MCAT Biology Chapter 5 Microbiology

what type of diseases do RNA viruses cause?

common cold, polio, and rubella

what are retroviruses?

- (+) RNA viruses that go through the lysogenic cycle - integrate into host genome as proviruses - produce dsDNA viral genome to integrate into our dsDNA genome - use reverse transcription to convert OG viral RNA into DNA using RNA-dependent DNA polymerase (reverse transcriptase) encoded by viral genome

which bacteria would be more susceptible to lysis when treated with lysozyme: Gram-positive or -negative?

- Gram-positive because they have no additional outer layer to protect from osmotic pressure after lysozyme degrades their cell wall made of peptidoglycan - Gram-negative have a thinner peptidoglycan layer and an additional outer layer to their cell wall, so they wouldn't be as likely to lyse from lysozyme treatment

what are examples of retroviruses?

- HIV (virus that causes AIDS), HTLV (Human T-cell Leukemia Virus)

are viruses living things?

- NO, viruses are not cells and they are not living organisms - they share some chars of living things inside cells (eg. can reproduce) - but outside cells, can't perform any chem reactions common to living things independently (eg. ATP synthesis, macromolecule synthesis)

what might limit the size of RNA genomes?

- RNA synthesis doesn't have any proofreading mechanisms in place - more errors are made, so if RNA genomes were too large, all copies made of the viral genome would be too screwed up that no infectious viruses would be made - DNA synthesis has built-in mechs to proofread and correct errors made

why don't RNA viruses carry around genes for enzymes involved in dNTP synthesis and DNA replication?

- RNA viruses have all they need to replicate their genome with RNA-dependent RNA polymerase - transcription is always occurring in all cells (in contrast to DNA replication), so NTPs are always present - RNA viruses have no need for enzymes involved in dNTP synthesis and DNA replication, so encoding these genes would be useless

what is a bacteriophage?

- a virus that infects bacteria

describe the lysogenic cycle of phages

- after infection, phage genome (= prophage) becomes part of bacterial host genome (lysogen) - silent prophage genes aren't expressed and no viral progeny are produced - bc transcription of prophage is blocked by phage-encoded repressor protein that binds to specific DNA elements in phage promoters (operators) - when host cell reproduces itself, prophage is reproduced along w it - eventually prophage is activated and removes itself from lysogen (=excision) - now enters the lytic cycle

describe the structure of a virus

- all have a nucleic acid genome covered in a protein shell (= capsid) - viruses are classified off the external capsid shape - capsid is made from repeating pattern of only a few proteins - helical capsids = rod-shaped // polyhedral capsids = multi-sided geometric figures - complex viruses might have a mix of shapes (ie. T4 bacteriophage has helical sheath & polyhedral head) - viral genome is located within capsid head - other parts of capsid are used during infection of host -> helps spread the viral genome - tail fibers & base plate are attached to surface of host cell - central shaft/sheath contract using ATP energy to inject genome into host - reflects the virus life cycle *entire viral capsid = protein // entire viral genome = nucleic acid

what additional structural component might an animal virus have? in contrast, what is a naked virus?

- an envelope that encapsulates the capsid = gotten from budding thru the host cell membrane - contains phospholipids, proteins, and carbs from host membrane + proteins encoded by viral genome (mix of both) - these enveloped viruses can only infect animal cells - new host is infected by fusing envelope with host PM -> uncovered capsid inside host cell = "naked virus" (w/o envelope)

what differences are there between phages and animal viruses?

- animal viruses don't have a special name like phages do - animal cells have PM proteins that act as specific receptors for viruses that are also imp for normal cellular function - another key part of specificity in recognition of animal cells by viruses is the distribution of receptors needed for adsorption (eg. HIV protein gpl20 binding to T cell mem protein CD4) - most animal viruses enter the host thru endocytosis, whereas phages do not - animal virus genome is then released from the capsid once inside the host (= uncoated) - from here, the animal virus can enter either the productive cycle or lysogenic cycle from here

what can destroy the bacterial cell wall?

