important in animal learning. Which of the following would increase the probability that such an element is studied throughout the animal kingdom?

A) the large number of copies of the creb gene within a genome
B) its unique to Drosophila
C) the finding that creb activates odor perception
D) the finding that creb is highly conserved
E) the interaction of creb with cAMP

Question 7

To introduce dsRNA into C. elegans, it is enough just to dip the worms into media that includes E. coli containing the dsRNA because _ .

A) C. elegans emit toxins that paralyze the bacteria
B) E. coli infect C. elegans and then the RNA is released
C) C. elegans feed on the transgenic bacteria
D) E. coli DNA integrates into the genome of C. elegans
E) E. coli emit chemicals that cause pores to open in the nematode body wall

Question 8

Which of the following tools/techniques would allow a researcher to measure the expression of a gene of interest in live organisms?

A) a lacZ reporter fused to the gene promoter
B) homologous recombination to replace the promoter of the gene of interest with a bacterial promoter
C) measuring the frequency of mutations by DNA sequencing
D) a transgene that fuses GFP to the gene of interest
E) RNAi targeting the promoter of the gene of interest

Question 9

What kind of analysis is needed to determine whether two mutations are in the same gene or in different genes?

Question 10

EMS (ethylmethane sulfonate) is mutagenic because .

A) it breaks phosphodiester bonds
B) it forms cross- links between DNA strands
C) it makes DNA more susceptible to radiation
D) it adds alkyl groups to bases
E) it causes chromosomal deletions

Question 11

In reverse genetics, what is the correct order in which the experimenter proceeds?

A) selection of mutants with a phenotype of interest and then mapping to locate the effected gene(s)
B) identification of a gene of interest followed by screening for mutations in that gene and studies of the phenotypes caused those mutations.
C) random bombardment of the DNA with a known mutagen, followed by observation of offspring for newly acquired traits
D) screening individuals by PCR/DNA sequencing to associate altered genes with the trait of interest
E) silencing the genes in question using RNAi, followed by mapping to locate the gene

Question 12

Which portion of a gene might you target with the CRISPR- cas system to interfere with splicing?

Question 13

If a gene in Drosophila is expressed only in imaginal disc (A) when it begins to differentiate, it is referred to as a homeotic gene. Recessive mutations in such genes often result in loss of function so that the structure does not develop. If a transgenic organism is made in which the gene is expressed in a different imaginal, disc (B), what is the predicted result?

A) deregulation of gene expression throughout disc A
B) loss of function of disc B's primary gene
C) gain of function of several inappropriate genes in disc A
D) deregulation of gene expression throughout disc B
E) gain of function in disc B of some of the structures usually seen in disc A

Question 14

In a disease associated with a nucleotide repeat, anticipation is often noticed in subsequent generations, usually associated with a more severe phenotype. Which of the following is a more likely cause of anticipation?

A) Highly repeated sequences are expressed more often.
B) Children of affected parents receive more attention from physicians than other children.
C) Alleles with a large number of repeats are unstable and change size from generation to generation.
D) The sequences have greater stability in later generations.
E) Family members are exposed to the same mutagens.

Question 15

A gene, VTE4, from the sunflower of known sequence and well- understood transcriptional regulation, is available from another lab. The product of this gene enables sunflowers to to produce a significantly increased amount of vitamin E from a substrate produced in all plants. The plant Brassica napus is harvested for canola oil. To produce canola oil with increased vitamin E, how would you proceed?

A) Clone VTE4 in A. tumefaciens and use these bacteria to produce transgenic Brassica.
B) Use a yeast system to engineer yeasts that produce the vitamin, and get manufacturers to add this to the canola oil during bottling.
C) Introduce the gene and necessary cis elements into Brassica, along with a reporter gene, then measure the vitamin E produced.
D) Introduce VTE4 into tomato plants or another food that humans eat more than Brassica.
E) Select Brassica plants with the highest titer of the vitamin, isolate the genes responsible, and cause these genes to duplicate.

Question 16

Before Muller's discovery that radiation induces mutation, scientists had to work on spontaneous mutants that were found solely by phenotype differences in natural populations. Which of the features of Drosophila made it a fortuitous choice for Morgan and his colleagues?

A) both sexual and asexual reproduction
B) well- known biochemical pathways
C) especially high rate of mutation
D) having a long life cycle
E) large number of visible phenotypes

Question 17

The reasons for using transposon- based mutagenesis include all of the following EXCEPT .

A) likely to cause only minimal effects on gene function
B) mutations are often 'tagged' by the nearby transposon
C) antibiotic selection can be employed during mutagenesis.
D) dramatic mutations which often cause null alleles
E) transposons are found in nearly all organisms

Question 18

A researcher wants to mutagenize an organism. She is not in need of a large number of mutants but is more concerned with being able to find and then to amplify the mutated sequence. Which of the following would therefore be more useful?

