Unit 3 Flashcards
What is transformation
uptake of free DNA from the environment
What is competence
When bacteria have the ability to take up foreign DNA
During transformation what type of DNA is taken up and why
Only ssDNA to prevent bringing in a virus/mutation
What are the two strategies for transformation
looking for a specific DNA sequence: 11bp sequence that tells bacteria the DNA is from their population or waiting for quorum so that only DNA from its population is taken up
what is transduction
Incorporation of foreign bacterial DNA mediated by viruses
What is the lytic cycle and what are bacteria called when they use this cycle
When bacteriophage infect a cell, replicate via rolling circle replication, then lyse the cell; baceriophage are virulent
What is the lysogenic cycle and what are the bacteria called when they use this cycle
Cell is infected, genome circularizes, then bacteriophage goes dormant due to lack of resources. Cell then gains resources or becomes stressed to virus ressurects itself, replicates, then lyses cell; temperate phage
What is generalized transduction
Random incorporation of any bacterial chromosomal fragments within an infectious phage
What is the process of generalized transduction
Viral DNA is injected into host, breaking up host chromosome. Packaging occurs when DNA is put into viral shells but some of the host DNA can be put in these shells. When cell is lysed bacteriophage leave to infect other cells. When shell goes to infect cells some receive host DNA that can be incorporated into new cell if advantageous
What is specialized transduction
Only happens in lysogenic cycle. When bacteriophage ressurects itself, it takes only certain parts of the genome (the parts directly next to it) thus, packaged viruses will be defective and host DNA can be incorporated into new cell when “infection” occurs
What organisms are intercellular mobile genetic elements and what does that mean
Plasmids and bacteriphages; means they can direct their own movement between bacterial genomes
What organisms are intracellular mobile genetic elements and what does it mean
Insertion Sequences and transposons; they can direct their own movement within bacterial genomes
What is methanogenesis in archaea
using anaerobic respiration to produce E; not much E is made so methanogens are just barely living
How is methanogensis in sediment environments an example of syntrophy between archaea and bacteria
Lack of O so bacteria must go through fermentation but products are toxin when in high concentration. Archaea use products to produce methane so no toxins for bacteria and archaea get food
How do bacteria and archaea work together in rumeneints
Volatile fatty acids (VFAs) along with H2 and CO2 are products of bacterial fermentation but are toxin when in high concentrations so archaea use those products for methanogenesis
Why do rabbits have two types of poop
They have regular poop to get rid of waste but also poop known as cecal pellets. These are pellets that have partially digested food in them that are then reingested to get more nutrients
How do microbes work in the human intestine
Microbes go through fermentation to break down material that we can’t. This creates short chain fatty acids that are a source of E for colonocyntes as they go into the mitochondria, through beta oxidation, into the TCA cycle to make reducing power to generate electrons for ATP synthesis
What are halophiles
Archaea that grow in very high salt concentrations and at lower O levels, produce pigments
How do halophiles produce pigment
via a bacteriorhodopsin that uses a light driven proton pump to generate PMF for ATP synthesis. They have retinal hydrocarbons that have two forms (cis or trans) that are switched between depending on light
How does halorhodopsin work
With chloride ions that enhance PMF creating more of a potential difference
How do sensory rhodopsin work
There are two; one that senses red/infared light and one that sense damaging/blue light. Archaea want to move towards the light but not too close. As such they move towards the red light via phosphorylation but also move away from blue via phosphorylation when too close.
