When you have only one plasmid to isolate, you need a new column for proper balance during
centrifugation
False
After using a micropipette, it is desirable to set the volume to the maximum.
True
You use yellow tips for 10 ul micropipettes.
True
We used RNA primers for PCR amplification.
False
LB media contains 0.2% glucose.
False
In Biol 160 it is our normal procedure to take out enzyme and put on ice until use.
False
For the separation of large DNA fragments, we use a polyacrylamide gel.
False
For agarose gel electrophoresis, agarose will be dissolved in H2O.
False
A DNA size marker is composed of different sizes of circular DNA fragments.
False
Excess use of 6x dye is not recommended because it will affect DNA migration on an agarose gel
False
We normally do not wash or rinse the flask used for dissolving agarose.
True
When we made an agarose gel, we added EtBr to the gel.
True
For plasmid isolation, vigorous mixing is recommended after adding lysis solution
False
We use the same spin columns for both plasmid isolation and PCR clean-up.
False
Many bacteria can sense quorum and do so by direct cell-cell communication using pili.
False
If the genes for luminescence in a bacterial species are under the control of quorum sensing signal, luminescence is dependent upon cell density.
True
If the genes for luminescence in a bacterial species are under the control of quorum sensing signal, luminescence happens in high cell density above certain concentration.
True
Bacteria move toward higher concentration of chemical attractants by remembering the previous concentration over time.
True
Chemoreceptor proteins for chemoeffectors (attractants or repellants) are found in bacterial cell membrane.
True
The production of the same AI-2 by different types of bacteria in the same community is one way for the bacteria to engage in ( ) communication.
Interspecies
This term is for a community of microorganisms immobilized and living on a solid surface exposed to air or liquid. The obvious advantage would be a formation of food webs via the coordination of different types of microorganisms. What is this?
Biofilm
Chemoreceptor proteins for chemoeffectors are also called ( four words ) (MCPs).
Methyl-Accepting Chemotaxis Protein
( ) are unique among the known prokaryotes in that the cells aggregate and construct multicellular fruiting bodies.
Myxobacteria
When cultures of B. subtilis undergo nutritional limitation and enter the stationary phase, 10 to 20% of the cells ultimately develop ( ), which allows the uptake of external DNA.
Competence
Bacillus subtilis has evolved ways to adjust to stressful changes in the natural environement. One of these ways is to ( a ) when faced with limiting supplies of a carbon or nitrogen source. The decision to ( a ) is regulated by a phophorelay signal transduction system.
Sporulate
The normal flora are always beneficial.
False
Temperature can be a signal for virulence gene expression for pathogens.
True
Endotoxins are secreted in soluble form by live bacteria,
False
An enterotoxin is a protein toxin released by a microorganism in the intestine.
True
The enzymatic activity of Cholera toxin is ADP-ribosylation.
True
mRNA can sense environmental signals.
True
This bacterium, ( ), killed 75-200 million European people (one-third of the population at that time) in 1347 to 1353, known as the Black Death.
Yersenia pestis
This bacterium, ( ) was first isolated by Italian anatomist, Filippo Pacini and also by Robert Koch as the cause of cholera.
Vibrio cholerae
This bacterium, ( ) is an opportunistic pathogen, meaning that can cause disease to an immunocompromised person, but not a healthy person. It typically infects lung, so it is a threat especially to a patient having Cystic fibrosis.
Pseudomonas aeruginosa
( ) species cause gastroenteritis, enteric fever, and septicemia (blood infections)
Salmonella
( ) species cause shigellosis and produces shiga toxin.
Shigella
This bacterium, ( ) is the causative agent of whooping cough. When you were very young, you probably got an immunization shot against this agent.
Bordetella pertusis
This bacterium, ( ) is the most common cause of staph infections, though it may exist as a commensal on human skin.
Staphylococcous aureus
( ) is the causal agent of Crown Gall disease (the formation of tumors) in over 140 species of flowering plants. The bacterium has a mega-sized Ti plasmid (tumor-inducing plasmid).
Agrobacterium tumefaciens
When glucose is added to E. coli culture media, you will see a lot of glucose inside the bacterial cell.
