MB 351 EXAM 2
F' strains mobilize large segments of the host chromosome to recipient cells at high frequency.
F
Free-swimming chemotactic bacteria power their transmembrane flagella motors with ATP.
F
Inducible prokaryotic operons under negative control have transcription factors requiring effector binding to induce transcription.
F
Lichens are a symbiois between a fungus and the root cells of an angiosperm plant.
F
Transformation is when DNA - released by a competent cell - is taken up by a donor cell.
F
Microbes unable to detoxify oxygen radicals would exhibit positive aerotaxis.
F
Most prokaryotic genomes are comprised of a pair of diploid, circular chromosomes.
F
Most prokaryotic transcriptional units are under the control of strong promoters to allow rapid, dynamic genetic response to changes in environment.
F
Neutral mutations often result in convergence.
F
Oxygen consumption in the animal intestinal tract is entirely due to obligate anaerobes.
F
Plasmids are typically responsible for functions essential for cell growth.
F
Plasmids replicate by the rolling circle mechanism before conjugation.
F
Prokaryotic genomes experience frequent transposition events.
F
Pseudomonads are polar flagellated rods with facultative anaerobic metabolisms.
F
Quorum sensing induces expression of operons involved in microbial metabolism, DNA replication and cell wall synthesis.
F
Repressible prokaryotic gene regulation systems use effectors to start gene transcription.
F
Rhizobium bacteriods provide fixed nitrogen for the water fern Azolla, leading to increased rice crop yields.
F
Oxygen consumption in the animal intestinal tract is entirely due to facultative anaerobes.
T
Planctomyces are the only bacterial lineage known to lack peptidoglycan entirely.
T
Plasmids may be circular or linear.
T
Positive genetic control involves regulatory proteins referred to as transcription factors.
T
Prokaryotic genomes experience frequent transposition events.
T
Purple non-sulfur bacteria are inhibited by high sulfide concentrations, they can appear orange, red, brown or purple and demonstrate phototaxis.
T
Purple sulfur bacteria grown in stagnant, anoxic waters using hydrogen sulfide for energy.
T
Repressors and transcription factors bind DNA sequences in the major groove.
T
Rhizobium bacteroids provide fixed nitrogen to their plant hosts in exchange for a stable environment.
T
Riftia tube worms are mutualistic symbionts with carbon-fixing sulfide oxidizers in geothermal vent ecosystems.
T
Some proteins can function as both repressors and transcription factors.
T
Specialized transduction can produce partial diploids. (merozygotes)
T
Specialized transduction is the result of a rare mistake of prophage excision.
T
Sulfate reducers dominate in marine sediments.
T
Syntrophy is also known as interspecies hydrogen transfer.
T
Syntrophy is common in anaerobic freshwater ecosystems.
T
The B. anthracis vaccine strain lacks a plasmid present in disease-causing B. anthracis strain.
T
The PatS oligopeptide is produced by the heterocyst at a constant rate.
T
The RecA protein facilitates proper DNA recombination and repair.
T
The carbon cycle requires carbon fixation by autotrophs to return the element of carbon to biosynthetic processes.
T
The first Bacillus anthracis vaccine strain was developed by Louis Pasteur.
T
The recombination frequencies of a pair-wise combination of genes can indicate the linear order of the genes.
T
There are estimated to be 4-6 x 1030 living prokaryotic cells on planet Earth.
T
There are two types of bacterial transcription termination - Rho-dependent and Rho-independent.
T
Transcription of a bacterial operon leads to a single mRNA which contains distinct translational control sequences for ribosome binding at each gene.
T
Transformation is likely the true horizontal gene transfer mechanism for prokaryotes.
T
Transformational competence is regulated by a quorum-sensing mechanism.
T
is Rho-independent - does not require the Rho protein and relies on specific sequences in the mRNA., is Rho-dependent - requires the Rho protein to displace RNA polymerase.
Termination of bacterial transcription (select all that apply)
Competent
This term describes a bacterium that has the capacity to take up DNA via transformation.
aqueous alcohol used with another compound
Tinctures
Prokaryotic metabolic processes are necessary to return vital nutrients from the land back to the sea.
F
Methylation of chemotaxis proteins decreases their sensitivity to increasing attractant concentrations.
T
Mycorrhizial symbionts provide water, minerals and protection to plant root cells.
T
Repressors and transcription factors sometimes bind at two distant sites forming a DNA loop.
T
Supercoiling is essential to pack the chromosome into a small volume.
T
The purpose of biological classification systems are to group and relate all organisms.
T
The relatedness of molecular clock sequences can be determined by distance, parsimony and likelihood methods of sequence analysis.
T
Topoisomerase overwinds the archaeal chromosome into a positive supercoil.
T
True.
True of False: Prokaryotic genes are often organized into operons.
True.
True or False: Promoters are either weak or strong. Bacterial promoters are not identical.
True.
True or False: The cAMP-CRP binding can act as overriding transcription initiator or repressor depending on the particular operon or regulon.
Vibrio strain A present in the light organ of a bobtail squid will be unable to produce light.
A Vibrio fischeri species, Vibrio strain A, produces an autoinducer molecule incapable of binding LuxR. What conclusion can you draw about Vibrio strain A?
