Exam 4 Module 9

Put the following steps in whole-genome sequencing in order from first to last. 1. Assemble the sequence reads with a computer into long contigs based on overlap. 2. Construct a genomic library. 3. Fragment many genome copies into overlapping segments. 4. Generate millions of short paired-end sequence reads.

2 4 3 1

T or F : After a plasmid vector has been linearized using one restriction endonuclease, DNA ligase cannot recircularize the plasmid unless it contains an insert DNA fragment to be cloned.

False

T or F : Restriction enzymes cut DNA only at specific sites. Therefore, they are not useful for making recombinant molecules.

False

T or F : When human DNA and plasmid DNA are both digested with the same restriction enzyme and mixed together, the two types of DNA will remain separate because their ends are incompatible.

False

T or F : In Sanger sequencing, the sequence of the newly synthesized strand is determined by separating the DNA fragments by size and then reading the gel one base at a time from bottom to top.

True

T or F : To join sticky ends, DNA ligase forms phosphodiester bonds.

True

T or F : To sequence DNA by Sanger sequencing, the DNA to be sequenced must first be denatured to form a single-stranded template.

True

Which polymorphism is most likely to affect an individual's phenotype? a) A SNP in the start codon of a protein-coding gene b) A DIP in an intragenic region between genes c) An SSR within a telomeric sequence d) A SNP in an intron of a protein-coding gene

a) A SNP in the start codon of a protein-coding gene

Herceptin® is a drug that is given to treat certain breast cancers. However, it is most effective on tumors that are overexpressing the gene HER2. Which of the following strategies would be best for determining whether Herceptin® would be effective in a given patient? a) Determine the patient's HER2 sequence and compare it to a database of known HER2 mutations to determine whether the overexpression allele is present; if the overexpression allele is present, give Herceptin® b) Sequence DNA from the patient's sperm or eggs to determine whether the patient's germ cells contain gain-of-function mutations in HER2, and treat with Herceptin® only if they do. c) Perform microarray analysis to determine the location of the patient's HER2 gene and give Herceptin® if the HER2 gene is not in the normal location. d) Determine the patient's HER2 sequence and compare it to a database of known HER2 mutations to confirm that the patient has a mutation in the gene; give Herceptin® if any mutation is found.

a) Determine the patient's HER2 sequence and compare it to a database of known HER2 mutations to determine whether the overexpression allele is present; if the overexpression allele is present, give Herceptin®

Which of these examples represents a gene family? a) Many genes in a genome that encode myosin motor proteins b) Orthogolous genes encoding a specific kinase in humans, chimps, and mice c) All of the genes that are required for gamete formation in humans d) Many pseudogenes present in a single genome e) All of the genes in an organism that are expressed in a single tissue

a) Many genes in a genome that encode myosin motor proteins

You are studying a disease that is known to be caused by a single nucleotide change in a single gene, although the effect this change ultimately has on the protein's structure and function is unknown. You have DNA samples from multiple patients that you suspect of having this disease. What is the most efficient way to test the samples for the relevant mutation? a) PCR amplification followed by Sanger DNA sequencing b) High-throughput genome sequencing c) Preimplantation genetic diagnosis d) PCR amplification followed by gel electrophoresis e) High-throughput exome sequencing

a) PCR amplification followed by Sanger DNA sequencing

Which is part of a DNA sequencing technique that is useful for high-throughput sequencing, but is not part of Sanger DNA sequencing? a) Removal of a chemical group that blocks the 3′ end of the new DNA strand b) Using dideoxynucleotides as chain terminators c) Separating DNA by size using gel electrophoresis d) Labeling deoxynucleotides with fluorescent tags e) Hybridization between the template and a primer

a) Removal of a chemical group that blocks the 3′ end of the new DNA strand

Identifying candidates for a disease gene by positional cloning depends on distinguishing DNA markers that are close to the disease gene from markers that are far away. When the disease gene is close to a marker, there will be ... a) a low rate of recombination between the disease gene and the marker. b) many alleles at the marker locus. c) a high number of mutations in the intervening DNA. d) a high chance of locus heterogeneity.

a) a low rate of recombination between the disease gene and the marker.

