mcb3020 4c 2
What is a common nucleotide range for a bacterial genome? Multiple choice question. 1-5 kilobases 1-5 megabases 100-500 megabases
1-5 megabases
ow do the genome sizes of archaea and bacteria compare? Multiple choice question. Archaea have, in general, smaller genomes than bacteria. Archaea have, in general, larger genomes than bacteria. Archaea and bacteria have similarly-sized genomes.
Archaea have, in general, smaller genomes than bacteria.
DNA alignment programs using a basic local alignment search tool are called ___ programs.
BLAST
Two technologies to study the expression level of many genes are _____ and _____. Multiple select question. Tn-Seq ChIP DNA microarrays RNA-Seq bioinformatics CRISPR
DNA microarrays RNA-Seq
In an electrophoretic mobility shift assay, a protein and the DNA fragment that it binds are mixed and then applied to a gel. How does the mobility of the DNA change upon protein binding? Multiple choice question. The protein-bound DNA moves faster than free DNA. The protein-bound DNA moves slower than free DNA.
The protein-bound DNA moves slower than free DNA.
A molecule of dGTP and a molecule of ddGTP are both able to pair with a cytosine residue in DNA. True false question. True False
True
A base-by-base comparison of two or more gene sequences is called a(n) ___
alignment
The science of manipulating and interpreting large quantities of information about biological organisms is called ___. It incorporates biology, mathematics, computer science, and statistics.
bioinformatics
An open reading frame that is presumed to encode a protein is called a __ sequence.
coding
Functional proteomics focuses on ___ and ___. Multiple select question. how proteins interact in the cell how proteins are expressed which proteins are exported how proteins are regulated
how proteins interact in the cell how proteins are regulated
In the first dimension of two-dimensional gel electrophoresis, proteins move through a pH gradient. This technique is called ___focusing.
isoelectric
Match the organism to the disease that it causes. Instructions leprosy tuberculosis Mycobacterium leprae Mycobacterium bovis
leprosy: Mycobacterium leprae tuberculosis: Mycobacterium bovis
Each spot of DNA on a microarray, representing a single gene or coding sequence, is called a __
probe
Two-dimensional gel electrophoresis is used to study mixtures of _____. Multiple choice question. proteins proteins and cDNA proteins and mRNA cDNA and mRNA
proteins
In preparation for mass spectrometry, a protein spot is cut from a gel and treated with ______. Multiple choice question. restriction enzymes a pH gradient proteolytic enzymes gel buffer
proteolytic enzymes
the entire collection of proteins that an organism produces is called its __
proteome
The study of the array of proteins that an organism produces is called ___
proteomics
When using a BLAST program to compare a DNA sequence of interest to a large database of sequences, the sequence of interest is called the _____. Multiple choice question. E value hit query
query
One advantage of metagenomic studies is that the sequences generated _______. Multiple choice question. can be manipulated in silico reflect the diversity of only the organisms that can be cultivated are generally homologous to those already in the database reflect the diversity in the environment
reflect the diversity in the environment
In tandem MS, the first spectrometer ______. Multiple choice question. determines the amino acid sequence performs isoelectric focusing separates proteins and peptide fragments
separates proteins and peptide fragments
To study gene expression by microarray technology, hybridization is performed between the single-stranded probe DNA and _______. Multiple choice question. single-stranded cDNA made from mRNA double-stranded cDNA made from mRNA single-stranded mRNA
single-stranded cDNA made from mRNA
In a DNA sequencing reaction, the DNA is sometimes immobilized on materials like beads or glass slides. These materials are called ___substrates.
solid
The phenomenon of orthologous genes being organized similarly in related organisms is called __
synteny
The Sanger method for DNA sequencing requires _____. Multiple choice question. ATP hydrolysis synthesis of a new RNA strand synthesis of a new DNA strand chemical degradation of a DNA strand
synthesis of a new DNA strand
The entire collection of mRNAs produced by an organism is its ___
transcriptome
Genome curation involves _____. Multiple choice question. establishing databases to maintain genomic data verifying the assignments identified by computer analysis identifying potential genes within a genome sequence storing representative microbes for future research
verifying the assignments identified by computer analysis
Which of the following environmental insults is Deinococcus radiodurans able to withstand? Multiple choice question. γ-radiation Cold temperatures High pressure Chloroform exposure
γ-radiation
Methods for DNA sequencing were developed at what time? Multiple choice question. 2000s 1970s 1950s
1970s
In automated DNA sequencing by the Sanger method, the products of the reaction are detected by ____. Multiple choice question. a fluorescent tag a radioactive label an antibody
a fluorescent tag
Single cell genomic sequencing is an important advance because ________. Multiple choice question. many types of bacteria cannot be cultured many types of bacteria are pathogens many cells have only a single copy of their chromosome
many types of bacteria cannot be cultured
The DNA to be copied in a Sanger sequencing reaction is called the _____. Multiple choice question. replicate primer template
template
The results of a DNA sequencing run are shown here. What type of sequencing reaction generated these results? Multiple choice question. Automated Sanger DNA sequencing Metagenomic sequencing Next-generation sequencing Sequencing by synthesis
Automated Sanger DNA sequencing
Which of the following is the term used to describe the process of studying the similarities between the nucleotide and protein sequences of different organisms? Multiple choice question. Bioinformatics Comparative genomics Functional genomics Systems biology
Comparative genomics
Order the following steps in RNA-Seq. Instructions Align results with genome sequence. Add adapter sequences. Sequence using NGS. Convert mRNA to cDNA.
