micro exam 4, Micro test 3, Mirco Exam 2 (second half), Micro Test 1
From the standpoint of fermentative microorganisms, the crucial product in glycolysis is
ATP and regenerated NAD+; the fermentation products are waste products
Which bacteria are positive when stained with an Acid-Fast stain?
Acid fast mycobacteria have a waxy coat
How do daptomycin and platensimycin kill bacterial cells?
Daptomycin kills gram positive bacteria by forming pores in the cytoplasmic membrane. Platensimycin is very broad spectrum and inhibits lipid biosynthesis
Who are fleming?
Dr. Flemming discovered a zone of inhibition on his plate and studied it further. He couldn't purify enough penicillin to be useful
Who was Robert Koch and why is he considered a co-founder of microbiology?
He was a german physician. He studied anthrax in mice. He found a way to culture bacteria
Why is isolating an organism's nucleic acid important?
Helps to determine if it has DNA or RNA, circular or linear, and single or double stranded
Did his experiment with the swan necked flask support or disprove spontaneous generation?
His experiment disproved spontaneous generation.
Would a host that lacked transferrin or lactoferrin be more or less resistant to infection?
Hosts that lack transferrin and lactoferrin would be less resistant to infection since they hide the iron so the pathogens can't use i
Given that penicillin inhibits the formation of new cell walls, would you categorize it as bacteriostatic, bacteriolytic or bactericidal?
I would categorize penicillin as bacteriostatic, since it slows growth but it does not kill
If someone is born with more receptors, would they be more or less susceptible to the viral illness?
If someone is born with more receptors will be more likely to get the virus and more likely to get sick
If they were born with less receptors, would they be more or less susceptible?
If they were born with less receptors would be less susceptible to the disease and would be less likely to get super sick from it
Why does an electron microscope have a much better resolution than a light microscope?
Increases the resolution by decreasing the wavelength
Why is it ineffective against viruses?
Ineffective against viruses because the filter holes are not small enough to filter viruses.
How do ionizing and non-ionizing radiation kill microbes?
Ionizing: can break the DNA and sterilize Non Ionizing radiation: can kill, but surface only.
How does filtration limit the spread of microbes?
It gets the microbes out of air or liquid
Why do cells need iron?
It is needed for ATP for the electron transport chain
Who debunked this treatment?
It was debunked in 1890 by the author of sherlock holmes
What are the three major functions of the plasma membrane?
Its function is that its a permeability barrier, protein anchor
Define Therapeutic index
LD50 (or TD50 for humans) / ED50. you want the LD50/ TD50 to be high and the ED to be low.
Was Robert Koch's treatment for tuberculosis an actual remedy for the disease?
No. the patients would get better for a bit but not actually get over the disease
Virus: cellular structure
Not a cell: protein coat around nucleic acid
Is the Sanger sequencing method commonly used today?
Not commonly used but is used sometimes.
Diagram the process of pyrosequencing.
Nucleotides are added slowly and one at a time. It is looking for pyrophosphate being converted into ATP. The ATP gets transmitted into light which is detected by a sensor
Eukaryote: Cellular structure
Nucleus surrounds chromosomes
Can OD readings distinguish between bactericidal and bacteriostatic drugs?
OD readings can not distinguish between bactericidal and bacteriostatic because it counts live and dead cells
During electron transport reactions
OH- accumulates on the inside of the membrane while H+ accumulates on the outside.
Why are two bottles inoculated when blood is sampled?
One bottle is cultured aerobically while the other is cultured without air. Automated system cultures, rolls, and reads the bottles.
What is the difference between PCR and RT-PCR?
Only RT-PCR produces cDNA.
What is the drawback of overly sensitive tests?
Overly sensitive tests will have more false positives but less negatives.
Can you use penicillin to treat chicken pox?
Penicillin does not work on viruses because it attacks the peptidoglycan and viruses don't have it
Do both penicillin and lysozyme kill non-growing cells? Why or why not?
Penicillin inhibits peptide cross-links which attacks growing cells. Lysozyme break 1, 4 bonds which doesn't matter if its growing or not. Gram positive are more complex.
Since glucose, a hexose, is the major source of energy for most prokaryotes, why would they need to have pentose sugars available?
Pentose sugars are needed for nucleic acid synthesis.
Why are two-component regulatory systems particularly useful for controlling gene expression in response to environmental signals?
Phosphorylation is a permanent change so genes are always turned on after signal.
Prokaryote: Respiration and photosynthesis
Plasma membrane for both processes
How could a host survive the first viral infection long enough to develop CRISPR based immunity?
Probably occurs when incoming virus is inactivated by environment or when restriction enzymes cleave invading DNA.
A notorious biofilm former implicated in cystic fibrosis is
Pseudomonas aeruginosa.
One way DNA differs from RNA is that ___.
RNA has uracil and DNA has thymine
RNA replicase
RNA viruses have dsRNA intermediate in their cycle which is made by an enzyme
Do DNA or RNA viruses have more mutations per generation?
RNA viruses typically have more mutations per generation.
Define Sanitation
Reducing the microbial population to safe levels
Who was the first individual to see a eukaryotic cell?
Rober hooke
Why do scientists use a chart to determine the susceptibility or resistance of a microbe to antibiotics?
Scientists use a chart because of all these variables, the distance measurement might not be the same of all of the antibacterials being tested.
How does microbial generation time influence their speed of evolution?
Short generation time means that they evolve very quickly.
What are the possible configurations of a virus? Can bacteria have an RNA genome? Single stranded genome?
Single stranded means viral. Bacteria can not have an RNA genome.
In general which molecules pass most freely - charged or uncharged molecules?
Small uncharged non-polar molecules can pass through the membrane. Large charged polar molecules can not pass through the membranes.
Would a microscope with a resolution of 25 micrometers be a better or worse microscope than one with a resolution of 5 micrometers, with all other variables being equal
Smaller the better. Makes them easier to see.
What microbe is commonly found in skin and wound infections? How is it identified?
Staphylococcus aureus (MRSA). Identified via chromogenic agar media which is selective and differential
Why doesn't sulfonamide harm a human host, but will kill bacteria?
Sulfanilamide prevents bacteria from producing folic acid. Humans and other mammals don't make their own folate so that's why the sulfonamide doesn't harm human hosts
DNA replication
Synthesis of DNA using DNA as a template
How does a TEM differ from an SEM?