Which of the following processes can generate orthologous genes over evolutionary time? a) gene duplication b) chromosomal inversion c) transcription regulation d) mutation that creates a new ATG e) protein cleavage

a) gene duplication

Pseudogenes are evidence of ... a) gene duplications. b) integrated viruses, or proviruses. c) natural selection for functional genes. d) de novo genes. e) proteins that are produced but have no function.

a) gene duplications.

Which enzyme copies an mRNA sequence into DNA during cDNA library construction? a) reverse transcriptase b) restriction endonuclease c) DNA polymerase d) RNA polymerase

a) reverse transcriptase

What information cannot be determined from the base-pair sequence of a cDNA clone? a) sequence of the promoter b) similarity to previously identified sequences c) sequence of the spliced mRNA transcript d) exon sequences e) amino acid sequence of the encoded polypeptides

a) sequence of the promoter

Approximately what proportion of the human genome is composed of the exome? a) 10% b) 2% c) < 0.1% d) 45% e) 20%

b) 2%

Which piece of evidence is most likely to indicate a gene within a genome? a) A sequence is 50% identical between human and chimp but does not include an open reading frame. b) A unique sequence within a genome is 80% similar in human, mouse, and zebrafish. c) An identical open reading frame is found in two species of fruit fly. d) A sequence is repeated multiple times in the human genome. e) A sequence is unique to a nematode genome.

b) A unique sequence within a genome is 80% similar in human, mouse, and zebrafish.

Which statement about SNPs in the human genome is true? a) Most SNPs are located in the introns of genes, and thus effect phenotype. b) Any two human genome copies will have on average 3 million single nucleotide polymorphisms. c) Most SNPs have an effect on phenotype. d) SNPs refer only to deletions or insertions, not base substitutions.

b) Any two human genome copies will have on average 3 million single nucleotide polymorphisms.

What technique can help identify a disease gene quickly by narrowing the focus? a) Use microarrays to identify silent mutations. b) Compare the genome sequences of different species to identify amino acids that are conserved in various encoded proteins. c) Determine genotypes of parents and children at all SSR loci. d) Filter the results to include only common polymorphisms.

b) Compare the genome sequences of different species to identify amino acids that are conserved in various encoded proteins.

Allele-specific oligonucleotides (ASOs) for the normal and disease alleles of a gene are in one section of a microarray. The disease is a recessive trait. If a probe made from an individual's genomic DNA hybridizes with both ASOs, what can be inferred about the individual? a) one of the individual's parents has the disease b) Each of the individual's children has a 50% chance of being a carrier. c) the individual has two normal alleles d) the individual has the disease

b) Each of the individual's children has a 50% chance of being a carrier.

The arms of human chromosome 2 are syntenic with two different chimpanzee chromosomes. What mechanism could have caused this pattern of synteny? a) an inversion in one of the chimpanzee chromosomes b) a translocation involving two chromosomes c) an inversion in the human chromosome d) gene duplication in the human chromosome e) exon shuffling in the chimpanzee chromosomes

b) a translocation involving two chromosomes

In the United States, most newborns undergo a screening test for up to 60 genetic disorders. A few drops of blood is taken from each baby and the levels of various blood components are determined. The screening identifies babies who might have a genetic disorder, but is not diagnostic. Further testing is required if the screen shows a blood component is out of the normal range. Which of the following technologies could potentially be a low-cost replacement for the current newborn screening and would test most babies directly for the presence of many genetic disorders? a) DNA profiling using CODIS SSRs b) exome sequencing and comparison with known mutations in databases c) PCR to amplify the PKU gene d) preimplantation genetic diagnosis

b) exome sequencing and comparison with known mutations in databases

Which disease results from deletion of the β-globin gene cluster LCR? a) mild β-thalassemia b) severe β-thalassemia c) severe α-thalassemia d) mild α-thalassemia e) sickle-cell disease

b) severe β-thalassemia

Which is the most common type of DNA polymorphism? a) simple sequence repeat b) single nucleotide polymorphism c) deletion/insertion polymorphism d) copy number variant

b) single nucleotide polymorphism

What is a reference sequence? a) A program to compare genome sequences. b) A program that identifies open reading frames. c) A single, complete, annotated version of a species' genomic DNA sequence that can be accessed for bioinformatic studies. d) A constantly updated collection of DNA sequences from all species that give the latest information for bioinformatic studies.

c) A single, complete, annotated version of a species' genomic DNA sequence that can be accessed for bioinformatic studies.

