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genetics > Lecture 14 > Flashcards

Lecture 14 Flashcards

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Biology 101 flashcards
1
Q

what is the goal of transcription regulation

A

to maintain internal environment and survive

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2
Q

parts of the lac promoter

A

cap…rna binding site…lac O…shine dalgaro…start codon

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3
Q

where does positive and negative regulation in response to glucose happen

A

the lac promoter

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4
Q

why does lactose bind to the repressor

A

so it cant bind to lac O and prevent RNA pol from binding

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5
Q

types of transcription regulation

A

2 component system, quorum sensing, attenuation and lamdda phage

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6
Q

2 component pathway

A

let bacteria respond to external stimuli
-the receptor will get a signla and autophosphorylate on a histidine side chain
-the receptor sends phosphate to response regulator (protein) whihc is a DNA binding protein that will regulate transcription

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7
Q

how do ecoli respond to changes in the osmotic environment?

A

they use omp c and omp f porin proteins to limit the influx of solutes

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8
Q

porin protein

A

form pores in the outer membrane allowing molecules/ water to go in and out

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9
Q

omp c

A

narrower than omp f
-less molecules will flow causing the cell to stop shrinking

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10
Q

EnvZ receptor sensory kinase

A

change shape and activity to respond to osmotic pressure by increasing osmolarity and kinase activity

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11
Q

increase osmolarity

A

increase molecules in external environment which will in turn decrease water potential outside bacteria cell

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12
Q

how does EnvZ work with omp c and f

A

it will phosphorylate omp r and omp r will then regulate osmolarity genes
-the genes are omp c and f
-EnvZ has to activate omp c and f using omp r
-these are genes that alter the cells permeability

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13
Q

increase osmolarity response

A

use omp c to close gates in membrane so solute doesn’t enter
-very salty

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14
Q

decreasing osmolarity response

A

omp f will open the gates bc the environment is less salty

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15
Q

How many omp r site do c and f have

A

many

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16
Q

high affinity

A

bind tightly
-omp r doesnt need to be phosphorylated to bind
-omp f

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17
Q

omp r gets phosphorylated when?

A

when it needs to bind to sites of high and low affinity bc it also has to bind downstream (low affinity) to block transcription of omp F and turn on C

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18
Q

what happens to kinase when omp r is unphosphorylated

A

it doesnt change shape

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19
Q

what else can omp r control

A

pathogenesis
-only if in proper osmotic conditions and host environment

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20
Q

pathogenesis pathway

A

phosphorylated omp r goes to Ssra with will phosphorylate SsrB and then phosphorylate the pathogenesis gene
-these genes ARE NOT omp c or f

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21
Q

fusing photosynthetic light sensory to EnvZ

A

when omp r phosphorylates to omp c it will trigger lac Z (reporter gene) and we will see a black output
-this proves that omp c drives lac Z transgene
-turns bacteria into photographic film

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22
Q

collective bacteria behaviors

A

virulence factors, biofilm, antibiotic production and bioluminescense

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23
Q

autoinducer

A

secreted by bacteria, increase bacteria increase autoinducers
-at high concentrations they can enter cells and regulate genes

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24
Q

what binds to autoinducer

A

lux R
-targets gene activation

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25
Q

lux I

A

a.i. producing enzyme

26
Q

lux r

A

needs autoinducer to binds @ operator and activate trancription
-the ligand must bind
-similar to CAP

27
Q

prokaryote

A

simultaneous transcription and translation

28
Q

where are bacterial structural gene coding regions

A

all on single polycistronic mRNA

29
Q

what does ribosome do when it reached stop codon

A

stops and slides to the next ORF

30
Q

trp operon

A

encodes enzyme for making amino acid tryptophan
-the regulation will depend on transcription and translation

31
Q

what inhibites trp operon

A

tryptophan the amino acid because once it is made we dont need to keep making more

32
Q

without tryptophan we cant?

A

there will be no dna binding and rna pol will not be blocked
-we can transcribe

33
Q

no lactose present

A

trp repressor binds to operator while being bound to tryptophan

34
Q

trpL

A

first trp operon
-makes short peptide for attenuation

35
Q

hairpins

A

control rna pol depending on which regions are touching

36
Q

1 and 2

A

pause

37
Q

2 and 3

A

antitermination
-rna pol can go faster
-rna pol will be waiting at the 1 to make tryptophan

38
Q

3 and 4

A

termination
-when rna pol is @ 2
-too much tryptophan so we kick rna pol off

39
Q

cells that are close together have similar?

A

transcription factors

40
Q

hershman chase

A

prove DNA is genetic material

41
Q

attentuation

A

makes it easy to make amino acid because base pairing with RNA hairpin
-this is easier than proteins binding to specific DNA

42
Q

lambda phage

A

goes into e.coli genome between gal and bio genes
-the spot it takes in the genome is determined by integration enzymes

43
Q

lambda lysis

A

-determined by lambda repressor (CI gene) and cro binding proteins
-CI and cro will enter the bacterial genome

44
Q

cro

A

kill

45
Q

ci

A

-repressor
-keeps rna pol more upstream away from cro
-dont kill

46
Q

ci decrease

A

cro wins, blocks ci, makes lysis gene

47
Q

UV damage

A

-cro responds to threat by activating an enzyme to repair DNA
-this enzyme will accidentally blocks cI and let cro win accidentaly

48
Q

euakryotes have

A

3 rna pol

49
Q

rna 2

A

transcribes protein coding region
-only binds when general transcription factors bind to DNA bc it can’t make RNA by itself

50
Q

rna 1

A

ribosomal rna genes

51
Q

rna 3

A

tRNA genes

52
Q

where does RNA pol 2 bind?

A

TATA box

53
Q

what binds at tata box aside from RNA pol 2?

A

-tata binding proteins (TBP)
-TATA binding complex (TFIID)

54
Q

what do TBP doa t the box

A

bend the DNA at the box by intercalating amino acids between base pairs

55
Q

what complexes recruite RNA pol 2 to core promoter

A

TFIIB and TFIIA

56
Q

what determines effectiveness of rna pol

A

cis regulatory region
-things like CAP and lux R

57
Q

enhancers

A

only in eukaryotes
-proteins that enhance RNA recuitment

58
Q

silencer

A

inhibit RNA recruitment
-inhibit turning on w out being a physical block
-repressor that does competitive DNA binding
-can happen it the activator would express a gene we dont want

59
Q

mediator complex

A

simtulate or inhibit rna pol 2

60
Q

shapes of transcription factors binding at DNA

A

helix loop helix, Zn 2+ inger (ions make the finger structures), leucine zipper (protein w zipper)

61
Q

combinatorial control

A

allowed by mutliple enhancers and transcription factors

62
Q

what can an enhancer with the right transcription factor do?

A

turn on a gene

genetics (16 decks)

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