Test Bank | Ch23 Functional Genomics & Proteomics – 7e

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1) A researcher isolates mRNA from healthy and diseased liver biopsies. Each mRNA sample is converted into cDNA and subjected to next-generation sequencing. Select all statements that describe this experiment and the possible results.

A) The researcher can identify transcripts that are more abundant in healthy liver than in diseased liver, which are candidate genes for further study.
B) The researcher can identify transcripts that are less abundant in healthy liver than in diseased liver, which are candidate genes for further study.
C) This is an RNA-Seq experiment.
D) This is a DNA microarray analysis.
E) Some genes' transcriptsmay be present in both samples but have different splice forms in healthy and diseased liver.
F) The intron sequences will be more abundant in the diseased liver samples.
G) The researcher should have combined the healthy and diseased mRNA samples before making cDNA, so that only one sample would need to be sequenced.

2) What field of study of genetics applies statistics and mathematical tools to genetic sequences in order to better understand the genetic information?

A) Structural genomics
B) Functional genomics
C) Proteomics
D) Bioinformatics

3) What can gene chips be used for?

A) To examine patterns of protein expression under various environmental conditions
B) To establish levels of genetic variation
C) To determine the mass of a gene
D) To identify the amount of a specific transcription factor in a cell

4) What does detection of a fluorescent signal from one of the spots of a DNA microarray indicate?

A) The probe hybridized to the sequences present in that spot
B) The probe did not hybridize to that particular gene
C) The experiment was not conducted correctly
D) That the probe was non-specifically trapped by the material present in the spot

5) _________ make it possible for researchers to study how an entire genome responds to an environmental stimulus.

A) Bioinformatics
B) PCR reactions
C) DNA microarrays
D) The BLAST program

6) Why is the proteome larger than the genome?

A) Different cell types contain different subsets of genes, making the proteome larger than the genome.
B) Not all genes are expressed in all cells at the same time, making the proteome larger than the genome.
C) Alternative splicing can lead to the production of several or many different polypeptides from the same pre-mRNA, increasing the number of proteins in the proteome.
D) The total amount of protein in a cell as measured by mass is always greater than the total amount of DNA.

7) What technique is used to separate cellular proteins for analysis?

A) PCR
B) Antibody microarrays
C) Two-dimensional gel electrophoresis
D) Functional protein microarrays

8) In a two-dimensional gel electrophoresis experiment, proteins are generally separated vertically by __________.

A) net charge
B) molecular mass
C) abundance
D) isoelectric point

9) In a two-dimensional gel electrophoresis experiment, proteins are separated horizontally by __________.

A) amino acid sequence
B) molecular mass
C) abundance
D) isoelectric point

10) The purpose of sodium dodecyl sulfate (SDS) in a two-dimensional gel electrophoresis experiment is that it allows proteins to separated __________.

A) by charge only
B) primarily by molecular mass
C) by size only
D) by net charge

11) Which technique can be used to identify a protein of interest after a two-dimensional gel electrophoresis experiment?

A) DNA microarray
B) Treatment with reverse transcriptase to isolate the DNA of interest
C) BLAST analysis
D) Mass spectrometry

12) What technique can be used to identify a protein's function?

A) Functional protein microarray
B) Antibody microarray
C) DNA microarray
D) RNA microarray

13) The program BLAST would bebest used for what purpose?

A) Determining what restriction sites are present in a fragment of DNA
B) Identifying a promoter sequence
C) Identifying splice donor and acceptor sites
D) Identify related sequences to a given DNA sequence in a database

14) What type of molecule is used in a protein microarray to measure protein expression?

A) cDNA
B) mRNA
C) Single-stranded DNA
D) Antibodies

15) What type of computer based search methodology would most likely be used to identify a potential promoter for a gene in a nucleotide sequence?

A) Search-by-signal
B) Search-by-content
C) Search-by-identity
D) Search-by-recognition

16) What is the term for two genes from two different species that are similar in sequence and serve the same function in each species?

A) Related genes
B) Paralogs
C) Gene family
D) Orthologs

17) The genes of a gene family that consist of two or more homologous genes are called __________.

