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