- antibiotics, like penicillion - lysozyme in tears, saliva and made by lytic viruses destroys the peptidoglycan => creates protoplast that crumbles under osmotic pressure

how can bacteria be classificed according to their carbon source and energy course?

- autotrophs = get carbon from CO2 as carbon source - heterotrophs = get carbon from organic nutrients created by other organisms & - chemotrophs = get energy from chemicals - phototrophs = get energy from light - each bacterium is either a chemotroph/phototroph & either an autotroph/heterotroph

why would all phages and plant viruses be naked?

- bacteria and plants both have an exterior cell wall - viruses need to get their envelopes by budding thru host membranes - when viruses need to exit the cell, the cell wall is ruined and the host membranes rupture -> no membrane thru which the viruses can bud, just escape in lytic explosion

how do we categories bacteria by their ability to tolerate different temperatures?

- bacteria can grow in a wide range of temps, each species has an optimal growth temp - outside of their ideal, bacteria don't grow and can die => boiling, fridges - mesophiles = bacteria that prefer moderate temp similar to humans and other organisms, 30 degrees C - thermophiles = can survive at up to 100 degrees C, near boiling hot springs, geothermal vents in ocean floor - psychrophiles = thrive at low temp, near 0 degrees

describe the climate of medical science in the 1800s and how viruses were discovered

- bacteria was identified as the cause of anthrax and other diseases - med science was headed towards germ theory as the explanation for all infectious diseases - but researchers discovered some microscopic germs were too small to be trapped by filters like bacteria = viruses (electron microscopy)

why would a bacterial gene, carried with a virus and integrated with viral genes into a new bacterial genome, not be repressed along with the viral genes during lysogeny?

- bacterial genes obtained thru transduction wouldn't be repressed initially bc they don't have the same promoters/operators that phages do - viral genome repressors wouldn't be able to bind to the bacterial promoters and stop them from being expressed

why would a bacteriophage inject its DNA, while animal viruses do not?

- bacteriophage needs to inject its DNA to bypass the bacterial cell wall, couldn't penetrate otherwise - animal viruses can more easily bypass the animal cell membrane (no cell wall present) by being internalized whole into the cells

why do dsDNA viruses carry around genes for host enzymes?

- bc even tho the host cell has enzymes for dNTP synthesis and DNA replication it will only make dNTPs when it reaches S phase (preparing for DNA replication) - if dsDNA virus wants to reproduce independently w/o waiting for the host to reach S phase, needs to encode for its own enzymes

what other bacterial structure is involved in adhering to surfaces besides pili and fimbriae? is it possible that the fimbriae play a role in infection by pathogenic organisms?

- capsule or glycocalyx also helps bacteria stick to smooth surfaces - yes, fimbriae facilitate adhesion to cells so bacteria can colonize a tissue

what is the plasmid?

- circular piece of dsDNA - much smaller than the genome - called an extrachromosomal genetic element - often encode gene products that'll be an advantage for bacterium with the plasmid eg. carry antibiotic-resistance genes => can break them down - most plasmids can replicate itself into many copies - also allow for conjugation, imp to exchange genetic info across bacterias

what are transmissible spongiform encephalopathies (TSEs)?

- class of disease caused by prions - cause degeneration in nervous system, esp in brain - misfolded proteins in nervous system are v resistant to degradation by other chems or heat = hard to combat - this is bc their abnormal structure prevents efficient binding at active sites of degradation enzymes - misfolded proteins cause degeneration of neurons (esp. in CNS) -> loss of coordination, dementia and death = ALWAYS fatal - characterized by long incubation period - can be several months to yrs in animals - several yrs to decades in humans - difficult to diagnose bc long incubation periods & symptoms overlap of other conditions

how are living organisms classified (taxonomy)?