False
A parasitic symbiotic relationship is detrimental to both partners.
is packaged into the virus capsid using a headful mechanism., refers to multiple, contiguous copies of the phage genome.
A phage concatemer (select all that apply) a. is packaged into the virus capsid using a headful mechanism. b. refers to a sequence in the host genome where the phage genome is inserted. c. refers to copies of the host genome that are packaged into the virus capsid. d. refers to multiple, contiguous copies of the phage genome.
Molecule that enters the Krebs Cycle
Acetyl CoA
Lowers microbial count Used for sanitizing utensils Surfactant
Acid-anionic Detergent
pH<6
Acidophiles
1. Make Media 2. Sterilize Medium & Plates 3. Inoculate Liquid or Streak Plate 4. Wait for Culture to Grow
Aerobic Cultivation (4 steps)
tolerates O2, but does not use it at all
Aerotolerant Anaerobes
contain solid media, typically what you see a smear on
Agar Plate
process that produces ethanol + CO2
Alcohol Fermentation
Denatures proteins, dissolves lipids (PM) Widely used
Alcohols
pH>9
Alkaliphiles
goes from ATP to complex molecules (build up)
Anabolism
organisms still go through respiration process but oxygen is not the final electron acceptor
Anaerobic Respiration
False
Anaerobic niches in marine or freshwater sediments are typically devoid of significant organic material, and therefore facilitate colonization by carbon and nitrogen fixing organisms only.
disinfection of living things
Antiseptic
lab techniques used to prevent microbial contamination
Aseptic Techniques
False
Assimilatory nitrate reduction (nitrate to ammonia) is an exclusively prokaryotic process.
pressurized steam, kills endospores, will denature heat labile substances (ex. Blood agar)
Autoclave
use inorganic CO2 for carbon source, carbon does not supply energy
Autotrophs
nonpathogenic microbes REQUIREMENTS - safety glasses, routine hand washing, surface decontamination
BSL 1
pathogens not easily transmitted REQUIREMENTS -BSL 1, Lab coats, gloves, Limited access, Same day decontamination
BSL 2
pathogens transmitted by air or contact REQUIREMENTS - BSL 2, Controlled access, No drains (only water in), Everything must be decontaminated, Protective lab clothing, Noncirculating Airflow
BSL 3
highly contagious pathogens causing fatal diseases REQUIREMENTS - BSL 3, Shower required, Full body suit, No running water or drains, Dedicated air exhaust system
BSL 4
population of cells arising from a single cell or spore, can also arise from a group of attached cells
Bacterial Colony (CFU)
Operon
Bacterial DNA genes are arranged in a(an) _____________, which allows for coordinated control of transcription of those genes.
kills bacteria but they still are intact
Bacteriocidal
lyses bacteria, living and dead
Bacteriolytic
stops growth of microbes, but does not kill them
Bacteriostatic
closed systems, short exponential growth
Batch Cultures
bacteriostatic and bacteriocidal, destroys cell's membrane, antiseptic and disinfectant, won't kill endospores
Biguanide
relates measured cellular activity to a fixed standard
Biochemical Activity
microbial communities that form and secrete a film from hydrated polysaccharides, the microbes start acting like a colony, can be very problematic if they are an infection
Biofilms
Disrupts PM, stops fatty acid synthesis Used as an antiseptic Phenol derivative
Bisphenols
protein found in milk
Casein
from complex molecules to ATP (breakdown)
Catabolism
Disrupts PM, denatures proteins Used as an antiseptic and disinfectant Surfactant
Cationic Detergents (Quat)
Surface exlusion
Cells carrying a plasmid will not conjugate with other cells containing the same plasmid. What is the term for this phenomenon?
False
Changes in heterocyst nitrogenase genes are reversible under high oxygen conditions.
exact amount of pure chemicals in media is known (ex. 20g Glucose, 0.5g MgCl2)
Chemically Defined Media
chemical energy source, CO2 carbon source
Chemoautotroph
chemical energy source, organic compound carbon source
Chemoheterotroph
replenish media constantly, allow for long periods of exponential growth
Chemostat (continuous) Culture
chlorine + ammonia
Chloramine
Strong oxidizing agent, alters cellular components Used as a disinfectant Halogen, can take on gas form
Chlorine
Gram-positive transformation begins when dsDNA binds to an outer membrane competence protein. This membrane protein binding is not DNA sequence specific. The bound DNA is then cleaved at binding site and a single DNA strand is taken up. The other strand is degraded outside the cell. If there is sequence homology between the transported DNA and the endogenote chromosomal sequences, RecA will promote crossing over and heteroduplex formation leading to replicative resolution of the donor sequence with the recipient cell chromosome. Gram-negative transformation is species specific and uptakes DNA in double-stranded form.
Compare and contrast Gram negative and Gram-positive transformation.
-plasmids are typically circular (some linear) molecules of supercoiled DNA (1/10th-1/100th the size of a chromosome) -plasmids not present in *all* archael or bacterial species -plasmids encode no functions essential to cell growth
Compare plasmics and chromosomes.
composed of natural mixtures where chemical composition is not known (ex. Blood)
Complex Media
False
DNA gyrase overwinds the archaeal chromosome into a positive supercoil.
True
DNA gyrase underwinds the bacterial chromosome into a negative supercoil.
newly formed cell, identical to mother cell
Daughter Cell
exponential loss of viable cells (reverse of log phase)
Death Phase
directional, linear and incomplete.
