New material for Final - Prep

consists of half of the final material; starts at viral latency and lysogeny - end of lectures

what is the lytic cycle?

when a virus infects a cell and immediately starts to replicate/make viral particles

What is an example of latent disease in humans?

shingles; b/c once chickenpox clears, there can be no symptoms for years → later on the virus can reemerge from neurons where it hid

* after infecting a cell, it is when a virus goes dormant, which allows a cell to “take care of the virus” to which it can then activate when it senses it needs to

What happens to the chromosome of a cell that is infected w/ shingles?

it will exist as a plasmid, causing it to circularize in the cell and just “hang out”, NOT actively replicating

What is latency?

when a virus is inside a host cell in some form -- like genetic information, etc. -- but it does not cause damage to the cell

What are the 2 ways latency can be accomplished?

Episome and Prophage/provirus

What is episome?

when viral DNA is maintained as an extra chromosomal element (like plasmid)

What is a prophage/provirus? What is the common prophage referenced in this class?

a viral genome that is integrated into the host chromosome/genome

* lambda prophage

What 2 abilities must a cell have to maintain latency?

1. avoid host cell destruction via some cell-mediated immunity


1. not activate replication of the virus -- meaning it must be able to go back into a lytic cycle to actively replicate, when ready

What is eventual reactivation?

some sort of physiological change in a host due to a response to stress or immunological suppression

What does it mean for a long-lasting virus to not technically be latent? What would this be in reference to (disease wise)

meaning it is integrated into the host chromosome like a latent virus, however, it remains actively replicating, just as a very low level → chronic diseases; HIV

What are are 3 main things latency can do to a host?

1. have positive effects
2. cause chronic diseases


1. cause cancer

What positive effects can latency have a host?

allow for protection from other infections, or similar viruses

* certain proviruses/prophages, if infected a host, can prevent us from being infected by other closely related things

How can latency to the host cause cancer?

allows for cell transformation, causing the viral infection to generate oncogenes, or regulatory sequences

What is an endogenous retrovirus? What is an example of this?

it makes viral genes work for our (human) bodies

* syncytins → viral envelope proteins that are used in placental synthesis

What would NOT be an example of a latent virus?

HIV b/c when it infects a host, it is still actively replicating at a low level → this is NOT latency b/c it is still replicating -- w/ latency, there should be NO level of replication at all

What are two other terms that can be used to describe latency?

temperate or lysogenic

What type of genome is the lambda phage considered? What does that mean as it becomes integrated into the host chromosome in comparison to when it is inside the virus?

dsDNA, AKA double-stranded DNA

when it is inside the virus, it is linearized -- when it’s injected into the host, it then circularizes itself for means of protection

* the ends of the DNA are joined together by DNA ligase

What would happen if lambda phage did not circularize in the host

the bacterial host would degrade it via exonuclease activity

Where will the lambda phage integrate at? What happens if it integrates elsewhere?

ONLY at the attB site -- if it does NOT integrate here, then it can cause a mutation

* this is rate though

Though some phages can integrate at multiple sites, what does that mean in terms of them sharing homologous sequences?

the sites don’t share homologous sequences

What are viral-encoded integrases responsible for? How do they work?

site-specific recombination

they MUST be expressed early in the infection for integration to happen in the first place

* b/c of this, it means that integrate enzyme will be one of the early proteins that need to be made right away to allow a virus to become latent

Maintaining latency refers to how does a virus turn itself “off”, what is the key protein used?

C1 repressor protein

Briefly explain the C1 repressor protein.

it is a lambda repressor; its a protein that encodes for a repressor protein to repress the expression of other viral genes

it will bind onto operator sequences in DNA in order to turn off **transcription**

as more repressors bind, the prophage sequences will bind to the promoters on either side, which causes loops on the sequences, which further inactivates the gene

What is the issue w/ C1 being made and causing viral replication to be shut off? What’s the solution?

once a virus is latent, it needs to stop being latent at some point in order to become lytic → solution = auto regulation

What is autoregulation?