- classified as either prokaryotes or eukaryotes - based on exam of their internal cellular structure - both able to carry out basic biochem processes of photosynth Krebs cycel, and oxphos to prod ATP - prokaryotes different from eukaryotes bc they don't contain mem-bound organelles (nucleus, mitochondria, lysosomes, etc.) - used to determine evolutionary relationship of organisms to one antoher - domain = largest taxonomic division: bacteria, archea, eukarya - bacteria & archea include prokaryotic organisms // eukarya includes eukaryotic organisms - kingdoms: eukaryotic - animalia, plantae, fungi // debate over kingdoms in other prokaryotic domains and in single-celled eukaryotes (protists)

a bacteriophage with an important capsid gene deletion infects the same cell as another virus w a normal copy of the same gene. at the time of host-cell lysis, what would happen?

- co-infection results when two viruses infect the same cell - a mix of the two viral genomes would be expressed -> some normal viruses and some defective genomes will get packaged into capsids made from proteins encoded by the normal virus - the latter could infect new hosts, but their progeny couldn't survive bc their capsid has been coded using the defective genome -> these phage couldn't cont the cycle by infecting new hosts - the original bacteriophage with the capsid gene deletion must've come from a co-infection as well* - these defective phage can only infect host cells and reproduce with the help of normal cells - a single virus can only carry a single genome -> it can only make one type of progeny

what is the productive cycle?

- cycle similar to lytic cycle in animal viruses, not phages - key difference is it doesn't destroy the host cell - possible bc enveloped viruses can exit w/o lysing host thru budding thru the host cell membrane and gets coated atst - host mem reseals as the virus leaves

some DNA viruses induce infected host cells to enter mitosis and may even override cellular inhibition of cell division so strongly that the cell becomes cancerous. what advantage does the virus gain by inducing host-cell division?

- during cell division, the cell produces its own dNTPs for DNA replication - the virus can hijack the cell's DNA replication machinery to reproduce its own DNA genome and use the cell's produced dNTPs

what are endotoxins and exotoxins? compare the two

- endotoxins = normal components of outer mem of Gram-negative bacteria ONLY - can have lots of diff structures, incl. lipopolysaccharide - aren't inherently poison, but v dangerous when lots of bacteria die and release their disintegrated outer mem into our bloodstream - induce an extreme reaction in our immune system -> releases too many chems and creates septic shock => aqueous part of blood leaks into tissues - drop in blood P and other problems, can lead to death - exotoxins = v toxic substances secreted by BOTH Gram-neg and -pos bacteria into outside - help compete w other bacteria (eg. normal gut bacteria) - cause diseases like botulism, diphtheria, tetanus, toxic shock syndrome

what is adsorption?

- first step in viral infection -> virus binds to exterior of host cell - in general, adsorption is termed the adhesion of atoms, ions or molecules from a gas, liquid or dissolved solid to a surface - process creates a film of the adsorbate on the surface of the adsorbent - differs from absorption, in which a fluid is dissolved by or permeates a liquid or solid, respectively

how are TSEs transmitted?

- from animal to animal eg. mad cow disease (transmitted from cows to sheep) kuru (found in cannibalistic tribes) -> stopped tradition to stop transmission - genetics -> mutations in gene that codes for prion protein eg. fatal familial insomnia (FFI) = autosomal dominant condition inherited on chromosome 20 Creutzfeldt Jakoh Disease (CFD) - spontaneous mutations *even in someone w/o family histroy but would be v rare (1-2 ppl/mil)

what are the 3 main retroviral genes?

- gag (codes for viral capsid proteins) - pol (polymerase codes for reverse transcriptase) - env (envelope codes for viral envelope proteins)

describe the variation between different viruses

- genome, protein capsule, and viral life cycle vary widely across different viruses - viral genome: DNA or RNA that can be either single or double-strandeded and either linear or circular - viruses use almost every form of nucleic acid in their genome - but important to know that one type of virus will only have one type of nucleic acid genome - mature virus only contains nucleic acid that makes up its genome

what are some exceptions to the rule that one type of virus will only have one type of nucleic acid genome?