How do bacteria adapt to living in hypersaline environments
They maintain homeostatsis via compatible solutes which don’t interfere with biochemical reactions and help maintain concentration intra and extracellularly
How do bacteria make it to a plant for crown gall disease
Rhizobacteriaceae move towards a wonded plant when they release metabolites and chemotaxis towards it and enter it
What causes the tumor to grow on plants for crown gall disease
The TI plasmid in the bacteria that causes a change in gene expression via conjugation
How do cyanobacteria fix N
They have specialized cells, heterocysts, that can fix nitrogen. They have specialized membranes that exclude oxygen from entering them so that they can fix N while the other cells can go through photosynthesis
How does symbiotic N fixation work between bacteria and plants
bacteria are attracted to plants via flavanoids. As bacteria move towards the plant, Nod factors are released which change gene expression in the plant as well as rhicadhesion which allow the bacteria to adhere to the root hair. Once bacteria infect the plant they proliferate to make a nodule. In the nodule nitrogenase enzymes are made that fix N. Nitrogenase breaks triple bonds in N to produce ammonia which is made into amino acids for bacteria
Where does does nitrogenase get the E to convert N to ammonia
Bacteroids convert sugar in organic acids which is put into the CAC then the ETC to make a PMF for ATP synthesis
What happens to bacteria once they make it into the plant for N fixation
A shepherd’s hook forms that wraps around the bacteria to hold it. An infection thread is made only in the presence of Rhizobium that moves thrughout the cell so that a symbiosome is formed, keeping the bacteria in one place. The bacteria then become bacteroids that contribute to ATP synthesis
What do bacteria do in nitrosification, whay do they use for it, and what else is needed for it
Converting NH4 to NO2 via ammonia monooxygenase (AMMO). Requires a lot of thylakoid membranes to increase SA for more AMO
what do methnotrophic bacteria use to convert CH4 to CO2 and what else is needed for it
methan monooxygenase (MMO) also requires a lot of thylakoid membranes to maximize MMOs
How are AMO and MMO similar
They have different functions but both will oxidize ammonia if given the opportunity
Explain the realtionship between sphagnum, archaea, and methanotrophic bacteria
Bacteria ferment the organic matter that is on the floor of the ocean, archaea eat the products of fermentation prodcuing methane, methanotrophic bacteria convert the methane into CO2 for the plant
What are microbial mats
microbes that lived in multispecie communites comprised mainly of primary producers
What are biofilms
Microbial mats but typically thinner and are not really made of primary producers
How are biofilms helpful for bacteria
They allow the bacteria to be able to secrete molecules that won’t freely diffuse so that a quorum can be sensed as well as molecules broken down for E
What is the life cycle of biofilms
Individual motile bacteria make their way onto a new surface, if good resources on surface, bacteria will diffrentiate and lose flagella so E can be used for replication. Bacteria move closer together to form a colony and make a capsule (Biofilm) that grows and remodels. Eventually the biofilm becomes overpopulated so diffrentiation happens again and motile bacteria leave tos start again
What is a virus
Genetic element capable of replication indepdent of host cell chromosomes but not of cells
What does it mean for viruses to be obligate intracellular parasites
They can’t survive without host cell
What type of genetic material do viruses use
RNA or DNA, ds or ss but never both, they will only use one
What type of viruses are more common among animal viruses
enveloped viruses as they have viral glycoproteins involved in adhesion to target cells and viral enzymes that free virus should it stick to cell bc of proteins
What is the eclipse period of bacteriophages
When infection has happened but there are no viruses since they are disassembled
What is the latent period of bacteriophages
When there are no extracellular viruses but there can be intracellular viruses
What is the rise period of bacteriophages
When the number of extracellular viruses begin to rise; lysis begins
What is burst size
number of viruses released from a single infected bacterium; varies from virus to virus
What is key part of the myoviridae bacteria
They have a contractile tail that twists so that noncontractile tube is driven into bacterial membrane so that DNA is released
Explain the infection process of T4 bacteriophage
Attach to cell via tail fibers (legs) attachment to OmpC, needed to ensure that virus infects correct host. Tail pins (teeth of “stomach”) unfold and are driven into cell. Contractile tail twists so tube is driven into cell causing infection. Lysozyme is driven into cell to degrade peptidoglycan of cell
Explain how restricion endonuclease works to defend bacteria
Enzymes, EcoR1, cuts DNA at palindromes so that H bonds are the only ones left. DNA is now restricted meaning its basically inactive. However to prevent restriction of cell genome a methyl group is added so identical sequences on genome to prevent restriction
Explain how the toxin antitoxin works to defend bacteria
Genes are built into chromosome so that bacteria doesn’t become food for virus to infect its brethren. LsoA is toxin while LsoB is antitoxin. Although viruses try to stop cell function, the enzymes are alreadly made so that the toxin will cause death. However Dmd protein is used by virus to bind to LsoA and act like LsoB so phage can replicate
Explain how CRISP works to defend bacteria
Immunity from previous bacteria are passed on during replication in genome. Spacer regions of genome hold DNA sequences that are similar to viral genomes. When bacteria is infected, spacer become trascribed and cleaved into small chunks that will bind to Cas protein as well as viral mRNA to cleave it
What is expressed in cells to supress the lytic cycle
Viral repressor gene represses lytic cycle through positive control. Which is controlled via the C1 protein through positive control. The C1 protein is broken down when lexA is broken down from the SOS regulon causing the viruse to resurrect itself
How does having a bacteriophage in the lytic cycle help bacteria?
