Deck 16: Recombinant Dna Technology and Its Applications

Question 1

Which is more likely to be the case for gene A found at the hub of a genetic network, compared to gene B, in the same network but not in a hub?

A) gene A is a nuclear gene, while gene B is mitochondrial
B) gene A is highly expressed
C) gene A encodes a transcription factor that controls the expression of one gene
D) gene A controls the expression of many genes
E) gene B encodes a protein that interacts with many different proteins

Answer 1

D

Question 2

What is the purpose of the two- hybrid system?

A) to discover how and whether two proteins interact
B) to locate the chromosomal position of hybridized genes
C) to study the interaction between an enhancer and a promoter
D) to explore a cDNA library to find interacting DNA sequences
E) to study the nature of two hybrid organisms at a time

Answer 2

A

Question 3

A researcher measures the quantity of cDNA that corresponds to the exons of a particular gene in mice using RNA- seq. They find that RNA for this gene isolated from the brain contains 4 exons, while RNA from the liver heart and skin contains 5 exons. What phenomenon likely explains this result?

A) there is a brain- specific allele compared to the other cells in the mouse
B) the skin, liver and heart cells differentiate before the brain and so have different exons
C) the mRNA in the brain is a pseudogene
D) the brain cell chromosome lacks the exon that is present in the other cells of the mouse
E) cells of the brain splice this mRNA differently than other cells in the mouse

Answer 3

E

Question 4

When Warnecke and colleagues were looking for genes that are involved in the digestion of lignocellulose by termites, they needed genes .

A) expressed when a termite is eating
B) for the bacterial enzymes found in the lignocellulose- digesting part of the gut
C) of the termites' mitochondria
D) from the sequences of the termite genome
E) genes found in cells of the termites mouth

Question 5

Interspecific genome comparisons can help to identify all but of the following except?

A) variation in nucleotides across a species breeding range
B) differences in nucleotide sequence between identical twins
C) biological fathers in cases of paternity
D) conserved nucleotides within a genus
E) the farms where produce at the supermarket comes from

Question 6

Celiac disease (CD) is a common, usually inherited human disorder of intestinal inflammation that is triggered by eating gluten, a major protein in wheat and other cereal grains. It is the most frequent food intolerance. One of the three genes involved encodes SH2B3, a protein involved in innate, nonspecific immune response to bacterial pathogens. Celiac sufferers frequently have a particular allele of this gene, an allele so common in the human population that which of the following might be hypothesized?

A) The allele must have been positively selected for during a period of especially frequent bacterial infections.
B) The gene must code for a T- cell receptor for a common bacterial component.
C) The non- celiac allele must have been selected against in previous human populations.
D) The gene must be common to all primate genomes.
E) The gene must be common in most mammalian genomes.

Question 7

Although whole- genome duplications that result in polyploidy are fairly common in plant species, which of the following are common in other eukaryotes?

A) miscellaneous aneuploidies in living members of a species
B) deletion of an entire haploid set of chromosomes
C) whole chromosome loss
D) duplication of whole chromosome arms
E) segmental duplications of small gene regions

Question 8

Shotgun sequencing requires all of the following except?

A) a computer
B) a genetic map
C) software capable of comparing DNA sequence
D) many overlapping DNA sequences
E) a DNA sequencing technology

Question 9

Previously unidentifiable microorganisms have now been identified through .

A) reverse transcription
B) evolutionary genomics
C) metagenomics
D) transcriptomics
E) proteomics

Question 10

Which of the following would likely exclude a sequence from being considered as an active gene?

A) introns missing the GT- AG splice junctions compared to other genes in this family
B) only one long exon
C) an exon followed by 3' processing signals
D) a promoter with signals identical to the promoter of another gene
E) exons in different reading frames from one another

Question 11

Recombination between two Alu elements can result in deletions of chromosome segments. In a recent study, researchers compared Alu recombination- mediated deletions of humans and chimpanzees. They identified 492 human- specific deletions of this type. Why is this finding important?

A) It shows that humans are not as genetically close to chimpanzees as researchers previously thought.
B) It demonstrates the importance of Alu recombination in shaping genome divergence.
C) It shows how much the chimpanzee genome has changed since the divergence of these two lineages.
D) It shows that the time of divergence of the two lineages is much older than was previously thought.
E) It shows that more deletions have occurred in humans than in chimps.

Question 12

When authors discuss gene annotation, to what do they refer?