False
In E. coli, glucose the best carbon source so if glucose is around, it represses the utilization of other carbon sources.
True
In E. coli, cAMP receptor protein is the transcriptional activator involved in catabolite repression. So, the effector (ligand) of the protein is glucose.
False
When E. coli cells see lactose (a decent carbon/energy source) outside, they always express lactose-utilization enzymes.
False
RNA polymerase prefers some DNA sites to bind to.
True
A transcription factor binds to target DNAs by recognizing a specific sequence.
True
Transcriptional activator helps RNA polymerase transcribe and repressor inhibits RNA polymerase from transcription.
True
In an operon, the binding site of a transcriptional activator always precedes the site for RNA polymerase (promoter).
True
In an operon, the binding site of a transcriptional repressor usually precedes the site for RNA polymerase (promoter).
False
Let’s say you know that the transcription of an operon strictly requires a transcriptional activator. Then the promoter for the operon is strong (& ideal).
False
How do you call DNA site to which a repressor binds?
Operator Region
Membrane protein cannot be a transcription factor.
True
Bacteria often use secondary messengers for environmental signals.
True
Obligatory anaerobes usually have oxygen-sensing transcriptional regulators such as FNR.
False
To kill host is the best interest for pathogenic bacteria.
False
Glucose is the best food for E. coli. So, glucose will repress utilization of any other carbohydrate in E. coli.
True
Many bacteria can sense quorum by direct cell-cell communication using pili.
False
There is no bacterium that can form multicellular fruiting bodies.
False
Several bacteria undergo sporulation when faced with nutrient excess.
False
In two-component systems, the sensor protein is always a transmembrane protein.
True
When bacteria encounter chemo-attractants (food), they tumble rather than swim.
False
mRNA can sense environmental signals.
True
Bacteria sense their environmental changes by recognizing signaling molecules and therefore there must be cellular components to bind to such signaling molecules.
True
All the environmental signaling molecules go into the cytoplasm in order to trigger appropriate adaptation mechanisms in bacteria.
False
Upon binding to signaling molecules, transcriptional regulators (or sensor proteins in two-component systems) undergo conformational changes (that is, there must be two protein forms in each case).
True
The regulation by altering protein’s activity is faster than that by changing the transcription level of the protein.
True
When glucose is NOT around, several glycolysis enzymes will be down-regulated through the alteration of the proteins’ activities.
False
The reactions catalyzed by regulatory enzymes are usually at a metabolic branch point.
True
Regulatory enzymes often catalyze reactions that are physiologically irreversible.
True
A positive allosteric effector would increase the Km of its protein.
False
For biosynthetic pathways, the end product is often a negative allosteric effector for a branch point enzyme. Such control is called end-product inhibition, or ( two words ), by an end product.
Feedback Inhibition
The ( ) is the substrate concentration yielding 1/2Vmax.
Km
When the effector binds to the ( ) site (the effector site), the protein undergoes a conformational change, and this changes its kinetic constants.
Allosteric
Regulatory enzymes typically show ( ) kinetics, while non-regulated enzymes show ( ) kinetics.
Sigmoidal, Michaelis-Menton
There are three recognized patterns of feedback inhibition in biosynthetic pathways. What are those?
Simple, Concertive, Cumulative
When the binding of one substrate molecule increases the affinity of the enzyme for a second substrate molecule or increases the rate of formation of product from sites already occupied. This is called ( ) cooperativity.
Positive
Positive cooperativity makes enzyme catalysis very ( ) to small changes in substrate level concentrations.
Sensitive
Covalent modification of enzymes or proteins occurs by the reversible attachment of chemical groups such as ( ) groups, ( ) groups, ( ) groups, ( ) groups, and ( ) groups.
Acetyl, Phosphate, Methyl, Adenyl, Uridyl
Sigma factors determine where RNA polymerase should bind.
True
The molecular weight of sigma32 is 32 kD.
True
Oxygen sensing proteins are all heme-containing proteins.
False
It is not the temperature per se that increases the activity and amount of sigma32, but rather the amount of ( ) protein.
Denatured
The toxic forms of oxygen include ( two words ), ( two words ), and ( two words ), which can damage molecules such as DNA, proteins, and lipids.
