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