TEM shows the details of internal structures. SEM fine details of exterior structures
Why is a special polymerase, such as Taq polymerase, required for PCR?
Taq polymerase is produced by an extremophile prokaryote and is able to work at relatively high temperatures.
How and why is tetrathionate broth made in a lab?
Tetrathionate broth is made by adding thiosulfate and a strong oxidant (iodine) to minimal media.
You experimentally change the DNA sequence directly upstream of a start codon of an operon in E. coli to investigate the function of this region of DNA. Analysis reveals that after the change the same amount of mRNA is made from the operon, but there are very few proteins made from the operon. What is the most likely function of the DNA sequence that you changed?
The DNA sequence likely functions as a ribosome-binding site.
Evolution
a change over time in gene sequence and frequency within a population of organisms, resulting in descent with modification
Culture
a collection of microbial cells grown using nutrient medium
Gram stain
a differential staining procedure that stains the cells either purple or blue
Pathogen
a disease causing microorganism
Explain the effects of Heavy metals
affect proteins by binding the heavy metal irreversibly to where the substrate is supposed to bind, so the active site of the enzyme becomes inactive.
Explain effects of Ethylene oxide
affects DNA by chemically altering it so it can no longer be copied. It is commonly used in a chemiclave.
Define Bacteriolytic
agents destroy the cells themselves
During a stringent response ___.
alarmones are produced by RelA
A population consists of
all of the individuals of one species in the same area.
Are all prokaryotes microbes?
all prokaryotes are not microbes
Flagella
allow for movement
Sequencing
allows you to determine the order of nucleotides.
How do amino acids get added to the correct tRNA?
aminoacyl tRNA synthetases
Explain effects of soap
amphipathic and will integrate into lipids and disrupt the plasma membrane. This leads to the outside of the cell coming in and the inside of the cell to leak out.
Which of the following is NOT required for homologous recombination?
an Hfr chromosome
An organism that cannot synthesize methionine is an example of __________.
an auxotroph
Wild type Salmonella use the ttrA gene locus to use tetrathionate as ____.
an electron acceptor for anaerobic respiration
Plasmid
an extrachromosomal genetic element that is not essential for growth
Regulation of lambda lifestyle. Cro protein:
activates lytiv events and represses cl
During positive gene regulation, the protein that binds the DNA is a(n)_______
activator
Attachment
adsorption of the virion
If you had 10 grams of glucose and fed it to non-reproducing cells in 3 different conditions: 1. Fermenting 2. Anaerobic respiration 3. Aerobic respiration Which condition would give you the most energy after 1 hour?
aerobic respiration
Soaps
are amphipathic meaning it has both hydrophobic and hydrophilic portions which disturbs the membranes.
Most metabolic pathways are amphibolic, which means they ___.
are both anabolic and catabolic
Variables influencing the zone of inhibition
are concentration of agent on disk, size of agent, diffusion rate, and effectiveness
Syntrophs
are organisms that accomplish the catabolism and degradation of a substance through a cooperative effort with one or more other microorganisms.
Lysins
are similar to lysozyme and will break down peptidoglycan
Calculating the burst size
assume 1 virus per bacterial cell and that the cell will lyse. The viruses started at approximately the same time, so will burst at the same time. If you had 100 bacteria and 10,000 phage appear at release, the burst size is 100. Numbers will vary but eukaryotic cells greatly yield more viruses.
The Griffith experiment demonstrated ___.
bacteria could pick up genetic material from the environment
Small, regulatory RNAs are important to a cell because they____.
base-pair with mRNA to regulate its expression
Why is the term microbe rather vague?
because commonly described as a living organism needing a microscope to be seen, but if it is a single celled organism, it can be quite large and still be considered a microbe. It can also be a virus, which are not considered living
What is the relationship between viruses and vaccines?
best treatment for viruses is vaccines
Genes transferred horizontally move ___.
between members of the same generation
Five-carbon sugars are used in the
biosynthesis of DNA and RNA.
Microbial growth on the two-carbon acetate substrate invokes
both the citric acid and glyoxylate pathways.
A mutation in the gene encoding the lactose repressor (lacI) that prevents lactose from binding to the LacI protein would result in
constant repression of the lac operon in the presence of lactose.
What is pure culture?
culture of the same cell
Abbe equation
d= 0.5(wavelength)/nsin0
Improperly functioning acyl carrier proteins (ACPs) would likely result in
death for a bacterium due to poor lipid bilayer integrity.
Which of the following is an example of a biofilm?
dental plaque
When damaged or single-stranded DNA activates the RecA protein, the RecA protein stimulates the cleavage of LexA. This results in
derepression of the SOS system.
A monophyletic group is a group that
descended from one ancestor.
The diversity of microorganisms in culture collections is representative of the diversity of microorganisms found in nature
false
True or false: The proton motive force is most often generated by splitting of H2.
false
True or false: The terminating step of moving electrons onto oxygen releases additional ATP during aerobic metabolism not made during anaerobic growth.
false
Which metabolic strategy does NOT invoke the proton motive force for energy conservation?
fermentation
Define Sterilization
kill all living organism
Define Disinfection
killing or removing pathogens from inanimate objects
Define Antisepsis
killing or removing pathogens from the surface of living tissue
What do viruses lack?
lack ribosomes and metabolic enzymes
Prokaryote
lacking a membrane enclosed nucleus and other organelles
Who was the first person to see a prokaryotic cell?
leeu wonhoek-duten
The enzyme responsible for joining Okazaki fragments together is ___.
ligase
The metabolic diversity of photosynthetic bacteria stems from different
light-harvesting complexes, electron donors, and organic compounds they produce.
How is lysogeny maintained?
lysogeny maintained by phage-encoded repressor protein. Inactivation of repressor induces lytic stage. Bacterial cell stress induces lytic pathway
What makes eukaryotic transcripts easier to isolate than bacterial transcripts?
mRNA is polyadenylated in eukaryotes.
Transcriptional regulators bind most frequently at the ________ site of DNA.
major groove
Virions
may contain pre-made enzymes needed for their "life" cycle
Chemorepellants
means less bacteria
Chemoattractant
means more bacteria
Define bacteriostatic
means that it inhibits growth of bacteria
Define bactericidal
means that it kills bacteria cells.
Define -Cidal
means that it kills microorganisms by binding tightly
Chemo neutral
means the same concentrations as the original solution.
