BI323 Final Exam Material from the new material Flashcards
what is a complete virus particle that is more than or equal to 1 molecule of DNA or RNA enclosed in a protein coat ? Hint, it may have additional layers
virion
what are some differences between viruses and cellular organisms?
cellular organisms are complex, contain both DNA and RNA, carry out cell division and only some are obligate intracellular parasites
this contains a nucleic acid and protein coat, capsid contains protein coat, protects genome, aids in transfer between host cells, contains protomer
nucleocapsid core
this is a capsid protein subunit, which is efficient and saves genome space, often spontaneous
protomer
what are three structures of a nucleocapsid core
helical, icosahedral, complex
this virion structure has hollow tubes with protein walls containing TMV (RNA in protomer grooves), diameter based on protomers, length based on nucleic acids. give an example
helical capsids, influenza is not as rigid and enveloped
this virion structure is a polyhedron with 20 equilateral triangular faces with a capsid constructed of capsomers which are ring/knob shaped units. give two examples
icosahedral, pentamers (SV40) and hexamers
what are examples of virions with complex symmetry
poxvirus, large bacteriophage (binal), vaccina virus
membrane structure surrounding some viruses, lipids and carbs usually host derived, proteins and virus specific with peplomers for attachment
viral envelope
what are peplomers
spikes for virus attachment
these are observed in some viruses associated with the envelope ex. influenza neuraminidase (viral release) and is located within the capsid that aids in nucleic acid replication ex. RNA dept and RNA pol for transcription and translation
viral enzymes
most DNA viruses are….
dsDNA, linear, circular, both
most RNA viruses are…
+, - strand, segmented genomes
what is a (+) strand RNA virus
viral genomic RNA, viral mRNA, euk viruses are capped, polyA
what is (-) strand RNA virus
viral genomic RNA that is complementary to viral mRNA
what is a segmented genome?
virions that contain >1 unique RNA usually in the same capsid ex. brome mosaic virus with 3 viral particles
these are stages of what? 1. adsorption 2. entry (penetrating/uncoating) 3. synthesis 4. assembly 5. release
replication of viruses (similar to bacteriophage reproduction)
this stage is when the interaction between the host membrane and virus occurs, viral surface proteins and/or enzymes mediate attachment to specific host receptors (some are exposed and some are hidden- immune), contains lipid rafts (microdomains)
adsorption
this stage is when the virus is enveloped (fusion of envelope/host membrane) or non enveloped, in some cases, only nucleic acids enter the host cell, both endocytosis
entry (penetration/uncoating)
this stage contains early genes, which are involved in the take over of host and synthesis of viral DNA/RNA, viral DNA replication (nucleus) and early mRNA synthesis (host RNA pol)
synthesis
this stage is when the capsid protein is encoded by late genes, naked (empty procapsids form and nucleic acids are inserted) vs enveloped virus assembly
assembly
this stage is when the naked viruses are released by lysis of the host cell and enveloped viruses release and envelop formation occur concurrently, virus encoded proteins are incorporated into the host membrane and the nucleocapsid buds outward surrounded by modified host membrane. give two examples
release, influenza and IV budding
virulent phage life cycles are typically _____ while temperate are ________
lytic (T4), lysogenic (lambda)
this is a complex, multi step process often involving oncogenes
carcinogenesis
this is where a neoplasia is found with abnormal new cell growth and reproduction and loss of regulation
tumor
this virus leads to Burkitt’s lymphoma, nasopharyngeal carcinoma due to the presence of Ab genome found in tumors
epstein barr vrius (EBV)
this causes hepatocellular carcinoma
hep b
this causes cirrhosis of the liver and liver cancer
hep c
this causes kaposi’s sarcoma
human herpesvirus 8 (KSHV)
this virus causes cervical cancer
human papillomavirus HPV 16, 18
this virus causes leukemia
human T cell lymphotropic virus (HTLV)
which mechanism of carcinogenesis is where the oncogene is carried into the cell and inserts it into the host genome
rous sarcoma virus, src gene
which mechanism of carcinogenesis is where the altered cell regulation due to changes in kinase activity or production of regulatory proteins occurs
HPV, p53 ubiquitylation
what are the random mutations that may lead to the survival of harder to infect bacterial populations, give an example
genetic resistance, expression of altered reception protein
what is the modification of bacterial DNA (methylation) and expression of enzymes that cleave unmodified DNA
restriction endonucleases (RE)
what does CRISPR stand for and what is it. which proteins interact with CRISPR regions
clustered repeat interspaced tandem short palindromic repeats, repeating sequences of bases found in bacteria and archaea with varied spacer sequences between them, Cas
each time the cell is infected but survives, a portion of the viral DNA is added to the ____ end of the region in CRISPR
3’
the addition of DNA sequences to the end of the region following survived infection
adaption stage
infection for the second time with the same virus, DNA in CRISPR is transcribed and processed into smaller crRNA molecules, each having 1 spacer and 1 repeat sequence, Cas/crRNA binds to viral DNA or mRNA leading to its destruction
interference stage
who were the scientists that founded CRISPR/Cas?
