Micro Exam 3

The phylogenetic analysis of complex microbial communities often targets small subunit (SSU) ribosomal RNA genes. This is because rRNA is found in all organisms and __________.

is highly conserved over evolutionary time

The term "phage" is generally reserved for the viruses that infect

Bacteria

The methodology of microbial ecology includes

enrichment and isolation of specific microbes, cell-staining, and gene, transcript, and protein characterization.

Which process listed below does NOT require homologous recombination to maintain the new genetic material in the recipient cell?

gene transfer through a genetic transfer agent

For microbial biodiversity studies, it is common to identify the ________ rather than the ________ as a measure of biodiversity.

genes / organisms themselves

A key concept in evolution is that all mutations are

random

What has occurred when organisms share a trait that was NOT inherited from a common ancestor?

convergent evolution

T/F At present there are four phyla in the domain Bacteria.

False

T/F The diversity of microorganisms in culture collections is representative of the diversity of microorganisms found in nature.

False

T/F The earliest nucleic acid was probably a simple DNA molecule.

False

Oxygen did not accumulate in the early atmosphere until it reacted with reduced materials, especially ________, in the oceans.

Ferrous Iron

A new chemotherapeutic agent is developed that alters the structure of all thymines in DNA. These thymines are then misread during the production of mRNA. Which of the following could NOT result from this type of mutation?

Frameshift Mutation

Which fluorescent molecule enables visualization of living microorganisms?

GFP

Why does the structure of plant and bacterial cells illustrate the reason for having few enveloped viruses that infect these cells?

Plant and bacterial cells contain cell walls that limit the virus from budding out and obtaining the envelope.

Chemical reactions involving ________ have been proposed as energy-yielding reactions for primitive organisms.

S, and H2

Competent cells are cells that

can take up DNA from their surrounding environment and integrate it into their own chromosomes by recombination.

Lysogeny probably carries a strong selective advantage for the host cell because it

confers resistance to infection by viruses of the same type.

A mutation that readily reverses to restore the original parental type would most likely be due to a(n)

point mutation

T/F Intercalating agents, like acridine orange and ethidium bromide, lead to mutagenesis by pushing DNA base pairs apart, which can lead to insertions or deletions.

TRUE

What most likely explains the recovery of live S strain cells from a mouse injected with heat-killed S strain mixed with live R strain cells?

The R strain picked up the S strain DNA, enabling it to produce a capsule.

What must occur for bacterial conjugation to take place?

The cells must come into contact with each other.

Which approach would help to identify biologically produced sulfur in a sediment sample?

isotopic fractionation

A silent mutation is so named because __________.

it has no effect on the overall amino acid sequence

T/F A lytic infection results in death of the host cell.

True

T/F In natural samples it is often difficult to differentiate live cells from dead cells or cells from nonliving matter.

True

T/F Oxygen was a driving factor in the formation of eukaryotic cells.

True

T/F Several fluorogenic dyes can be used simultaneously in a sample as long as they each emit light at a different measurable wavelength.

True

If a bacterium carrying a plasmid that confers resistance to ampicillin is placed into medium without ampicillin, it may

lose the plasmid because there is no selection for ampicillin resistance

Viruses go through phases during which they are actively replicating and destructive to the host cell, or dormant within the host cell. During which part of the bacteriophage life cycle will the viral genome be replicated in synchrony with the host cell?

lysogenic phase

Phylogenetic stains, such as those used in FISH, hybridize with

ribosomal RNA

Metagenomics involves the analysis of a microbial community by __________.

sampling and sequencing all of the genes in an environment

An organism that cannot synthesize methionine is called __________.

An auxotroph

Which of the following is true about viral infection?

Viruses are very specific in which cells they infect. For a virus to be taken up by a cell, it must find a cell with appropriate receptors on the surface. It cannot be taken up by cells without the appropriate receptors.

A change in the base sequence of DNA that is passed on to daughter cells is __________.

a mutation

Increasing genetic variability by the uptake of DNA from the environment is __________.

transformation

Reverse transcriptase is a(n)

RNA-dependent DNA polymerase.

A NASA ecologist wants to design an instrument to send to Mars on the next space probe to determine whether living organisms ever carried out carbon fixation on that planet. Suggest an assay that she could use on Martian soil samples.