Define Horizontal Gene Transfer.
-The ability of a cell to be competent recipient for transformation is regulated by quorum sensing regulation mechanism
Define and explain quorum sensing regulation
Because diverse populations are more likely to survive. Genetic diversity enhances the long term survival of any population of organisms. Why? Because diverse populations are more likely to survive environmental changes; diet, climate, predators, disease, etc. This principle applies to microbial populations too. Genetic diversity is created in plants and animals by sexual reproduction. Genetic diversity is achieved in prokaryote populations mostly by horizontal gene transfer and to a lesser extent, mutation
Define and explain the need for genetically diverse populations.
When homologous DNA sequences are aligned by RecA they crossover and then undergo recombination. DNA strands from odd numbered crossover events cannot resolve successfully as they destroy the structure of a closed circular DNA chromosome. Even numbered crossover events can resolve themselves successfully.
Define crossover.
Donor/Exogenote (red) DNA strand sequences are aligned to recipient/endogenote (blue) homologous DNA sequences by RecA followed by strand invasion with the displaced strand forming a heteroduplex/D loop. Subsequent resolution of the two strands generates a recombinant cell with a new allele.
Define strand invasion.
Transformation competent Gram-negative cells express a sequence-specific DNA binding membrane protein/type IV pili. These proteins recognize 8-11 bp DNA repeats found in homologous genomes - meaning this binding and uptake is intended for genetic, not nutritional, purposes.
Define transformation competence.
True
Deinococci are known for their extreme radiation and ultraviolet (UV) light resistance.
False
Deinococci are the only bacterial lineage to lack peptidoglycan entirely, having a protein cell wall.
1. NO3- 2. NO2- 3. NO 4. N2O 5. N2 (gas)
Denitrification Process Steps (5)
allows for the separation of organisms based on visible change in the media
Differential Media
doesn't differentiate between living and non-living cells. Spits culture up into grid and counts, average taken. Labor intensive, bacteria move quickly
Direct Microscopic Count
disinfection of non-living objects
Disinfectants
reduces number of microbes to prevent diseases
Disinfection
evaluates the efficacy of a chemical agent, disk soaked in a chemical is places in an inoculated agar plate
Disk-Diffusion Method
measures weight/volume after centrifuge, very sensitive
Dry/Wet Weight
False
E.coli cells moves in the direction of increasing attractant concentrations via a random walk.
False
Ectomycorrhizae produce haustauria, which penetrate through plant root cell walls - growing into the root cells.
describes the flow of electrons generated through the oxidation of NADH and FADH2. Creates a proton gradient
Electron Transport Chain
another name for Glycolysis
Embden-Meyerhof Pathway
A donor cell, transfers a fragment of its chromosome (exogenote DNA) into a recipient cell with its endogenote DNA. The resulting cell - termed the merozygote - briefly contains two copies of similar sequence. After these DNA sequences recombine, the resulting recombinant cell typically inherits most of its chromosome from the recipient/endogenote and only a minority of its genes from the donor/exogenote.
Endogenote vs exogenote
use of specific compounds to enrich and isolate an organism with specific capabilities, may contain a specific growth factor
Enrichment Cultures
microbes that live in guts, typically pathogenic
Enteric microbes
Prokaryotic horizontal gene transfer occurs via three mechanisms; Transformation - DNA released by a donor cell is taken up by a recipient cell. Transformation appears to be the most common form of Horizontal Gene Transfer/HGT. Conjugation is when a donor cell with a plasmid - in direct contact with a recipient cell- transfers its plasmid DNA directly into the recipient cell cytoplasm. Transduction is when donor cell DNA is accidentally packaged within a phage capsid and is subsequently injected by the phage into a recipient cell. Horizontal gene transfer is much less common in eukaryotes.
Explain the process used to generate genetically diverse prokaryotic cell populations.
16S rRNA phylogenies describe three major lines of descent - or kingdoms.
F
A group of transcriptional units controlled by the same regulatory protein is called an operon.
F
A symbiotic relationship in which both partners benefit is known as commensal.
F
All flagellated chemotactic cells in a liquid medium move via run and tumble motion.
F
All prokaryotic genomes are comprised of a single, circular DNA chromosome.
F
Antisense RNA anneals/binds to complementary DNA, disrupting polymerase assocation and terminating transcription.
F
Conjugation and transduction mapping score neutral phenotype mutations in recombinant cells after genetic crosses.
F
Cyanobacteria are known for their extreme radiation and ultraviolet (UV) light resistance.
F
Sigma factor association with RNA polymerase is irreversible, and thus progression to an alternative sigma factor requires transcription and formation of new RNA polymerase complexes.
F
The Lac operon directly controls cAMP production.
F
The carbon cycle requires macromolecular hydrolysis by heterotrophic organisms to return the element of carbon to biosynthetic processes.
F
The first E. coli linkage map was created using massively parallel DNA sequencing.
F
The spoA cascade is initiated by a series of sigma factors.
F
There are three types of bacterial transcription termination.
F
Transcription of a bacterial operon leads to a single mRNA and a single polyprotein, which is then cleaved into individually functional proteins.
