Deck 23: Genomics II: Functional Genomics, Proteomics, and Bioinformatics

Question 1

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.

Answer 1

A

Question 2

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.

Answer 2

B

Question 3

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.

Answer 3

False

Question 4

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

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

Question 5

What technique can be used to identify a proteins function?

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

Question 6

The genes of a gene family that consist of two or more homologous genes are called ___.

A)Orthologs
B)Paralogs
C)Polylogs
D)Homologs

Question 7

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

Question 8

The program BLAST would be best 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 the Genbank database

Question 9

A cluster analysis is used when reading a DNA microarray to identify genes whose expression follow a similar patterns.

Question 10

Genetic sequences may be useful in predicting protein structure because

A) there is a high statistical frequency of specific amino acids within a given secondary structure
B) the folding of the protein is based on how the mRNA folds.
C) the physical and energetic properties of the DNA influence protein folding.
D) knowing what specific codons are used for each amino acid in the protein can help predict its structure.

Question 11

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)identify protein-protein interactions.

Question 12

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

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

Question 13

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

Question 14

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

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

Question 15

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

Question 16

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.

Question 17

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

Question 18

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

Question 19

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

Question 20

To identify a functional protein motif that might be shared by several different proteins what type of recognition strategy would most likely be used?

A) Pattern recognition
B) Sequence recognition
C) Identity recognition
D) Search-by-content

Question 21

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 spectometry. 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.

Question 22

In analyzing microarray data if the ratio of mRNA present before and after a particular treatment is 1 it indicates that

A)there was no change in mRNA levels before and after treatment.
B)the gene was not expressed either before or after treatment.
C)gene expression could not be detected.
D)mRNA was not detected before treatment.

Question 23

What is a reason that the proteome is larger than the genome?

A)Alternative splicing
B)Proteins are constantly being synthesized and degraded.
C)Each protein has a specific function which are quite varied while the genes in the genome are only transcribed
D)Each protein has multiple functional domains whille each gene consists of three basic parts.

Question 24

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

A) ChIP assay used with a DNA microarray
B) Mass spectometry of proteins in the cell
C) 2-D gel electrophoresis
D) Antibody microarray

Question 25

Why is the proteome larger than the genome?

A)Proteins may be modified by covalent addition of a variety of molecules
B)Not all genes are expressed in all cells at the same time
C)Each gene will produce multiple mRNAs which will produce multiple proteins so the ratio of the number of protein molecules the number of genes is greater than 1.
D)The total amount of protein in a cell as measured by mass is always greater than the total amount of DNA.

Question 26

In a two-dimensional gel electrophoresis experiment, proteins are separated horizontally by ____.

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

Question 27

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

A)by charge only
B)primarily by molecular mass
C)by a combination of both size and mass
D)net charge

Question 28

_________ 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

Question 29

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.

Question 30

The figure below represents the results of a DNA microarray experiment that compared a cell line before and after treatment with drug. What would be an appropriate conclusion to draw from this data?

A)At one hour post induction none of the mRNAs that are in the figure are producing protein
B)Some of the genes that are presented may have significant amounts of mRNA in the cell prior to induction.
C)The amount of protein for each gene presented will show a similar increase as the mRNA.
D)At seven hours post-induction the treated cells should have the maximal amount of mRNA for each gene.

Question 31

cDNA uses chromosomal DNA as its template.

Question 32

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

Question 33

What technique is used to separate cellular proteins for analysis?

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