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BIO 315 > Midterm 4 > Flashcards

Midterm 4 Flashcards

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Biology 101 flashcards
1
Q

regulons

A

genes that are coordinated to respond to the same regulatory systems

(this means multiple sets of operons)

bigger than an operon has more than one promoter

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2
Q

Catabolite repression

A

shutdown of several systems that utilize various nutrients when glucose is present

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3
Q

the SOS response

A

a multigene system for wide scale DNA repair

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4
Q

jean jacques weigle

A

showed uv exposure induces nonspecific repair mechanisms in bacteria

bacteria were pre-exposed to uv light, then infected with damaged phages, repaired the phage DNA but also introduced more mutations

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5
Q

what does the sos response allow cells to do?

A

recognize and respond to serious dna damage

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6
Q

weigle experiment

A

uv light to damage phage. infect e coli with it and infect e coli that was exposed to uv light with it.

you see that a lot of phages are made from the ecoli that were exposed to the uv light because uv induces the repair response and it extends to the phages.

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7
Q

once they knew that the sos response existed, they wanted to know _______

A

which genes were involved in it. they used a promoter probe reporter lacZ gene transposon to figure it out.

When it was inserted next to a gene that was expressed in response to DNA damage, it was also expressed

this showed which genes were required for DNA damage repair

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8
Q

how to screen to identify genes involved in sos regulation

A

screen for mutant e coli cells in the presence pof DNA damging mitomycin C. made containing ampicillin, C-gal and mitomycin C.

pick all the blue e coli that are expressing b galactosidase indicate a high level of expression of genes that respond to dna damage and isolate them.

replica plate colonies on media without mitomycin C. white colonies confirm gene expression is in response to DNA damage (these are din genes that belong to the SOS regulon)

white are on when dna damage and off when not

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9
Q

RecA is a ___ for din gene

A

inducer

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10
Q

LexA is a _____ for the din gene

A

repressor

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11
Q

blue is ____

A

constitutively expressed

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12
Q

white is _____

A

unable to be expressed

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13
Q

RecA binds ____

A

single stranded DNA.

when it binds it, it is activated. then it cleaves the LexA repressor

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14
Q

heat shock genes are a __

A

regulon

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15
Q

what do sigma factors do?

A

in bacteria the use of different sigma factors directs RNA polymerases to certain genes

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16
Q

sigma 54

A

regulating nitrogen utilization in genes

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17
Q

sigma 32

A

heat shock protein gene regulator

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18
Q

sigma 38

A

general stress response gene regulation

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19
Q

post initiation control of gene expression

A

post transcriptional regulation

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20
Q

Regulatory RNAs

A

genomes carry regions of DNA coding for non-translated RNA

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21
Q

sRNA

A

control gene expression at transcription or translation points

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22
Q

quorum sensing

A

gene regulation process that allows bacteria to talk to one another

a number of members of a group that must be present in order to conduct business

cells release autoinducer molecules into the environment as the population density increases

detecting changes in autoinducer levels causes regulation of gene expression

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23
Q

lux

A

example of quroum sensing system

can live freely in symbiosis with the hawaiian bobtail squid. the cells only emit light (via enzyme luciferase) when in the light organ of the squid– this helps the squid evade prey.

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24
Q

how does lux work?

A

tldr AHL has to hit a threshold to induce light emission

when grown to high density, the cells produce N-acyl-homoserine lactose (AHL)

this autoinducer stimulates luminescence

the luxI protein catalyzes AHL synthesis

at low density the cells don’t produce enough AHL to induce light emission

examination of how cells detect levels of AHL has been an area of active research

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25
Q

LuxR

A

regulator/transcriptional activator interacts with AHL when it reaches a high enough concentration.

AHL is like a coactivator.

