MCB Exam 3
solid substrates
In a DNA sequencing reaction, the DNA is sometimes immobilized on materials like beads or glass slides. These materials are called
the environment under study
In a metagenomic analysis, DNA is extracted from ________.
True
PCR can be used to amplify DNA from any source.
dATP, dGTP, dTTP, dCTP
The four deoxynucleoside triphosphates are ____, ____, ____, and ____.
Venter and Smith
Which of the following scientists developed methods for whole genome shotgun sequencing?
alignment
A base-by-base comparison of two or more gene sequences is called
mobility shift assay
A common method to study protein-DNA interaction is EMSA, an electrophoretic
pathogenicity islands
A section of a genome that derived from a mobile genetic element and encodes virulence factors is called a(n)
genomic island
A section of a genome that is derived from a mobile genetic element is called a(n)
messenger RNA
An open reading frame (ORF) encodes a _____.
coding
An open reading frame that is presumed to encode a protein is called _____sequence.
a few femtograms (10-15 grams)
Approximately how much DNA is present in a single bacterial cell?
Protein-protein sequence comparisons DNA-DNA sequence comparisons
Comparative genomics involves which two of the following types of analysis?
plasmids bacteriophage
Comparative genomics reveals that horizontal gene transfer has occurred frequently. This type of transfer may be mediated by _____.
BLAST programs
DNA alignment programs using a basic local alignment search tool are called
annotation
Determining the location and nature of genes on a newly sequenced genome is called genome
True
During the PCR, the hydrogen bonds of the double-stranded DNA molecules are broken by the enzyme helicase
probe
Each spot of DNA on a microarray, representing a single gene or coding sequence, is called a
microarrays
For transcriptome analysis, a solid support with DNA attached in an organized grid fashion is called a DNA
the process of placing genomic sequence information into a biological context
Functional genomics is best described as _____.
how proteins interact in the cell how proteins are regulated
Functional proteomics focuses on
verifying the assignments identified by computer analysis
Genome curation involves _____.
Genome size is measured in ____.
Genome size is measured in ____.
a. The molecular organization of genomes b. The gene products that genomes encode c. All of the choices are correct d. The information content of genomes
Genomics is the study of
Archaea have, in general, smaller genomes than bacteria.
How do the genome sizes of archaea and bacteria compare?
64
If you start with one double-stranded DNA molecule and you perform SIX cycles of PCR, how many double-stranded copies of the DNA will you have?
the intensity of the fluorescent dye the color of the fluorescent dye
In a microarray hybridization experiment, the level of expression of each gene is quantified by _____. (Choose two.)
four ddNTPs four dNTPs
In addition to a primer, which two of the following are required for the Sanger method of DNA sequencing?
The protein-bound DNA moves slower than free DNA.
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?
a fluorescent tag
In automated DNA sequencing by the Sanger method, the products of the reaction are detected by ____.
short pieces of DNA with adapters at each end
In contrast to Sanger DNA sequencing which uses long genomic DNA strands, next-generation sequencing technologies use _____.
genes are grouped according to level of expression
In hierarchical cluster analysis, __________.
Red, green, black
In hierarchical cluster analysis, the results are imaged in which colors?
pH
In isoelectric focusing, proteins are applied to what kind of gradient?
many copies of the same fragment, which are sequenced simultaneously
In massively parallel sequencing techniques, the DNA to be sequenced is amplified by PCR. This results in ___________.
proteolytic enzymes
In preparation for mass spectrometry, a protein spot is cut from a gel and treated with ______.
separates proteins and peptide fragments
In tandem MS, the first spectrometer ______.
determines the amino acid sequence
In tandem MS, the second spectrometer _____.
the amount of reads that match each gene
In the RNA-seq process of mRNA sequencing, the mRNA is quantified by measuring
isoelectric focusing
In the first dimension of two-dimensional gel electrophoresis, proteins move through a pH gradient. This technique is called
E
In the output of a BLAST program, the hits are each given a(n)____ value, value, which measures the probability of obtaining that alignment by chance.
From the negative pole of the gel to the positive pole.
In the second dimension of the two-dimensional gel electrophoresis, how do proteins migrate?
The smallest peptide travels farthest on the gel.
In the second dimension of the two-dimensional gel electrophoresis, how do proteins migrate?
RNA-Seq
It is now possible to directly sequence mRNA, in a process called _____.
change the phenotype of the host cell
Lysogenic conversion genes are genes from temperate bacteriophage that _____
1970s
Methods for determining DNA sequence were developed at what time?
tuberculosis
Mycobacterium bovis
leprosy
Mycobacterium leprae
reflect the diversity in the environment
One advantage of metagenomic studies is that the sequences generated _______.
convert mRNA to cDNA Add adapter sequences sequence using NGS Align results with genome sequence
Order the following steps in RNA-Seq.
many types of bacteria cannot be cultured
Single cell genomic sequencing is an important advance because ________.