when C1 reaches the highest levels, the repressor will eventually shut off the expression of the repressor itself → allowing for replication of the virus to begin (entering the lytic cycle)

* \*b/c in order to be lytic again, you need to get rid of all the C1 protein

What does filling the third operator on either side of the promoter cause (in terms of auto regulation of the C1 protein)?

it will turn off the repressors own transcription, which causes the C1 protein to no longer work → allowing for lytic cycle to take place

What is induction?

a signal form the cell and the environment that tells the virus that “its time to enter the lytic cycle and begin replicating”

When would a cell consider going into the lytic cycle? What does it signal for?

when events occur that negatively affect the host, which signals for the induction of lysis

What is an example of Induction?

UV exposure b/c it causes damage to the DNA of the host, to which the virus will respond by becoming lysis.

Briefly explain UV exposure’s relation to the induction of lysis.

during DNA repair of UV-mediated damage, RecA will bind ssDNA intermediates for it to become activated

RecA will then degrade a host repressor, LexA, to keep the SOS response off

When RecA detects DNA damage, it becomes a protease → cuts up other proteins in the host cell. What is the main target of RecA?

LexA; b/c it is a repressor that keeps the SOS response genes off, since most times it is NOT needed

When the DNA repair system is activated, when under UV damage, what does that mean ?

you’re getting ride of the C2 repressor and activating the viral lytic cycle

To get a lytic cycle, what do you need from the promoters?

them to actively transcribe the genes needs to do viral replication

What happens when the lambda repressor is gone?

phage genes can be expressed, followed by the rest of lytic genes -- in order to undergo lysis

What is the role of the cro gene (when beginning to undergo lysis)?

Cro will be produced first for the purpose of inhibiting the production of the C1 protein → allowing for the expression of the rest of the genes

* recombination occurs → DNA replication → Capsid production → host cell lysis
* \*don’t want to go backwards after the removal of the C1 protein

What determines the virus’s initial decision to undergo the lytic path?

the condition of the host cell

To undergo lysogeny, what 3 proteins are used and what for?

C3 and C2 proteins protect C1 → to which host cell proteases can degrade the enzymes

What is a key protease to look for when determining the virus’s initial decision to go lytic or lysogenic? What does this protease do?

Hfl

* it’s sensitive to nutrient levels in the cell → will determine whether or not the condition of the host cell is good
* high glucose → LOW cAMP → HIGH hfl

What does Hfl do?

it will degrade the C1 protein, causing MORE Hfl → less C1 → LYSIS

Why will high numbers of infecting particles/viruses cause?

more C1/2/3 production → lysogeny

What is a protease? What would lots of it cause (terms of C1 repressor)?

enzyme that degrades protein

lots of it → destroying C1 repressor protein → become lytic

Briefly describe a situation where a viral particle would want to become lytic.

if there is one healthy cell that a single virus has gotten into, but is surrounded by a bacterial population full of healthy cells → you’d want to spread as quickly as possible (as a virus), therefore you would wan to become lytic to begin replication of viral particles to attack the healthy bacterial population

Under what cell condition would a latent lambda phage undergo induction and switch to the lytic cycle?

when the cell is undergoing stress or when the cell is growing quickly

* you would want to begin replication before more damage occurs to the host cell -- like when the host cell is in danger
* growing quickly means more opportunities for the virus to infect the cell

If a cell is doing OK and NOT growing quickly, what will a virus likely do once infected into the host cell?

simply hang out and be latent b/c there is no danger to the host cell, nor are there opportunities for the virus to infect the surrounding bacterial population

What is a symbiosis?

any stable interaction between 2 or more organisms -- NOT always a positive interaction for both members

Mutualism

if they don’t exist together, then neither organism will survive on its own; obligatory

Cooperation

when two organisms are together, they do better BUT the presence of one another is NOT necessary for survival; not obligatory

Commensalism v. Amensalism

A benefits B v. A harms B

Amensalism, predation, and parasitism are all very similar. Predation and Parasitism is more specific. Briefly explain both.

predation is when there’s a predator/prey species and the predator hunts the prey

parasitism is when a parasite lives within a host and causes harm to the host

Competition

one outcompetes the other for resources OR both will coexist at lower levels b/c they share a limiting resource

What are 4 pieces of evidence that mitochondria and chloroplasts arouse from a symbiosis between bacterial ancestors?