E. Charpentier and J. Doudna
direct counts are often performed by an ________ to count particles
electron microscope
this count is used to determine relative viral quantity ex. hemagglutination assay to determine highest dilution of viruses that cause rbc clotting
indirect
this method of measuring concentration of infectious units is where dilutions of the virus prep are made, plated on lawn of host cells then incubated, number of plaques counted
plaque assays
this method of measuring concentration of infectious units is where you determine the smallest amount of virus needed to cause infection or death of 50% exposed host cells or organisms
infectious/lethal dose assays
these are infectious agents composed of only circular ssRNA and have a rod like shape, they don’t act as mRNA molecules, no proteins are encoded and some are ribozymes, causes disease in plants, RNA may be replicated by rolling circle method with the host RNA pol
viroid
this is an infectious proteinaceous agent that causes neurodegenerative diseases such as scrapie, bovine spongiform encephalopathy, creutzfeldt jakob disease, have a normal and abnormal form
prions
what are three categories of enzyme expression
constitutive, inducible, repressible
the presence of substrate increases enzyme expression ex. many catabolic enzymes
induction
the presence of end product decreases enzyme expression ex. biosynthetic enzymes
repression
this is when initiation is inhibited ex. repressor proteins
negative transcriptional control
this is when initiation is permitted ex. activator proteins
positive transcriptional control
this is when the repressor is active without the inducer so the catabolic enzyme is not made without the substrate
inducible enzyme for negative control
this is when the repressor requires corepressor for activity so the biosynthetic enzyme is not made when the end product is present
repressible enzyme for negative control
for the lac operon, this is an example of _______ control and ______ genes, it contains the Lacl which acts as the ____, the operator which _____ and the operon and _____ in the presence of lactose
negative, inducible, repressor, binds repressor, turn on genes
what happens when there is no lactose present
Lacl is expressed and active, binds operator
what happens when there is lactose present
Lacl is expressed but inactive, allolactose binds Lacl repressor and inactivates
what happens when Trp is abundant, when its low
the Trp repressor is active, Trp repressor is inactive
what is the relationship between the lac operon and catabolite repression
glucose first then lactose second in a diauxic biphasic growth
this is selective substrate uptake from media that offers choices, 5-10% of all bacterial genes subject ti this
catabolite repression
what does the catabolite activator protein do (CAP)?