The ends of DNA molecules can be joined together by ... a) DNA polymerase. b) restriction endonucleases. c) DNA ligase. d) primase. e) helicase.

c) DNA ligase.

E. coli cells that are sensitive to ampicillin are mixed with many copies of a plasmid that has a gene for ampicillin resistance and then plated on medium containing ampicillin. What will happen next? a) E. coli cells with and without a plasmid will grow and form colonies. b) The plasmid is resistant to ampicillin, so it will survive and replicate outside of the bacterial cells. c) Only E. coli cells that have taken up a plasmid will grow and form colonies. d) Only E. coli cells that have not taken up a plasmid will grow and form colonies.

c) Only E. coli cells that have taken up a plasmid will grow and form colonies.

Which is a challenge of using pedigrees for positional cloning? a) Pedigrees are not based on DNA sequences. b) Recombination occurs during meiosis. c) Some matings may not be informative. d) Many individuals in a pedigree are unaffected.

c) Some matings may not be informative.

A gene desert is ... a) a gene that is transcribed only in dry climates. b) a region of a genome containing many open reading frames but no promoter. c) a region of a genome containing very few genes. d) a region of a genome in which all genes are transcribed at low levels. e) a unique sequence of DNA in a genome.

c) a region of a genome containing very few genes.

When a dideoxynucleotide is incorporated into one new DNA strand by DNA polymerase, ... a) nucleotides are removed only from that strand and then new nucleotides are added. b) nothing changes. c) addition of nucleotides only to that strand ceases. d) addition of nucleotides to all new strands stop. e) addition of nucleotides only to that strand speeds up.

c) addition of nucleotides only to that strand ceases.

Which experiment would best determine which genes are expressed in a Drosophila embryo? a) identifying all the open reading frames in the Drosophila genome b) identifying all the promoters in the Drosophila genome c) analysis of a cDNA library from Drosophila embryos d) analysis of a cDNA library from adult male Drosophila e) analysis of a Drosophila genomic DNA library

c) analysis of a cDNA library from Drosophila embryos

Most polymorphisms do not result in a phenotypic difference because they are typically ... a) either missense mutations or are in promoter regions. b) nonsense mutations. c) either silent mutations or are in non-coding regions. d) either missense or neutral mutations.

c) either silent mutations or are in non-coding regions.

Reverse transcriptase is an enzyme encoded in the genomes of ... a) red blood cells. b) E. coli. c) retroviruses. d) phage λ. e) yeast.

c) retroviruses.

Positional cloning depends on knowing what? a) the function of a gene b) the sequence of a gene c) the map location of markers that are linked to a gene d) the expression pattern of a gene

c) the map location of markers that are linked to a gene

A BLAST search can be used for which of these applications? a) to display the reading frame of a nucleotide sequence b) to analyze microarray data c) to compare a nucleotide or amino acid sequence to databases from a variety of species d) to visualize the locations of all the genes on a single chromosome e) to determine whether a gene has an essential function in an organism

c) to compare a nucleotide or amino acid sequence to databases from a variety of species

How can microarrays differentiate between a wild-type allele and a disease allele that differ at only one nucleotide? a) Polymerase chain reaction primers amplify DNA from one allele, but not the other. b) Microarrays are not capable of detecting a difference between those alleles. c) The DNA sequences of both alleles are determined. d) Oligonucleotides hybridize with the two alleles differently.

d) Oligonucleotides hybridize with the two alleles differently.