Nucleus
membrane enclosed organelle that contains cells DNA
Describe in your own words the properties ALL cells share: metabolism, growth, evolution
metabolism: cells take up nutrients, transform them and expel wastes: genetic or catalytic Growth: more cells Evolution: cells evolve to display new properties
The Calvin Cycle and nitrogenase fixation are both ___.
methods to harvest cellular materials from the air, reductive processes, energy intensive
Define Mircobial death
microbes are considered dead when they are no longer able to grow in conditions known to support their growth
the F (fertility) plasmid contains a set of genes that encode for the ________ proteins that are essential in conjugative transfer of DNA.
pili
Aerobic respiration and anaerobic respiration will always use different ____.
terminal electron acceptors (TEA)
Based on the figure below, which compound listed has the highest standard reduction potential (Eo)?
tetrathionate
True or false: Organisms grown with CO2 as its sole carbon source must have energy in the form of ATP as well as reducing power.
true
Mixotrophs
use inorganic compounds for energy and organic compounds as a carbon source.
Chemolithotrophs
use inorganic electron donors and CO2 as a carbon source.
Chemotrophs
use inorganic or organic chemicals as energy sources.
Phototrophs
use light as an energy source and CO2 as a carbon source.
Heterotrophs
use organic carbon as their carbon source.
Gluconeogenesis is the process of synthesizing __________.
glucose from other compounds
The Embden-Meyerhof-Parnas pathway is another name for
glycolysis.
Culture-independent approaches avoid issues associated with
growing organisms in the lab.
Some antibiotics bind to the bacterial enzyme, _____, which effectively stops bacterial growth because bacteria need this enzyme to complete replication. Eukaryotic cells are not harmed because they are linear and don't use the same type of this enzyme.
gryase
How does Hemophilus harvest iron?
harvests iron from blood cells
How do archaella differ from flagella?
has half the diameter of bacterial flagella move by rotation like flagella. Composed of several different filament proteins with little homoly to bacterial flagellin powered by ATP not PMF
Gram positive cells
have a thick layer of peptidoglycan, single membrane under this thick layer, this traps the crystal violent making these cells purple in a gram stain. Also they have teichoic acid and lipoteichoic acid
A starving bacterial cell will typically ____.
have more uncharged tRNAs than charged
Eukaryote
having a membrane-enclosed nucleus and various other membrane enclosed organelles
How did climate change contribute to an anthrax outbreak in 2016?
hawing of permafrost allowed anthrax endospores to germinate and grow on an infected reindeer. They form from nutrient depravation and stress, DPA dries out the cell and stabilizes the DNA, and small acid soluble proteins dry DNA and are an energy reserve.
Middle and late proteins
head and tail proteins and enzymes required to release mature phage proteins.
Endospores
highly differentiated cells resistant to heat, harsh chemicals, and radiation. "Dormant" stage of bacterial life cycle that can survive multiple environmental stressors. Only in some gram positive cells
In Bacteria, sensor kinases that respond to extracellular signals transfer this signal to the cytoplasmic machinery by typically phosphorylating the residues.
histidine
Lysogen
host cell that harbors temperate virus can result in lysogenic conversion with new properties.
Define Transcriptomics
identifies how genes are expressed
Streptobacilli
in chains because they divide along same plain.
Staphylococci
"grape like"; they divide in random phases
Penetration
(entry, injection) of the virion nucleic acid
Prokaryote: Relative size
-20-100 microns in diameter
Eukaryote: Relative size
-5-10 microns diameter
Virus: Relative size
0.01-0.2 microns in diameter
The net gain of ATP per molecule of glucose fermented is
2
A codon is made up of ___.
3 bases of mRNA
Bases are always added to the ___ end of a growing chain.
3'
Gram negative
A bacterial cell with a cell wall containing small amounts of peptidoglycan and an outer membrane
Compare and contrast a simple and a differential stain
A simple stain colors everything the same color. Differential stain will show different organisms different colors. Can not identify with simple stain.
Who was Louis Pasteur and how did he cure "sick wine"?
He cured sick wine with pasteurization
What was his training?
He was a french chemist
Why is pressure added to an autoclave?
An autoclave is a device that uses steam under pressure. We use pressure because the pressure allows the temp to get above 100 degrees C (about 121 degrees C). This can kill endospores.
What is the envelope?
An envelope is an outer layer made up of lipids and proteins
How do dyes and antibody staining differ from using GFP?
Antibody and dye staining kills the sample.
Many pharmaceutical drugs specifically inhibit transcription in Bacteria but not Archaea or Eukarya. Why would drugs that inhibit transcription only affect Bacteria and not Archaea even though they are both prokaryotes?
Archaea and Eukarya have very similar RNA polymerases that are different than bacterial RNA polymerases.
You identify the prokaryotic cells you've found as a species of bacteria. These bacteria appear to be living off of nutrients and sulfur compounds released from the vents on the sea floor. Over time, the bacteria must have evolved extreme metabolic and enzymatic capabilities to allow them to tolerate and even benefit from the extreme depths, the lack of oxygen, the low pH of the surrounding waters, high temperatures due to volcanic releases, and the unique nutrient source of the vents. Choose the characteristics and their impact on enzyme activity that are not correct from the following statements.
Archaea are able to tolerate highly acidic pH environments and have proteins that will not denature in the low-pH environments that the bacteria are found in.
Which came first - free oxygen in the atmosphere or microbes?
Bacterial and archaeal cells came first. They produced the free oxygen that is in the atmosphere, specifically cyanobacteria and photosynthesis.
Why are antifungal drugs typically more toxic than antibacterial drugs?
Because fungi are eukaryotes, there aren't as many targets as in bacteria. Much of the cellular machinery is similar or the same.
Why is isoniazid a narrow-spectrum drug?
Because it only affects the production of mycolic acid which is only in mycobacteria.
Why not erythromycin?
Because that attacks the home ribosomes which they don't have. Antimicrobial act on unique features such as 70s ribosomes or peptidoglycan. Antivirals tend to tranget unique viral enzymes and processes
Whether a molecule is oxidized or reduced in a redox reaction depends on its reduction potential relative to the available electron donors and acceptors present that the organism can utilize. Given the following reduction potentials for various redox half reactions, in a lithotroph capable of utilizing ammonia as an energy source, which substances would be potential terminal electron acceptors for respiration? NO2 -/NH3 +0.34 VNO3 -/NO2 - +0.43 VO2/H2O +0.82 V
Both O2 and NO3 - are possible electron acceptors
Which of the following is an example of one codon?