A) using DNA sequencing to detect genes of unknown function
B) gene expression measurements for all coding genes in a genome
C) comparison of conserved sequences
D) describing protein expression patters
E) use of computers to guess at gene location and function based on comparison to known genes

Question 13

To study the maximum amount of genome diversity in humans, which of the following provides the most information?

A) SNP variation
B) ortholog comparisons
C) sequencing of one or more specific genes
D) karyotyping
E) DNA fingerprinting

Question 14

Which type of sequencing involves first creating a physical map?

A) clone- by- clone sequencing
B) paired- end sequencing
C) whole- genome shotgun sequencing
D) annotation sequencing
E) metagenomic sequencing

Question 15

Subtelomeres are blocks of homologous DNA sequences close to the ends of chromosomes. When sequences of chromosomes 4q and 10q subtelomeres were analyzed from a world- wide population, only seventeen 4q haplotypes and and eight 10q haplotypes were found among African, European, and Asian groups, making these the least diverse subtelomeres shared by these ethnic groups. Which conclusion do these data support?

A) a conclusion that assigning chromosomal origin is only possible in a population with the same ethnic origin
B) a conclusion that all haplotypes were present before the human population migrated from Africa
C) finding that few or no interchromosomal exchanges can occur among these chromosomes
D) reporting that haplotype polymorphism shows no response to natural selection
E) humans have made multiple migrations out of Africa

Question 16

It has been predicted that genes may be involved in smoking behavior. Previously, large twin and family studies have provided evidence of this and an estimate of heritability (genetic contribution) of 46- 59%, depending on sex. A large group of researchers from several institutions composed a pathway- or- systems- based series of studies including SNP analysis, cellular location and protein interaction, replication with other samples, statistical analysis, and bioinformatics. What is a likely result?

A) Two specific genes, one for a transporter protein and one for an opioid receptor, are clearly shown to be causative in all members of each sample.
B) A group of genes that tend to code for proteins with similar biological function have been identified to contribute significantly.
C) The samples used also correlate with behaviors like depression, often associated with smoking, and they may be finding depression- associated genes.
D) The study is unlikely to produce meaningful results because it is too diffuse in its methods.
E) Genome- wide association studies are of no practical use in studying human behaviors.

Question 17

Which of the following describes genome tiling arrays?

A) use of one or more arrays that together contain all sequences of a genome
B) use of high- throughput DNA sequencing technology
C) use of RNA- based arrays
D) aligning chromosomes based the sequence of short pieces of DNA
E) use of cDNA arrays

Question 18

Which of the following defines the essential gene set of an organism such as a species of yeast?

A) genes whose mutations result in haploinsufficiency
B) the fewest genes that an organism needs to divide
C) genes that, when mutated, are conditionally lethal in special environments
D) genes whose deletion alleles are lethal
E) genes that, when mutated, reduce the growth of a heterozygous organism

Question 19

Groups of genes that are evolutionarily related are called .

A) metagenomes
B) gene domains
C) gene duplications
D) gene families
E) SNPs

Question 20

Transcomplementation is a name sometimes given for a test to see whether a gene from one organism can "rescue" a loss- of- function mutant of a different organism with a homologous gene. To which of the following processes might this term apply?

A) replacement of a cdc25- with a cdc13+ gene to rescue a cell cycle dysfunction
B) introduction of a human WEE1 gene into a yeast culture with wee1- mutant yeast
C) use of Drosophila heat shock gene promoters to regulate heat shock genes in the model fish, fugu
D) replacement of a nonfunctional globin gene with a globin pseudogene
E) substitution of a drought- resistant gene from potato plants with a drought- resistant gene from a cactus species

Question 21

Human genes often occupy a larger part of the chromosome compared to the homologous gene in yeast, yet the number of amino acids in more homologous human and yeast proteins are not very different. What structure explains this difference?

Question 22

A gene in a sheep- like species has been found to differ from that in related species by the inclusion of a variable number of tandem repeats of a short sequence. These repeats or duplications arise from what process?

Question 23

An inherited human disorder, familial dysautonomia, results from a nucleotide mutation in the gene IKAP that is expressed in the nervous system. The decreased IKAP protein leads to abnormal development, and the resulting disease is usually fatal by age 30. The nucleotide change alters splicing. If this change affects only the nervous system and not the immune system, in which the gene is also expressed, what feature must be found in this gene?

