Deck 24: Genomics Ii: Functional Genomics, Proteomics, and Bioinformatics

Question 1

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.

Answer 1

A

Question 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

Answer 2

D

Question 3

________ 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

Answer 3

C

Question 4

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 5

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 6

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 size only
D) net charge

Question 7

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 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

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 10

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 11

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 12

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 13

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 14

What technique can be used to identify a proteins function?

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

Question 15

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) Many coding genes are transcribe into mRNA which can be alternatively spliced, and those transcripts produce different 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 16

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

Question 17

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 while each gene consists of three basic parts.

Question 18

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 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

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.

Question 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.

Question 22

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

Question 23

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.

Question 24

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.

Question 25

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 26

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

Question 27

________ 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 28

cDNA uses chromosomal DNA as its template.

Question 29

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 spectrometry of proteins in the cell
C) 2-D gel electrophoresis
D) Antibody microarray

Question 30

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

Question 31

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

Question 32

________ 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