CAG
Alternative autotrophic routes to the Calvin cycle such as the reverse citric acid cycle and the hydroxypropionate pathway are unified in their requirement for
CO2.
How does a capsule differ from a slime layer?
Capsules are firmly attached but the slime layers are not.
Explain why chaperonins are critical to a cell's survival.
Chaperonins aid in the correct folding of proteins, as well as refolding partially denatured proteins
How does cold affect microbial growth?
Cooling affects microbial growth by slowing (not kills) microbial growth.
What is the current recommendation for polio and smallpox vaccination in the US?
Current recommendation is to give the killed version of the polio because wild type is not here.
How can DNA binding proteins (DBP) regulate transcription?
DNA-binding proteins can catalyze transcription.DNA binding proteins can activate transcription.DNA-binding proteins can block transcription.
Prokaryote: Genetic material
DS DNA; single circular chromosome w/ many plasmids
The template for RNA polymerase is ________, and the new RNA molecule is ________ to the template.
DNA / antiparallel and complementary
In the process of transcription, promoters are specific sequences of ________ that are recognized by ________.
DNA / sigma factors
The SOS regulatory system is activated by
DNA damage.
Identify 7 different cellular targets of antibiotics?
DNA gyrase, cell wall synthesis, proteins synthesis 50S, 30S, and tRNA, folic acid metabolism, and lipid biosynthesis.
Virus: genetic material
DNA or RNA; single or ds
The main enzyme of DNA replication (that is responsible for elongation) is _____.
DNA polymerase III
The flow of biological information begins with
DNA replication
List the steps of the central dogma of molecular biology in the correct order.
DNA → RNA → protein
Compare and contrast the Stanford E. coli experiment and the Griffith experiment. What cellular structures were demonstrated to be virulence factors by these experiments?
E.coli uses pili to attach to the intestinal surface. In the experiment test subjects were given normal e.coli and got sick. A second group that got the e.coli without pili did not get sick.
Which are more resistant to killing - vegetative cells or endospores?
Endospores are much more resistant to microbial killing than vegetative spores.
What would happen if you mutate the enzyme I or the enzyme II system of a PTS transporter?
Enzyme I system is shared by all systems, this mutation would likely be lethal as it would prevent multiple sugars from entering. Enzyme II system is specific to different sugars, this mutation would compromise the ability of some sugars to get into the cell
Inducer exclusion happens because ____.
Enzyme II from glucose intake inhibits LacY action
Distinguish how fermentation and respiration differ.
Fermentation forms organic acids and takes place in the absence of oxygen, while respiration forms water and carbon dioxide in the presence of oxygen.
How do flagellin mutants (FliC) differ from cheW mutants? Do these two mutants form different sized colonies? Why or why not?
Flagellin mutants means that its lacking the flagellin CheW means its lacking signal transduction. When they damaged the Flagellar synthesis or function the colonies were very small.
When Beijerinck enriched for nitrogen fixers, he inoculated soil into two types of liquid media: one containing mineral salts and mannitol but no nitrogen source (flask A), and one containing mineral salts, mannitol, and an ammonium salt (flask B). After incubation in the presence of air, what types of organisms did he expect to find in each flask?
Flask A would contain nitrogen fixers that could grow both with or without ammonium; flask B would not contain nitrogen fixers but would contain organisms that could use ammonium.
Who were florey and chain?
Florey and Chain were able to purify penicillin to be useful. Alber alexander was the first human patient treated with penicillin. Thus began the age of penicillin!
Where is most of the nitrogen and phosphorus in the biosphere found (be specific)? How are microbes important in agriculture? Particularly to soybean and dairy farmers?
Found in soil. They help with nitrogen fixation and breaks down the plant material.
Would you expect to see more genes in a free living, parasitic or endosymbiotic species?
Free living. The trend is that the less dependent you are on hosts, the more DNA and ORFs you have
What adaptations do photosynthetic bacteria have to help them succeed in their ecological niche?
Gas vesicles keep bacterial cells afloat impermeable to water and solutes. Enable bacteria to have adaptations that enable the bacteria to float, efficiently fix carbon dioxide and generate energy
How does differential media differ from general purpose and selective media?
General-purpose media grows everything. Selective media selects for target microbes. Differential media may be used to differentiate between bacteria. Media can be both differential and selective.
As discussed in the introductory text, archaeans do NOT appear to use the Embden-Meyerhof-Parnas (glycolytic) pathway. Instead, they use alternate pathways to metabolize sugars. What is the function of this pathway in organisms that do use it? Choose the best answer.
Glucose is split into two molecules of pyruvate with a net gain of 2 ATPATP and 2 NADHNADH (regenerated to NAD+NAD+ to maintain redox balance in the third stage of glycolysis)
Compare and contrast Pili and Flagella
Gram negative cells make pili and these are few in number and longer than fimbriae. Sex pili bind 2 cells together, enabling the transfer of DNA without the producing offspring. Because they are so widely distributed, viruses often target pili proteins
When a physician doesn't know the cause of a disease (e.g. pneumonia has the same symptoms but multiple causes), would he or she prescribe a narrow or broad-spectrum drug?
Look at the relative effectiveness of different agents on the organism causing the infection. Is the causative agent known? If not, a narrow spectrum will likely be used. The tissue levels of each drug that are attainable in vivo.
How would the loss of Cas gene function, methylase gene function, or restriction enzymes affect a bacterial cell's resistance to viral attack?
Losing the CAS gene function they become more susceptible to infection. If it couldn't methylate its own DNA less restriction enzyme activity. Deleting the restriction enzyme genes it will be more susceptible.
Can the MLC be a lower dose than the MIC?
MLC is always higher than MIC because in MIC cells could just not be growing instead of dying.
Why do researchers study viruses?
Major cause of disease (potential new source of therapies), ecological balance of aquatic ecosystems, Important in evolution ( transfer genes), and model systems in molecular biology(hershey-chase)
When and how is ethylene oxide used as an anti-bacterial agent?
Materials are sterilized by the chemiclave which is flooded by ethylene oxide which makes it usable.
How do Microbes Fulfill all the qualities of life?
