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Final Exam Study Sets > BI323 Final Exam Material from the new material > Flashcards

BI323 Final Exam Material from the new material Flashcards

1
Q

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

A

virion

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2
Q

what are some differences between viruses and cellular organisms?

A

cellular organisms are complex, contain both DNA and RNA, carry out cell division and only some are obligate intracellular parasites

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3
Q

this contains a nucleic acid and protein coat, capsid contains protein coat, protects genome, aids in transfer between host cells, contains protomer

A

nucleocapsid core

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4
Q

this is a capsid protein subunit, which is efficient and saves genome space, often spontaneous

A

protomer

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5
Q

what are three structures of a nucleocapsid core

A

helical, icosahedral, complex

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6
Q

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

A

helical capsids, influenza is not as rigid and enveloped

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7
Q

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

A

icosahedral, pentamers (SV40) and hexamers

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8
Q

what are examples of virions with complex symmetry

A

poxvirus, large bacteriophage (binal), vaccina virus

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9
Q

membrane structure surrounding some viruses, lipids and carbs usually host derived, proteins and virus specific with peplomers for attachment

A

viral envelope

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10
Q

what are peplomers

A

spikes for virus attachment

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11
Q

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

A

viral enzymes

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12
Q

most DNA viruses are….

A

dsDNA, linear, circular, both

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13
Q

most RNA viruses are…

A

+, - strand, segmented genomes

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14
Q

what is a (+) strand RNA virus

A

viral genomic RNA, viral mRNA, euk viruses are capped, polyA

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15
Q

what is (-) strand RNA virus

A

viral genomic RNA that is complementary to viral mRNA

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16
Q

what is a segmented genome?

A

virions that contain >1 unique RNA usually in the same capsid ex. brome mosaic virus with 3 viral particles

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17
Q

these are stages of what? 1. adsorption 2. entry (penetrating/uncoating) 3. synthesis 4. assembly 5. release

A

replication of viruses (similar to bacteriophage reproduction)

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18
Q

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)

A

adsorption

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19
Q

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

A

entry (penetration/uncoating)

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20
Q

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)

A

synthesis

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21
Q

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

A

assembly

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21
Q

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

A

release, influenza and IV budding

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21
Q

virulent phage life cycles are typically _____ while temperate are ________

A

lytic (T4), lysogenic (lambda)

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21
Q

this is a complex, multi step process often involving oncogenes

A

carcinogenesis

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21
Q

this is where a neoplasia is found with abnormal new cell growth and reproduction and loss of regulation

A

tumor

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22
Q

this virus leads to Burkitt’s lymphoma, nasopharyngeal carcinoma due to the presence of Ab genome found in tumors

A

epstein barr vrius (EBV)

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23
Q

this causes hepatocellular carcinoma

A

hep b

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24
Q

this causes cirrhosis of the liver and liver cancer

A

hep c

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25
Q

this causes kaposi’s sarcoma

A

human herpesvirus 8 (KSHV)

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26
Q

this virus causes cervical cancer

A

human papillomavirus HPV 16, 18

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27
Q

this virus causes leukemia

A

human T cell lymphotropic virus (HTLV)

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28
Q

which mechanism of carcinogenesis is where the oncogene is carried into the cell and inserts it into the host genome

A

rous sarcoma virus, src gene

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29
Q

which mechanism of carcinogenesis is where the altered cell regulation due to changes in kinase activity or production of regulatory proteins occurs

A

HPV, p53 ubiquitylation

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30
Q

what are the random mutations that may lead to the survival of harder to infect bacterial populations, give an example

A

genetic resistance, expression of altered reception protein

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31
Q

what is the modification of bacterial DNA (methylation) and expression of enzymes that cleave unmodified DNA

A

restriction endonucleases (RE)

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32
Q

what does CRISPR stand for and what is it. which proteins interact with CRISPR regions

A

clustered repeat interspaced tandem short palindromic repeats, repeating sequences of bases found in bacteria and archaea with varied spacer sequences between them, Cas

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33
Q

each time the cell is infected but survives, a portion of the viral DNA is added to the ____ end of the region in CRISPR

A

3’

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34
Q

the addition of DNA sequences to the end of the region following survived infection

A

adaption stage

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35
Q

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

A

interference stage

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36
Q

who were the scientists that founded CRISPR/Cas?