CRP/cAMP regulator is required for expression by binding CAP to binding site and allowing RNA pol to bind, when active cAMP is bound, when glucose is absent cAMP is high
what is the significance of catabolite repression
multiple catabolic operons are affected, flagellar genes controlled (don’t have to search for nutrients), important for competition in natural environments
this is the halting of transcription elongation prior to termination, forming paus/loops based on metabolite availability ex. riboswitches that act in the differential folding of mRNA leader region affecting RNA pol activity and folding
attenuation
operons controlled by same regulator protein associated with common function such as HS
regulon
regulon with operons also controlled separately such as catabolic repression
modulon
this is when different sigma factors lead to different promotors, the substitution of these factors, changes in gene expression and many genes and operons
alternative sigma factors
this acts in prokaryotic signal transduction that links outside events with cell response, control of gene expression by the transfer oh phosphate groups, contains sensor kinase and response regulator, sk/rr=two component regulatory system
phosphorelay systems
TM protein that transmits EC changes in global regulation
sensor kinase
DNA binding and transcriptional control in global regulation
response regulator
what are some important factors of B subtilis sporulation
multiple control mechanisms, vegetative growth, starvation, KinA, Spo0A
auto phosphorylates in response to environmental signals such as starvation
sensor kinase KinA
active transcription regulator that activates production and sporulation
response regulator Spo0A
this binds chemoattractant that stimulates ccw rotation, dimer bound to CheW and CheA
methyl accepting chemotaxis proteins (MCP) of E.coli
no attractant is bound to MCP, this auto , runs and tumbles, phosphorylates and phosphorylates CheY
sensor kinase CheA
this leads to FliM, causing cw rotation and tumbles
response regulator CheY
……… CheA autophosphorylase is inhibited to ccw run, less tumbles, directional movement, dephosphorylation of CheY
this is when the attractant is bound to MCP
what is important to know about quorum sensing global regulation
AHL synthase (luxl) is positively upregulated, LuxR transcription activator requires AHL
this diffuses out, accumulates and diffuses back into the cell, activating _________
AHL, LuxR
AHL is also known as…
an autoinducer
these are heritable changes in nucleotide sequences that may or may not affect the phenotype
mutation
this develops in the absence of any added agent and is thought to arise randomly
a. errors in DNA replication such as tautomeric shifts and frameshifts) b. DNA damage c. transposon insertion
spontaneous mutations
this is caused by an exposure to mutagens, caused by chemical or physical agents that damage or alter DNA chemistry and interfere with DNA repair
induced mutation
alteration in H binding of nucleotides, contain normal (keto watson and crick) and abnormal (enol)
tautomeric shifts
the deletion or addition of base pairs that alters reading frame
frameshift
what are some examples of induced mutations
base analogs, DNA modifying agents, intercalating agents, DNA damaging agents (UV, radiation, free radical peroxide)
what are some effects of mutations
forward mutations, reverse mutations with a suppressor mutation at a second site, silent mutations, missense mutations (one base substitution leads to one AA change), nonsense mutations (early termination) and frameshift, resistance mutations, biological, conditional, lethal, morphological, regulatory, tRNA and rRNA mutations affecting protein synthesis
this biosynthetic pathway mutant cannot synthesize the product of the pathway required for growth
auxotrophs
this grows in minimal media without supplements
prototrophs
how are mutants detected?
phenotypic observation, replica plating techniques detect autotrophic mutants
prokaryotes divide in ________ with no meiosis and how do they increase their fitness?
