Study Question 4-1: Oct 31 - Nov 4

How does the long T4 DNA genome get packaged into the small viral nucleocapsid?

A packaging motor attaches to the prohead and starts to discard scaffold proteins and pack in the DNA in a spiral form in the head

What are the cellular filaments of fungi called. What are the dispersal cells of fungi called. Where do you find the dispersal cells on the fungi.

cellular filaments are what grow on a substrate, called hyphae, which is separated into cellular compartments dispersal cells of fungi are called conidia (also called spores) they are found at the ends of aerial hyphae (when the hyphae grows upward)

How does the majority of fungi obtain their nutrients for growth?

chemoorganotrophs -nourish themselves by secreting enzymes that digest polymeric materials into monomers, then up-take the monomers

What is the name of the club-like structure that a fungal sexual spore grows out of? What is the name of the type of fungus that makes these structures?

club-like structure = basidium fungus = basidomycete *spore = basidiospore*

For the endomycorrhizae, what is the hyphopodium and what is the arbuscules.

hyphopodium (anchor) - penetrates fungus epidermis, outer cortex, and inner cortex to form arbuscles arbuscles - do not penetrate cytoplasm, but are surrounded by cell membrane called apoplast

if a virus is spherical in shape, what type of symmetry does the virions have?

icosahedral (20 sides) symmetry

What type of individuals are susceptible to fungal infections?

immunocompromised (sick, young, and old people)

What is the process called where the lysogenic prophage becomes lytic?

induction

What enzyme promotes lambda integration into the chromosome.

integrase

What are some viral proteins/enzymes that can be found contained in the viral nucleocapsid.

integrase- used to integrate their genome into the host genomes replicase- replicate the DNA or RNA nucleic acid lysozyme- degrades bacterial cell wall so the virus can exit neuraminidase- destroy glycoproteins and glycolipids allowing liberation of viruses from animal cells

How does T4 DNA protect its genome from its own nucleases?

it contains 5-glucosylated hydroxymethyl cytosine INSTEAD of cytosine it evolved to disguise its DNA to not look like DNA to prevent attacks

The fungus Microsporidia lacks mitochondria, so how can it grow?

it exists as spores outside of the host, and extends a helical tubes that penetrates the host cytoplasm when near it -injects sporoplasm into host, replicates and lyses the host for growth

How does T4 Phage protect from host defenses like Crisper?

it forms viral factories (viroplasms) to compartmentalize itself from host defenses like Crisper

What does the CIII transcription factor do for Lambda?

it works with CII to promote CI expression to repress lytic growth of Cro

What is the difference between lysogeny and lytic growth?

lysogeny- phage inhibits lytic replication, viral genome integrates into host genome (phage conversion) lytic- replicate in cell and lyse

What enzyme does the virus make that allows them to "lyse" its host? What cellular structure does this enzyme use as a substrate?

lysosome beta 1u-4 linkages conjugated bond system of bacterial cell wall

What is the difference between the lytic viral lifestyle and a lysogenic viral lifestyle?

lytic pathways - viruses replicate and destroy the cell once inside → called a virulent infection lysogenic - the virus' nucleic acid integrates with the host genome → the host becomes a time bomb eventually the virus becomes lytic and produces more of the virus to kill the host

If a T4 gene encodes capsid proteins, would you expect that gene to be considered a early or a middle/late protein?

middle/ late proteins for DNA packaging functions, caspids, tails and

What are monomers of the cells walls of fungi called? What other microbe contains similar type molecules? What are polymers that make up the fungal cell wall called?

monomers → n-acetylglucosamine polymers → chitin serves similar purpose to cellulose → plants and peptidogylcan → bacteria (cell wall)

If the lambda genome is circular in the cytoplasm, how does it replicate to make linear genomes in the viral nucleocapsid?

rolling circle mechanism - positive strand is peeled off template as its being replicated

What is the name of the sac-like fungal structure that encapsulates sexual spores? What is the name of the type of fungus that makes these structures?

sac-like fungal structure that encapsulates spore = ascus (inside a sac) fungus = ascomycete *the spore is an ascospore*

When the T4 genome enters the cytoplasm, why does the middle/late genes NOT get expressed at the same time as the early genes?

sigma factors that regulate when the middle/late proteins need to be made?? takes energy to synthesize these middle/late proteins so the bacteriphage only want to do this when the cell is healthy? T4 first has to take over all of the machinery of the victim cell(DNA/RNA polymerase) in order to make sure its own DNA is not destroyed by the victim cell and to destroy the bacterias own genome to make sure it can't fight back. (via nuclease). ?