13C/12C stable isotope analysis

Which of the following populations would be most likely to demonstrate genetic drift?

A researcher transfers bacteria into fresh medium but accidentally collects only a very small quantity of bacteria in the process.

What is the benefit, for a virus, to be a temperate or lysogenic virus?

A single infection event can produce millions of new viral particles instead of hundreds of viral particles.

The genetic code is degenerate. Which of the following answers describes an example of the degenerate nature of the code?

AUU, AUC, and AUA all code for Ile

Why would it be highly advantageous to a cell to form a mutualism with a prokaryote capable of aerobic cellular respiration?

Aerobic cellular respiration involves an electron transport chain with oxygen as the terminal electron acceptor. This produces large amounts of ATP as the electron transport chain produces the greatest amount of ATP in cellular respiration.

When determining the number of bacterial virus particles in a suspension, why is the number obtained always less than the actual viral titer?

Because all of the virus particles do not infect with 100% efficiency.

Which type of transposon would contain a gene for transposase?

Both simple and complex transposons

The major source of carbon was _________ for early cells and the major fuel for energy was __________ for early cells.

CO2 ; H2

Consider a mutation in which the change is from UAC to UAU. Both codons specify the amino acid tyrosine. Which type of point mutation is this?

Silent mutation

The element(s) that have proven useful for stable isotope studies are

Carbon, sulfur, nitrogen

What are the minimal components needed for a virion?

Caspid and genome

How do complex transposons differ from simple transposons?

Complex transposons code for additional genetic elements, such as antibiotic resistance genes; simple transposons only code for the transposase gene essential for the tranposon itself.

Bacterial conjugation is often referred to as bacterial sex. Why is this term inaccurate?

Conjugation does not result in the formation of new offspring.

Which statement about conjugation is false?

Conjugation is a process of bacterial reproduction.

Which of the following attaches the target gene to a desired location?

DNA ligase

Which of the following statements is FALSE concerning enrichment bias?

Enrichment bias favors organisms that grow quickly.

Some viruses, especially animal viruses, have an envelope surrounding their nucleocapsid. This envelope may have viral proteins embedded in it. Why are the viral proteins more readily recognized and targeted by the immune system than the envelope?

Enveloped viruses are often coated with animal cell membrane as they leave the cell. This membrane is a major component of the viral envelope. The viral proteins are more readily recognized by the immune system, as they are more distinct from the materials normally found in and on the cells. However, the envelope can contain several types of viral components as well.

A change in allele frequencies in a set of organisms over time is called __________.

Evolution

T/F All unicellular organisms belong to the same domain of life.

False

T/F In specialized transduction, virtually any genetic marker can be transferred from donor to recipient.

False

T/F Laboratory-based genetic systems have been difficult to develop for Archaea, because they do NOT naturally undergo conjugation or transduction.

False

T/F Lysogeny is unique to bacteriophages; similar relationships have not been found among the animal viruses.

False

T/F Once a putative pure culture has been obtained from the environment, it is no longer necessary to check its purity.

False

T/F Penetration requires that the entire virus is inserted within the host.

False

T/F Penicillin selection is a positive selection for the isolation of mutants with growth factor requirements.

False

T/F Sequencing technology and molecular phylogenetic analyses have had very little impact on our understanding of the evolution and diversity of life on Earth.

False

T/F The 16S rRNA sequence is an approximately 1,500 bp linear strand of single stranded RNA.

False

T/F The MPN technique is rarely applied in the food industry because any microbial presence in food is unsafe.

False

How is generalized transduction different from specialized transduction?

Generalized transduction is initiated during lytic cycle of a virulent bacteriophage; specialized transduction is initiated during the lysogenic cycle of a temperate bacteriophage.

Transformation is a useful technique for making genetically modified bacteria in the laboratory. There have been efforts to transform Archaea, but it has been more difficult than transforming Bacteria. One reason that it has been difficult is that Archaea lack a peptidoglycan cell wall. Why does that affect the ability of researchers to develop techniques to transform them?

Genes for resistance to penicillin and related antibiotics can't be used as selectable markers.

Based on your knowledge of cellular and viral processes, which of the following would be (an) appropriate target(s) for antiviral drugs?

Integrases

Why would a recombinant DNA molecule be inserted into a host cell?

