Week 10 Assignment MCB3020
What is a common nucleotide range for a bacterial genome?
1-5 megabases
Methods for DNA sequencing were developed at what time?
1970s
Which two of the following examples represent situations that might be studied by transcriptomics via microarrays?
A comparison of genes expressed in a microbe when growing in pure culture and when growing symbiotically A comparison of genes expressed in mutant and wild type strains
Two species of Bacillus, for example B. anthracis and B. cereus, would be expected to exhibit what degree of synteny in their chromosomes?
A high level of synteny
How do the genome sizes of archaea and bacteria compare?
Archaea have, in general, smaller genomes than bacteria.
A section of a genome that is derived from a mobile genetic element is called a(n) _________ island.
Blank 1: genomic
A common method to study protein-DNA interaction is EMSA, an electrophoretic ________ ________ assay.
Blank 1: mobility Blank 2: shift
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?
Comparative genomics
Two technologies to study the expression level of many genes are Blank______ and Blank______.
DNA microarrays RNA-Seq
The Sanger method for DNA sequencing involves synthesis of a new strand of DNA by the enzyme
DNA polymerase
Which two methods needed to be developed for efficient bacterial genome sequencing?
DNA sequence assembly software Whole genome shotgun sequencing
ddNTPs and dNTPs differ in which portion of the nucleotide?
Deoxyribose sugar
Which two of the following are examples of metagenomic studies?
Determining the genomic sequences of organisms present in a marine sponge. Determining the 16S rRNA sequences present in the human mouth.
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
Why is so little known about Treponema pallidum?
It cannot be cultured in vitro.
Why is DNA sequencing performed on a solid substrate?
It does not require preparation of a genomic library.
Which fact about Treponema pallidum was inferred from its genome sequence?
It lacks TCA cycle enzymes.
What information is obtained about a protein from two-dimensional gel electrophoresis and mass spectrometry?
Its probable amino acid composition
What are the four stages of whole-genome shotgun sequencing?
Library construction, random sequencing, fragment alignment and gap closure, and editing.
What type of information is generated by proteomics?
Post-translational modification of proteins
Comparative genomics involves which two of the following types of analysis?
Protein-protein sequence comparisons DNA-DNA sequence comparisons
In hierarchical cluster analysis, the results are imaged in which colors?
Red, green, black
Which two effects does SDS (sodium dodecyl sulfate) have on proteins?
SDS denatures protein. SDS coats protein with a negative charge.
The second dimension in two-dimensional gel electrophoresis is
SDS polyacrylamide gel electrophoresis
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?
The protein-bound DNA moves slower than free DNA.
True or false: A molecule of dGTP and a molecule of ddGTP are both able to pair with a cytosine residue in DNA.
True
Which of the following scientists developed methods for whole genome shotgun sequencing?
Venter and Smith
Approximately how much DNA is present in a single bacterial cell?
a few femtograms (10-15 grams)
A base-by-base comparison of two or more gene sequences is called a(n)
alignment
The field of transcriptomics is the study of
all RNAs produced at any one time by an organism
The core genome consists of those genes found in Blank______ member(s) of a species or other taxon being compared, whereas the pan-genome consists of those genes found in Blank______ member(s) of the species or taxon.
all/any
Determining the location and nature of genes on a newly sequenced genome is called genome
annotation
Fill in the blank question. Genes that encode informational proteins involved in DNA replication, transcription, and translation are generally considered to be a part of the _____________ genome of a species
core
The four deoxynucleoside triphosphates are
dATP, dGTP, dTTP, dCTP
The first step of RNA-Seq requires which two of the following components?
dNTPs reverse transcriptase
In tandem MS, the second spectrometer _____.
determines amino acid sequence
The most frequently used next generation sequencing technique takes place in a
flow cell
In hierarchical cluster analysis, Blank______.
genes are grouped according to level of expression
The process of manually inspecting and assessing computer gene prediction is termed
genome curation
The output of a BLAST program is called a(n)
hit
Functional proteomics focuses on Blank______ and Blank______.
how proteins are regulated how proteins interact in the cell
Fill in the blank question. In the first dimension of two-dimensional gel electrophoresis, proteins move through a pH gradient. This technique is called ______ focusing.