It bins to the lux box, DNA regulatory site and this leads to the transcription of luxA/luxB

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26
Q

Lux operon has _____

A

positive control

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27
Q

LuxI

A

always on at a basal level but when LuxR binds to the lux box in the presence of high AHL it really ramps up production – this makes the luminscence

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28
Q

mechanisms controlled by quorum sensing:

A

motility
conjugation –> transformation
biofilm formation
pathogenesis

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29
Q

autoinducers may ________

A

play a role in competition interrupting or inhibiting a control pathway in other organisms in the environment

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30
Q

two component regulatory systems

A

use one protein as a sensor and another to control transcription

  • this allows for response to changes in the environment
  • signal transduction induced inside the cell alters it to repsond appropriately
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31
Q

____ and _____ are examples of two component systems

A

sensor kinase (to detect environmental stimulus) and response regulator (to regulate transcription)

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32
Q

A tumefacians

A

example of two component reg system

vir genes found on the Ti plasmid

  • only expressed under conditions similar to a plant wound site
  • virA/virG are required for expression of the other virulence genes
  • virA is a transmembrane protein HPK
  • vir G is a transcription activator RR protein
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33
Q

chemotaxis

A

move toward things we want away from things we dont

controlled at the level of protein activity rather than via changes in gene expression

chemotactic bacteria sense changes in chemical gradients over time

changes induce altered direction and duration of flagellar rotation leading to directed movement over time

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34
Q

chemotaxis experiment

A

mutants outside of cap tube regular ones go into the cap tube

cap tube is filled with nutrients. so that makes sense normal functioning ones go in and mutants dont

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35
Q

che proteins are ______

A

two component regulatory systems

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36
Q

CheA & CheY

A

works as a sensor kinase becoming phosphorylated

phosphorylates CheY the RR protein
-the phosporylated RR proteins do not bind DNA they bind to the flagellar motor and change its activity

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37
Q

when attractant is bound

A

flagella moves in the diredction it was going

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38
Q

when attractant (MCP) isn’t bound

A

tumble occurs flagella changes direction

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39
Q

genomic library

A

collection of cloned dna fragments that represents the entire genome of an organism

the number of cloned fragments needed to encompass an entire genome can be determined by the formula

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40
Q

genetic libraries

A

the method of obtaining the library varies depending on the desired outcome

-a true genomic library is generated by shearing the genome and cloning the fragments

a library of expressed mRNA molecules of a cell can be formed as a complementary DNA library using reverse transcriptase

41
Q

transcriptomes

A

collection of transcribed mRNA molecules in a cell

northern blots

all Rnas including sRNAs

42
Q

northern blots

A

separation of RNA fragments by electrophoresis followed by blot transfer and probing with labeled DNA fragments

43
Q

microarrays

A

method of examining transcriptional activity of all genes in a cell simultaneously

the technique is miniatured, automated reverse of northern blots

  • probe DNA fragments are amplified by PCR and placed on glass slide in a known pattern
  • total cell mRNA is converted to cDNA by reverse transcriptase, labeled with a fluorescent molecule and passed over the microarray slide
  • the more intensely a spot on the microarray lights up the more cDNA ergo, the more mRNA is present
44
Q

comparative genomics

A

the study of evolutionary processes using the tools of genomics

  • genetic variability
  • different genes may have arisen from duplication events
  • paralogs = genes that are different from each other yet arose from a duplication vent

-orthologs - genes that have evolved from the same ancestor with the same function in different organisms

45
Q

paralogs

A

= genes that are different from each other yet arose from a single duplication event in the same ancestor

46
Q

orthologs

A

-orthologs - genes that have evolved from the same ancestor with the same function in different organisms

47
Q

to reproduce viruses must:

A
  • get into permissive host
  • acquire resources needed for replication
  • evade host defenses
  • spread to new hosts
48
Q

acute infections

A

short duration, signs/symptoms observed, infection is cleared (immunity usually results)

ex. common cold = rhinovirus
or flu

49
Q

latent infections

A

period of acute infection followed by latency
-virus is still present but replication is shutdown

reactivation may occur leading to recurrence of acute infection signs and symptoms

ex. include lambda phage and herpesviruses

50
Q

herpesviruses latent

A

maintain circular episome during latency

latency associated transcripts (LATs) help maintain latency

51
Q

reactivation events ______

A

typically damage the host cell

52
Q

is hiv latent chronic or acute?