A

E. Charpentier and J. Doudna

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37
Q

direct counts are often performed by an ________ to count particles

A

electron microscope

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38
Q

this count is used to determine relative viral quantity ex. hemagglutination assay to determine highest dilution of viruses that cause rbc clotting

A

indirect

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39
Q

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

A

plaque assays

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40
Q

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

A

infectious/lethal dose assays

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41
Q

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

A

viroid

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42
Q

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

A

prions

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43
Q

what are three categories of enzyme expression

A

constitutive, inducible, repressible

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44
Q

the presence of substrate increases enzyme expression ex. many catabolic enzymes

A

induction

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45
Q

the presence of end product decreases enzyme expression ex. biosynthetic enzymes

A

repression

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46
Q

this is when initiation is inhibited ex. repressor proteins

A

negative transcriptional control

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47
Q

this is when initiation is permitted ex. activator proteins

A

positive transcriptional control

48
Q

this is when the repressor is active without the inducer so the catabolic enzyme is not made without the substrate

A

inducible enzyme for negative control

49
Q

this is when the repressor requires corepressor for activity so the biosynthetic enzyme is not made when the end product is present

A

repressible enzyme for negative control

50
Q

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

A

negative, inducible, repressor, binds repressor, turn on genes

51
Q

what happens when there is no lactose present

A

Lacl is expressed and active, binds operator

52
Q

what happens when there is lactose present

A

Lacl is expressed but inactive, allolactose binds Lacl repressor and inactivates

53
Q

what happens when Trp is abundant, when its low

A

the Trp repressor is active, Trp repressor is inactive

54
Q

what is the relationship between the lac operon and catabolite repression

A

glucose first then lactose second in a diauxic biphasic growth

55
Q

this is selective substrate uptake from media that offers choices, 5-10% of all bacterial genes subject ti this

A

catabolite repression

56
Q

what does the catabolite activator protein do (CAP)?

A

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

57
Q

what is the significance of catabolite repression

A

multiple catabolic operons are affected, flagellar genes controlled (don’t have to search for nutrients), important for competition in natural environments

58
Q

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

A

attenuation

59
Q

operons controlled by same regulator protein associated with common function such as HS

A

regulon

60
Q

regulon with operons also controlled separately such as catabolic repression

A

modulon

61
Q

this is when different sigma factors lead to different promotors, the substitution of these factors, changes in gene expression and many genes and operons

A

alternative sigma factors

62
Q

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

A

phosphorelay systems

63
Q

TM protein that transmits EC changes in global regulation

A

sensor kinase

64
Q

DNA binding and transcriptional control in global regulation

A

response regulator

65
Q

what are some important factors of B subtilis sporulation

A

multiple control mechanisms, vegetative growth, starvation, KinA, Spo0A

66
Q

auto phosphorylates in response to environmental signals such as starvation

A

sensor kinase KinA

67
Q

active transcription regulator that activates production and sporulation

A

response regulator Spo0A

68
Q

this binds chemoattractant that stimulates ccw rotation, dimer bound to CheW and CheA

A

methyl accepting chemotaxis proteins (MCP) of E.coli

69
Q

no attractant is bound to MCP, this auto , runs and tumbles, phosphorylates and phosphorylates CheY

A

sensor kinase CheA

70
Q

this leads to FliM, causing cw rotation and tumbles

A

response regulator CheY

71
Q

……… CheA autophosphorylase is inhibited to ccw run, less tumbles, directional movement, dephosphorylation of CheY

A

this is when the attractant is bound to MCP

72
Q

what is important to know about quorum sensing global regulation

A

AHL synthase (luxl) is positively upregulated, LuxR transcription activator requires AHL

73
Q

this diffuses out, accumulates and diffuses back into the cell, activating _________

A

AHL, LuxR

74
Q

AHL is also known as…

A

an autoinducer

75
Q

these are heritable changes in nucleotide sequences that may or may not affect the phenotype

A

mutation

76
Q

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

A

spontaneous mutations

77
Q

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

A

induced mutation

78
Q

alteration in H binding of nucleotides, contain normal (keto watson and crick) and abnormal (enol)

A

tautomeric shifts

79
Q

the deletion or addition of base pairs that alters reading frame

A

frameshift

80
Q

what are some examples of induced mutations

A

base analogs, DNA modifying agents, intercalating agents, DNA damaging agents (UV, radiation, free radical peroxide)

81
Q

what are some effects of mutations

A

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

82
Q

this biosynthetic pathway mutant cannot synthesize the product of the pathway required for growth

A

auxotrophs

83
Q

this grows in minimal media without supplements

A

prototrophs

84
Q

how are mutants detected?

