BMS 503 Exam 3

spontaneous mutations

without external intervention

specialized transduction

-a page transfers its DNA into a host cell and the DNA is incorporated into that genome (the lysogenic cyle) -when the lytic cycle is induced, the DNA splits into plasmids (just trying to package the phage DNA, but bacterial DNA can get in by accident) that are packaged into virions and sent into the environment -only bacterial genes that are located near the phage DNA are packaged

generalized transduction

-bacterial DNA is accidentally packaged into a virion (part of lytic cycle of bacteriophage just trying to infect a host) and transferred to another cell -those genes are then incorporated into a new cell

phylogenetic tree -branch length -branch order

-represents the amount of change on that branch -order of descent and the anscestry of the nodes

enrichment bias

unnatural amount of nutrients available in the enrichment compared to what is found in the organisms natural environment...leads to an underrepresentation of the actual population dilution to help fix

repair of one strand of dsDNA damage uses what as the template

use oppositte strand as template

silent mutation

usually a point mutation that results in no change in the amino acid sequence

viral replication is independent of _________________ but dependent on ________________

viral replication is independent of the host cell's DNA but dependent on the host cell's enzymes and metabolism

missense mutation

wrong protein made because the wrong AA sequence is read

transposable elements

segments of DNA that move as a unit from one location to another within other DNA molecules

ionizing radiation

forms oxygen radicals

6 characteristics of viruses

1. Viruses do not belong to any of the three domains: Bacteria, Archaea, and Eukarya. 2. Viruses cannot replicate on their own. 3. The genetic information of a virus can be in the form of RNA or DNA. 4. Viruses are unable to perform replication on their own. 5. Viruses are as old as Bacteria and Archaea. 6. Viruses are smaller than Bacteria and Archaea.

steps necessary for PCR microbial community analysis

1. microbial sample collection 2. DNA extraction 3. PCR of target genes 4. sorting by electrophoresis 5. analysis

3 concerns when performing a plaque assay

1. plaques must be at an appropriate density to be counted on the plate 2. plaques must be clearly visible in order to be accurate (can't use this technique with viruses that don't cause clear cellular damage) 3. the count may underestimate the total number of virions because not all viruses may be able to infect

ideal antimicrobials have 5 characteristics

1. safe 2. effective 3. specific 4. resistant to counterattack by microbe 5. inexpensive

what is the benefit to being a temperate or lysogenic virus?

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

Suggest an assay that she could use on Martian soil samples.

C12/C13 stable isotope analysis

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.

T/F conjugation is a process of bacterial reproduction

FALSE

T/F lysogeny is unique to bacteriophages, similar relationships have not been found in animal viruses

FALSE

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

FISH

T/F The 16S rRNA sequence is a 1,500bp sequence of single-stranded DNA

False

Which fluorescent molecule enables visualization of living microorganisms?

Green Flourescent Protein

what kind of DNA must be analyzed in order to determine the phylogenetic relationship between two organisms?

HOMOLOGOUS REGION

phylochip analysis

Microarrays that have been designed to screen samples for specific groups of bacteria by taking a specific segment of 16S primer and inserting it into the sample....it binds to similar bacteria sequence and bind which causes flouresence

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.

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

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.

In Griffith's mice experiments with S. pheumoniae - R strain vs S strain - heat-killed S strain and live R strain

R strain: absense of capsule makes it able to be phagocytized by the mice's white blood cells S strain: Capsule allows the virus to evade the mice's immune system Heat-killed S + live R strain: the R strain acquired genes to form a capsule to allow the virus to survive in the mouse and kill the mouse host

reverse transcritase is a ________________-dependent _____________polymerase

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

retrovirus

RNA viruses that replicate through DNA intermediate, enveloped, contain reverse transcriptase makes DNA from RNA

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

different species same genus

T/F selection does not cause mutations, it only selects for advantageous mutations

TRUE

bacteriophage genomes consist of (ssRNA, dsRNA, ssDNA, dsDNA)

double stranded DNA

evolution

a change in allele frequencies over time

In order to quickly determine the approximate number of reproducing bacteria in a sample, it would best to use __________.

a flourescent viability stain

mutant

a strain of any cell or virus differing from parental strain

minus sense DNA

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

When a transducing phage interacts with a new host cell... a) the new host cell will be lysed. b) the DNA from the previous host can recombine with the new host chromosome. c) it will cause the new cell to produce more transducing phage.