- hep B virus has circ DNA genome that is part single stranded & part double stranded - takeaway: virus not outisde host cell contains only its genome which is always the same - but there are also some special situations where piece of host genome accidentally becomes part of the viral genome - a true cell will contain its own genome, plus RNA (m, t, and rRNA)

describe the lytic cycle of phages

- host polymerases and/or ribosomes start transcribing and translating phage genome - early genes = group of genes expressed right after infection and include special enzymes needed to express viral genes - one of these is hydrolase = hydrolytic enzyme that degrades all of the host genome - multiple copies of phage genome produced using materials from broken down - capsid proteins also produced - late gene lysozyme produced (also in human tears and saliva) destroys bacterial cell wall - osmotic pressure no longer is fighting with cell wall -> host bacterium lyses - ~100 progeny viruses released into ECF -> can start another round of the cycle

how might decrease in temp increase bacterial growth rate?

- if the decrease in temp causes the temp to become closer to the bacteria's optimal range, this could improve bacterial growth rate - eg. from 20 to 0 degrees C, would help psychrophiles - these bacteria might possess enzymes that may be optimally active at low temps => better growth

what are subviral particles?

- infectious agents even smaller than viruses - more simple too - includes prions and viroids

what are prions?

- infectious agents that don't follow the Central Dogma of Molecular Biology - self-replicating proteins - a misfolded verion of a protein that already exists - prion meets normally folded protein and alters shape of normal protein by acting as a template

why do retroviruses theoretically not need to carry reverse transcriptase and only encode it?

- its (+) RNA ss genome can be infective and be immediately translated by host ribosomes upon infection - reverse transcriptase is produced and can now transcribe a dsDNA viral genome from the RNA genome - despite this HIV still does carry reverse transcriptase in its capsid

why is the T4 bacteriophage commonly used in research?

- its host is the bacterium E. coli

if the ratio of A to T in a DNA virus is not one to one, what can be said about the genome of this virus?

- its nucleic acid genome consists of single-stranded DNA (could be either linear or circular) - A pairs to T in double-stranded DNA -> if it was double-stranded, A:T = 1:1 - this strand wouldn't have any T

what are pili?

- long projections on bacterial surface that helps attach to diff surfaces - sex pilus = special pilus attaching F+ (male) and F- (female) bacteria that facilitates formation of conjugation bridges - fimbriae = smaller structures not involved in locomotion/conjugation, only sticking to surfaces

what direction is the mRNA read in bacterial ribosomes?

- mRNA is fed into the ribosome 3' end first, with the free end being the 5' end - elongation of mRNA proceeds 5' to 3' - proteins are made from N to C, so the free end of the polypeptides is the N terminus

describe the modern medical science climate with regard to viruses

- modern molecular biology has allowed us to learn lots ab viruses (ie. able to determine nucleotide sequence of entire viral genomes) - but still lots more to learn ab viruses -> HIV remains a major public health threat

what diseases do viroids cause?

- most diseases caused by viroids found in plants - Hepatitis D = only viroid human disease, can only enter hepatocytes (liver cells) if contained in a capsid w a binding protein - viroids don't have capsids so successful Hep D infection reqs co-infection w Hep B to get its capsid

what is chemotaxis?

- movement of bacteria towards attractants/away from toxins - chemoreceptors on cell surface bind attractants/toxins and transmit signal that changes direction of flagellar rotation (blindman's bluff) - response depends on change in concen over time

what proteins must a (-) RNA virus encode or carry in its capsid?

- must encode RNA-dependent RNA pol and carry one in its capsid

what proteins must a (+) RNA virus encode or carry in its capsid?