A

technically chronic but after its short acute phase

however it must be making a certain amount of infectious virions to be able to be transmitted as we have discussed

53
Q

types of transmission

A

horizontal
vertical
zoonotic (horizontal)
mechanical (horizontal)

54
Q

horizontal transmission

A

transfer individual to individual within the same species

requires a mode of exit and a mode of entry

this is what people commonly think of when they think of catching something from someone

55
Q

vertical transmission

A

still transmission within the same species from mother to fetus or newborn

virus may be transmitted by placenta or during birth (rubella, hepatitis B and C, HIV)

viruses can be transmitted via breast milk (HIV MMTV)

a few viruses can even be transmitted via germ cells infection. these are endogenous retroviruses

56
Q

endogenous retroviruses

A

have confluence of interest with the host. dont want to harm host best thing they can do would be silent

most germ cell transmitted mmtv do not cause active infection in offspring as would be expected

those that do represent recent integration events that have not yet been silence

silent endogenous retroviruses make up at least 8% of the human genome

57
Q

why have hiv rates decline in the us?

A

antiretroviral drug therapies and c sections

58
Q

if untreated, roughly ___ infected mothers will infect their infants w hiv

A

1/3

2% now in US

59
Q

reservoir

A

continual source of infective pathogens

60
Q

zoonosis

A

disease that can be transmitted from non human animals to humans

usually humans are the dead end in the transmission cycle

still horizontal event

ex rabies (direct transmission) and west nile (indirect transmission)

61
Q

direct transmission

A

reservoir is other mammals

62
Q

indirect transmission

A

reservoir is bird populations even tho you get bit by mosquito

there’s a vector bw you and the reservoir

63
Q

mechanical transmission

A

intraspecies facilitated transfer of virus from host to host via another vector (e.g myxoma virus, yellow fever)

mosquito vector is NECESSARY

64
Q

how is zoonotic transmission different from mechanical?

A

same species = mechanical

different species = zoonotic

65
Q

ways viruses can cause cells to die:

A

necrosis –> direct

apoptosis –> indirect

66
Q

necrosis

A

viral-induced cellular destruction

the cell bursts
sometimes due to overfilling the cell with new viruses
other times due to viral impairment of normal cell functions

67
Q

apoptosis

A

viral-induced cellular destruction

the cell commits suicide (usually to stop the spread of the virus). often, the virus provokes the host cell to produce interferons which trigger apoptosis in surrounding cells

68
Q

how do some viruses cause cancer?

A

transformation events produce changes in a cell that make it cancer like

some viruses possess oncogenes, genetic material capable of inducing transforming events in host cells

tumorigenesis may result from viral protein inducing a normally quiescent (not dividing) cell to enter the cell cycle

69
Q

DNA tumor causing viruses =

A

papillomaviruses

noneveloped icosahedral dsDNA viruses

infects epithelial cells, causing warts

may also induce transformation through e6/e7 viral proteins (leads most commonly to cervical cancer)

not all strains possess genes for transformation

vaccine exists against most common e6/e7 carrying strains

70
Q

how do e6/e7 cause cancer?

A

Rb and p53 normally keep the cell cycle under control. they are tumor suppressor genes/proteins

Rb and p53 inhibit progression of the cell cycle in different ways

E6 and E7 block their action and encourage cells to enter S phase and reproduce

71
Q

RNA tumor causing viruses

A

very few RNA viruses seem to cause cancer. MAINLY RETROVIRUSES DO THO WHY?

retroviruses may act indirectly to induce cancer

via altering proto-oncogenes (genes that code for regulation of the cell cycle)

cis-acting retroviruses integrate genomes, activating a cellular proto-oncogene

transducing retroviruses acquire a cellular gene and bring it with them into a newly infected cell

72
Q

cis acting retroviruses

A

– Cis-acting retroviruses integrate their genomes, activating a cellular proto-oncogene.

after conversion of rna to cDNa occurs

the point of integration may alter expression of a proto-oncogene

73
Q

transducing retroviruses

A

may have acquired a cellular proto oncogene during previous infections

if that proto oncogene is overexpressed cancer results

if that proto oncogene becomes altered it may alter the normal function within a cell usually then called an oncogene

74
Q

how do tranducing rna tumor causing viruses possibly work

A

retrovirus effects by turning proto oncogene into oncogene

75
Q

seasonality effects of covid

A

when little to no immunity exists in a population seasonality effects can be diminished

76
Q

if you were interested in expressed mRNAs – how would you gather them to put them into a genetic library?