b) the DNA from the previous host can recombine with the new host chromosome

mutator strain

bacteria that benefit from increased mutation rates

plus sense DNA

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

Metagenomics involves the analysis of a microbial community by __________. a) sampling and sequencing all of the genes in an environment b) sequencing all of the community RNA in an environment c) generating a complete sequence of the genomes of all of the organisms in an environment d) generating a phylogenetic tree based on all of the versions of a gene in an environment

a) sampling and sequencing all of the genes in an environment

how do bacteriophage effect bacterial evolution

a) they transfer genetic information through transduction, causing increased genetic diversity among microorganisms

reversion

act on point mutations, deletions or insertions

a prophage replicates

along with the host while the lytic genes are expressed

metabolism of primitave cells

anaerobic and likely chemolithotrophic

earliest stromatolites were probably formed by

anoxygenic phototrophs

restriction is a) the viral process where... b) the general host mechanism to prevent virus particles from further infective action c) the viral process whereby... d) a general host mechanism to invent invasion of a foreign nucleic acid

b) a general host mechanism to prevent virus particles from further infective action

microarrays are helpful for assessing ___________ a) enzyme activity. b) gene expression and the presence of specific rRNA sequences. c) gene expression. d) the presence of specific rRNA sequences.

b) 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 a) cellular components of small microbes because of the limits of magnification. b) genetic and functional diversity of microorganisms in the habitat under study. c) absolute cell concentration. d) physical microbial interactions as found in nature.

b) genetic and functional diversity of microorganisms in the habitat under study

Analyses of sulfur isotopes have been used as evidence against life on the Moon, because the sulfides in lunar rocks have a) exactly equal amounts of 34S and 32S. b) an isotope composition similar to marine sulfate, which is enriched in 34S. c) an isotope composition similar to igneous rocks. d) an isotope composition similar to marine mud, which is depleted in 34S.

c) an isotope composition similar to igneous rocks

Which of the following statements is FALSE concerning enrichment bias? a) Enrichment bias resulted in the underestimation of prokaryotic diversity. b) Enrichment bias is impossible to overcome in some oligotrophic environments. c) Enrichment bias favors organisms that grow quickly. d) Dilution of the inoculum may help to avoid enrichment bias in some cases.

c) enrichment bias favors organisms that grow quickly

what are the minimal components needed for a virion

capsid and genome

for early cells: major source of carbon major source of energy

carbon source: CO2 energy source: H2

3 elements that have proven useful for stable isotope studies

carbon, nitrogen, and sulfur

penicillin inhibits

cell wall synthesis (transpeptidation)

transposase enzyme may be coded for on 3 things...

chromosome, phage or plasmid

F-Plasmid

circular DNA to regulate DNA replication and allow the plasmid to be incorporated into the recipient cell

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

confers resistance to infection by viruses of the same type

why is conjugation not referred to as "bacterial sex"?

conjugation does not result in the formation of new offspring

pan genes v. core genes

core genome is a set of genes shared by all members of a species pan genome is those genes shared by all members of a species and those not shared by all members

Which of the following is NOT a way in which viruses are different from living organisms? a) Viruses are acellular and all living things are made up of cells b) Viruses depend on their host to synthesize the essential components of new viruses (e.g., genetic material and proteins), while living organisms are capable of synthesizing these components even if they require a host for food, shelter, or other necessities. c) Viruses have DNA or RNA, not both d) Viruses are obligate parasites and no living organisms are obligate parasites.

d) Viruses are obligate parasites and no living organisms are obligate parasites.

virus repressor protein controls a) does not control the phage's life cycle b) different things in different situations c) lytic genes but not incoming genes of the same virus d) both they lytic genes on the prophage and prevents an incoming virus of the same type

d) both the lytic genes on the prophage and prevents an incoming virus of the same type