1. looking at their division process, both use FtsZ and Min proteins
2. protein synthesis begins w/ f-Met
3. ribosomes closely resemble bacterial type


1. have circular chromosomes w/ no histones

Many bacterial genes have been transferred from what?

organelles to nucleus

Which endosymbiosis came first (between mitochondria and chloroplasts)?

mitochondria (1.7-2 bya) then chloroplast (1 bya)

What is the likely mitochondrial ancestor?

rickettsia

Apicoplast in protists is another symbiosis. Explain

related to chloroplasts → converted from photosynthesis to other functions

Kinetoplast is another symbiosis. Explain

they are specialized mitochondria in some protozoa, usually found in association w/ the flagella/cilia

Aphid and Buchnera is a common Bacterial/Insect mutualism. Briefly explain it.

Aphis CAN’T synthesize 10 amino acids and the same ones are not provided in their diet -- Buchnera lost many amounts of genes, but retains amino acid biosynthesis in their plasmids → species have coevolved

* vertical transmission → Buchnera replicates and is passed down during the replication of Aphid cells, rather than being transmitted after → THEREFORE buchnera cells do NOT have to reinfect a new host cell every time
* \*coevolving means that whenever an aphid lineage splits, a buchnera linage also splits

What 2 things would you expect to see if you were observing a bacterial endosymbiont that is very far along in the process of becoming an organelle?

1. some of the genes from the bacterium are transferred into nuclear DNA
2. the bacterium provides an important function for host cell survival

What is the symbiosis between Rhizobium and plants considered?

commensalism or cooperation

Briefly explain the Rhizobium and plant symbiosis (4 kind of steps)

plants will excrete flavonoids (acting as chemoattractants) to attract bacteria to their root hairs to bind → induces the expression of nod genes in bacteria (nod = nodule forming)

rhizobium will then secrete enzymes to break down plant cell wall for them to enter the root hair → releasing nodulation factors, causing the root hairs to curl

rhizobium will then travel along infected sites → plant will respond by starting nodule formation

finally, as a nodule forms, bacteria will differentiate into nitrogen-fixing forms -- the plant will produce leg hemoglobin to bind O2 and keep its concentration low around the nodule (since it is doing N2 fixation -- sensitive to O2)

What is the purpose of plants producing leghemoglobin (symbiosis w/ rhizobium)

to keep the rhizobium in an anaerobic environment, since it will be doing N2 fixation -- the leghemoglobin will bind O2, keeping it away from the rhizobium

What are ruminants?

mammals that rely on a microbial community in their gut to convert plant material into digestible forms

Where does the symbiosis between mammals and their gut microbes take place?

the rumen → anaerobic fermentation chamber

\*kind of like a mammals “pre-stomach”

Explain the symbiosis that occurs in ruminants and the role the rumen plays.

a community of bacteria, fungi, and protozoa create an anaerobic ecological system that breaks down cellulose into sugars (bc cellulose is indigestible), to which it then ferments those sugars -- all in the rumen

* volatile fatty acids are formed from the fermentation absorbed by the ruminant
* saliva production maintains pH balance in the rumen

in the rumen, the stomach kills microbes and makes their biomass available for the ruminant for absorption

* microbes not already destroyed by the acid, will be degraded by an acid-resistant lysozyme in the ruminant

What is a syntrophy?

similar to commensalism, BUT, one microbe produces a waste product that another microbe will then consume as nutrients

* could benefit both organisms b/c the waste product accumulation could inhibit growth

Briefly explain the interspecies metabolite transfer (5 steps).