It can be copied, transcribed, and translated into a desired protein.

Viruses infecting ________ are typically the easiest to grow in the laboratory.

Prokaryotes

Which of the following best explains the endosymbiont hypothesis?

Prokaryotes capable of cellular respiration and prokaryotes capable of photosynthesis took up residence in larger prokaryotes, forming obligate mutualisms. The prokaryotes capable of cellular respiration evolved into mitochondria and the prokaryotes capable of photosynthesis evolved into chloroplasts.

Molecular sequencing suggests that mitochondria arose from a group of prokaryotic organisms within the

Proteobacteria.

Which of the following groups contains some representatives with genomes that are so small that they may have as few as two genes?

RNA Viruses

Viruses rely on the host cell machinery to make new viruses, but they sometimes provide their own enzymes (such as reverse transcriptase, which is an RNA-dependent DNA polymerase). Which of the following types of enzymes would a virus need to provide in order to replicate within a cell? In other words, which of these enzymes would not normally be found in a cell unless a virus provided it?

RNA replicases (RNA-dependent RNA polymerases) for RNA viruses

The most widely used molecule in sequence-based evolutionary analyses are ________ genes.

SSU rRNA

Which of the following would result in a frameshift mutation?

The deletion of two nucleotides in a codon

How do viability stains usually distinguish between living cells and dead cells?

The dye specifically targets intact cytoplasmic membranes.

Plaque assays are often used to estimate the number of virions in a sample of a particular volume (the titer). The count is given as plaque-forming units. Which of the following is NOT generally a concern that must be considered in evaluating the results of plaque assays?

The largest problem is that single viruses may create multiple plaques, resulting in overestimates of the number of viruses present.

A single base substitution happens to cause a nonsense mutation early in the gene for a protein. What will be the result?

The protein will be truncated so much that it is unlikely to function normally.

How do restriction enzymes cut DNA sequences?

They cut DNA at sites, called recognition sites, that have specific nucleotide sequences.

In a culture of bacteria, there are some individuals that are unable to synthesize histidine. What is the best and most likely description of how these individuals differ from the other bacteria in the culture?

They differ in their genotype and in their phenotype.

In general, how might recombinant DNA technology be used to prevent a genetic disorder caused by a mutation in a single gene?

To insert a desirable gene, remove an undesirable gene, or replace a defective gene with a functioning gene

What is unique about transduction compared to normal bacteriophage infection?

Transduction transfers DNA from the chromosome of one cell to another.

T/F The establishment of DNA as the genome of the cell may have resulted from the need to store genetic information in a more stable form than RNA.

True

Frameshift mutations can be very severe. What is one reason why they are often so serious?

When a frameshift mutation occurs, it causes changes in many bases downstream and can affect many of the amino acids in the protein.

Systematic analysis now commonly includes ________ to identify, characterize, and determine relationships between new strains of bacterial species.

Whole genome analysis

There is a small lake on campus that students like to use for recreational activities. A study has begun on the microbial community in the lake at different times of the year. In order to quickly determine the approximate number of reproducing bacteria in a sample, it would best to use __________.

a fluorescent viability stain

A "point mutation" refers to mutations involving

a substitution, deletion, or addition of one base-pair.

Some viruses have plus sense RNA genomes. Which of the following could describe one of those viruses?

a virus that contains RNA with the same nucleotide sequence as the functional mRNA that its host cell will translate to produce viral products

The earliest RNA probably functioned in

both catalysis and self-replication.

Winogradsky columns are used primarily for enrichment of

aerobes, anaerobes, and phototrophs.

Analyses of sulfur isotopes have been used as evidence against life on the Moon, because the sulfides in lunar rocks have

an isotope composition similar to igneous rocks.

Phylogenetic trees for bacteria are constructed by which of the following?

analyzing molecular similarities and then using computer algorithms or optimality criteria to construct phylogenetic trees showing hypothesized evolutionary relationships

ALL viral particles

are metabolically inert.

You would like to determine the rate of production of carbon dioxide in a specific microbial habitat. How could you do this without growing the microorganisms in the lab?

by using a microsensor

You are studying 12 new isolates from the human skin. The isolates have 16S rRNA sequences that are 97% similar and share important phenotypic traits. Their genomes have 55% of their genes in common. The isolates would most likely be

classified as individual strains of the same species.

