Studied by 3 people
MBioS 450 at WSU
Lecture 17
Lecture 17
In bacterial nitrogen fixation, what is N2 converted to?
NH4+
What is the anammox (chemical) reaction equation?
NH4+ + NO2- → N2 + 2H2O
Where does nitrification occur in a fish tank?
In the water column
What is the product of denitrification?
Nitrogen gas (N2)
What is the purpose of assimilatory nitrate reduction?
To remove Nitrate
To produce ammonium for cellular use
To gain energy
Lecture 18
Lecture 18
What is the acid mine drainage?
Wastewater from abandoned metal mines
Wastewater from abandoned coal mines
When sulfur-oxidizing bacteria oxidized sulfide (H2S, HS-, S2-) to H2SO4, how low can the pH go?
pH1
What is the purpose of reverse electron flow in chemolithotrophic bacteria?
Reduce NAD+
What is the physiologic function of dissimilatory sulfur reduction?
To oxidize organic compounds and gain energy for growth
What do heterotrophic bacteria often oxidize sulfide to?
Thiosulfate
Lecture 19
Lecture 19
What does the microbial community in sediments of freshwater lakes without O2 and alternative electron acceptors converts complex organic compounds to?
CO2 + CH4
What does the microbial community in cow rumen converts complex organic compounds to?
CO2 + CH4 + short chain fatty acids
Why do anaerobic protozoa often harbor methanogens and hydrogenosomes in their cytoplasm?
The association allows sugar fermentation to acetate and H2, producing more ATP
Which short chain fatty acid is a major carbon and energy source for the human intestinal tissue?
Butyric acid
How does the carbon cycle primarily interact with nitrogen cycle under anaerobic conditions?
Dissimilatory nitrate reduction
Lecture 20
Lecture 20
Why is lipid A synthesis a target for antibiotic drug development?
Essential to only Gram-negative bacteria
LamB is a porin. What type of solutes does it preferentially transport?
Oligo saccharides
Where is Lipopolysaccharide (LPS) commonly present?
Outer layer of the outer membrane
Which part of lipopolysaccharide (LPS) is the endotoxin?
Lipid A
Why does EcoRI not cut the E. coli chromosome?
EcoRI methylase methylates the EcoRI binding site and protects it from EcoRI.
Lecture 21
Lecture 21
What is a SOS response in a cell?
A global response to DNA damage, including repair and inhibition of cell division.
What is the phenotype of the minE-deletion mutant growing at 30°C?
Minicells
Which protein provides the scaffold for the assembly of the divisome?
FtsZ
Which protein inhibits the Z-ring formation?
MinC
Which protein separates DNA into the two daughter cells?
FtsZ
How long is the round trip of MinCDE oscillation at room temperature?
1 minute
Lecture 22
Lecture 22
Hypothetical Mechanisms of Biofilm Resistance? (there are 4)
Sequestered or enzymatically inactivated by EPS
Inhibits cells at biofilm core; starved (low metabolic activity)
Are adapted to resist antibiotics and are a large enough colony to increase chances of survival
Made of Persister cells (Highly protected, possibly spore-like cells)
What organism is responsible for cystic fibrosis?
Pseudomonas aeruginosa
Cystic fibrosis patients of what age group are 2.6x more likely to die within 8 years?
Children
Why can autoinducer analogues inhibit biofilm development?
They disrupt the timing of gene expression required for biofilm development
How many stages are there in biofilm development by Psuedomonas aeruginosa?
5 stages
Which quorum sensing system regulates rhamnolipid biosynthesis in Psuedomonas aeruginosa?
The RhI system
Which is important in surface attachment in the biofilm development of Psuedomonas aeruginosa?
Flagella and Type 4 pili
Which properties make biofilm more resistant to antibiotics?
EPS layer slows the diffusion of hydrophobic antibiotics
Persister cells are more abundant in biofilms than in planktonic cells
Drug resistant genes are abundantly expressed in mature biofilms
Lecture 23
Lecture 23
What can you learn from a sequenced bacterial genome?
All the genes of the genome and their potential functions of the bacterium
What does Halobacterium salinarum use to harvest light energy for growth?
Bacteriorhodopsin
What can you learn via RNA-seq with a sequenced bacterial genome?
The expression of the genes in the bacterium
What is the percentage of identify between the microbial species of two unrelated persons on average?
80-90%
What can we learn from metagenomic studies in a specific environment?
Identify microbial processes in the environment
Identify new species in the environment
Identify dominant microorganisms
Lecture 24
Lecture 24
Why acn TA pairs induce the formation of persister cells?
Some toxins degrade mRNA, which arrests the growth of cells
What is the function MazF?
Sequence-specific RNA endoribonuclease
What is the function of HipA?
It phosphorylates glutamyl-tRNA synthetase to stop the production of charged tRNAGlu
What are persister cells?
Persister cells commonly present in normal culture as a small subpopulation
Since they are metabolic dormant, they are not sensitive to antibiotics
Persister cells randomly revive to generate a normal microbial population
Why does a toxin-antitoxin pair stabilize a plasmid in a bacterial population?
Toxin is stable
Antitoxin is unstable
Toxin kills the cells after the cells lose the plasmid
Lecture 25
Lecture 25
What is Aequorin, and what does it produce when reacting with O2?
Aequorin is a luciferase produced by jelly fish, producing Blue light
What element is usually required for maturation of GFP?
Oxygen
What causes GFP to become different colors?
mutagenesis
Why are fluorescent proteins so easy to isolate?
Proteins are extremely stable and can be identified by their fluorescent color
What molecular structure are fluorescent proteins held within?
Beta barrel proteins
Why is green light produced when aequorin produces blue light?
GFP takes in blue light and produces green light
What is aequorin from Aequorea victoria?
enzyme that is activated by calcium (Ca2+)
A luciferase
An enzyme uses O2 to oxidize coelenterazine to produce light
What is green fluorescent protein (GFP)?
It is a barrel shaped protein with the chromophore made up of 3 amino acid residues
Which amino acid residue change converts GFP to enhanced GFP (EGFP)?
The conversion of serine at position 65 (counted from N-terminus) to threonine
Which amino acid residue change converts GFP to yellow fluorescent protein (YFP)?
The conversion of threonine at position 203 (counted from N-terminus) to tyrosine
Why some Red fluorescent proteins (RFPs) are green when first synthesized but are gradually converted to red?
GFP contains a single double bond, and REP contains two double bonds
The chromophore in RFP is not completely matured
The formation of the second double bond in REP is slow
Lecture 26
Lecture 26
What will synthetic biology do?
To construct biological systems biological systems, but to make changes as desired.
To construct new biological systems biological systems not found in nature.
Computer is used to design and create models for testing.
What are key enabling technology for synthetic biology?
Synthetic gene regulators so that the gene expression strength and timing can be designed
Chemical synthesis of DNA
Assembling plasmid or viral genomes
How can a bacterial genome be chemically synthesized?
Small fragments are chemically synthesized, assembled in yeast, and then transformed into a bacterial host to replace the host genome.
Why does a biological toggle switch have memory (Using the example given in the lecture)?
The promoter (pMerT) is repressed by MerR, and the promoter (pLac) is repressed by LacI
When Hg2+ is added, pMerT is on to produce LacI and other activities.
LacI represses MerR expression so that MerR is no long present and pMerT is on even without Hg2+
What is leghemoglobin?
It is a plant-produced hemoglobin
Lecture 27
Lecture 27
Note 
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