Reactive oxygen species can oxidatively damage guanine to form ( ), which triggers GO system in bacteria.
8-oxoguanine
The most common (& bad) outcome of DNA damage by UV light is (two words)
Thymine Dimers
When E. coli cells are exposed to H2O2, OxyR is required to transcribe a set of genes for cellular defense and therefore will be activated. The active form of OxyR has an intramolecular ( two words ) between two cysteine residues.
Disulfide Bond
List four functions of the E. coli heat-shock proteins:
1. Folding newly synthesized proteins at all temperatures
2. Export of proteins at all temperatures
3. Refolding of misfolded polypeptides
4. Proteolysis of improperly folded
proteins
Acidic environment is easier for ATP generation via ATP synthase, so it is optimal for bacterial growth.
False
Bacteria maintain their internal pH and osmolarity by controlling water permeation (blocking/allowing water permeation) through the cell membrane.
False
Turgor pressure has nothing to do with bacterial cell growth and division.
False
In bacteria, turgor pressure is generally exerted across the outer membrane.
False
No bacterium can live in 5 M NaCl environment.
False
In the presence of high salt concentrations inside bacterial cells, ionic interactions (e.g. between amino acids in a protein) are weakened.
True
Bacteria can be found growing in habitats that vary in pH from 1 to 11. However, regardless of the external pH, the internal pH is usually maintained within 1 to 2 units of neutrality, which is necessary to maintain viability. Thus, bacteria maintain a pH gradient (DpH) across the ( two words ).
Cell membrane
The regulation of intracellular pH is mostly a consequence of controlling the flow of protons across the cell membrane. On the other hand, for bulk proton to take place, the pumping must be done ( ). For example, when the cytoplasm becomes too basic, protons are brought in via exchange with outgoing ( ) or ( ).
Electroneutrally, K+, Na+
In alkaliphiles, the use of Na+/solute symporters is advantageous because solute transport is driven by the ( two words ) rather than the ( two words ), the latter being low because of the inverted ( ).
Sodium Potential, Proton Potential,Δ pH
In acidophiles, the maintenance of the large DpH requires an ( two words ) at low pHout. In turn, this is due to an inward flux of ( ) greater than an outward flux of ( ).
Inverted Membrane Potential, K+, Protons
It looks like an acidophile has an advantage of having pre-existing proton potential, thus generating ATP through ATP synthase. But there is a problem without any compensatory mechanism. What is the problem?
It costs energy to maintain the gradient
An alkaliphile should maintain the pH condition above. Then, what is the main challenge for these bacteria?
Very little H+ outside the cell so it's difficult to make ATP
Mechanosensitive channels exist in the cell membrane. (T/F)
True
Mechanosensitive channels are proteins. (T/F)
True
Mechanosensitive channels proteins should have strong interaction with lipid molecules. (T/F)
True
SoxR and OxyR are involved in transcriptional regulation by sensing superoxide and hydrogen peroxide, respectively. Then, their activity is DNA binding. (T/F)
True
What could be the main job(s) of heat shock proteins in bacteria (well, let's say E. coli) when temperature is higher than normal condition?
Renature proteins or dispose of the denatured protein
Role of rpoD
Housekeeping sigma factor
Role of rpoH
Genes induced by heat shock
Role of rpoS
Genes for stationary phase
Role of rpoE
Genes for very high temperature
Role of rpoN
Genes for nitrogen metabolism
Role of mutS
Identify basepair mismatch problem
Role of mutL
Methylation
Role of mutH
Add nick to DNA
A. - ("simple")
B. -/- ("concerted")
C. -/- ("cumulative")
If Km is high, this means: The enzyme has ( ) affinity to the substrate
Low
Which curve (A or B) shows more sensitivity in terms of enzyme activity in response to change in substrate level?
A (sigmoidal curve)
1. Binding of + effector will (increase or decrease) Km of the enzyme.
2. Binding of - effector will (increase or decrease) Km of the enzyme.
1. decrease Km
2. increase Km
All the molecules below can be environmental signaling molecules in bacteria. Which one will penetrate cell membrane freely?
a) NO3-
b) K+
c) Inorganic phosphate
d) N-hexanoyl homoserine lactone