Is lambda integration considered general recombination or site-specific recombination.

specific - integration occurs between 2 specific regions Site-specific recombination between the gal and bio region of the chromosome

What are strigolactones? Who produces them and what are the consequences of the molecule?

strigolactones are factors that stimulate germination and growth of arbuscular mycorrhizae toward the plant roots plant roots produce strigolactones

What is the difference between superficial and subcutaneous fungal mycosis?

superficial - skin, hair and nails layers caused by dermatophytes Trichophyton spp → spores are everywhere subcutaneous - spores from soil enter skin abrasions so fungi can break the dermis and invade into deeper tissue Chromoblastomycosis - found in tropical and suptropical countries; spores enter through puncture wounds sporothrix, fonsecaea, cladosporium, schenckii

How does T4 DNA penetrate the bacterial peptidoglycan cell wall?

tail contracts allow an injection tube to penetrate the outer membrane and enzymatically make a pore through the cell wall

The T4 genome is circularly permuted; however, the genome is linear. What does circularly permuted mean?

that each genome has different ends, but contains the same complement of genes

Where does T4 get its nucleotides for DNA synthesis?

the bacteriophage encodes its own DNA polymerase and other DNA replication machinery proteins consisting of repeated genes these genes are used for recombination and replication early proteins subvert host proteins to making the virus and replicate the genome encodes a nuclease that degrades the host genome

If you have a bacteria that became lysogenic with the phage lambda, what would happen if you superinfect it with bacteriophage that came from the clear plaque in question 35?

the clear plaque was infected with lytic bacteria, so the cell would turn lytic??? isnt the phage immune to the new infection?

How does the lipid envelope help virus infect?

the envelope contains proteins that allow the virus to attach and gain -entry into the cell energy is usually a membrane fusion process ( fusion of the viral envelope and the host cell membrane) the enveloped can contain host proteins in addition to specialized viral proteins used for infection and also used for viral release

In the lambda virion, lambda is a linear molecule. However in the host cytoplasm, it is circular. How does this happen?

the lambda genome cyclizes at its cohesive ends the circular genome uses integrase to recombine into the host between the gal and bio regions the integration occur here because there is some sequence homology between the phage and the bacteria

If lambda had a mutation in the CI gene, what would happen if you infect that mutant into E. coli?

The cells would likely go lytic because the there would be nothing to repress the Cro gene

What bacterial cell structures can a bacteriophage use for attachment?

receptors can be flagellum, pilus, membrane transport protein, LPS

If the E. coli has a mutation in Fth, what would happen if it was infected with lambda bacteriophage with a mutation in CIII?

.If Fth is mutated, CII will not be degraded but if CIII is mutated, it cannot induce and stabilize CII. It would most likely go lytic due to Cro not being inhibited. C1 and CII is not degraded since there is a mutation in Fth so it goes lysogenic***

What transcription factor keeps lambda in the prophage lifestyle?

CI prophage - when the viral DNA integrated its chromosome into the host chromosome this is inherited some genes of the prophage is still expressed, and can confer survival advantage to it host

What protein must be degraded in order for lambda to go into the lytic lifestyle.

CI repressor protein

If the E. coli has a mutation in Fth, what would happen if it was infected with lambda bacteriophage?

CII and CI levels build up to great amounts, thus causing the cell go enter the lysogenic cycle

What does the CII transcription factor do for Lambda?

CII is used in the decision of lambda going lytic or lysogenic promotes lysogenic growth promotes CI expression to repress lytic growth induces and stabilizes CI expresion

If lambda had a mutation in the CII gene, what would happen if you infect that mutant into E. coli?

CII would not be there to help stabilize CI so the cell would most likely go lytic

If lambda had a mutation in the CIII gene, what would happen if you infect that mutant into E. coli?

CII's stability is disrupted, resulting in decreased production of CI. Decreased CI causes lytic growth

Name all of the different types of nucleic acid genomes that can be found in viruses.

DNA & RNA Single stranded DNA Double stranded DNA Single stranded RNA Double stranded RNA

If the T4 genome was not circularly permuted, what parts of the T4 life cycle will be disrupted? Why?

DNA replication, because it requires an RNA primer early proteins the genome would not get replicated

What is the relationship between the Fth protease and lambda bacteriophage?

