Deck 10: Genome Annotation

Question 1

How do the genes in the β-globin locus differ from each other?

A)They use different template strands for transcription.
B)They are expressed at different times in development.
C)They evolved from different ancestral genes.
D)They are dispersed on different chromosomes.
E)Some are expressed in all cells; others are expressed only in red blood cell precursors.

Answer 1

B

Question 2

Which of the following is a potential mechanism through which proteins can acquire novel domain architectures over evolutionary time?

A)protein cleavage
B)exon shuffling
C)mutation in a pseudogene
D)duplication and divergence
E)de novo mutation

Answer 2

B

Question 3

Which of the following processes can generate orthologous genes over evolutionary time?

A)protein cleavage
B)transcription regulation
C)gene duplication
D)chromosomal inversion
E)mutation that creates a new ATG

Answer 3

C

Question 4

A BLAST search can be used for which of these applications?

A)to compare a nucleotide or amino acid sequence to databases from a variety of species
B)to display the reading frame of a nucleotide sequence
C)to determine whether a gene has an essential function in an organism
D)to analyze microarray data
E)to visualize the locations of all the genes on a single chromosome

Question 5

A student analyzes a genomic DNA sequence of 100 nucleotides in order to determine if it is part of a gene.When she translates the sequence beginning at the first nucleotide, she finds that the tenth codon is UAA.What should she do next?

A)Tell her professor that the sequence does not represent an exon.
B)Tell her professor that the sequence encodes a peptide with nine amino acids.
C)Translate the sequence in the other five reading frames.
D)Use the genomic DNA to make a cDNA of the sequence.

Question 6

What do you predict would be the effect of an inversion of the β-globin gene cluster with respect to the LCR?

A)No globin genes will be expressed and the fetus will die in utero.
B)ε-globin will be expressed first during development.
C)The order of globin gene expression will be reversed; the effect on the fetus cannot be predicted.
D)The individual will develop sickle-cell disease in adult life.

Question 7

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.

Question 8

How are open reading frames or exons predicted from genomic sequence?

A)If the open reading frame is at least 10 sense codons long, it is considered an exon.
B)If the sequence is absent from mRNA, it is considered an exon.
C)If there is a splice donor and acceptor site at the ends of the open reading frame, it is considered an exon.
D)If an open reading frame is longer than 21 sense codons, it is predicted to be an exon.
E)If an enhancer and promoter sequence are present, the downstream sequence is considered an exon.

Question 9

Reverse transcriptase is an enzyme encoded in the genomes of

A)red blood cells.
B)phage λ.
C)retroviruses.
D)yeast.
E)E.coli.

Question 10

Use the BLAST tool at http://blast.ncbi.nlm.nih.gov/Blast.cgi and click "Protein blast" to find out the identity of the protein with the following amino acid sequence: CCKHPEAKRM PCAEDYLSVV LNQLCVLHEK TPVSDRVTKC CTESLVNRRP

A)myosin
B)actin
C)albumin
D)DNA polymerase
E)tubulin

Question 11

What is a RefSeq?

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

Question 12

What is one way that genes can be predicted in genome sequences?

A)identifying the sequences most conserved between different species
B)identifying the sequences least conserved between different species
C)identifying the regions most conserved between individuals of the same species
D)identifying regions that have undergone the most rapid evolution
E)identifying sequences that have been duplicated

Question 13

Which piece of evidence is most likely to indicate a gene within a genome?

A)A unique sequence within a genome is 80% similar in human, mouse, and zebrafish.
B)A sequence is unique to a nematode genome.
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 50% identical between human and chimp but does not include an open reading frame.

Question 14

Which of the following is a way that protein function can be modified AFTER translation?

A)protein cleavage
B)transcription regulation
C)gene duplication
D)exon shuffling
E)gene rearrangement

Question 15

Which experiment would best determine which genes are expressed in a Drosophila embryo?

A)analysis of a Drosophila genomic DNA library
B)analysis of a cDNA library from adult male Drosophila
C)analysis of a cDNA library from Drosophila embryos
D)identifying all the open reading frames in the Drosophila genome
E)identifying all the promoters in the Drosophila genome

Question 16

What information cannot be determined from the DNA sequence of a cDNA clone?

A)exon sequences
B)sequence of the promoter
C)similarity to previously identified sequences
D)amino acid sequence of the encoded polypeptides
E)sequence of the spliced mRNA transcript

Question 17

Which disease results from deletion of the β-globin gene cluster LCR?

A)sickle-cell disease
B)mild α-thalassemia
C)severe α-thalassemia
D)mild β-thalassemia
E)severe β-thalassemia

Question 18

Which enzyme copies an mRNA sequence into DNA during cDNA library construction?

A)RNA polymerase
B)DNA polymerase
C)reverse transcriptase
D)restriction endonuclease

Question 19

Approximately what proportion of the human genome is composed of the exome?

A)< 0.1%
B)2%
C)10%
D)20%
E)45%

Question 20

What is the advantage of having different forms of hemoglobin?

A)Multiple forms allows for speciation.
B)The multiple forms all have the same function so that one can be mutated without affecting the individual.
C)There is no advantage because the forms arose by random chance.
D)The different forms are adapted to most efficiently carry oxygen in different stages of development.
E)The different forms are adapted to most efficiently carry oxygen in different climates.

Question 21

If four genes are in the same region of a eukaryotic chromosome, then

A)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.
B)the four promoters must be oriented such that all four genes are transcribed using the same strand as the template.
C)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.
D)the genes can be transcribed from different strands only if their promoters are more than 1 kilobase apart.
E)the genes must be in a gene family.

Question 22

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 the human chromosome
B)an inversion in one of the chimpanzee chromosomes
C)gene duplication in the human chromosome
D)exon shuffling in the chimpanzee chromosomes
E)a translocation involving two chromosomes

Question 23

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 primary transcript?

A)alternative splicing
B)gene divergence
C)gene duplication
D)exon shuffling
E)gene rearrangement

Question 24

Which of these examples represents a gene family?

A)A genome includes many genes that encode myosin motor proteins.
B)All of the genes that are required for gamete formation in humans.
C)A gene encoding a kinase is similar in humans, chimps, and mice.
D)A genome includes many pseudogenes.
E)All of the genes that are expressed in a single tissue.

Question 25

A gene desert is

A)a unique sequence of DNA in a genome.
B)a region of a genome containing very few genes.
C)a gene that is transcribed only in dry climates.
D)a region of a genome containing many open reading frames but no promoter.
E)a region of a genome in which all genes are transcribed at low levels.

Question 26

Each human α-globin locus contains two α-globin genes, α1 and α2, and most individuals have two copies of the locus.Which of the genotypes would result in the most severe phenotype? (A"-" represents a deletion allele. )

A)α1 α1 / α2 α2
B)α1 - / α2 -
C)α1 α1 / - -
D)α1 - / α2 α2
E)α1 - / - -