Metabolism, growth, evolution, and central dogma
What does yeast do for bread and beer? Why are microbes a problem in food microbiology (2 reasons). Is spoilage the same as foodborne disease? Can unspoiled food be unsafe to eat? Can spoiled food be safe to eat?
Microbes are important to the process of fermentation and yeast makes carbonation. Microbes also spoil food. And foodborne disease which can cause unspoiled food to be unsafe
Why are microbes important in the production of ethanol from corn or switchgrass?
Microbes use plant material for energy and release ethanol as a waste product
Eukaryote: Respiration and photosynthesis
Mitochondria and chloroplasts
How do microbial growth and metabolism, microbial proteins, antibody production and molecular biology techniques enable clinical labs to identify microbial pathogens?
Modern identification of pathogens requires a combination of microbiological(microbial growth and metabolism), immunological(microbial proteins and antibody responses), and molecular biological techniques ( microbial genes). Blood cultures and cerebrospinal cultures are methods that are testing for bacteremia or septicemia. Blood cultures are the only way of isolating and identifying the causative agent of septicemia.
Which works better - moist heat or dry heat?
Moist heat works better than dry heat because it penetrates better and denatures proteins.
Why is it important for a bacterial cell to be small?
More nutrients in, More waste out, Short generation time, and Growth and evolution
Are drugs that target the cytoplasmic membrane more or less toxic than those that target peptidoglycan?
More toxic since our cytoplasmic membrane isn't super different than bacteria cytoplasmic membrane.
Where are most antibiotics used? Which are the most commonly used?
Most antibiotics are used in vivo or in the body. If the causative agent is not known a broad spectrum antibacterial is used but if the causative agent is know you would use a narrow spectrum antibacterial
Which of the following statements is FALSE?
Most available nitrogen is in organic forms.
Are most microbes found in pure culture in nature?
Most cells are not found in a pure culture in nature.
Are most of these cultured in lab?
Most numbers, most biomass and metabolic diversity.
Eukaryote genetic material
Multiple linear chromosomes made up of DNA and proteins
How do mycobacterial cell envelopes differ from most bacterial cell envelopes?
Mycobacteria have a complex, waxy cell envelope which makes it hard to get nutrients in so it slows the growth but it protects the cell, making mycobacteria hard to kill.
Would penicillin be effective against mycoplasmas?
Mycoplasma lack peptidoglycan they have cholesterol in their membrane to strengthen it and walking pneumonia is caused by mycoplasma and can not be treated with penicillin. Penicillin would not work because the cross links are different.
Which is less fragile naked or envelope virus?
Naked viruses are less fragile
How does a negative stain enable researchers to see structures?
Negative stain the background is stained not the target.
Prokaryote: Cellular structure
No nucleus but a nucleoid instead
Would microbe that shows no zone of inhibition would be considered resistant or susceptible to a given antibiotic?
No zone of inhibition means resistant while large zone of inhibition means susceptible.
Are all microbes prokaryotes?
No, not all microbes are prokaryotes
Do surgeons sterilize human skin prior to surgery?
No, surgeons no not sterilize human skin prior to surgery because that would kill ALL living organisms, including our cells
Can the viable cell count ever be higher than the total cell count?
No, viable cell count can never be higher than total cell count
You calculate a different protocol to have a D value of 8 minutes and another protocol with a D value of 15 minute, which is the better protocol to kill microbes?
The better protocol is 8 minutes, since it takes you 8 vs 15min to do the same thing.
How do polysomes illustrate the energy efficiency of a cell?
The cell can translate multiple copies of a protein from a single piece of mRNA.
Which of the following would result in a frameshift mutation?
The deletion of two nucleotides in a codon
Which would be safer, an antibiotic with a T.I. of 50 or one with a T.I. of 5?
The larger the T.I value, the safer. So a TI of 50 is safer than TI of 5
Which statement below demonstrates why the majority of organisms are heterotrophs?
The majority of organisms obtain their carbon from organic sources.
Are overly specific tests more prone to false positives or false negatives?
The more specific a test, the less likely there will be false positives, but increase risk of false negatives.
Archaeans also differ in their use of the pentose phosphate pathway. It may be absent or different from the pathway found in other domains. What is the function of the pentose phosphate pathway in organisms that use it?
The pentose phosphate pathway is important for breaking down glucose and The pentose phosphate pathway is important for the biosynthesis of pentoses and other sugars
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.
To calculate the free energy (ΔG0′) of a reaction, you can subtract the free energies of formation (Gf0) of the reactants from those of the products. Given the following data, what will be true of this reaction? C6H12O6 + O2 → CO2 + H2O Gf0 : -917.3 0 -394.4 -237.2
The reaction will be exergonic.
Metabolic reactions can be assimilative or dissimilative. Which term, "assimilative" or "dissimilative," describes the reduction of sulfate by the sulfate-reducing bacteria (SRB) that have a symbiotic association with ANME?
The reduction of sulfate by SRB using electrons from ANME is dissimilative.
What is the relative abundance of microbial vs visible life?
The relative abundance of the microbial life is 2x10^3 organisms on earth.
Which response best explains why promoters for the same sigma subunit do not have identical sequences?
The sequences within the promoter region at -10 and -35 are the most important for recognition by the sigma subunit
Gram positive
a bacterial cell whose cell wall consists chiefly of peptidoglycan and lacks a membrane
Bioinformatics
is where you can use computers to store and analyze the sequences and structures
How is anaerobic respiration different from aerobic respiration?
The terminal electron acceptor in anaerobic respiration is not oxygen.
Chlorophyll and bacteriochlorophyll pigment molecules absorb light energy for photosynthesis. Each specific version of these molecules absorbs a different range of wavelengths of light, allowing different species of phototrophs to coexist by partitioning their use of the light spectrum. What controls the absorption spectrum of each particular chlorophyll/bacteriochlorophyll?
The various substituents on the tetrapyrrole ring alter the absorption properties of the pigments.
What are the basic guidelines used to keep both lab workers and the public safe? Why are lab precautions so important?
There are different microbiology safety standards, such as restricted access areas, good personal hygiene, wearing PPE, vaccination, handling specimens safely, and decontamination. This limits the spread of infection
Are viruses single or double stranded
They could be both
How do viruses avoid CRISPR-mediated cleavage?
They evolve. Mutations of PAM regions and production of cas inhibitors
Why are our resident microbes important to human health? Give 3 different examples of their influence.