binary fission, HGT and mutations
this is the rearranging of more than or equal to 1 nucleic acid molecules to produce a new nucleotide sequence generating a new combination of genes
recombination
the transfer of DNA from donor organism to recipient via conjugation, transformation and transduction including exogenote, endogenote, merozygote
horizontal gene transfer
this is the most accepted model of recombination where reciprocal exchange between homologous chromosomes, results from DNA strand breakage and reunion leading to crossing over and catalyzed by rec proteins
homologous double stranded break recombination
incorporation of DNA single strand into chromosome creating heteroduplex DNA
homologous nonreciprocal recombination
this is the recombination where the insertion of primarily nonhomologous DNA into chromosome only short region of homology, often during viral genome integration where enzymes responsible are specific for virus and host
site specific recombination
this is the recombination that accompanies replication of genetic material used by genetic elements ex. transposons
transposition
widespread mobile DNA segments found in all 3 domains that carry required genes but don’t require large homology regions with no life cycle and can’t replicate autonomously. give two examples
transposable elements, insertion sequences and composite transposons
these are the simplest sequences that possess only genes encoding enzymes required for transposition such as transposase that are bound by inverted repeat
insertion sequences
these carry genes in addition to those needed for transposition such as antibiotic resistance, the central region is flanked by IS elements
composite transposons
these are cut and paste transposons where insertion generates direct repeats of flanking host DNA
simple transposition
this is where transposase makes cuts, strands are exchanged and ligated together forming cointegrate, gaps are filled by DNA pol and sealed by ligase, resolvase catalyzes recombination and makes them into two separate structures each with a copy of the transposable element
replicative transposition
what are some effects of transposition
mutation of coding region, arrest of translation or transcription, activation of genes, generation of new plasmids, R1 plasmid
what’s special about the R1 plasmid
multiple drug resistance plasmid due to transposon accumulation
single circular dsDNA molecules that are replicons with their own origin with single or multiple copies
plasmids
these can exist with or without integrating
episomes
these transfer copies via conjugation with genes encoding pili, in E coli contain F factor to transfer genes using tra operon
conjugative pili
this is the integration mediated by insertion sequences (IS)
fertility factors (F)
these contain plasmids with antibiotic resistance genes that destroy/modify antibiotics such as beta lactamase, some are conjugative, usually non integrative
resistance factors (R)
these encode colicin which is a type of bacteriocin that destroys closely related bacteria by targeting membrane integrity, RNA/DNA/ peptidoglycan and kills E coli
col plasmids
these carry virulence genes that confer resistance to hose defense mechanism and encode toxins
virulence plasmids
these carry genes for metabolic processes that encode degradative enzymes for pesticides and nitrogen fixation
metabolic plasmids
what as important about the U tube experiment
Davis 1950 showed that contact is required for conjugation, the filter prevented contact and no prototrophs were obtained
F+ is the _____ and F- is the ______
donor which possesses the F factor, the recipient which has no F factor
what happens in F+ x F- mating
rarely prototrophs, chromosomal genes are rarely transferred just the F factor, rolling circle mechanism
recipients become ______ and donor is ______
F+, F+
high frequency of recombination, the donor has the F factor integrated into chromosome which allows the transfer of chromosome, both of the plasmid genes and chromosomal genes are transferred here
Hfr strain
formed by incorrect excision of F factor from chromosome containing more than or equal to 1 gene from the chromosome, can transfer from plasmid to recipient
F’ plasmid
according to fredrick griffith, living S cells led to ____, living R cells led to______ heat killed S cells led to _____ and heat killed S cells + living R cells ______
died, healthy, healthy, died
what’s the conclusion from griffith’s experiment?
R bacteria were transformed into pathogenic S bacteria by a substance from the dead S cells
the uptake of DNA from the environment that’s incorporated in a heritable form usually natural from the donor bacterium which is lysed
transformation
this is capable of taking up DNA and is complex based on the growth stage and protein secretion, natural transformation in some genera such as N. gonorrhoeae, B subtilis, streptococcus, pseudomonas
competent cell
this form of artificial transformation uses a calcium chloride treatment for temporary competence, HS DNA and recover/plating
chemical transformation
this form of artificial transformation makes protoplasts, cells + DNA in cuvette, apply current then recovery/plating
electroporation
transfer of bacterial genes by bacteriophages
transduction
this type of bacteriophage reproduces using lytic life cycle
virulent
this type of bacteriophage reproduces using lysogenic life cycle
temperate
this type of transduction is when any of the bacterial genome can be transferred which was initially discovered by lederberg and zinder from u tube experiment, takes place during lytic life cycle, during viral assembly fragments of host DNA mistakenly packaged into phage head
generalized transduction
this type of transduction is restricted, by temperate phages established lysogeny, only specific portion of bacterial growth genome is transferred ad occurs when prophage is incorrectly excised and there’s an error in the lysogenic cycle
specialized transduction