The presence of a selectable marker on a plasmid allows the researcher to determine if ... a) the polylinker is present in the plasmid. b) the gene of interest has been inserted in the plasmid. c) the plasmid DNA can be separated from the bacterial DNA. d) a bacterial cell has taken up the plasmid.

d) a bacterial cell has taken up the plasmid.

A single eukaryotic gene can produce two different forms of a protein, one that is membrane bound and one that is secreted. Which of these mechanisms allows a single gene to produce two different proteins from one type of primary transcript? a) gene rearrangement b) gene duplication c) exon shuffling d) alternative splicing e) gene divergence

d) alternative splicing

The primer used in Sanger sequencing ... a) has a nucleotide sequence complementary to the 5' end of the template, just outside the region to be sequenced. b) must have a sequence beginning and ending with the same nucleotide. c) is made up of all Ts. d) has a nucleotide sequence complementary to the 3' end of the template, just outside the region to be sequenced.

d) has a nucleotide sequence complementary to the 3' end of the template, just outside the region to be sequenced.

Which of the following is a way that protein function can be modified AFTER translation? a) exon shuffling b) gene rearrangement c) gene duplication d) protein cleavage e) transcription regulation

d) protein cleavage

Which does a successful PCR require? a) at least 100 starting DNA template molecules b) a double-stranded DNA template of at least 100 kb to amplify c) an undamaged DNA template with intact chromosomes d) some sequence information about the region to be amplified e) a cloned cDNA of the region to be amplified

d) some sequence information about the region to be amplified

If four genes are in the same region of a eukaryotic chromosome, then ... a) the genes can be transcribed from different strands only if their promoters are more than 1 kilobase apart. b) the genes must be in a gene family. c) the four promoters must be oriented such that all four genes are transcribed using the same strand as the template. d) the four promoters may be oriented such that some of the genes are transcribed using the Watson strand as template, and others use the Crick strand. e) the four promoters must be oriented such that two genes are transcribed using the Watson strand as a template and two genes use the Crick strand.

d) the four promoters may be oriented such that some of the genes are transcribed using the Watson strand as template, and others use the Crick strand.

How are open reading frames or exons predicted from genomic sequence? a) If there is a splice donor and acceptor site at the ends of the open reading frame, it is considered an exon. b) If the open reading frame is at least 10 sense codons long, it is considered an exon. c) If an enhancer and promoter sequence are present, the downstream sequence is considered an exon. d) If the sequence is absent from mRNA, it is considered an exon. e) If an open reading frame is longer than 21 sense codons, it is predicted to be an exon.

e) If an open reading frame is longer than 21 sense codons, it is predicted to be an exon.

The most common mutant allele of the PAH gene, which is responsible for the metabolic disorder PKU, has a SNP in the splice donor site of one intron. What is the simplest way to detect this allele? a) PCR using genomic DNA as template and two primers, one on either side of the SNP, followed by gel electrophoresis b) Direct exome sequencing using a microarray c) Whole-genome sequencing d) PCR using genomic DNA as template and two primers, one complementary to the region containing the SNP, followed by gel electrophoresis e) PCR using two primers, one on either side of the SNP, followed by sequencing the PCR products

e) PCR using two primers, one on either side of the SNP, followed by sequencing the PCR products

Which of the following is a potential mechanism through which proteins can acquire novel domain architectures over evolutionary time? a) de novo mutation b) protein cleavage c) mutation in a pseudogene d) duplication and divergence e) exon shuffling

e) exon shuffling

What is one way that genes can be predicted in genome sequences? a) identifying the sequences least conserved between different species b) identifying sequences that have been duplicated c) identifying the regions most conserved between individuals of the same species d) identifying regions that have undergone the most rapid evolution e) identifying the sequences most conserved between different species

e) identifying the sequences most conserved between different species

What are sticky ends? a) different from cohesive ends b) double-stranded DNA sequences that are generated by blunt cuts c) single-stranded DNA sequences that are generated by blunt cuts d) double-stranded DNA sequences that are generated by staggered cuts e) single-stranded DNA sequences that are generated by staggered cuts

e) single-stranded DNA sequences that are generated by staggered cuts