F
prefers to O2 but will survive without it
Faculative Anaerobe/Aerobe
cells use organic materials as electron acceptor, but does not go through an electron transport chain (substrate level only) or Krebs cycle
Fermentation
False
Free-swimming chemotactic bacteria power their transmembrane flagella motors with ATP.
time for one binary fission to occur (bacterial doubling time)
Generation Time
Starting reactant of Glycolysis
Glucose
End product of Prep Stage of Glycolysis
Glyceraldehyde 3-Phosphate
small organic compounds the compound can't synthesize on its own (Amino acids, Purines/pyrimidines (nucleic acid), Vitamins (enzymes))
Growth Factors
True
Heterocysts lose photosystem II and undergo significant morphological differentiation.
produces lactic acid and other compounds
Heterolactic Fermentation
use organic carbon sources for energy, H, & O
Heterotrophs
produces only lactic acid
Homolactic Fermentation
True
Host legume symbiosome cells produce leghemoglobin molecules to maintain a low oxygen concentrations for Rhizobium bacteriods.
-Bacteria use DNA *gyrase* to underwind the relaxed, closed-circular, double stranded DNA molecule into a negative supercoil -Archae use *topoisomerase* to overwind their genomes into positive supercoils
How do the supercoiling of bacteria and archae differ?
-they have comparatively fewer nucleotides -prokaryotic average intergenic distances range from 3-9 nucleotides compared to 150-350 nucleotides founder in larger species genome
How does the amount of nucleotides in prokaryotes compare to larger species?
horizontal gene transfer and to a lesser extent, mutation.
How is genetic diversity achieved?
-Sigma proteins (σ) assist RNA polymerase with promoter binding and dissociate after transcription initiation. The sigma protein is responsible for recognizing promoter sequences. -The RNA polymerases in archaea and eukaryotes have multiple subunit RNA polymerases, but no subunit equivalent to sigma (σ). Specific regulatory proteins recognize and bind sites adjacent to promoters.
How is the promoter recognition different in bacteria than with archaea or eukarya?
tool used to spread inoculant (microbes) on to a plate
Inoculating Loop
65 ⁰C to 120 ⁰C (opt. over 75)
Hyperthermophile
E. coli will use the glucose until it is depleted and then begin to use the lactose.
If E. coli is grown in liquid media containing equal amounts of glucose and lactose, which sugar will the bacteria use as a carbon source?
Hungarian physician who made people wash their hands before delivering babies
Ignac Semmelweis
The bacterial population in the light organ had reached saturation and is beginning to die.
In lecture 20, you were prompted to watch a video of Dr. Bonnie Bassler discussing an example of quorum sensing using the Hawaiian bobtail squid and its symbiont, Vibrio fischeri . Each morning the squid pumps out 95% of the bacteria present in the light organ. Why? a. The squid senses that the concentration of autoinducer has become too low. b. The bacterial population in the light organ had reached saturation and is beginning to die. c. The squid senses that the concentration of autoinducer has become too high. d. The bacteria begin to turn on virulence genes that could harm the squid.
both the Azolla fern and the Anabaena cyanobacteria
In the Azolla/Anabaena symbiotic relationship, cyanobacterial nitrogen fixation supports the growth of ________. a. only the Anabaena fern b. both the Azolla cyanobacteria and the Anabaena fern c. both the Azolla fern and the Anabaena cyanobacteria d. only the Azolla cyanobacteria
acts as a transcription factor., turns on synthesis of sigma factor H.
In the endospore formation cascade, SpoOA (select all that apply) a. acts as a transcription factor. b. turns on synthesis of sigma factor H. c. is phosphorylated by KinB. d. is the sensor that becomes phosphorylated.
AraC binds the effector, arabinose, and acts as a transcription factor.
In the presence of arabinose, a. AraC acts as a transcription factor to turn on transcription of the genes for arabinose synthesis. b. AraC acts as a repressor to turn off transcription of the genes for arabinose synthesis. c. AraC binds the effector, arabinose, and acts as a transcription factor. d. AraC binds the effector, arabinose, and acts as a repressor.
Strong oxidizing agent, inhibits protein function Used as an antiseptic Halogen
Iodine
organic molecules with iodine
Iodophors
Xrays, gamma rays, & electron beams
Ionizing Radiation
True
Irreversible DNA rearrangements occur in the mother cell during endosporulation.
lactic acid produced
Lactic Acid Fermentation
time it takes culture to adapt to new media, no cell division occurs, cells "gear up" for new environment
Lag Phase
number of cells will begin to double over time, cells are very active
Log Phase
surgeon who sterilized surgical equipment and OR environment, read about Pasteur and Koch
Lord Lister
selective and differential media
MacConkey Agar
C,H,N,O,P,S Nutrients usually needed in mg amounts
Macronutrients (6)
-The resulting polycistronic mRNA molecule transcribed from these operon structural genes contains ribosome binding, translation initiation, and transcription termination sequences.
Many prokaryotic transcriptional and translational controls are built into the prokaryotic operon DNA sequence. What do the resulting polycistronic mRNA molecules do?
measures amount of nitrogen or protein gives total number of cells, only practical for research labs
Measurement of total N or P
10 ⁰C to 45 ⁰C (opt. 20-40)
Mesophile
CO2 -> CH4 (archaeans only)
Methanogenesis
prefers small amounts of O2
Microaerophile
True
Microbial waste products accumulate in high concentrations near the cells and low concentrations a few millimeters away.