A

make a poly U rich area and the poly As will come to it

77
Q

most material to least material in genetic library:

A 
genome = DNA
transcriptome = RNA
Proteome = Proteins
Metabolome = sugars, nucleotides amino acids
78
Q

t or f transcriptomes include all RNAs including sRNAs

A

yes

79
Q

SNOW DROP

A

southern dna
northern rna
western protein

80
Q

dna and rna have a ____

A

negative charge to them so they go to the positive side of the electric field in electrophoresis

81
Q

proteomes

A

collection of expressed proteins in a cell

can be studied by multiple methods including

  • 2D polyacrylamide gel electrophoresis (PAGE)
  • mass spec
  • xray crystallography
  • NMR
82
Q

comparative genomics

A

is the study of evolutionary processes using the tools of genomics

can show genetic variability, and how/when different genes may have arisen from duplication events

paralog families can become very large

83
Q

genomes have characteristics G+C nucleotide content

A

E coli = 50% G+C
Streptomyces coelicolor = 72%
saccharomyces cerevisiae = 38%

areas of genome with significantly lower or higher G+C content than the rest of the genome are likely areas where horizontal transfer has occurred

identifying and studying these areas can lend further insight into comparative genomic studies

84
Q

genomic islands

A

DNA segments of 10-200kB associated with tRNA genes, transposable elements, plasmids, or bacteriophages

endogenous prophages are those that are considered a stable part of bacterial genome

some do conjugation some do transformation

acts like a parasite of the virus interfering with the normal biology of phages to promote their own spread

85
Q

core genome vs accessory gemone

A

transposable elements can go between taxa, orders, phyla and even kingdoms

THEY DONT KNOW HOW

accessory is the genes not present in all of strains of a species

core genomes are genes present in all genomes

86
Q

metagenomics

A

involves construction and analysis of gene libraries from DNA extracted directly from complex microbial communities

this field is changing our understanding of life on earth, finding evidence for newly discovered organisms in very diverse and challenging locations

87
Q

e coli shiga toxin example

A

e coli acquire shiga toxin prob through transduction

shiga toxins are expressed by genes considered to be something of the genome of lambdoid prophages

shigella and e coli are closely related

88
Q

cellulose in gut w cows is _____

A

mutualism

89
Q

parasitism

A

one species does obvious harm to the other

90
Q

commensalism

A

one species benefits but nothing happens to other species

91
Q

mutualism

A

both species happen

92
Q

endophytes

A

plant endosymbionts

93
Q

rhizobia

A

endophytes that can infect plant root cells fixing nitrogen and forming root nodules

94
Q

endosymbionts go ____

A

into cells

we don’t have true endosymbionts –> mitochondria kinda they are anciently symbiotic

95
Q

mutualism in plant bacteria example

A

plant provides leghemoglobin

binds oxygen similar to hemoglobin in red blood cells
prevents it from damaging nitrogen in a form the plant cells can use

the bacteria provide valuable nitrogen in a form the plant cells can use (often ammonium ion)

96
Q

root nodule formation

A

bacterial nod genes are expressed in presence of plants

an infection thread is formed to invade the root

the nodule forms providing a low O2 environment

the root cells form leghemoglobin to assist
the plant provides carbon compounds to the bacteria while bacteria provide ammonium in return

97
Q

nodule metabolism

A

is it just sugar that the plants provide to the bacteria

no it turns out that C4 dicarboxylic acids are provided by the plant, not sucrose

these compounds are then inserted into the TCA cycle to produce ATP for the bacteria

98
Q

lichens

A

a different arrangement

they have microbes/microbe symbionts

BIO 315 (4 decks)

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