Degrades CI & CII, Cro wins what the phage does depends on the state of the cell when the phage infects if the cell is healthy, it produces a lot of cellular protease (Fth) this protease degrades CII protein and "Cro wins" → lytic growth is promoted for the phage, a metabolically fit host means the phage can produce a high burst; if low, then CIII inhibits FtH and CI accumulates to repress lytic genes so the phage goes lysogenic

What are some examples of superficial mycosis? How does one get exposed to fungi that can cause superficial growth? What do you guess these fungi use for nutrients?

athletes foot, ring worm, jock itch through shared damp areas such as showers or gyms feeds on keratin from our skin

If one was able to individually sequence the whole individual genomes from each T4 virion, what sequences do you expect to vary between virions? Why does this variability not have a deleterious effect on the viral lifestyle?

Circularly permuted (does not mean circle) is a repeated genome. All the genes are there but some have spare copies that differ between organisms. This spare is for the T4 replication of DNA. The repeating sequence acts as a primer. the ends of each will be different but still contain the full genome

What does the CI transcription factor do for Lambda?

Cl is used in the decision of lambda going lytic or lysogenic seen in early gene expression represses lytic growth genes including Cro and promotes lysogenic growth

Of the 5 groups of eukaryotes, which super group includes both fungi and animals?

Opisthokonta

What can a temperate virus do that a lytic virus cannot?

Enter lysogeny- phage conversion The bacteriophage inhibits the lytic replicative mode

What does the Cro transcription factor do for Lambda?

Promotes lytic growth

What is the name of the region on the lambda genome that is involved in integration.

att (attachment) between the gal and bio region because there is some sequence homology between the phage and bacteria

If a transposon hopped into gene in E. coli, and the phenotype was that the E.coli became resistant to T4 adsorption, what cellular process would you guess that gene would be involved in?

T4 needs lipopolysaccharide to adsorb onto a cell. E.coli with disruption in genes that produce lipopolysaccharide would prevent absorption

If lambda had a mutation in the Cro gene, what would happen if you infect that mutant into E. coli?

The Cro gene would not be able to promote lytic growth and the phage would favor the lysogenic cycle.

If a baker yeast has a mating type of a, how can it change its mating type and become mating type alpha?

S. cerevisiae has genes for A and alpha a MAT locus transcribes the active gene, degrades it, & a copy is recombined downstream of an active promoter to express the new gene from a → alpha

You mixed 1000 bacteriophages with 10 E. coli, wait 1 minute, spin down the E. coli in a centrifuge, wash the E. coli a few times. In experiment A, you waited 5 additional minutes, then plated everything. In experiment B, you waited 10 additional minutes after the initial infection, then plated everything. In experiment C, you waited 15 minutes after the initial infection, then plated everything. For experiment A you see 10 plaques, For experiment B you see 10 plaques but for experiment C you see 1000 plaques on your Petri plate. Why did the number of plaques change?

Infectious virus slowly accumulates, therefore it is likely that in 5-10 minutes the virus is in its eclipse period in which nothing is infective and therefore will not cause cell lysis (in the latent period) As the time continues, more viral particles are able to mature and assemble their capsids and package their viral genome into new virions causing the cell to lyses leaving a plaque behind (end of the latent period)

What is the term used for a Eukaryotic virus infection that is analogous to lysogeny of bacterial viruses.

Latent infection (exist as a provirus-similar to lysogeny and prophages)

What does the endomycorrhizae produce in response to the strigolactones and what consequence does that have on the plant root?

Myc factors → stimulate plant to accept fungus invasion Produces arbuscular mycorrhizae consequences - plant roots grow more extensive and slows growth at the top of plants

You discovered a new bacteriophage called T1000. You mixed 1000 bacteriophages with 10 E. coli, wait 1 minute and spin down the E. coli in a centrifuge, wash the E. coli a few times to remove the phage from the mixture, then place the E. coli on a Petri plate containing a lawn of other E. coli (this is called "plating the cells"). The next day, you see 10 plaques (ie. clearings/holes) in the bacterial lawn. Why did you see 10 plaques (and not 0 or 1000) if you thought you washed the phages away? Where did the plaques come from?

We saw 10 plaques because only 10 cells were infected before the phage was washed away and plated. when culturing lytic viruses one uses serial dilutions of the virus on a cell culture plate in order to determine the quantity of the virus, in this case that is 10 counting the number of plaques allows one to estimate the concentration of virus

A chemical called chloroform can poke holes in E. coli. You mixed 1000 bacteriophages with 10 E. coli, wait 1 minute, spin down the E. coli in a centrifuge, wash the E. coli a few times. In experiment D, you add chloroform at 5 minutes after the initial infection, removed the chloroform and then plated everything. In experiment E, you add chloroform at 10 minutes after the initial infection, removed the chloroform and then plated everything. In experiment F, you add chloroform at 15 minutes after the initial infection, removed the chloroform and then plated everything. For experiment D, you see 0 plaques, For experiment E you see 10 plaques and for experiment F you see 1000 plaques on your Petri plate. Why did the number of plaques change? Why are the number of plaques either different or the same as the cognate time points in question 16?