K, Ca, Na, Mg, Fe (" Kari Can Numb My Feet"), AKA micronutrients
Mineral Ions (5)
type of chemically defined media, only provides exact nutrients needed for growth
Minimal Media
True
Molecular chronometers provide evidence of evolutionary relatedness while avoiding the confusion of convergence.
False
Most prokaryotic transcriptional units are under the control of strong promoters to allow rapid, dynamic genetic response to changes in environment.
True
Most prokaryotic transcriptional units have one or more regulatory sites controlling the rate of transcription.
UV light
Nonionizing Radiation
requires O2 to survive
Obligate Aerobe
requires O2 absent (becomes toxic because of free radicals)
Obligate Anaerobe
a, d
Of the following statements, what is TRUE of the transport between the heterocyst and adjacent vegetative Anabaena cells. (select all that apply) Select one or more: a. The amino acid glutamine is transported from the heterocyst to the adjacent vegetative cells. b. Ammonia is transported from the heterocyst to the adjacent vegetative cells. c. Vegetative cells provide ATP directly to heterocyst cells. d. Vegetative cells provide sucrose to feed the core metabolic energy pathways of the heterocyst cell to generate ATP.
1. Glycolysis 2. Kreb's Cycle 3. Electron Transport Chain
Processes of Cellular Respiration (3)
1. Glycolysis 2. Fermentative Pathways
Processes of Fermentation (2)
enz yme that catalyzes an oxidation reaction (oxidizing agent, but itself is reduced)
Oxidase
formation of ATP from the ETC (one compound oxidized while another is reduced)
Oxidative Phosphorylation
generates ATP from the phosphorylation of ADP, NADH and FADH2 are oxidized
Oxidative Phosphorylation
reduces spoilage, does not sterilize
Pasteurization
protein source, can contain lipids
Peptone
Disrupts PM, denatures enzymes & proteins Used as antiseptic and disinfectant Used by Lister, rarely used now
Phenol Compounds
light energy source, CO2 carbon source
Photoautotroph
light energy source, organic compound carbon source
Photoheterotroph
organisms that are free living (have flagella)
Planctonic
False
Plasmids replicate by the rolling circle mechanism before conjugation.
False
Polycistronic mRNA contains transcriptional control sequences for ribosome binding and translational termination.
True
Prokaryotic cells exclusively convert nitrates to N2 gas.
True
Prokaryotic genomes contain multiple transposons and insertion sequences.
False
Prokaryotic genomes typically have 25-50 nucleotides between genes.
False
Proteins recognize the difference between DNA base pairs viewed from inside the DNA helix but not from outside of the DNA helix.
-10 ⁰C to 20 ⁰C (opt. 10-20)
Psychrophile
1. Sterilize media & hardware 2. Introduce Isolated Cells or Pure Cultures 3. Isolate single cells to obtain pure cultures
Pure Culture Technique (3 steps)
True
Purple sulfur bacteria grown in stagnant, anoxic waters using hydrogen sulfide for energy.
False
Purple sulfur bacteria grown in stagnant, anoxic waters using organic sulfur for energy.
End product of Glycolysis
Pyruvate
means of communication between bacteria, sometimes even between species
Quorum Sensing
False
Quorum sensing allows cells to begin production of certain compounds only upon reaching a certain size.
True
Quorum sensing induces expression of operons involved in biofilm, surfactant and antibiotic production.
True
Recombination is a separate process from replication in a prokaryotic cell.
enzyme that catalyzes a reduction reaction (reducing agent, but itself is oxidized)
Reductase
False
Rhizobium bacteriods provide fixed nitrogen for the water fern Azolla, leading to increased rice crop yields.
nutrients, fermentation
Ruminants provide __________ to their microbial symbionts, and then absorb the products of symbiont __________.
False
STARI is a red, expanding "bulls eye" lesion around a lone star tick bite caused by Borrelia burgdorferi.
True
Sea floor methane hydrate is metabolized through a syntrophic relationship between methanotrophic archaea and sulfate-reducing bacteria.
inhibits growth of unwanted organisms, supports the growth of desired organisms ("selective")
Selective Media
organisms in the Biofilm (have lost flagella)
Sessile
False
Sigma proteins assist RNA polymerase with promoter binding in all prokaryotes and dissociate after transcription initiation.
True
Since Hfr formation is reversible, every Hfr or F+ culture is a mixture of both.
placed in test tubes, can hold samples longer, prevent contamination
Slant Cultures
surface active agent, physically removes microbes from an area
Soap
True
Specialized transduction can be used to understand the cis/trans nature of a regulatory region or protein.
False
Specialized transduction can transfer DNA across great evolutionary distances.
True
Spirochetes are characterized by their periplasmic endoflagella.
for microbes that don't like to grow on the surface of solid media, it must be "stabbed" to form a cavity for microbes to grow in
Stab Cultures
nutrients & space become limited, Dying Cells = Dividing Cells, endospores will form
Stationary Phase
1. Cell Elongates, DNA replicated 2. Cell Wall & PM form cleavage 3. Cell wall completely divides 4. Cells Separate
Steps in Binary Fission (5)
removes all viable microbes including endospores
Sterilization
False
Strains of E. coli either contain the F plasmid (F+) or lack the F plasmid (Hfr).