Horizontal gene transfer

complicates the construction of phylogenetic trees and the interpretation of specific traits in relation to evolution.

A transducing phage

contains fragments of the host chromosome instead of the viral genome.

Mutations contribute to the vast diversity of viruses. What viral genetic type has the most stable genome and the lowest mutation rate?

double-stranded DNA virus

What technique(s) can be used to characterize the phylogenetic composition of a microbial community without culturing any of the members?

fluorescent in situ hybridization

Which molecular method allows for the detection of a specific organism within a diverse microbial community?

fluorescent in situ hybridization

The killing of cells by UV irradiation involves

formation of pyrimidine dimers.

Microinsertions and microdeletions often result in ________ mutations.

frameshift

Metatranscriptomics and metaproteomics are favored over metagenomics when ________ is of more interest than ________.

function or gene expression / gene presence

Microarrays are useful for assessing

gene expression and the presence of specific rRNA sequences.

The biggest limitation of traditional light microscopy and electron microscopy methods is that they are unable to reveal

genetic and functional diversity of microorganisms in the habitat under study.

Culture-independent approaches avoid issues associated with

growing organisms in the lab.

What characteristics make a gene a good candidate for determining the evolutionary relationships between organisms?

highly conserved and universally distributed

The pan genome of a microbial species is constantly changing because of

horizontal gene transfer

The science of microbial ecology deals with

how the activity and biodiversity of microbial communities affect microbial interactions with each other and the environment.

Viral replication is

independent of the host cell's DNA but dependent on the host cell's enzymes and metabolism.

Select the option that lists the steps necessary for PCR microbial community analysis in the correct order.

microbial sample collection; DNA extraction; PCR of target genes; sorting by electrophoresis; analysis

Which technique would be used to estimate the concentration of naturally occurring Escherichia coli in a wastewater sample?

most probable number (MPN) method

The best choice for estimating the viable cell number of a water sample would be the __________.

most probable number method

Which taxonomic tool would scientists use if they wanted to determine if an outbreak of food poisoning was caused by a particular strain of a pathogen?

multilocus sequence typing

What is the process that will amplify DNA from a single cell isolated from a natural microbial community?

multiple displacement amplification

While studying protein synthesis in the lab, you experimentally induce a mutation in a bacterium's DNA. You assess the proteins in the mutated bacterium and find that one of them is significantly shorter than its wild-type counterpart. Based on this information, what type of mutation did you induce?

nonsense mutation

The mutagens 2-aminopurine and 5-bromouracil are examples of

nucleotide base analogs.

The designations Phe-, Leu-, and Ser+ refer to an organism's

phenotype

Microarrays that have been designed to screen samples for specific groups of bacteria are called __________.

phylochips

The evolutionary history of a group of organisms is called its ________ and it is inferred from ________.

phylogeny / nucleotide sequence data

Genes that change over evolutionary time as organisms diverge are called orthologs. Organisms with identical or very similar orthologous genes belong to the same __________.

phylotype

When solutions of host cells and infectious virions are mixed and spread on an agar plate, ________ form where viruses lyse the host cells.

plaques

Enrichment cultures are often effective for isolating bacteria from complex communities in natural samples because they __________.

select both for and against certain bacteria

Evolution is driven by

selection pressure applied to random mutation.

Mice that are injected with only the R strain of Streptococcus pneumoniae

stay healthy, because their immune systems can kill this strain easily.

When a transducing phage interacts with a new host cell,

the DNA from the previous host can recombine with the new host chromosome.

What characteristic of the S strain allows it to evade the immune system of the mice?

the cells have a capsule

When dealing with stable isotopes, enzymes tend to favor

the lighter isotope.

Microorganisms were probably restricted to the oceans and subsurface environments until

the ozone layer was made.

The genes for 16S rRNA are used to determine genetic relatedness because __________.

these genes are of adequate length to show deep relationships

Which statement most closely expresses our present understanding?

The chloroplast arose from the incorporation of a cyanobacterial-like organism.

Both deletions and insertions occur during the evolution of microbial genomes. Insertions bring in new genes that may be useful for the cell, but deletions

may increase fitness of a microorganism by eliminating unneeded genes.

The term axenic is used to describe a(n)

pure culture