Convert mRNA to cDNA. Add adapter sequences. Sequence using NGS. Align results with genome sequence.
The Sanger method for DNA sequencing involves synthesis of a new strand of DNA by the enzyme ______. Multiple choice question. Reverse transcriptase RNA polymerase DNA polymerase
DNA polymerase
Which two methods needed to be developed for efficient bacterial genome sequencing? Multiple select question. DNA sequence assembly software Fluorescent labels conjugated to nucleotides PCR on solid supports Whole genome shotgun sequencing
DNA sequence assembly software Whole genome shotgun sequencing
Comparative genomics involves which two of the following types of analysis? Multiple select question. Metabolomics In silico translation of nucleic acids DNA-DNA sequence comparisons Protein-protein sequence comparisons
DNA-DNA sequence comparisons Protein-protein sequence comparisons
ddNTPs and dNTPs differ in which portion of the nucleotide? Multiple choice question. Ribose sugar Phosphate group Deoxyribose sugar Nitrogenous base
Deoxyribose sugar
Which two of the following are goals of the field of structural proteomics? Multiple select question. Determining the three-dimensional structures of proteins Correlating protein abundance and expression data Correlating genome structures with protein expression Predicting the structures of proteins by modeling
Determining the three-dimensional structures of proteins Predicting the structures of proteins by modeling
Microbiologists involved in systems biology may study a single metabolic pathway in isolation to work out the minute details of molecular systems interactions. True false question. True False
False
In the second dimension of the two-dimensional gel electrophoresis, how do proteins migrate? Multiple choice question. From the positive pole of the gel to the negative pole. They are uncharged so they do not migrate at all. From the negative pole of the gel to the positive pole.
From the negative pole of the gel to the positive pole.
Which of the following can be validly concluded about this DNA sequence? Multiple choice question. It cannot encode a protein because neither strand has an ATG. It cannot encode a protein because there is no ribosome binding site. It can encode an internal portion of a protein because one reading frame has no stops
It can encode an internal portion of a protein because one reading frame has no stops.
Why is DNA sequencing performed on a solid substrate? Multiple choice question. Reactions proceed much faster when the DNA is immobilized rather than in solution. DNA sequencing reagents are more stable in solid phase. It does not require preparation of a genomic library.
It does not require preparation of a genomic library.
What information is obtained about a protein from two-dimensional gel electrophoresis and mass spectrometry? Multiple choice question. Its probable amino acid sequence Its probable amino acid composition The size of the proteolytic fragments
Its probable amino acid composition
Which of the following statements is correct regarding structural proteomics? Multiple choice question. Known protein structures can be used to predict the structures of related proteins. It is believed that proteins can fold into an infinite number of shapes. Structural proteomics researchers group proteins according to their molecular weight.
Known protein structures can be used to predict the structures of related proteins.
What are the four stages of whole-genome shotgun sequencing? Multiple choice question. Library construction, random sequencing, fragment alignment and gap closure, and editing. Library construction, random sequencing, fluorescence detection, and editing. Library construction, PCR amplification, Sanger sequencing, and editing.
Library construction, random sequencing, fragment alignment and gap closure, and editing.
As a representation of the number of genes, genome size is measured in ____. Multiple choice question. ORFs megabytes (Mb) megabases (Mb)
ORFs
What type of information is generated by proteomics? Multiple choice question. Subcellular localization of proteins Whether the protein is secreted Post-translational modification of proteins
Post-translational modification of proteins
Metatranscriptomics is best described as the study of _____. Multiple choice question. RNA molecules produced by a cell under specific conditions DNA molecules obtained from an environment RNA molecules obtained from an environment RNA molecules that are downregulated under specific conditions
RNA molecules obtained from an environment
It is now possible to directly sequence mRNA, in a process called _____. Multiple choice question. reverse transcription isoelectric focusing Sanger sequencing RNA-Seq
RNA-Seq
In hierarchical cluster analysis, the results are imaged in which colors? Multiple choice question. Red, yellow, green Red, green, black Red and green
Red, green, black
Which of the following elements must be present in an open reading frame for it to be considered a putative protein-coding gene? Multiple select question. Ribosome binding site Stop codon Promoter sequence At least 100 codons
Ribosome binding site At least 100 codons
Which two effects does SDS (sodium dodecyl sulfate) have on proteins? Multiple select question. SDS coats protein with a negative charge. SDS precipitates proteins from solution. SDS denatures protein. SDS raises the pH of a protein.