1. organic material will be processed -- usually in anaerobic conditions, leading to fermentation
2. extracellular hydrolysis occurs to generate soluble, transportable carbon compounds
3. fermentation is performed
4. fermentation products are used by other organisms within the chain, until you end up w/ CO2 and/or CH3


1. acetate → both
2. formate → H2 + CO2, or CH4
3. fatty acids/alcohols → CO2
5. inhibitory/toxic waste products are removed → allowing reaction equilibriums into a more favorable spot

Briefly explain commensalism in a dental context (3 steps)

1. first colonizer are commensals -- streptococcus and actinomycetes → set up initial biofilm by attaching to the tooth surface further colonization by
2. pathogenic/acidifying bacteria causes harm (2 reasons)


1. fermentation acidifies the environment → weakens tooth enamel
2. gingivalis invades the gum tissue → gingivitis


3. biofilm will continue to develop & tartar buildup will continue to protect bacterial populations

\*bacteria are the organisms that are benefiting from this symbiosis

Which bacteria are the ones causing damage to teeth and gums during the commensalism in a dental context?

the late colonizing (facultative) anaerobic bacteria

* fermentation weakens enamel due to acidifying environment
* bacteria invades the gum tissue causing gingivitis

Briefly explain the amensalism between ant farmers protecting their crops w/ weaponized microbes (4 steps)

recall: amensalism is when one organism is directly causing harm to another organism

\*though this interaction is an amensalism, it can also be considered a commensalism → the ant gives home to the microbes -- the microbes give the ant means of self defense


1. ants grow fungal gardens to feed
2. parasitic fungi then want to eat the ants food (escovopsis)
3. ants evolved w/ actinomycete to be a good host environment
4. the actinomycete creates a good antibiotic that controls the growth of escovopsis phialophora (yeast) to keep the number of “cheaters” in check


1. this yeast is constantly eating some microbes, to which it ~~makes~~ the microbes pressured to continue maintaining antibiotic production

What does “cheating” refer to?

when a whole colony of bacteria want to do a certain activity

Why would too many cheaters not producing antibiotics be a danger?

it would harm the ant b/c it means there would be less pressure for the microbe to produce the antibiotic → decreasing the amount of antibiotic production

Briefly explain Toxoplasma gondii

is a parasitic protist → performs sexual reproduction in a cat (as its main host)

* will colonize the git and release oocytes that will then spread through the feces of the cat

rodents and humans are secondary hosts

Briefly explain how toxoplasma gondii works

1. oocysts will begin reproduction, BUT are impeded by a strong immune system response
2. most oocysts are then destroyed or remain dormant within the tissue of the host
3. in RODENTS: infected rats/rodents are shown to become attracted to cat urine → increasing their chances for being eaten and passing the parasite back into a cat for it to complete its lifecycle


1. in HUMANS: infection can lead to acute symptoms

Briefly explain Cordyceps

they are an example of parasitism; they consist of an ascomycetes genus of many species

* their spores infect target insects at their respiratory tract, causing mycelia to grow towards their brain → compounds are secreted into the brain that disorient the host
* BUT infected insects have evolved in a way where they will move away form offers of its species as a defense
* as the fungus continues to grow, it will kill the host and form fruiting bodies → ready to disperse spores

Briefly explain the predation chain among bacteria, protists, other bacteria, and animals.

bacteria/other microbes are often prey for other organisms:

bacteria → other microbes → protists → animals

Myxococcus and Bdellovibrio are examples of bacteria preying on other bacteria. Briefly explain Bdellovibrio (5)

Bdellovibrio is a bacterial predator


1. begins as a motile predator
2. invades the periplasm CAUSING the loss of the flagellum
3. cell membrane is then disrupted, allowing it to feed on nutrients
4. will then grow and divide into multiple motile daughters
5. finally escaping

Briefly explain antibiotics and how its considered an amensalism.

they re secreted compounds that are toxic to other types of cells -- they can kill or inhibit the growth of organisms

\*antibiotic production of bacteria → linked to predation

What are bacteriocins? Briefly explain

small peptide molecules that inhibit growth of its targets

* they are NOT classified as antibiotics, but have similar effects
* target can be closely-related species, OR not -- can have a narrow or broad spectrum
* can be used industrially

What are siderophores? Briefly explain in terms of competition

competition for iron → allow bacteria to grab all the iron before before any other organism

What is an example of waste products being inhibitory to other organisms?

ethanol

* competition of resources, like nutrients or space to grow

What do most elemental conversion processes come from?

redox reactions

What is the potential use of microbes in recycling man-made materials?

plastics or chemicals

Briefly explain Carbon cycling

* \~50% of a cells weight


* can come in multiple forms (4):
* CO2, methane, organic, inorganic
* autotrophs can fix CO2
* occurs in territorial and marine life

What does the cycling of ORGANIC Carbon result in?

respiration or fermentation

Briefly explain the elemental conversion process of Oxygen.