again, viruses need to be inside a healthy cell in order to divide. When chloroform is added the cell is no longer healthy. Additionally, it takes time for a viral genome to replicate. It must go through a latent period in which it synthesizes new capsids, proteins, and genetic material, then it will mature and package the viral genome into xfnew virions. At this point, the cell is infected and will lyse. when chloroform is added at 5 mins all the e.coli is destroyed before the virus has a chance to fully replicate, thus leading to 0 plaques when chloroform is added after 10 mins, some viral genome has had the ability to replicate, but other cell in the latent period will be stopped by the addition of chloroform, thus resulting in reduced number of plaques when chloroform is added after 15 mins, all the viral genome has already replicated and ended its latent period before chloroform could stop it, therefore you see 1000 plaques

For bacteriophage T4, what is the function of the tail fibers?

allow phage to randomly scan the cell surface until suitable site of entry, generally when all of the tail pins are in good contact with the host

Does the fungus absorb nutrients from the plant from the hypopodium or the arbuscules?

arbuscules

Does bakers yeast produce spores in an ascus or on a basidium?

ascus

What are the protein shells of viruses called?

capids

What are the repeating subunits called that make up the protein shell of the virus.

capsomeres multiple proteins repeating

If a T4 gene encodes an enzyme that modifies cytosine to 5-hydroxymethyl cytosine, would you consider that gene to be an early or a middle/late gene?

early gene subvert (trick) host proteins to making the virus and replicating the genome

What is the definition of the viral eclipse period and the viral maturation period and the viral latent period. What is the time scale for these terms as they relate to the bacteriophage T1000, as experimentally dissected in questions 16, 17 and 18?

eclipse- synthesis of virus nucleic acid and proteins 5 minutes maturation- assembly of capsids and packaging of the viral genome into new virions 10 minutes latent- includes both the eclipse phase and the maturation phase whose end is marked by cell lysis 15 minutes

What is the difference between the maturation phase and the eclipse phase of a lytic bacteriophage viral life cycle?

eclipse- synthesis of virus nucleic acid and proteins nothing infective is made at this point maturation- assembly of capsids and packaging of viral genomes into new virions infectious virus slowly accumulates if broken open, some of the virions are infective

Under what conditions do you expect lysogeny lifestyle to be preferred over the lytic lifestyle?

f the cell is not in a healthy metabolic state no protease will be produces and therefore there will be an accumulated of CI or multiple infections of viruses accumulate large amounts of CI that will not be degraded fast enough

If a virus have a lipid envelop, where did it get it from?

gain their envelopes through a budding out process surrounded by bits and pieces of the host that they came out of

What is the name of the fungus that has symbiotic relationship with plants?

glomeromycota phylum -Endomycorrhizae/arbuscular mycorrhizae

What does the plant provide the fungus?

hexose sugar - this is in exchange for the nutrients ^

You did an experiment and infected a population of 1000 temperate bacteriophages on a lawn of E. coli on a Petri dish. The next day you see 999 cloudy plaques and 1 clear plaque. The fact that you see 1000 plaques on the Petri plate tells you what about lytic/lysogeny decision in the original 1000 phage infection? Why are majority of the plaques cloudy? What do you guess happened in the clear plaque?

most of the bacteriophages decided to enter into the lysogenic pathway this tells us that the cells are likely not in a healthy metabolic state causing little protease to be produced and more C1 to the produced causing lysogenic growth majority of the plaques are cloudy because those cells are infected with lysogenic bacteriophages the one clear plaque is a result of an infection from a lytic bacteriophage Temperate phage makes plaque cloudy because inside the plaque there are bacteria immune to being infected. "Immune" because it became lysogenic. There are live, growing bacteria. Lytic phage makes plaque clear because all cells lyse. First infection always goes lytic. In subsequent rounds of infection, the virus goes lysogenic. The first genes that are made are cro (makes virus go lytic) and CIII -> CII -> CI which makes it go lysogenic and inhibits cro. FTH protease degrades CII. CIII inhibits FTH protease. Cells have a limited amount of FTH protease. Mutation in CI makes it go lytic.