They help us digest food. They affect how drugs are absorbed. They also influence mood, behavior, and weight.
explain how this mechanism enables bacteria to move toward a chemoattractant.
They run more than they tumble when they see a chemoattract.
How do bacteria store carbon, phosphorus, and sulfur?
They store carbon as a glycogen (glucose polymers) or PHB. This is stored in membrane-bound inclusions. Poly phosphate granules. Sulfur granules are the product of hydrogen sulfide oxidation and are stored. Sulfur granules are in the periplasm making these bacteria
How do researchers visualize pili, flagella, and capsules?
They use polysaccharide coating for capsules and its a negative stain. Flagella is a leifson stain stains flagella red-brown. Pili use labeled viruses. Pili and capsules are virulence factors
Would a cell that lacked siderophores grow better or worse in an iron-poor environment?
They would not grow as well in an iron-poor environment
What is a Microbe?
This is a minute life form; requires a microscope to be seen. They live in dense community or microorganism called a biofilm.
How is the MIC and MLC calculated in a lab?
This is done using a disc diffusion assay. It uses solid media, and the antibacterial agent is added to a filter paper disc and diffuses into the agar. The MIC is reached at some distance. The zone of inhibition is the area of no growth around the disc
How does the proton motive force lead to production of ATP?
Translocation of three to four protons drives the F0 component of ATPase which in turn phosphorylates one ADP into ATP.
Almost all plasmids are double-stranded DNA.
True
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
One gene may have multiple promoters, each that is recognized by a separate sigma factor.
True
T or F: Microbes are essential for life as we know it and the processes that support life (e.g., in biogeochemical cycles and plant and/or animal microflora).
True
T or F: The structure and function of microorganisms have been revealed by the use of microscopy (including bright field, phase contrast, fluorescent, and electron).
True
T or F; Cells, organelles (e.g., mitochondria and chloroplasts), and all major metabolic pathways evolved from early prokaryotic cells.
True
Toxigenicity in Corynebacterium diphtheriae is due to phage conversion.
True
True or False: Bacteria and Archaea have specialized structures (e.g., flagella, endospores, and pili) that often confer critical capabilities
True
True or False: Bacteria have unique cell structures that can be targets for antibiotics, immunity and phage infection.
True
True or False: In electron transport systems, the electron carriers are membrane associated.
True
True or False: The replication cycles of viruses (lytic and lysogenic) differ among viruses and are determined by their unique structures and genomes.
True
True or False: The synthesis of viral genetic material and proteins is dependent on host cells.
True
True or false: Photolytic systems REQUIRE a membrane to function.
True
DNA polymerase can only add nucleotides to a free 3(-hydroxyl group on a nucleic acid strand. As a consequence, all EXCEPT which of the following statements are true of DNA replication?
Uracil is not found in DNA
Why is confocal microscopy an innovative technique, especially where biofilms are concerned?
Uses a computer to models cells in a biofilm. Can determine the order of microbes top to bottom
Can a light microscope be used to examine prions or viruses? Why or why not?
Viruses are too small to be used to examine viruses
Which of the following examples describes a type of catabolite repression?
When glucose is present, the lac operon is inhibited.
The replisome is a large complex of proteins that contains many enzymes involved in DNA replication. Hypothesize why these enzymes function best together.
With the replisome, it can replicate both strands of DNA at the same time.
The researchers used Cybb whose white blood cells lacked the enzymes to make an oxidative burst. When they infected these mice with ttrA- mutants (Salmonella that cannot reduce tetrathionate). Given this mix, would you expect to detect tetrathionate in the guts of these infected mice? (why or why not)
You wouldn't expect tetrathionate because thiosulfate wouldn't be oxidized by Cybb- white blood cells.
The path of electron flow in oxygenic phototrophs is referred to as the ________ scheme.
Z
Colony
a macroscopically visible population of cells growing on solid medium, arising from a single cell
A change in the nucleotide sequence of DNA that is passed on to daughter cells is referred to as __________.
a mutation
Peptidoglycan
a polysaccharide composed of alternating repeats of N-acetylglucosamine and N-acetylmuranic acid
cell wall
a rigid layer present outside the cytoplasmic membrane; it confers structural strength on the cell
Koch's postulates
a set criteria for proving that a given microogranism causes a given disease
Hypertonic
a solution has a higher solute concentration than another solution. water particles will move out of the cell, causing crenation
Hypotonic solution
a solution that has a lower solute concentration than another solution. water particles will move into the cell, causing the cell to expand and eventually lyse
Isotonic
a solution that has the same solute concentration as another solution. there is no net movement of water particles and the overall concentration on both sides of the cell membrane remains constant.
To determine if you have identified a functional open reading frame (ORF), you should have found __________ within the sequence.
a start codon and a ribosomal binding site (RBS)
Ribosome
a structure composed of RNAs and proteins upon which new proteins are made
Ferrous iron oxidation
can be aerobic or anaerobic; only small amounts of energy can be produced in acidic environments even though many of the organisms using this are acidophilic.
High affinity transporter
can become saturated when their target is at relatively low concentrations(no faster with more solute).
What data can be gathered from genomes concerning the function of genes?
can give insight to metabolic pathways and gaps, virulence traits, transport mechanisms, biosynthesis mechanisms, and other life functions. The complement of genes defines its capabilities. Metabolic genes are the most abundant class in microbes, followed by protein synthesis.
A chemoorganotroph and a photoautotroph in the same environment would NOT compete for
carbon and oxygen.
Carboxysomes are structures where ____.
carbon dioxide is fixed by Rubisco
The rising of bread dough is the result of
carbon dioxide produced by fermentation.
Whether an organism is classified as a photoheterotroph or a photoautotroph depends on its
carbon source
Regulation of lambda lifestyle. Cl protein
causes repression of lytic events, it represses cro proteins
Metabolism
cells take up nutrients, transform them and expel waste
Organisms use different sources of carbon and energy. Archaeans do NOT use glycolysis and do NOT always use the pentose phosphate pathway, but use variations on these pathways for similar purposes. What is the best classification of this type of catabolism?
chemoorganotrophs
Most of the carbon in amino acid biosynthesis comes from
citric acid cycle intermediates and glycolysis products.
Lysogeny probably carries a strong selective advantage for the host cell because it
confers resistance to infection by viruses of the same type.