A) orthologs
B) paralogs
C) polylogs
D) homologs

18) A database is defined as __________.

A) a large collection of files stored in one place
B) a small collection of files that are stored in different places
C) files that are only used by the BLAST program
D) a large collection of files that are not annotated

19) _______ can be used to determine the amino acid sequence of a protein or peptide.

A) X-raycrystallography
B) Nuclear magnetic resonance
C) Mass spectrometry
D) The ChIP assay

20) DNA microarrays may be paired with chromatin immunoprecipitation (ChIP) to __________.

A) assay the use of substrates by different enzymes
B) determine mRNA folding patterns
C) identify DNA sequences bound by specific proteins
D) identifyprotein-protein interactions

21) Gene knockouts in mice can be useful because __________.

A) they can be used to develop models of human disease
B) they identify DNA binding proteins
C) they limit mRNA production both from the knockout as well as the normal allele in diploids
D) only genes that are actively transcribed in the embryo are susceptible to being knocked out

22) What would be the most reasonable technique to use to determine if a drug is capable of inhibiting the binding of a transcription factor?

A) ChIP assay
B) Mass spectrometry of proteins in the cell
C) 2-D gel electrophoresis
D) Antibody microarray

23) A population of cells is treated with a polypeptide hormone that induces mitosis and the hormone's cell surface receptor is isolated after 15 minutes and subjected to fragmentation and mass spectrometry. Several of the peaks show a slight shift as compared to the same protein from cells not treated with the hormone. What is the most likely explanation of this phenomenon?

A) Phosphorylation of some amino acid residues
B) mRNA editing resulting in a slightly different amino acid sequence
C) Alternative exon usage
D) Proteolytic processing

24) The term that best describes how the components of a genome interact to produce an organism's traits is __________.

A) proteomics
B) functional genomics
C) structural genomics
D) genomics

25) _________ involves an examination of how the proteins encoded by genes interact to produce cell and tissue types.

A) Proteomics
B) Functional genomics
C) Structural genomics
D) Genomics

26) A multiple sequence alignment is shown for a kinase that is highly conserved among species. What amino acid do you predict is essential for function of the kinase? Dots are indicative of gaps where the sequences do not line up.
Species 1 SGPEDPAFTWRAAVTTNQGWEDTTNVAY
Species 2 SGLEDPAFTWR.............NQGWEDTTNVAQ
Species 3 AAPEDPAFTWRAAVTTLLGWEDTTNVAY
Species 4 ...........DPLSCWRAAVTTN.............TTNVAY
Species 5 SGPEDEAFTCCAAVTTNQGWEDSSNVCY
Species 6 SGPEDPAFTWRAAVTTNQGWEDTT...........

A) D in position 5
B) S in position 1
C) W in position 10
D) T in position 23
E) V in position 26

27) Amino acids froma hypothetical proteasefromHomo sapiensare compared to the same protease in other species using the BLAST program.The following results are obtained. The sequence from whichspecies has the highest E value?
H. sapiens SSTNQLLKHRRAALSTMVIITNQKRSAA
P. catodon SSTNQLLKHRSAALSTMVIITNQKRSAA
M. mulatta SSTNQIIKHRRAALSTMVLLTNQKRSAK
F. cattus ASTNQLLKHRSAALSTMVIITNQKRSAK
C. cristata SSTNQLLKHRRAALSTMVIITNQKRSAA

A) P. catodon

B) M. mulatta

C) F. cattus

D) C. cristata

28) In two dimensional gel electrophoresis, proteins are first treated with SDS, separated according to molecular mass, and then separated by their net charge at a specific pH.

⊚ true
⊚ false

29) A pattern recognition algorithm examines a string of nucleotides for sections that match a specific sequence parameter.

⊚ true
⊚ false

30) Two genes that share a common ancestral gene will probably have significant homology.

⊚ true
⊚ false

31) cDNA uses chromosomal DNA as its template.

⊚ true
⊚ false

32) A functional protein microarray can be used to establish the function or substrates for a given group of proteins.

⊚ true
⊚ false