High energy phosphate bonds broken to form ATP from ADP
Substrate Level Phosphorylation
True
Syntrophy is common in anaerobic freshwater ecosystems.
A Sigma protein equivalent has not been identified in archaea or eukarya.
T
A modulon is group of operons controlled by the same global control system.
T
An accurate molecular chronometer is universal, changes at a constant rate and is large enough for the changes in it to be statistically significant.
T
Antisense RNA anneals/binds to complementary mRNA sequences, blocking translation and therefore protein production.
T
Bacterial promoters with consensus base sequences from multiple bacterial promoters are considered ideal.
T
Catabolite repression is the inhibitory effect of a preferred carbon and energy source on the induction of enzymes for the transport and metabolism of other carbon and energy sources.
T
Charles Darwin first proposed groups of organisms sharing similar features are related by descent from a common ancestor.
T
Directed cell movement in response to light intensity is termed phototaxis.
T
Geothermal vent ecosystems are based on bacterial chemoautotrophic symbionts.
T
Heterocysts lose photosystem II and undergo significant morphological differentiation.
T
Hfr strains mobilized large segments of the host chromosome to recipient cells at high frequency.
T
Horizontal gene transfer among distantly related organisms confuses phylogenies.
T
Hyperthermophilic bacteria have optimal growth temperatures between 70 and 85 degrees Celsius.
T
In many symbioses the prokaryote partner provides fixed nitrogen.
T
Initiation of endospore development is regulated by quorum sensing.
T
Interrupted mating experiments allow scientists to create linkage map of relative gene distance by exploiting bacterial conjugation.
T
Many prokaryotic cells demonstrate negative chemotactic responses away from repellents.
T
usually circular and found in a nucleoid.
The bacterial chromosome is
Negative control of a repressible operon.
The binding of an effector molecule to a repressor protein activates the repressor protein to bind DNA. What form of transcriptional control will result?
False
The genes controlling conjugal plasmid transfer are normally expressed.
True
The high viscosity of most bacterial environments results in little to no coasting when bacteria engage in a tumble.
involves a virus.
The horizontal gene transfer process known as transduction
b
The host-pathogen relationship is an example of what type of symbiosis? Select one: a. commensalism b. parasitism c. mutualism
b, d
The legume's roots excrete a mixture of chemical compounds into the soil that function (select all that apply) Select one or more: a. to act as a chemorepellent to non-symbiotic strains of bacteria. b. to begin to establish symbiosis. c. to kill parasitic bacteria in the soil environment. d. to act as a chemoattractant to specific strains of rhizobium bacteria.
True
The nitrifying bacteria are mostly obligate chemoautotrophs capable of oxidizing ammonia or nitrite for energy.
False
The spoA cascade is initiated by a series of sigma factors.
False
The sulfate-reducing bacteria are found wherever organic matter is decomposing aerobically.
True
The sulfate-reducing bacteria are ubiquitous in anaerobic environments and predominant in marine sediments.
True
There are two types of bacterial transcription termination - Rho-dependent and Rho-independent.
40 ⁰C to 75 ⁰C (opt. over 50)
Thermophile
False
Transcription of a bacterial operon leads to a single mRNA and a single polyprotein, which is then cleaved into individually functional proteins.
False
Transformation is when DNA - released by a competent cell - is taken up by a donor cell.
-insertion sequences or transposons.
Transposable elements are either what and what?
True. Instead, antisense or silencing RNA (SiRNA) molecules bind to complementary mRNA molecules forming double stranded RNA molecules. The resulting double-stranded RNA molecule cannot bind a ribosome or serve as a template for translation. This stops any production of the protein encoded on the mRNA strand. An example of translational regulation of gene expression in a prokaryotic cell is the regulation of the OmpF and OmpC porin proteins of E.coli.
True or False: Translational regulation of gene expression does not increase or decrease transcription of the gene in question.
False. the same direction.
True or false: Transcriptional units in prokaryotic chromosomes are often transcribed in a *different* direction as the chromosomal DNA is replicated.
fast and nondestructive estimation in clear media, measures how much light gets through the sample, dead cells counted
Turbidity Measurement (Spectrophotometer)
6.5-7.5 pH
Typical pH Range
actively dividing cells
Vegetative Cells
successively dilutes sample then counts # of colonies, total # found by multiplying the counted # by amount diluted
Viable Cell Count
-relaxed, cytoplasmic loops of chromosomal DNA- supercoiling eliminated by DNA gyrase nicking
What are domains?
-group of operons, each operon with its own unique transcription control proteins, sharing a common, overriding, secondary transcriptional control system regulating their cumulative expression in response to an environmental change.
What is a modulon?
-sigma factors
What is an example of global genetic regultion in bacteria?
Flagella
Which of the following structures is responsible for the run and tumble movements observed in motile bacteria? a. Flagella b. Pili c. Autoinducer d. Cilia
-for rapidly controlling diverse groups of operons in prokaryotic cells
Why are global regulation systems essential?
-Seven E. coli sigma factors bind the RNA polymerase core enzyme and then bind modulon promoter sequences
Why are sigma factors important during specific environmental conditions?
Promoter strength is matched to the amount of gene product needed by the cell. Strong/consensus promoters produce constant/constitutive amounts of protein. Operons under a dynamic control - like the lac operon - use weak promoters in conjunction with a transcription factor to provide a wide range of dynamic control over gene expression.