If a virus is called a temperate virus, can it go through a lytic lifestyle?

no - temperate bacteriophages and lysogeny (Lambda) is when the lytic mode is inhibited (summarized explanation below) the bacteriophages (now called a prophage) integrates its chromosome into the host chromosome some genes of the prophage are expressed and can confer survival advatange against its host phage conversion = lysogenic conversion after injecting its genome, the genome forms COS sites these COS sites promote early gene expression Cro promotes lytic growth CIII, CII & CI promote lysogenic growth CII promotes CI, which represses lytic growth (including the Cro factor) CIII & CII induce CI expression if protease is low or sufficient CIII is made, the CIII inhibits FtH to accumulate CI and repress lytic genes, so that the phage becomes lysogenic if the cell is superinfected by a lot of Lambda, a lot of CIII, CII, & CI are made

If a fungus is in the Ascomycota, do you think it would look like a mushroom?

no because Ascomycota develops into ascus (inside sac) only basidiums (outside sac) look like mushrooms

If one has two haploid baker yeast cells of mating type a, will those two cells form a diploid cell?

no because you need two different mating types in order to form a diploid cell This is why some cells will randomly switch mating types in cases of a majority of only one mating type, so that they can continue to reproduce

Is the linear lambda genome circularly permuted like the linear T4 genome?

no it's just a circle Circularly permuted is a linear genome where the genes are continuously repeated. * where genes are randomly repeated at the ends of the virus genome

What does the fungus provide the plant?

nutrients - the fungi break down matter so the plant roots uptake them -endomycorrhizae help uptake phosphate and nitrate

What is a persistent viral infection and how is that different from a latent viral infection?

persistent viral infections do not kill the host. they only use it for a perpetual viral factory latent viral infections are similar to lysogeny where the bacteriophage inhibits lytic replication and goes through a process called induction. it integrates its own chromosome into the host chromosome and becomes a phage. the phage excises from the chromosome to form virions and eventually lyses the host

Are pathogenic fungi common or rare?

rare

If a virus mutated for the enzyme in question 33, what do you expect to happen during the infection?

the virus would not be able to escape the bacteria cell and would eventually die from lack of nutrients (bacterial cell would also die due to competition with the virus)??? The virus would be trapped inside of the dead bacteria with no way to lyse the cell to get out. It would require an outside force to break/lyse the dead cell open for the virus to be released. ( Virus will not die because it is not alive and once matured/nucleocapsid is assembled, it shouldn't use/need additional resources. (i think)

Why are viruses not considered alive?

they are a genetic entity that can only replicate inside a host they rely on the host for energy, metabolic intermediates and protein synthesis

How does aquatic fungi spores disperse under water? What is the name of their spores?

they are flagellated in order to promote dispersion under water these are called zoospores

In fungi, what is a gametangia? Are cells in the gametangia sexual or asexual?

they are specialized hyphae (unicellular gametes) that sexual spores develop from the cells in gametangia are sexual

Why are plant viruses able to infect many different types of plants?

they have a wider host range because they are no dependent on viral-receptor interactions no receptors = less specific

If you have a bacteria that became lysogenic with the phage lambda, what would happen if you superinfect it with more lambda?

usually if the cell is super infected by a lot of lambda, then collectively a lot of CIII, CII, and CI are made this leads to a lysogenic pathway

If the nucleocapsid is not spherical in shape, then what other shapes can it have?

usually rod

A chemical called chloroform can poke holes in E. coli. You mixed 1000 bacteriophages with 10 E. coli, wait 1 minute; spin down the E. coli in a centrifuge, wash the E. coli a few times, then you add chloroform to the cells; then removed the chloroform and placed the resulting mixture on a Petri plate containing a lawn of other E. coli (this is called "plating the cells"). The next day, you see 0 plaques (ie. clearings/holes) in the bacterial lawn. Where did the plaques go?

viruses can only replicate in healthy cells because they need to be given nutrients in order to divide. Thus, if chloroform is added and pokes holes into the E.coli, it is no longer healthy and cannot support the division of viral genome without the replication of viral genes, no plaques will appear

If one has a woody compose pile that requires decomposition, what complex polymer needs to be broken down and what organism can do it?

white rot fungi -produce enzymes needed to break down lignin

What morphological form of fungi causes systemic mycosis?

yeast

If a fungi does not produce the tubular filaments, then what are fungi called?

yeasts

Does an enveloped virus still contain a nucleocapsid?

yes - there are just extra layers composed of lipids and proteins within the envelope the nucleocapsid is inside the envelope

If one has two cultures (hundreds of thousands of cells each), each originally started from a single haploid cell of mating type a, would you find diploid cells in both cultures? Why?

you could because they can change their mating types each cell has the genes for both types (alpha and a)

What is the name of a sexual fungal spore that has a flagellum?

zoospore - exists in aqueous environments, so needs flagellum to swim