What type of DNA viruses are most prevalent
dsDNA
Which is one major difference between anaerobic and aerobic respiration?
electron acceptor
Early proteins
enzymes needed for DNA replication and transcription
Which type of genes contain introns, a poly A tail and 5' cap?
eukaryotic only
If ΔG0 is negative, the reaction is
exergonic and energy will be released.
Bacterial mating (or conjugation) is a bidirectional process where nucleic acids (DNA or RNA) are transferred between two cells.
false
Green fluorescent protein (GFP) is used for detecting translational activity of a fused protein, whereas lacZ reporters are used to detect transcriptional activity of a fused gene.
false
How do computer programs identify ORFs?
for start and stop codons, ribosome binding sites, ORFs that are similar to known sequences, and similar codon bias that matches with other genes
How does a colony form?
forms by growing on a medium
Microinsertions and microdeletions often result in ________ mutations.
frameshift
The functional unit of genetic information is the
gene
Bacteriorhodopsin is a molecule that is used by bacteria to ___.
generate a proton motive force
Pure fermenters have an ATP synthase that they use to ___.
generate a proton motive force
Which metabolic cycle or pathway is LEAST likely to be invoked during the biosynthesis of DNA?
gluconeogenesis
Which of the following would NOT be required to grow an autotroph?
glucose
Darkfield
increase contrast
The synthesis of ββ-galactosidase is regulated by __________.
induction and catabolite repression
Tamiflu
inhibits the release of viral particles so if it's late there have released so many already it doesn't matter.
intercellular communication
interactions between cells using chemical signals
Nitrification
involves the aerobic oxidation of ammonia or nitrite.
Triclosan
is a competitive inhibitor of the enzyme that adds to the tails of the phospholipids and bacteria can't make new membrane
What is the MiniION?
is a mini sequencing device. It was used in the Ebola outbreak and was able to sequence the Ebola genome.
Genome annotation
is converting raw sequence data into a list of genes present in the genome.
Aerobic ammonia oxidation
is performed by Archaea and Bacteria and produces nitrite; Bacteria may oxidize the nitrite to nitrate.
Anaerobic oxidation of methane (AOM)
is performed by Archaea, often in sewage and in freshwater sediments; CO2 is often reduced using H2.
Acetogenesis
is performed by obligate anaerobes that use H2 as the major electron donor; both ion pumps and substrate level phosphorylation are used to conserve energy.
Annotation
is the "bottleneck".
Define Specificity
is the ability to recognize only the target pathogen which minimizes false positives
Define Sensitivity
is the actual minimum amount of pathogen needed for a test to detect it which minimize false negatives.
codon bias
is the differences in frequency of synonymous codons, since multiple different codons can be one amino acid. I.e. arginine has 6 codons.
d value, or decimal reduction time
is the length of time it takes an agent or condition to kill 90% of the population
Define MIC
is the smallest amount of an agent needed to inhibit growth of a microorganism
Nitrogenase is an enzyme that ___.
is unique to prokaryotes
The lac operon is an example of ________ control in which the presence of an ________ is required for transcription to occur.
negative / inducer
Ecological theory states that for every organism there is at LEAST one ________, and the microenvironment where the organism is most successful is called the ________.
niche / prime niche
Are ddNTPs used in pyrosequencing ?
no
Horizontal gene transfer
no offspring formed but genes are moved around and joined with different genes
Alcohol
non-polar it dissolves lipids
If an electrophoresis gel is run with RNA and then a DNA probe is used to identify the fragments of interest, what is the process called?
northen blotting
If you add polyT (segment of DNA that has TTTTTTT (many Ts) , and ribosomes, you'd expect to see ____ form.
nothing (ribosomes don't bind DNA)
The mutagens 2-aminopurine and 5-bromouracil are examples of
nucleotide base analogs.
Assembly
of capsids and packaging of viral genomes into new virions
Release
of mature virions from the host cell.
Synthesis
of virus nucleic acid and protein by host cell metabolism as redirected by virus
Phase contrast
offset some light increases contrast
Domain
one of three main evolutionary lineages of cells: the bacteria, archaea, and eukarya
Magnification
optical enlargement of an image
Fermentation occurs when there is no usable external electron acceptor (like O2) available for respiration. Fermentation products are made following glycolysis as a result of reactions that __________.
oxidize NADH so that NAD+ can be reused again in glycolysis
If you have a sieve or filter that allowed prokaryote cells to pass through, but retained the eukaryotic cells, would you expect most viral particles to pass through or be retained?
pass through because viral particles are smaller than prokaryotic cells
Autotrophs
perform CO2 fixation and utilize CO2 as their sole carbon source.
A sensor kinase will ____.
phosphorylate a response regulator
What powers the rotation of the flagella?
polar lophotrichous, peritrichous, increase or decrease rotational speed relative to strength of proton motive force. Gram postive differ from gram negative. The negative have an outer membrane. Positive have basal bodies that lack the outer membrane
Which of the following represents increasing microbial diversity?
population-guild-community
DNA replication is started with a(n) ________, which, in most cases, in vivo is a short stretch of ________.
primer / RNA
Arrange the different types of microbes (viruses, prions, prokaryotic cells, eukaryotic cells, and helminths). In the correct order, from largest to smallest.
prion, virus, prokaryotic, eukaryotic, helminthe.
The ability of an enzyme (e.g. RNA polymerase) to stay on the DNA and make RNA is called the enzyme's ____.
processivity
RNA polymerase and a ribosome can bind to the same mRNA molecule at the same time in ____.
prokaryotes
mRNA combined with ribosomes and charged tRNA will yield ____ in a test tube
protein
Bacteria produce auto-inducers such as AHL as part of their ____ pathways.
quorum sensing
According to ecological theory, each organism has one place where it will be most successful, called the __________.
realized niche
The role of an enzyme includes all EXCEPT which of the following?
reducing the rate of a reaction to allow for better control
Regulatory proteins
regulate transcription, bind specific DNA sites, and can be influenced by small molecules
Considering the catabolite repression mechanism, which observation would make you suspect it IS occurring?
relatively low intracellular cyclic AMP levels
The genes encoding green fluorescent protein (GFP) and β-galactosidase are typically used in cloning as
reporter genes.
In negative regulation, the protein binding to the DNA is a(n)________.
repressor
Which type of regulator(s) specifically binds to operator regions of DNA?
repressors
Activation energy is the energy
required for a chemical reaction to begin.