- must encode RNA-dependent RNA polymerase (does not have to carry it)* - needed to copy the RNA genome so the virus can replicate itself bc the host will never make RNA from RNA (wouldn't occur in cytosol naturally)

what proteins must a retrovirus encode or carry in its capsid?

- must encode reverse transcriptase

mutation of the cell-surface receptor that viruses attach to would be a means for an organism to become resistant to viral infection. why is this mechanism not common?

- mutation of the cell-surface receptor would disrupt many other functions important for the cell as well which would likely prevent it from surviving - therefore, we wouldn't see this mutation as all the cells with it would've died off - another reason is that viruses generally evolve very rapidly so they can keep up with any host evolutionary changes - however, this isn't always the case since our immune cells keep us healthy by keeping up to speed w most microorganisms' tricks

describe the genome of bacterial cells

- no membrane bound organelles - single ds circ DNA chromosome (not in nucleus or assoc w any histone proteins) - transcription and translation occur in same place same time - ribosomes start translating before completely transcribed - many ribosomes translate a single piece of mRNA form into polyribosomes

do (-) strand RNA viruses use host enzymes to catalyze RNA production in transcription or in replication of the genome?

- no, RNA-dependent RNA pol transcribes the (-) strand into the (+) strand that encodes viral proteins - RNA pol also replicates the genome - host enzymes are only used to translate the viral proteins from the (+) strands

after integration of a retrovirus into the host genome, reverse transcriptase inhibitor is added to the cell. will production of new viruses by blocked?

- no, because reverse transcriptase has already done its job converting the OG viral RNA genome into dsDNA to be integrated into the host genome - production of new viruses doesn't require reverse transcriptase, only the normal host enzymes to transcribe viral mRNA and new viral RNA genomes

would an infectious virus be produced if the genome of an enveloped (+) strand RNA virus is added to an extract prepared from the cytoplasm of eukaryotic cells that can translate but can't replicate DNA or do host gene transcription?

- no, because the enveloped (+) strand RNA virus wouldn't be able to generate new enveloped viruses without any host PM to be infectious - the (+) strand RNA virus could still produce viral genomes and proteins tho

a disease agent is isolated from a human cannot reproduce on its own but can reproduce in a culture of human cells. in its pure form it possesses both RNA and DNA. could this be a virus?

- no, because this disease agent contains both RNA and DNA, whereas viruses would contain one but not the other - this must be another kind of obligate intracellular parasite (ie. certain bacteria like chlamydia)

if lysozyme was an early gene instead of a late gene, would this help the virus

- no, the bacterium would lyse before the virus has the chance to take over the host replication machinery and create more copies of itself - wouldn't be able to continue replicating - needs time to replicate and assemble

can viruses use flagella to find host cells?

- no, viruses can't produce any energy of their own - only rely on diffusion to find host cells

what is a virus?

- obligate intracellular parasite = only able to reproduce within cells - infect all organisms on Earth (incl. plants, animals, protists, and bacteria) - bundle of nucleic acid that needs to overtake reproductive machinery of their host cell to make more copies of itself - relies on host machinery whenever possible "nasty 35-year-old man living in its mom's basement"

what proteins must a dsDNA virus encode or carry in its capsid?

- often encode enzymes req for dNTP synthesis and DNA replication

what are dsDNA viruses?

- often have large genomes w genes for enzymes involved in dNTP synthesis and DNA replication

what is the terminology assoc. with bacterial cells' flagella?

- one/more flagella = motile bacteria - monotrichous = flagellum - amphitrichous = flagella at both ends - peritrichous = multiple flagella

what is a flagellum in bacterial cells?

- only some bacteria have this - only way for bacteria to move - complicated structure, polygenic trait - made of protein flagellin - remember that all prokaryotes: 9+2 arrangement of microtubules - in contrast, eukaryotic flagella are made of both microtubules and dynein - major parts: filament, hook, basal structure - bs has rings that anchor flagellum to mems + rotate the rod/flagellum powered by proton grad

what is the capsule/glycocalyx?