What technique(s) can be used to characterize the phylogenetic composition of a microbial community without culturing any of the members? a) stable isotope techniques b) green fluorescent protein tagging c) radioisotope experiments d) fluorescent in situ hybridization

d) flourescent in situ hybridization

consequences of viral infection of an animal cell (4)

d) rapid lysis, latent infections, persistent infections, or cancer

frameshift mutation

deletions or insertions of 1 or more base pairs that often results in the complete loss of gene function

the first self-replicating organisms probably contained (ssRNA, dsRNA, ssDNA, dsDNA)

dsRNA

induced mutations

environmentally or deliberately from radiation which leads to oxygen radicals being formed

phylogeny

evolutionary history of a group of organisms inferred indirectly from nucleotide sequence data (HOMOLOGOUS REGION)

homologous DNA

exact or very similar DNA inherited from different species with a common ancestor

synthesized sulfa drugs do what to bacteria and help people how?

folic acid is necessary for DNA synthesis - humans get it in their diet - bacteria have to make folic acid give synthesized sulfa drugs because they mimic the building block to folic acid but the bacteria can't use it to make folic acid so they die and the person doesn't

killing of cells by UV irradiation forms

forms pyrimidine dimers

TRA-genes

genes important in conjugation to allow transfer of DNA from one cell to another by contact with a sex pili

orthologs

genes that diverge over evolutionary time

selectable mutations

give growth advantage in certain conditions

mutation

heritable change in DNA sequence

microbial ecology

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

FISH technique ID's organisms based on ______

hybridization of a flourescent probe to a specific rRNA sequence

a strain of an organism with an increased mutation rate is known as _________________

hypermutable or mutator strain

nonsense mutation

incomplete protein made because a stop codon is read too early

where did the chloroplast arise from ?

incorporation of cyanobacyterium-like organism

why is the mutation rate not constant and close to zero all the time?

increased mutations are a sign that the microorganisms can no longer replicate their DNA and are about to die

transformation

increasing genetic variability by the uptake of DNA from the environment

nonionizing radiation

purines and pyrimidines strongly absorb UV light and form pyrimidine dimers

the Ames test

looks for an increased in mutations when there is a possible mutagen present

in a natural population of diverse slow-growing prokaryotic cells, which type of virus would you expect to be most common?

lytic bacteriophages

insertions bring in new genes but deletions..... a) always result in a severe loss of fitness for the microorganism. b) always result in a severe loss of fitness but keep microbial genomes compact. c) are uncommon because they are usually lethal. d) may increase fitness of a microorganism by eliminating unneeded genes.

may increase fitness of a microorganism by eliminating unneeded genes

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?

multilocal sequence typing

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

multiple displacement amplification

direct reversal

mutated base is still recognizable and can be fixed without referring to another strand

auxotroph

mutation of an organism that results in the inability of the organism to synthesize a compound needed for its growth they have a nutritional requirement for growth

nonselectable mutations

no advantage

phylotype

organisms with identical or very similar orthologous genes

recombination

physical exchange of DNA between genetic elements

homologous recombination

process that results in genetic exchange between homologous DNA from two different sources

mitochondria arose from

proteobacteria

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

select both for and against certain bacteria

Phylogenetic trees for bacteria are constructed by

sequencing and algorithims

simple v. complex transposons

simple transposons contain genes for only the transposase enzyme complex transposons contain genes for the transposase enzyme and a favorable trait like antibiotic resistance

treat lyme's disease with

tetracycline family of drugs interferes with small subunit of ribosomal function

fitness

the ability to produce progeny and contribute to the genetic makeup of future generations

what must occur for conjugation to take place

the cells must come in contact (sex pili from donor)

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

the dye attaches to intact cytoplasmic membranes

point mutation

the insertion, deletion, or swap of any one base pair

wild type

the sample isolated from the environment

why are frameshift mutations so dangerous

they cause the amino acid sequence to be severely different downstream of the mutation

winogradsky column top v. bottom used primarily for enrichment of ________________ (3)

top: higher oxygen concentration bottom: H2S concentration higher aerobes, anaerobes, and phototrophs

reverse transcriptase

transcribe complimentary DNA from RNA in retroviruses so that the DNA can be integrated into the host cell's genome

what is unique about transduction compared to the normal pattern of bacterial infection?

transduction involves the transfer of DNA from the chromosome of one cell to another

transformation v. transduction

transformation: virus DNA is taken into cell and incorporated transduction: DNA is transferred from one cell to another through a bacteriophage (virus)

T/F Many viruses contain their own nucleic acid polymerases.

true

T/F enrichment cultures can prove the presence of an organism but cannot prove its absence

true

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

true