SDS coats protein with a negative charge. SDS denatures protein.
The second dimension in two-dimensional gel electrophoresis is ______. Multiple choice question. isoelectric focusing SDS polyacrylamide gel electrophoresis agarose gel electrophoresis
SDS polyacrylamide gel electrophoresis
Which of the following scientists developed the most commonly used method of sequencing DNA? Multiple choice question. Venter Watson and Crick Maxam and Gilbert Sanger
Sanger
In the second dimension of the two-dimensional gel electrophoresis, how do proteins migrate? Multiple choice question. The smallest peptide travels farthest on the gel. The most negatively-charged peptide travels farthest on the gel. The largest peptide travels farthest on the gel. The most positively-charged peptide travels farthest on the gel.
The smallest peptide travels farthest on the gel.
Which of the following would be a possible application of microarray technology for the study of gene expression? Multiple choice question. To determine the abundance of tRNAs within the cell. To determine how often initiation occurs at the origin of replication. To determine how gene expression is regulated in response to environmental changes.
To determine how gene expression is regulated in response to environmental changes.
Systems biologists recognize that the change of a single gene or protein may have far-reaching physiological effects for the cell. True false question. True False
True
The analysis of gene expression using microarray technology is based on hybridization between nucleic acids. True false question. True False
True
Which of the following scientists developed methods for whole genome shotgun sequencing? Multiple choice question. Venter and Smith Maxam and Gilbert Watson and Crick Sanger
Venter and Smith
Approximately how much DNA is present in a single bacterial cell? Multiple choice question. a few micrograms (10-6 grams) a few nanograms (10-9 grams) a few picograms (10-12 grams) a few femtograms (10-15 grams)
a few femtograms (10-15 grams)
In massively parallel sequencing techniques, the DNA to be sequenced is sheared into small pieces, and small oligonucleotides called ___ are attached to the ends of the DNA fragments.
adapters
In massively parallel sequencing techniques, the DNA to be sequenced is sheared into small pieces and small oligonucleotides called adapters are attached to the ends of the DNA fragments. These adapters function to ___ and ___. Multiple select question. produce the dNTPs required in the reaction anneal to a PCR primer attach the DNA fragment to a solid substrate attach the DNA fragment to Taq polymerase
anneal to a PCR primer attach the DNA fragment to a solid substrate
Determining the location and nature of genes on a newly sequenced genome is called genome
annotation
Determining the location and nature of genes on a newly sequenced genome is called genome ___
annotation
To identify an open reading frame in DNA sequence, the sequence of _____ must be analyzed. Multiple choice question. both strands for a total of six reading frames both strands for a total of three reading frames one strand for a total of three reading frames
both strands for a total of six reading frames
Lysogenic conversion genes are genes from temperate bacteriophage that _____. Multiple choice question. change the phenotype of the host cell change the secretion processes of the cell encode lytic enzymes alter the life cycle of the cell
change the phenotype of the host cell
The four deoxynucleoside triphosphates are ____, ____, ____, and ____. Multiple choice question. ATP, GTP, TTP, CTP dATP, dGTP, dUTP, dCTP ddATP, ddGTP, ddTTP, ddCTP dATP, dGTP, dTTP, dCTP
dATP, dGTP, dTTP, dCTP
The first step of RNA-Seq requires which two of the following components? Multiple select question. NTPs dNTPs RNA polymerase reverse transcriptase thermostable DNA polymerase ATP
dNTPs reverse transcriptase
In tandem MS, the second spectrometer _____. Multiple choice question. separates proteins and fragments determines the amino acid sequence performs isoelectric focusing
determines the amino acid sequence
In the output of a BLAST program, the hits are each given a(n) __ value, which measures the probability of obtaining that alignment by chance.
e
In a microarray hybridization experiment, the target nucleotides are labeled with ______. Multiple choice question. heavy isotopes fluorescent dyes radioactive nucleotides
fluorescent dyes
In addition to a primer, which two of the following are required for the Sanger method of DNA sequencing? Multiple select question. four ddNTPs four dNTPs and one ddNTP four dNTPs four NTPs three dNTPS and UTP
four ddNTPs four dNTPs
The process of placing the information from a genome sequence into a biological context is called __ genomics.
