Microbial Physiology Exam 3

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)

1. Sequestered or enzymatically inactivated by EPS
2. Inhibits cells at biofilm core; starved (low metabolic activity)
3. Are adapted to resist antibiotics and are a large enough colony to increase chances of survival
4. 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