Why are there two different promoter strengths for operons?
-It's essential to pack the chromosome into the small volume of the prokaryotic cell
Why is supercoiling essential?
clearing around disc
Zone of Inhibition
Ectomycorrhizae produce haustauria, which penetrate through plant root cell walls - growing into the root cells.
F
Hypochlorous acid (HOCl)
Bleach
100 deg C for 30 mins, kills everything except endospores
Boiling
Deinococci stain gram positive despite lacking peptidoglycan within their cell wall due to a thick protein S-layer.
F
MCP
This transmembrane protein binds chemoattractant and initiates a signaling pathway that alters flagella rotation.
a consensus sequence comprised of the conserved base sequences from multiple bacterial promoters are considered strong promoter sequences. Each base in the consensus sequence is the base most commonly appearing at that position.
What are considered strong promoters?
-The transposase enzyme and inverted repeats give insertion elements the ability to move/transpose their location within the genome. -More complex transposons are comprised of two insertion sequences- one nonfunctional- bracketing other genes - often antibiotic resistance genes. The transposase repressor protein is expressed constitutively -keeping transposition a rare event.
What are insertion sequences?
-Operons are comprised by multiple structural/transcribed loci/genes grouped together into a single transcriptional unit, under the control of a single promoter DNA sequence.
What are operons?
-circular, some linear, molecules of supercoiled DNA -
What are plasmids?
-group of antibacterial compounds (ie. Cipro) that interfere with DNA gyrase and topoisomerase IV enzymatic activity -inhibit supercoiling, strand nicking, and supercoil relaxation -as a result, prok. DNA replication is prevented
What are quinolones?
*Antibiotic resistance*, *Metabolism of exotic organic compounds*, *Plasmid incompatibility* - which are the genes for plasmid DNA replication, *Segregation* - which determines which cytoplasm a plasmid occupies during cell division, *Conjugation* - cell-to-cell plasmid transfer, and *Host chromosome DNA transfer* - performed by a subset of conjugative plasmids
What are the gene functions encoded by plasmids?
The first is Nonreplicative, - the transposable element is physically removed from its original genome site and reintegrated into the genome at new site - a cut and paste mechanism. The second mechanism is Replicative - one transposable element remains at its original site while a second copy is inserted elsewhere. Transposition can occur between two distant chromosome locations because they may exist adjacent to each other in a supercoiled nucleoid.
What are the two types of replication?
-DNA sequences capable of changing their location in a host genome. Transposable elements are sometimes referred to as jumping genes. Transposition is a rare cellular event.
What are transposable elements that are contained in prokaryotic genomes?
Bacterial operons with significant sequence differences from consensus are considered weak promoters, recognized less effectively by RNA polymerase.
What are weak promoters?
-single, circular, supercoiled DNA chromosome -some are comprised of multiple, haploid chromosomes -some comprised of linear and circular chromosomes
What chromosome are most prokaryotic genomes comprised of?
-conditions such as carbon limitation, nitrogen limitation, and high temperature.
What conditions are many operons and regulons a part of in a larger-scale response system?
Southern Tick Associated Rash Illness
What disease causes a rash, a red, expanding "bulls eye" lesion around a tick bite, followed by fatigue, fever, headache, muscle and joint pains?
Bacterial RNA polymerases easily recognize and efficiently initiate transcription from consensus/strong promoters.
What do bacterial RNA chromosomes do?
d. sulfate
What form of sulfur can be used as an electron acceptor in anaerobic respiration? Select one: a. hydrogen sulfide b. No form of sulfur is used as an electron acceptor in anaerobic respiration. c. sulfite d. sulfate
carbon dioxide
What greenhouse gas is also a common end-product of many microbial fermentations? a. carbon dioxide b. nitrogen gas c. sulfate d. hydrogen sulfide
-it can then bind to specific DNA sites and regulate the transcription of various operons and regulons.
What happens when the effector molecule cAMP binds the allosteric CRP protein?
-is the inhibitory effect of a preferred carbon and energy source - glucose - on the induction of enzymes used in the transport and metabolism of other carbon and energy sources
What is Catabolite repression?
OmpF is a membrane transport protein made under conditions of low salt concentration/low osmolality. OmpF porin has a diameter of 1.2 nm. When the osmolarity/solute concentration in the environment suddenly increasestranscription of the ompc and mycF genes increases and the mycF gene product is an RNA molecule with a sequence complementary to the Shine-Delgarno/ribosome binding sequence of the ompF mRNA. This prevents their translation, stopping synthesis of the ompF protein. Meanwhile the ompC protein- with a smaller protein diameter is translated - helping the E.coli cell retain more solutes in higher osmolarity environments
What is OmpF?
RecA is a DNA strand exchange protein. Polymers of RecA bind to single-stranded (ssDNA) and double-stranded (dsDNA) DNA as helical filaments. RecA polymers promote the pairing of homologous DNA sequences. Homologous DNA sequences are similar -but not identical to each other. RecA promotes crossing over and strand invasion- leading to the formation of a heteroduplex/D-loop. RecA dissociates from ssDNA after strand exchange. RecA requires ATP hydrolysis to bind as well as disassociate from DNA.
What is RecA protein?