isoelectric
The advantage of two-dimensional gel electrophoresis over one-dimensional gel electrophoresis is that
it permits visualization of thousands of proteins
The study of RNA molecules obtained directly from the environment is
metatranscriptomics
For transcriptome analysis, a solid support with DNA attached in an organized grid fashion is called a DNA
microarray
The smallest genomes in all three domains belong to
parasitic microbes
The most frequently used next generation sequencing technique is
reversible chain termination sequencing
In tandem MS, the first spectrometer Blank______.
separates proteins and peptide fragments
Next genomic sequencing (NGS) methods differ from Sanger DNA sequencing in several ways. Rather than sequence long genomic DNAs, NGS methods sequence Blank______.
short pieces of DNA attached to a solid substrate
Genome curation involves
verifying the assignments identified by computer analysis
Parasitic microbes are distinctive in that their genome structure is Blank______.
very small
Which element is not required in an open reading frame for it to be considered a putative protein-coding gene? -35 and -10 promoter sequences At least 100 codons Transcriptional terminator sequence at the 3' end A ribosome binding site
-35 and -10 promoter sequences
Order the following steps in RNA-Seq
1. Convert mRNA to cDNA 2. ADD ADAPTER SEQUENCES 3. sequence using NGS' 4. Align results with genome sequence
Fill in the blank question. A section of a genome that is derived from a mobile genetic element and encodes virulence factors is called a(n) _________ island.
Blank 1: pathogenicity, pathogenic, or pathogen
The field of study that seeks to integrate cellular components with pathways for metabolism, regulation, and microbial behavior is ______ biology.
Blank 1: systems or system
Which two of the following are goals of structural proteomics?
Determining the three-dimensional structures of proteins Predicting the structures of proteins by modeling
Which two genes are most likely a part of the core genome?
Gene encoding the sigma subunit of RNA polymerase Gene encoding a ribosomal protein
What is the core genome?
Genes that are common to all members of a species (or other monophyletic taxonomic group)
The second dimension in two-dimensional gel electrophoresis is __________.
SDS polyacrylamide gel electrophoresis
Which of the following scientists developed the most commonly used method of sequencing DNA?
Sanger
Which statement about synthetic biology is correct?
Systems biologists recognize that the change of a single gene or protein may have far-reaching physiological effects for the cell.
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 Blank______ and Blank______.
attach the DNA fragment to a solid substrate anneal to a PCR primer
The science of manipulating and interpreting large quantities of information about biological organisms is called _____ It incorporates biology, mathematics, computer science, and statistics.
bioinformatics
Lysogenic conversion genes are genes from temperate bacteriophages that
change the phenotype of the host cell
An open reading frame that is presumed to encode a protein is called a ________ sequence.
coding
In addition to a primer, which two of the following are required for the Sanger method of DNA sequencing?
four ddNTPs four dNTPs
Two technologies, RNA-Seq and DNA microarrays, are important in the study of
gene expression
In massively parallel sequencing techniques, the DNA to be sequenced is amplified by PCR. This results in
many copies of the same fragment, which are sequenced simultaneously
Single cell genomic sequencing is an important advance because
many types of bacteria cannot be cultured
DNA sequencing methods that sequence thousands of identical DNA fragments at the same time are referred to as
massively parallel sequencing
An open reading frame (ORF) encodes a Blank______. Multiple choice question.
messenger RNA
The systematic study of a cell's small molecules at a particular time is called .
metabolomics
The process of studying the genomes present in an environment is called
metagenomics
Technologies developed to sequence DNA faster and more cheaply are referred to as_____ sequencing
next generation
Comparative genomics reveals that horizontal gene transfer has occurred frequently. This type of transfer may be mediated by
plasmids bacteriophages
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
proteins
In preparation for mass spectrometry, a protein spot is cut from a gel and treated with
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
query
In contrast to Sanger DNA sequencing which uses long genomic DNA strands, next-generation sequencing technologies use
short pieces of DNA with adapters at each end
Fill in the blank question. 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 Blank______.
single stranded DNA
To study gene expression by microarray technology, hybridization is performed between the single-stranded probe DNA and
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 Blank______.
synthesis of a new DNA strand
In a microarray hybridization experiment, the level of expression of each gene is quantified by Blank______ and Blank______.
the intensity of the fluorescent dye the color of the fluorescent dye
Two limitations of Sanger sequencing (in the context of whole genome sequencing) are that it is
time-consuming expensive
The entire collection of mRNAs produced by an organism is its
transcriptome