functional or comparative
Two technologies, RNA-Seq and DNA microarrays, are important in the study of _____. Multiple choice question. gene expression genome sequence proteomics mutagenesis
gene expression
In hierarchical cluster analysis, __________. Multiple choice question. genomes are grouped according to phylogenetic position genes are grouped according to chromosome position genes are grouped according to level of expression
genes are grouped according to level of expression
The process of predicting genes (often by computer programs) and inspecting the assignments to verify the prediction is termed _____. Multiple choice question. genome annotation genome curation genome sequencing next-generation sequencing
genome curation
A section of a genome that is derived from a mobile genetic element is called a(n) ___ island.
genomic
The output of a BLAST program is called a(n) _____. Multiple choice question. query E value hit
hit
The advantage of two-dimensional gel electrophoresis over one-dimensional gel electrophoresis is that ______. Multiple choice question. it permits the study of more complex organisms it provides a 3d structure of the proteins under study it permits visualization of thousands of proteins
it permits visualization of thousands of proteins
Match these "-omics" terms with their field of study. Instructions lipidomics glycomics metabolomics small molecule profiles cellular lipid profiles cellular carbohydrate profiles
lipidomics: cellular lipid profiles Glycomics: cellular carbohydrate profiles metabolics: small molecule profiles
In massively parallel sequencing techniques, the DNA to be sequenced is amplified by PCR. This results in ___________. Multiple choice question. many copies of the same fragment, which are sequenced simultaneously many copies of the same fragment, which are sequenced sequentially copies of the fragment which differ in length and terminate with a dideoxynucleotide
many copies of the same fragment, which are sequenced simultaneously
An open reading frame (ORF) encodes a _____. Multiple choice question. ribosomal RNA regulatory RNA transfer RNA messenger RNA
messenger RNA
The systematic study of a cell's small molecules at a particular time is called __
metabolomics
The study of RNA molecules obtained directly from the environment is _____. Multiple choice question. structural proteomics transcriptomics metagenomics metatranscriptomics
metatranscriptomics
The study of RNA molecules obtained directly from the environment is _____. Multiple choice question. transcriptomics structural proteomics metatranscriptomics metagenomics
metatranscriptomics
For transcriptome analysis, a solid support with DNA attached in an organized grid fashion is called a DNA ___
microarray
A common method to study protein-DNA interaction is EMSA, an electrophoretic __ __ assay.
mobility Blank 2: shift
In isoelectric focusing, proteins are applied to what kind of gradient? Multiple choice question. Agarose Temperature Acrylamide Denaturant pH
pH
The smallest genomes in all three domains belong to _____. Multiple choice question. parasitic microbes bacteriophage pathogens methanogens photosynthesizers
parasitic microbes
A section of a genome that is derived from a mobile genetic element and encodes virulence factors is called a(n) __ island
pathogenic
Comparative genomics reveals that horizontal gene transfer has occurred frequently. This type of transfer may be mediated by _____. Multiple select question. liposomes plasmids RecA bacteriophage histones
plasmids bacteriophage
In contrast to Sanger DNA sequencing which uses long genomic DNA strands, next-generation sequencing technologies use _____. Multiple choice question. DNAs synthesized in vitro with ddNTPs short pieces of DNA with adapters at each end PCR products with adapters at each end denatured RNA with adapters at each end
short pieces of DNA with adapters at each end
The process of DNA sequencing of a bacterial genome by constructing a genomic library is called whole-genome ___ sequencing.
shotgun
The template for the Sanger method of DNA sequencing is _____. Multiple choice question. double stranded DNA single stranded DNA
single stranded DNA
In a microarray hybridization experiment, the level of expression of each gene is quantified by ___ and ___. Multiple select question. the concentration of the fluorescent dye the color of the fluorescent dye the identity of the fluorescent dye the intensity of the fluorescent dye
the color of the fluorescent dye the intensity of the fluorescent dye
In a metagenomic analysis, DNA is extracted from ________. Multiple choice question. the environment under study the predominant organisms in the environment each organism in the environment
the environment under study
In the RNA-seq process of mRNA sequencing, the mRNA is quantified by measuring ___. Multiple choice question. the abundance of each mRNA relative to a control RNA the number of reads that match the mRNA pool the number of reads that match each gene
the number of reads that match each gene
Functional genomics is best described as _____. Multiple choice question. identifying growth conditions under which genes are expressed the process of determining the function of genes that lack orthologues the process of placing genomic sequence information into a biological context identifying the ecological role of organisms identified only be metagenomics
the process of placing genomic sequence information into a biological context
The entire collection of mRNAs produced by an organism is its _____. Multiple choice question. transcriptome genome proteome
transcriptome mRNA= transcript