Encoded in the DNA sequence at the end of the operon is an inverted repeat sequence of DNA. When the inverted repeat is transcribed by the RNA polymerase, the mRNA complementary sequence forms a stem-loop structure. Immediately following the inverted repeat DNA sequence is a series of adenine nucleotides. The combination of the inverted repeat RNA and the series of adenines act in concert to dissociated the RNA polymerase from the DNA strand terminating the transcription
What is Rho-independent transcription termination?
Rho is a protein that binds single-stranded, mRNA molecules. Rho proteins clamp around mRNA molecules as they are being synthesized - pulling the mRNA through its central pore until the Rho factor molecules catch up to the RNA polymerase. Rho then displaces the RNA polymerase - terminating mRNA transcription.
What is Rho?
internal glucose concentrations. Low internal Glucose levels cause the adenyl cyclase enzyme to phosphorylate AMP molecules -increasing cAMP levels. As a result of the increased cAMP-CRP levels, Lac operon transcription inititation is up-regulated. High internal glucose levels cause the adenyl cyclase enzyme to dephosphorylate cAMP molecules - decreasing cAMP levels. As a result of decreased cAMP CRP levels - of Lac operon transcription initiation is down-regulated - even in the presence of lactose.
What is adenyl cyclase activated by?
-by protein transcription factor CRP and the effector molecule cyclic AMP (cAMP)
What is catabolite repression regulated by?
-prokaryotic gene expression and chromosome replication
What is domain formation crucial for?
-DNA gyrase and DNA topoisomerase enzymes
What is supercoiling a consequence of?
The first is *Rho-dependent transcription termination*.
What is the first type of bacterial transcription termination?
d
What is the function of the Xis protein in heterocyst development? Select one: a. Xis determines heterocyst spacing. b. Xis acts as a transcription factor to turn on expression of nifD and fdxN. c. Xis fixes nitrogen gas into ammonia. d. Xis performs two irreversible DNA rearrangements.
a. methanogens
What is the predominate group of microbes in freshwater sediments? Select one: a. methanogens b. aerobic and sulfate-reducing microbes c. sulfate-reducing microbes d. methanogens and sulfate-reducing microbes e. aerobic microbes
-indirectly controls cAMP concentration.
What is the purpose of glucose permease?
-Rho- independent transcription termination
What is the second type of transcription termination?
-Only when the glucose in the growth medium is exhausted/used up is the lac operon finally expressed
When is beta-galactosidase made?
(a. spirochete)
Which drawing in the figure represents the pathogenic bacterial species responsible for syphilis, Lyme disease, and relapsing fever?
Attachment to a solid surface prevents cells from being washed out of a flowing habitat., Biofilms protect microbial cells from predation by eukaryotic microbes.
Which of the following are advantages to biofilm formation? (select all that apply) a. Biofilms prevent quorum sensing. b. Biofilms decrease horizontal gene transfer. c. Biofilms protect microbial cells from predation by eukaryotic microbes. d. Attachment to a solid surface prevents cells from being washed out of a flowing habitat.
a, c, e
Which of the following are characteristics of dead zones? (select all that apply) Select one or more: a. A dead zone is a low oxygen or hypoxic area in an ocean or lake. b. Water containing too much dissolved oxygen causes most marine animal life to die or flee. c. The northern Gulf of Mexico has one of the largest dead zones in the world. d. Dead zones are exclusively the result of human activity. e. The purple bacteria are found in anaerobic environments like marine dead zones. f. Algael digestion of the microbial life can quickly deplete the dissolved oxygen in the water.
The lac repressor is bound to the lac operator in the absence of lactose.
Which of the following best describes the regulation of the lac operon? a. The lac repressor is bound to the lac operator in the absence of lactose. b. The lacI repressor is an effector molecule that regulates transcription of the lac operon. c. Lactose binds the promoter and helps initiate transcription of the lac operon. d. The lac repressor is bound to the lac operator in the presence of lactose.
a. marine sediment b. intestinal tract c. freshwater sediment
Which of the following ecosystems are anaerobic? a. marine sediment b. intestinal tract c. freshwater sediment d. marine water column e. freshwater water column
All of these are features of prokaryotic classification.
Which of the following is NOT a feature of prokaryotic classification? a. All of the these are features of prokaryotic classification. b. None of the these are features of prokaryotic classification. c. Since prokaryotes do not reproduce sexually, they are not grouped by species using the same criteria as eukaryotes. d. Horizontal gene transfer among prokaryotes makes genetic classification more difficult. e. Prokaryotes are grouped based on differences in their 16s rRNA sequence.
All genetic changes are beneficial because they increase genetic diversity.
Which of the following is NOT true of genetic diversity? a. Genetic diversity is created in prokaryote populations by mutation and horizontal gene transfer. b. All genetic changes are beneficial because they increase genetic diversity. c. Genetic diversity can lead to advantageous adaptions to changing environmental conditions. d. Transformation, conjugation, and transduction all create genetic diversity.
Various sigma factors recognize different promoter sequences.
Which of the following statements is CORRECT about bacterial transcription? a. A single RNA polymerase produces all RNA transcripts. b. Rho protein is required for termination of transcription. c. The mRNA is extensively modified before transcription. d. Various sigma factors recognize different promoter sequences. e. It occurs in the periplasm.