Comparative genomics
Study of similarities between nucleotide and amino acid sequences among organisms to infer gene function and evolution is called
template
The DNA to be copied in a Sanger sequencing reaction is called the _____.
DNA polymerase
The Sanger method for DNA sequencing involves synthesis of a new strand of DNA by the enzyme ______.
synthesis of a new DNA strand
The Sanger method for DNA sequencing requires _____.
it permits visualization of thousands of proteins
The advantage of two-dimensional gel electrophoresis over one-dimensional gel electrophoresis is that ______.
transcriptome
The entire collection of mRNAs produced by an organism is its
dNTPs reverse transcriptase
The first step of RNA-Seq requires which two of the following components?
Hot vents
The most likely source of the Taq polymerase used in PCR is a bacterium that lives in ______.
hit
The output of a BLAST program is called a(n) _____.
Shotgun squencing
The process of DNA sequencing of a bacterial genome by constructing a genomic library is called whole-genome____
funcational
The process of placing the information from a genome sequence into a biological context is called________genomics.
genome curation
The process of predicting genes (often by computer programs) and inspecting the assignments to verify the prediction is termed _____.
bioinformatics
The science of manipulating and interpreting large quantities of information about biological organisms is called____. It incorporates biology, mathematics, computer science, and statistics.
SDS polyacrylamide gel electrophoresis
The second dimension in two-dimensional gel electrophoresis is
parasitic microbes
The smallest genomes in all three domains belong to _____.
metatranscriptomics
The study of RNA molecules obtained directly from the environment is _____.
proteomics
The study of the array of proteins that an organism can produce is called
metabolomics
The systematic study of a cell's small molecules at a particular time is called
single stranded DNA
The template for the Sanger method of DNA sequencing is _____.
both strands for a total of six reading frames
To identify an open reading frame in DNA sequence, the sequence of _____ must be analyzed.
single-stranded cDNA made from mRNA
To study gene expression by microarray technology, hybridization is performed between the single-stranded probe DNA and _______.
true
True or false: A molecule of dGTP and a molecule of ddGTP are both able to pair with a cytosine residue in DNA.
False
True or false: Microbiologists involved in systems biology may study a single metabolic pathway in isolation to work out the minute details of molecular systems interactions.
True
True or false: Systems biologists recognize that the change of a single gene or protein may have far-reaching physiological effects for the cell.
true
True or false: The analysis of gene expression using microarray technology is based on hybridization between nucleic acids.
A high level of synteny
Two species of Bacillus, for example B. anthracis and B. cereus, would be expected to exhibit what degree of synteny in their chromosomes?
DNA microarrays RNA-Seq
Two technologies to study the expression level of many genes are _____ and _____.
gene expression
Two technologies, RNA-Seq and DNA microarrays, are important in the study of _____.
proteins
Two-dimensional gel electrophoresis is used to study mixtures of _____.
Library construction, random sequencing, fragment alignment and gap closure, and editing.
What are the four stages of whole-genome shotgun sequencing?
Its probable amino acid composition
What information is obtained about a protein from two-dimensional gel electrophoresis and mass spectrometry?
1-5 megabases
What is a common nucleotide range for a bacterial genome?
Post-translational modification of proteins
What type of information is generated by proteomics?
Broadly affects gene expression and cellular physiology
When observing a microbe in which one gene has been deleted, you often find that the product of the missing gene
Paralogs
When two or more genes from the same genome have nucleotide sequences so alike that they most probably arose from gene duplication those genes are called _______.
query
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 _____.
Ribosome binding site At least 100 codons
Which of the following elements must be present in an open reading frame for it to be considered a putative protein-coding gene?
γ-radiation
Which of the following environmental insults is Deinococcus radiodurans able to withstand?
Comparative genomics
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?
Sanger
Which of the following scientists developed the most commonly used method of DNA sequencing DNA?
Known protein structures can be used to predict the structures of related proteins.
Which of the following statements is correct regarding structural proteomics?
To determine how gene expression is regulated in response to environmental changes.
Which of the following would be a possible application of microarray technology for the study of gene expression?
Whole genome shotgun sequencing DNA sequence assembly software
Which two methods needed to be developed for efficient bacterial genome sequencing?
Predicting the structures of proteins by modeling Determining the three-dimensional structures of proteins
Which two of the following are goals of the field of structural proteomics?
SDS denatures protein. SDS coats protein with a negative charge.
Which two of the following effects does SDS (sodium dodecyl sulfate) have on proteins?
It does not require preparation of a genomic library.
Why is DNA sequencing performed on a solid substrate?
Deoxyribose sugar
ddNTPs and dNTPs differ in which portion of the nucleotide?
attach the DNA fragment to a solid substrate anneal to a PCR primer
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 _____. (Choose two.)
The proteome
the entire set of proteins expressed by an organism