- only some bacteria have this - sticky layer of polyssacharide goo surrounding one/many bacteria - makes the immune system's job of fighting off the bacteria harder - allows bacteria to stick to smooth surfaces (ie. rocks, respiratory tract lining)

a 1k bp region of viral genome encodes 2 polypeptides unrelated in aa sequences during eukaryotic cell infection. if 1 polypeptide is 250 aa's long and the other is 300, how would u explain this?

- overlapping multiple reading frames - the virus must contain at least 750 bp's (to code 250 aa's) and 900 bp's (300 aa's) of genetic info for unrelated peptides in 1000 bp of DNA - this is impossible if the reading frames don't overlap

what encapsulates the bacterial cytoplasm?

- plasma membrane - rigid cell wall that provides support and stops the bacterium from exploding made of peptidoglycan = complex polymer unique to prokaryotes - peptidoglycan has cross-linked chains of sugars and aas

how do prions violate the Central Dogma?

- prions (misfolded proteins) cause other proteins to misfold - diff from the Central Dogma, which states DNA --transcription--> mRNA --translation--> protein - prions take transcription and translation out of the process => proteins shaped based on other proteins (= self-replicating)

what are the pros and cons of the lytic cycle?

- pro: quick way for a virus to rapidly reproduce - con: all the host cells are destroyed = not evolutionarily ideal

what are prokaryotes?

- prokaryote = "before the nucleus" -> evolutionarily older domain - include bacteria, archea (extremophiles), and blue-green algae (cyanobacteria)

what are the pros and cons of the lysogenic cycle? what does the term transduction mean?

- pros: prophage is reproduced along w the host cell + virus keeps host alive while still replicating - cons: activation of viral genome while separating from lysogen will remove part of host genome too -> host genome will become incorporated & replicated along w viral genome as well -> stolen host DNA will be injected into subsequent new hosts => manifest in new traits that infected host didn't have before (= transduction)

what diseases can (-) strand viruses cause?

- rabies, measles, mumps, influenza

bacteria cultured in the presence of S-labeled cysteine and P-labeled phosphates are infected w phage T4. when phage from this culture are used to infect a new unlabelled bacterial culture, which isotope will be found inside the newly infected bacteria?

- radiolabelled phosphates bc these would be incorporated into the bacterium's genome - when phage T4 infects the bacterium and its hydrolase breaks the host genome down, these labelled dNTPs would be incorporated into the newly produced phage T4 progeny - rmb that PO4 is one of the components of a nucleotide, along w pentose sugar and nitrogenous base* - when these phage infect a new unlabelled bacterial culture, radiolabelled phosphate would be found inside - cysteine would be incorporated into the viral coat proteins, however after injection into the new bacteria, the capsid would remain on the exterior

describe viral infection

- regardless if the virus is enveloped or naked, the host cells it can infect are determined by the virus surface - highly specific process: virus binds to host receptor and is either internalized thru fusion w/ PM (enveloped) or receptor-mediated endocytosis (naked) - only cells w/ receptor matching virus's will be infected* -> virus will infect specific species/cell types - viral surface also imp for our immune system to recognize

how do viroids replicate?

- replication of some viroids is like replication of RNA viruses: - viroid RNA-dependent RNA polymerase synth a (-) strand - RNA ligase derived from host makes (-) strand into a circle - this round, rolling templase is used to make more (+) copies of the OG RNA viroid seq - an alt mechanism: - (-) strand left in more linear state that still acts as template for (+) strand creation and then becomes circular - other cases: - viroids hijack the cells' DNA dependent RNA polymerase - directs it to read RNA templates - no one understands this

what similarities are there between phages and animal viruses?

- same general outline of the viral life cycle - viruses bind to specific type of host cell, inject viral genome into host, take over host machinery, replicate self & assemble, then escape to infect a new cell - phages enter the lytic/lysogenic cycle, whereas animal viruses enter the productive (similar to lytic)/lysogenic cycle

how do ribosomes used to translate viral proteins compare to host ribosomes?