* oxygen gas was generated by microbes → cyanobacteria evolved O2 first
* microbial O2 synthesis in oceans accounts for more than half of O2 production on earth → diatoms

\

Briefly explain the elemental conversion process of Methane.

* Methane cycling links to carbon/oxygen and sulfur cycling → lots of overlap
* Archaea and bacteria combine the process of REDUCING sulfate and OXIDIZING methane
* some utilize bacteria to cycle out sulfide via oxidation in order to push the equilibrium to a more favorable direction
* archaea will directly transfer e- to bacteria via their pilus ?

What is an ANME?

an anaerobic methanotrophic archaea → archaea that can break down methane anaerobically

Briefly explain the elemental conversion process of Nitrogen.

* something ONLY prokaryotes can do


* is 80% of the atmosphere
* N2 fixation is important for life on earth → if this did NOT occur, then there would be NO nitrogen compounds for others to use
* ex. soil would be depleted quick -- we need soil for fertilizers so that we can grow food
* is fixed biologically and chemically

What is assimilation?

the conversion of a nutrient used for biosynthesis (building of things)

* nutrients are REDUCED and incorporated into cell material

What is assimilatory nitrate reduction?

NO3- (nitrate) serves as a nitrogen source → it is reduced into ammonia and then incorporated into the biomass of the cell

What is dissimilation?

the breakdown of nutrients to use as an energy source

* can be a reduction or oxidation
* oxidation of ammonia to nitrate
* reduction of oxidized nitrogen compounds (as a terminal e- acceptor) in anaerobic respiration

What is dissimilatory nitrate reduction?

NO3- will serve as the terminal e- acceptor during anaerobic respiration

What is nitrification, denitrification, and anammox examples of?

energy generating processes, AKA dissimilatory processes -- breaking things down and NOT saving Nitrogen; will just be a WASTE product

Briefly explain nitrification.

the oxidation of ammonia to nitrate via a nitrate intermediate

* consist of 2 steps, 2 organisms
* nitrifiers → chemolithoautotrophs
* grow in close proximity to one another

\*NH4 → NO2- → NO3-

Briefly explain comammox.

complete ammonia oxidation (CAO); is the direct conversion of ammonia to nitrate in one organism

\*is an example of convergent evolution -- genes evolved independently

NH4+ → NO3-

Briefly explain denitrification. What are the most common denitrifyers

a series of reductions from nitrate into nitrogen gas: NO3- → NO2- → NO → N2O → N2

\*using O2 as at the terminal e- acceptor

* heterotrophic denitrifyers are most common
* each reaction is often done by a different microbe in a communities

During nitrification, if there’s NO O2 available, but nitrate available, what might happen? What is the consequence of this?

the microbe will express a nitrate reductase so that it can use nitrate as an e- acceptor instead of O2 -- BUT, b/c nitrogen is getting turned into N2, it results in the loss of Nitrogen to the system

* w/ O2 as terminal acceptor, you’re not losing nitrogen in the process of making N2

Briefly explain Anammox. What type of organisms do this?

Anaerobic Ammonia Oxidation (AAO); NH4+ + NO2- → N2 + H2O -- oxidizing ammonium to nitrogen

* organisms that do this are anaerobic autotrophs
* responsible for majority of N2 generation from the ocean

What are Planctiomycetes?

organisms that perform anammox

* discovered in wastewater treatment -- very slow growing & difficult to culture

What are anammoxosomes?

similar to carboxysome; they generate a PMF for ATP synthesis AND sequesters toxic intermediates