The repressor protein that prevents virus resurrection also prevents new infection but only from identical viruses
When will a bacteriophage go into lysogeny
When there are a lack of resources meaning less viruses would be able to be made and when there is a high multiplicity of infection (MOI) meaning that should the virus lyse the cell, there would be no host for those viruses to infect
What type of virus is polio virus
a + ssRNA virus
How do babies receive passive immunity
They receive IgG from their mothers through the placenta or milk. Lasts only a few weeks and allows babies to develop own immunity
What was the benefit of Salk’s vaccine
Prevented viremia (infection getting into blood) via IgG but required boosting
What was the benefit of Sabin’s vaccine
oral vaccine, easy for kids, and made it so that polio couldn’t spread via mucosal layer (had IgA antibodies)
How does polio bind to a host
The viral proteins of the virus bind to necl-5 receptor. VP 2 and 3 specifically bind to the receptor causuing a conformational change of proteins so that the viral RNA genome is injected into the host
How does polio replicate
Instead of capping a 5’ methyl cap, polio uses ires sites to trick ribosomes into binding to it to start translation. This creates a giant protein that goes through autoproteolytic activity to create protiens. One of which is RNAP then makes a new RNA copy resulting in - ssRNA which serves as a template to make more + ssRNA.
What is site specific recombination
Moving of DNA that does not depend on recA or DNA similarity but specific sequences of DNA
How are insertion sequences different to transposons
ISs only have one gene that encodes tranposase and IRs on each end for movement while transposons (Tns) contain IS elements as well as multiple genes
What are composite transposons
when two ISs flank tranposase and other genes
What are noncomposite transposons
When IRs flank transposase and other genes, usually antibiotic resisitance
What is conservative transposition, what it another name for it, and how does it affect the copy number
transposon is cut out and moved to a new site AKA cut and paste. Same copy number
What is replicative transposition and how does it affect the copy number
transposon is replicated and copy is placed somewhere else. Adds to the copy number
How does replicative transposition work
Plasmid or chromosome is nicked at target sites then join together forming cointegrate. Replication occurs so there are two circles making an 8. Resolvase enzyme recombines internal resoultion sites (IRS) so that circles are broken apart.
What are integrons
Mobile pieces of DNA with the ability to acquire novel genes
How do integrons work to take in new DNA
instead of IRs, integrase takes new DNA. int brings DNA between aatC and aatI via integrase site. recombination allows the gene to be replicated intot the genome directly after aatI site, pushing all “novel” genes back
What is the difference between Salk’s vaccine and Sabin’s vaccine for Polio
Salk’s vaccine uses IgG serum so it provided antibodies in the bloodstream. People were protected from the diesase but not from being infectious. Sabin’s vaccine used both IgG and IgA serums so it protected agaisnt infection and the disease, however it could cause paralytic poliomyleitis
What is the poliovirus life cycle
- Attaches to cell via necl-5 receptors and tail fibers
- +ssRNA enters the cell with its VPg protein
- Genome is translated into a giant protein
- Protein goes through autoproteolytic activity
- A bunch of new proteins are made in waves
- +ssRNA is made from -ssRNA