- same host ribosomes, since the virus doesn't have its own ribosomes - the virus and host use the same ribosomes

what are viroids?

- short piece of circular, single-stranded RNA (200-400 bases long) w extensive self-complementarity (= can base-pair w itself to create ds regions) - generally don't code for proteins - no capsids - some viroids are catalytic ribozymes - others when replicated produce siRNAs that silence normal gene expression

what limits the size of viral genomes?

- size! - viruses are way smaller (avg )100-200 nm) than the hosts they infect (prokaryotic: 1-2 microns and eukaryotic: 10-20 microns

treating an enveloped animal virus w mild detergent solubilizes several proteins from the virus, although the genome doesn't become accessible. describe the proteins released from this process and how the infectivity of the virus would be affected?

- some proteins released by detergent might be encoded by the infected cell, along w the virus's own proteins - some evelope proteins are encoded by the virus and others are taken from the host membrances during budding - taking away the virus's envelope would impair adsorption and limit infectivity

where do some viruses obtain ATP?

- stolen from previous host - use ATP to power penetration

how to bacterial ribosomes differ from eukaryotic ribosomes?

- structure, even tho both function the same way - bc of this, we can prescribe various antibiotics which interfere w bacterial translation w/o disrupting our own eg. mycin and tetracycline only bind to bacterial ribosomes

what happens when cyanide is added to a culture of virus-infected mammalian cells?

- the mammalian cells would be killed and viral replication would be stopped, but the culture would remain infectious - cells need ATP from the ETC -> addition of cyanide would kill htem - viruses need cells for ATP and enzymes to replicate -> replication would stop - any viruses already replicated before cyanide was added would be unaffected -> culture is still infected

if a viral genome is (+) strand RNA, what is used as a template by the RNA-dependent RNA polymerase?

- the original viral genome's transcribed complementary strand => referred to as the (-) strand RNA - this will be produced as an intermediate before the RNA-dependent RNA pol generated new (+) strand genomes

what else limits the size of viral genomes?

- the rigid protein shell can't expand past the small size of the virus to fit a larger viral genome

what is the difference between the animal virus lysogenic cycle and the phage lysogenic cycle?

- the viral genome inserted into the host genome is termed a provirus instead of a prophage eg. Herpes simplex 1 virus causes oral herpes - after infection, remains dormant as provirus for unknown time - reactivates when host encounters stress

what would likely happen if a viral genome tripled in size?

- the viral genome will likely no longer fit inside the normal structure -> genome wouldn't be packaged into infectious viral particles

when phage are first added to a bacterial culture, the infective viruses initially decreases before it later increases. explain why this happens?

- this happens bc at first, the viruses must inject their genome into a host bacterium, leaving an empty genome-less virus outside the host cell - this causes the initial decrease -> at this point when many phage have injected their genomes, they're no longer infectious - after some time when the bacterium has time to overtake the host cell's machinery to replicate and assemble more copies, then lyses the bacterium to escape into the ECF, the phage number increases

how do we use the bacterial call wall to classify bacteria?

- two types of bacterial cell wall are distinguished in Gram staining: 1. Gram-positive = strong stain, dark purple - thick peptidoglycan layer outside cell mem - that's it 2. Gram-negative = weak stain, light pink - thinner peptidoglycan layer in cell wall - in between: periplasmic space -> sometimes enzymes that degrade antibiotics - additional outer layer of lipopolysaccharide - weak staining bc extra protection from environment - more resistant to antibiotics *think IG = pink/purple, so G+ => purple => thick cell wall w no extra outer layer

what factors are used to classify viruses/target viruses for therapeutic intervention?