Question 24

The BLAST program from NIH enables a researcher to look for homologous genes. It does so in general by searching for identity in what?

Question 25

Often, in the absence of experimental data, computerized algorithms are used to predict gene structures from large sequences. What is this approach known as?

Question 26

Interspecific (between species) genome studies show us conserved sequences, but intraspecific (within species) comparisons identify what?

Question 27

is a strategy that compiles genome sequence from many overlapping DNA sequences each corresponding to a random location in the target genome.

Question 28

In a simple bioinformatics exercise, students are asked to locate the beginning of an ORF among the six possible reading frames for a hypothetical DNA molecule. The first step in their process should involve looking for what sequence?

Question 29

A researcher has produced groups of contigs that are linked via paired- end sequences, although these include some sequence gaps. What are these groups called?

Question 30

A researcher is annotating a newly- sequenced chromosome that they constructed from contigs sequenced from a sample of Antarctic ice. The cell/organism that the chromosome came from is not known, however it yielded a single circular chromosome. You are asked to run a BLAST search to help this researcher identify the most related organism in GenBank. What would be the best strategy?

A) Perform many careful one- by- one comparisons between the newly- discovered DNA sequence and species selected from GenBank, one at a time.
B) Look for an exact match to the whole chromosome.
C) Look for a nearly identical match to a very small part (20- 40 bp) of the chromosome from all known ice bacteria.
D) Use several ~1000bp portions of the DNA sequence to search for the closest matches from among the entire available database.
E) Compare the most unusual portion of this newly- discovered chromosome to al known animal genomes.

Question 31

Species whose ancestors might once have been free living may now be present as parasites. Would their genomes now tend to be larger, smaller, or approximately the same in size and complexity?

Question 32

In 2000, when then- President Clinton along with Francis Collins of the Human Genome Project and Craig Venter of Celera announced the completion of a "draft" of the human genome, the event did not, in fact, represent true completion because most of what types of sequences were not included?

Question 33

In humans, a large number of genes associated with immune function share sequence similarity and are evolutionarily related. Together these genes are referred to as what kind of group?

Question 34

Researchers look for segments of chromosomes, larger than genes, that are similar in arrangement between distant species. Such segments may reveal relatedness and chromosome rearrangements that have happened in the evolutionary past. What are such segments identified by?

Question 35

Mammalian genomes all have a number of genes for globin polypeptides. Several of these genes are functional, but several are never expressed. What are the nonfunctional ones known as?

Question 36

The set of transcripts present in a cell or organism is called the .

Question 37

A gene product might be initially hypothesized from comparative genomics but should be confirmed how?

Question 38

can lead to the evolution of a gene with new functions while maintaining the ancestral function.

Question 39

In general, which part of a coding gene shows the most evolutionary conservation?

Question 40

Conserved noncoding sequences (CNGs) are usually sequences involved in what kinds of functions?

Question 41

If an entire genome is fragmented and then a large number of pieces are sequenced, the approach is known as the approach.

Question 42

What evidence has been found from genomics that support the conclusion that whole genome duplication has happened in the past?

Question 43

The movement of genes from one species into the genome of another is referred to as
.

Question 44

Explain the role that gene duplication may play in genome evolution.

Question 45

Provide a reasonable explanation for the discovery of a gene in the human genome that has no homolog in chimpanzees, but does have homologs with E. coli and other bacteria.

Question 46

Compare and contrast the two approaches to genome sequencing (whole- genome shotgun sequencing and clone- by- clone sequencing).

Question 47

The process of finding the location of genes and functional (e.g., regulatory) sequences and their functions within a genome sequence is called .

Question 48

The use of computational approaches to understand DNA sequence information is called
.

Question 49

Conservation of DNA sequence within an intron across wide taxa suggests that this sequence is important for .

Question 50

Under what circumstances is a metagenomic analysis preferable to analysis of a gene or genes from a single species?

Question 51

A genome sequence is considered to be complete when all its sequences are included, as well as reasonable amounts of repetitive sequences.

Question 52

Finding only the coding sequence of an ancestral gene, no introns or promoter, in a new location in a genome suggests what mechanism of gene birth gave rise to this sequence?

Question 53

How and why is the two- hybrid system used to find where two proteins interact?

Question 54

Genome- wide expression patterns can be studied using _ .

Question 55

Sequencing of DNA from a community of organisms rather than from a single individual is known as .