A

phenotypic observation, replica plating techniques detect autotrophic mutants

85
Q

prokaryotes divide in ________ with no meiosis and how do they increase their fitness?

A

binary fission, HGT and mutations

86
Q

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

A

recombination

87
Q

the transfer of DNA from donor organism to recipient via conjugation, transformation and transduction including exogenote, endogenote, merozygote

A

horizontal gene transfer

88
Q

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

A

homologous double stranded break recombination

89
Q

incorporation of DNA single strand into chromosome creating heteroduplex DNA

A

homologous nonreciprocal recombination

90
Q

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

A

site specific recombination

91
Q

this is the recombination that accompanies replication of genetic material used by genetic elements ex. transposons

A

transposition

92
Q

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

A

transposable elements, insertion sequences and composite transposons

93
Q

these are the simplest sequences that possess only genes encoding enzymes required for transposition such as transposase that are bound by inverted repeat

A

insertion sequences

94
Q

these carry genes in addition to those needed for transposition such as antibiotic resistance, the central region is flanked by IS elements

A

composite transposons

95
Q

these are cut and paste transposons where insertion generates direct repeats of flanking host DNA

A

simple transposition

96
Q

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

A

replicative transposition

97
Q

what are some effects of transposition

A

mutation of coding region, arrest of translation or transcription, activation of genes, generation of new plasmids, R1 plasmid

98
Q

what’s special about the R1 plasmid

A

multiple drug resistance plasmid due to transposon accumulation

99
Q

single circular dsDNA molecules that are replicons with their own origin with single or multiple copies

A

plasmids

100
Q

these can exist with or without integrating

A

episomes

101
Q

these transfer copies via conjugation with genes encoding pili, in E coli contain F factor to transfer genes using tra operon

A

conjugative pili

102
Q

this is the integration mediated by insertion sequences (IS)

A

fertility factors (F)

103
Q

these contain plasmids with antibiotic resistance genes that destroy/modify antibiotics such as beta lactamase, some are conjugative, usually non integrative

A

resistance factors (R)

104
Q

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

A

col plasmids

105
Q

these carry virulence genes that confer resistance to hose defense mechanism and encode toxins

A

virulence plasmids

106
Q

these carry genes for metabolic processes that encode degradative enzymes for pesticides and nitrogen fixation

A

metabolic plasmids

107
Q

what as important about the U tube experiment

A

Davis 1950 showed that contact is required for conjugation, the filter prevented contact and no prototrophs were obtained

108
Q

F+ is the _____ and F- is the ______

A

donor which possesses the F factor, the recipient which has no F factor

109
Q

what happens in F+ x F- mating

A

rarely prototrophs, chromosomal genes are rarely transferred just the F factor, rolling circle mechanism

110
Q

recipients become ______ and donor is ______

A

F+, F+

111
Q

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

A

Hfr strain

112
Q

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

A

F’ plasmid

113
Q

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 ______

A

died, healthy, healthy, died

114
Q

what’s the conclusion from griffith’s experiment?

A

R bacteria were transformed into pathogenic S bacteria by a substance from the dead S cells

115
Q

the uptake of DNA from the environment that’s incorporated in a heritable form usually natural from the donor bacterium which is lysed

A

transformation

116
Q

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

A

competent cell

117
Q

this form of artificial transformation uses a calcium chloride treatment for temporary competence, HS DNA and recover/plating

A

chemical transformation

118
Q

this form of artificial transformation makes protoplasts, cells + DNA in cuvette, apply current then recovery/plating

A

electroporation

119
Q

transfer of bacterial genes by bacteriophages

A

transduction

120
Q

this type of bacteriophage reproduces using lytic life cycle

A

virulent

121
Q

this type of bacteriophage reproduces using lysogenic life cycle

A

temperate

122
Q

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

A

generalized transduction

123
Q

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

A

specialized transduction

Final Exam Study Sets (6 decks)

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