- type of genome* > likely most important -> has imp consequences for how infection proceeds - naked/enveloped virus - nature of cell-surface proteins - type of life cycle

describe the life cycle of a bacteriophage (initial phase that's common to all bacteriophages before the lytic/lysogenic specific parts kick in)

- viral genome has genes that redirect the host to produce viral products - attachment/adsorption = bind to exterior of bactierium - penetration/eclipse = inject viral genome into host cell - this process is named eclipse bc capsid remains on outer surface of cell while genome disappears into cell -> removes infectious virus from ECF - from here, a phage follows enters either the lytic cycle or the lysogenic cycle

how do viruses reproduce?

- viral genome initiates production of new genome & protein packaging copies

how do viral genomes accomodate their small size?

- viral genomes have evolved to save space w some pretty smart adaptations - carries v few genes -> virus relies on host proteins for transcription, translation, and replication - encode >1 protein in the same section of genome -> use more than 1 reading frame so genes can overlap

if antibodies to a viral capside aren't blocking infection very well, what can we infer about this virus?

- virus could be enveloped -> antibody can't reach its epitope on the capside surface - epitope = part of an antigen molecule to which an antibody attaches itself

what is a (-) RNA virus? how does it function?

- virus whose genome is complementary (-) to RNA that encodes viral proteins (+) - acts as the template for viral mRNA production - can't be translated into any useful polypeptides -> must encode RNA-dependent RNA pol and carry one in its capsid - after entering the host, RNA pol will transcribe a (+) strand from the genome - host machinery can then use (+) strand -> prod viral proteins and proceed thru viral life cycle

what is a (+) RNA virus? how does it function?

- virus with a simple-stranded RNA genome -> serves as mRNA - simplest viral genome possible - once inside host cell, acts directly as RNA so host ribosomes start translating genome => prod viral proteins - viral proteins produced due to translation will be RNA-dependent pol, which will then go on and copy the RNA genome - injecting this isolated genome into a host cell will cause virus production (= infective genome)

what are adenoviruses?

- viruses that have a single linear dsDNA genome - contain numerous diff promoters regulated during infection - transcription is carried out by cellular RNA pol - but need the viral E1A gene product to transcribe most viral genes -> if deleted/inactivated, no longer infectious - code most of their own replication machinery (incl. DNA pol)

if co-infection occurred w 2 diff adenoviruses, one w a deleted E1A gene and another w a deleted DNA pol gene, what would happen?

- yes, bc these viruses would complement each other - the virus w the deleted DNA pol gene would still be transcribed and its E1A gene product could make up for the other virus's deleted E1A gene, permitting its transcription - this would yield a DNA pol that could help the virus replicate its genome whose DNA pol gene was deleted - this process must've occurred previously, otherwise these viruses wouldn't exist - these would be helper viruses towards each other (complementary)

would a protoplast moved from salt water to fresh water shrivel or burst?

- yes, osmosis would cause water to travel from the external medium into the protoplast, which cause it to burst

would treatment of an HIV-infected person w a soluble form of CD4 protein affect the infectivity of the virus?

- yes, the free-floating CD4 protein would bind to the virus's CD4 receptor gp120 - this would prevent it from attaching to T cells

what situations are needed for the DNA virus to replicate?

1. provide all necessary components itself (enzymes needed for dNTP synthesis and DNA replication) 2. infect a cell that's dividing 3. induce the cell it's infected to divide

what are the 3 shapes of bacteria and their proper names?

1. round/cocci (pl.)/coccus (sing.) 2. rod-shaped/bacilli/bacillus 3. spiral-shaped/spirochetes or spirilla/spirochete or spirillum

what is the cell theory?

Robert Hooke: 1. all living things are made of one/more cells and their products 2. cells are the monomer for any organism 3. new cells come from pre-existing living cells modern extensions: - no matter what species, the chem composition of cells is similar - DNA is the course of hereditary programming passed between cells - organism's activity determined by total activity of its cells - biochem energy flow occurs within cells => verified from vast improvements both in microscopy and biochem + genetic testing