A) a chemical mutagen
B) UV radiation
C) transposon insertion
D) ionizing radiation
E) search for spontaneous mutant

Question 19

Besides the obvious fact that chemical mutagens are dangerous to handle, another major disadvantage to their use is that _.

A) chemical mutagens activate transposons which cause widespread genetic damage
B) they alter all A- T and C- G base pairing
C) they often result in only dramatic alterations of gene function
D) most of these mutations are immediately lethal
E) most chemically induced changes are detectable only by genetic mapping and sequencing

Question 20

In Drosophila, mutation screening usually involves use of a balancer chromosome that includes three elements: a set of overlapping inversions, an easily recognized dominant mutation, and a recessive lethal mutation that prevents balancer homozygotes from surviving. Which one, or combination, of these elements is necessary and sufficient to suppress crossovers?

A) lethal recessive
B) inversions plus dominant
C) inversions
D) lethal plus inversions
E) dominants

Question 21

The GFP gene is useful as a reporter gene because the cells and tissues with it emit fluorescence when treated with what, which functions as a substrate?

Question 22

In a given situation, reduced or missing function in gene A results in a viable but noticeable phenotype. The same is true for gene B. However, when both gene A and gene B products are reduced or missing in the same organism, the result is lethality. What is this called?

Question 23

In positional cloning, the researcher begins with a phenotype. To move toward identification of its DNA sequence, she must begin with what step?

Question 24

Reporter genes such as GFP can be integrated into a native gene to study the expression pattern of a target gene. If a researcher wishes to make a fusion of the GFP protein to the protein expressed by the target gene, where must the GFP gene integrate?

Question 25

Libraries of insertion strains can be screened, primarily by which common technique, to identify mutations in a gene of interest?

Question 26

If an experimenter wants to use the GFP method but needs to detect the presence or absence of several proteins at the same time, he can take advantage of mutational variants of GFP that emit what?

Question 27

Suppose a scientist works with a mouse strain B75 and isolates an interesting recessive mutant that they call glyph. The researcher wants to identify the gene affected in glyph by complementation cloning. Which strain would the researcher use as the source of DNA for transformation?

Question 28

A single nucleotide in a genome can be targeted for mutagenesis using the technique, adapted from a bacterial defense system.

Question 29

Why is only a fraction of an organism's genes represented in any cDNA library?

Question 30

Chemical mutagens are preferred to because they have a broader mutation spectrum, including generating alleles that affect only a single codon.

Question 31

You have performed an analysis of a gene promoter using a genetic reporter and a series of deletions. From this analysis, you identify a small deletion upstream of the start codon that causes increased expression of the reporter gene, compared to the expression of the reporter when it is fused to the wild type promoter. How do you explain the increased expression of the reporter in the mutant?

Question 32

A genetic strategy that starts with knowing the DNA sequence and works toward identifying an associated phenotype is known as _ _.

Question 33

In an organism, X, it is found to be impossible to generate loss- of- function mutants for most genes. There is an alternative method of introducing random mutations that can later be screened for the gene(s) in question. This can be accomplished by using insertions due to what genetic entities?

Question 34

What method allows researchers to reduce the expression of a target gene, even in wildtype organisms that have not previously been genetically modified?

Question 35

Why are conditional alleles useful in studying genes with functions in essential cell processes?

Question 36

You have performed a mutagenesis screening in a population of organisms. Describe how you would identify mutations that are dominant. Describe how you would identify mutations that are recessive.

Question 37

In nature, RNAi protects cells against infection by what kind of pathogen?

Question 38

Which technique can be used to replace an endogenous gene with one constructed in vitro?

Question 39

DNA markers that are found to segregate with a mutation of interest can be used to determine the mutation's distance from the markers by looking at what?

Question 40

A balancer chromosome includes a recessive lethal allele, a marker dominant allele, and
.

Question 41

A friend of yours claims to have identified a gene that causes a human disease! Your friend says that they have sequenced the DNA of someone with the disorder and compared that to a healthy individual. They found a nucleotide difference in a gene called Hsr12 that encodes a protein that functions cell- to- cell communication. What is wrong with your friends claim?

Question 42

In TILLING, a population of inbred organisms is mutagenized to saturation. DNA from mutagenized lines is isolated and amplified by PCR. PCR products are denatured and allowed to reanneal and then treated with an endonuclease. Why is the denaturation/re- annealing step important for the detection of mutant alleles?

Question 43

Design an experiment that uses enhancer trapping to drive the expression of a gene of interest.

Question 44

Transgenic fusions between a gene and a reporter are used to determine whether a gene is expressed. Which of these components allows the researcher to work with living specimens, and why?