The function of tmRNA is to ___.
rescue trapped ribosomes bound to degraded mRNA
What type of genes would you NOT expect to see on a plasmid?
ribosomal proteins
The research team infected different sets of mice with 3 different strains of Salmonella. Wild-type (with a ttrA gene that enables the bacteria to use tetrathionate), ttrA- (loss of function mutant that cannot use tetrathionate), and ttrA restored (lacking ttrA on its chromosome, but present on the plasmid). They harvested the cecal contents to make the figure below:
serial dilutions and colony counts
If an oxidation reaction occurs
simultaneous reduction of a different compound will also occur, because electrons do not generally exist alone in solution.
Electron carriers used in electron transport chains are always found in membranes. Which one of the following statements is NOT a reason why electron transport chains are found in membranes?
so that they can transport NADH out of the cell to the periplasm
Differentiate
some microbes form spores
Which metric describes the proportion of EACH species present in a community?
species abundance
What type of RNA is most prevalent
ssRNA
ORF
stands for open reading frame. It is a sequence of DNA that encodes a string of amino acids long enough to encode a protein.
Recognizing pathogens that contain multiple unique proteins which enable the human immune system to recognize just one and mount an effective response has opened the door on development of some vaccines only being
subunit vaccines
Given the paper and the data below, what can you infer about the value of tetrathionate to these Salmonella? The research team infected different sets of mice with 3 different strains of Salmonella. Wild-type (with a ttrA gene that enables the bacteria to use tetrathionate), ttrA- (loss of function mutant that cannot use tetrathionate), and ttrA restored (lacking ttrA on its chromosome, but present on the plasmid). They harvested the cecal contents to make the figure below
tetrathionate respiration is more efficent than fermentation
Define -Static
that it inhibits growth
RNA polymerase adds bases to ____.
the 3' end of any growing RNA
Resolution
the ability to distinguish two objects as distinct and separate when viewed under the microscope
Contrast
the ability to resolve a cell or structure from its surroundings
Nucleoid
the aggregated mass of DNA that makes up the chromosome of prokaryotic cells
horizontal gene transfer
the asymmetrical and unidirectional transfer of DNA from one cell to another
The proton motive force (PMF) is driven by __________.
the difference in charge across the plasma membrane with protons outside the membrane
____ does not provide carbon intermediates for the biosynthesis of amino acids or sugars.
the electron transport chain
The reduction potential (E0′) of a substance reflects its tendency to donate or accept electrons. The larger the difference (ΔE0′) between the reduction potentials of the electron donor and the electron acceptor, __________.
the greater the change in free energy (ΔG0′), and the greater the energy released
The Lac I protein will bind to ___ and act as a(n) ______.
the operator:repressor
The first step of translation begins when __________.
the ribosome binding site (RBS) on the mRNA binds to the 16S rRNA to begin the formation of the initiation complex
Gram negative cells
thin peptidoglycan layer that is protected by an outer membrane, periplasm, contain lipopolysaccharide, and "protect" their peptidoglycan so it doesn't trap much crystal violet, LPS, PINK they have a second membrane. They have they have LPS with holes are called porins. The porin concentration can be increased or decreased depending on environmental stress vary between species.
Acid-Fast
this a property of mycobacterium species in which cells stained with the dye basic fuchsin resist decolorization with acidic alcohol
In complementary base pairing of DNA, adenine pairs with ________ (or ________ in RNA) and cytosine always pairs with ________.
thymine / uracil / guanine
Which of the following is NOT a role of carotenoids?
to produce singlet oxygen
Attenuation is a type of regulation that can control
transcriptional activity exclusively.
Which form of horizontal gene transfer requires a virus to transmit the DNA from one bacterial cell to another?
transduction
Competent cells are required for ___ to take place.
transformation
Increasing genetic variability by the uptake of DNA from the environment is __________.
transformation
The ribosome, mRNA and tRNAs are key components of ____.
translation
Which of the following is the correct abbreviation for a mutation in a gene that synthesizes one of the enzymes involved in tryptophan production?
trpC1
An effective way to introduce DNA into plant cells is using the Ti plasmid, which comes from a plant pathogen.
true
Many Bacteria isolated from nature are natural lysogens.
true
Throughout the living world, the genetic code is generally universal; however, there are slight variations.
true
True or False: In natural samples it is often difficult to differentiate live cells from dead cells or cells from nonliving matter without special dyes
true
True or False: Many defined growth media that support microbial growth lack malonate, which is an important precursor for biosynthesis of lipid membranes. Based on this, we can infer cells also must have a metabolic pathway to generate malonate from other compounds.
true
True or False: Regeneration of oxaloacetate is essential for the citric acid cycle to be cyclical.
true
True or False: The net result of electron transport is the generation of a pH gradient and an electrochemical potential across the membrane.
true
How much do we owe microbes?
used in valuable human products, energy generation and clean up bioremediation. In Agriculture they are used to help with nitrogen fixation and breakdown complex plant material. Fermentation helps with chocolate. Yeast makes carbonation
quorum sensing
used to coordinate genetic responses to the environment
Influenza
uses hemagglutinin to get into a cell and neuraminidase to leave
sanger sequencing
uses the chain termination method. Where the chain was terminated, the base was incorporated.
Virulent
viruses always lyse and kill host after infection
Temperate
viruses integrate and replicate their genomes WITH host genome and without killing host, establishing long-term, stable relationship
species specificity
viruses that attack certain species examples are ICAM-1 is the receptor for common cold
What is salvarsan and what is the active segment of this drug and what was it used to treat?
was used to treat syphilis in the civil war. It is effective against syphilis but toxic to humans due to the arsenic ring.
brightfield microscope
when sample is in direct light path
Enzyme induction occurs
when the substrate is present.
Cells that have "insertional inactivation" of the lacZ gene are
white
When tryptophan is abundant, the tryptophan leader sequence will ___.
will form a Rho-independent terminator to stop transcription
The third base in a codon is called ____ and leads to ____ of the genetic code.
wobble:degeneracy
Low affinity
work best when target is at high concentrations; do not get saturated easily
Do viruses self-assemble?
yes most do but, others need scaffolding
Which intermediate compound(s) in the citric acid cycle is/are often used for biosynthetic pathways as well as carbon catabolism?
α-ketoglutarate, oxaloacetate, and succinyl-CoA
