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Lecture 15 Flashcards

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Biology 101 flashcards
1
Q

regulation methods

A

-transcriptional cascade
-splice
-polyadenylation, mRNA cap and translation regulation
-RNAi and miRNA

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2
Q

what determines mammal gender

A

transcriptional cascade bc it runs off certain transcription factors

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3
Q

what supports the theory of regulation

A

different somatic cells have the same genomic code so they must be expressing different regions

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4
Q

where is the enhancer

A

before the core promoter

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5
Q

what tells the enhancer what genes to turn on

A

insulators bc they can go in either direction and where they are means transcription is going the opposite way
ex: if insulator is upstream we are going to express genes downstream

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6
Q

what can block promoter access

A

sequence between enhancer and promoter (insulator)

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7
Q

what do insulators do to DNA

A

put it in loops and the enhancer will only bind to transcription activator on the loop that is being activated
-the other loop is not being expressed

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8
Q

CTCF

A

protein that bind insulator to DNA
-causes the loop

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9
Q

chip assay

A

identify DNA base pair sites, extract DNA with proteins still attached and then use antibodies to get the transcription factors of interest, selectively purify antibody and it will take anything bound to it, then sequence and map genome

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10
Q

one transcription factor has

A

thousands of sites and sequences

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11
Q

male vs female determined by

A

SRY TF
-when it is present it causes male development
-you can have an XY without SRY which will lead to a female XY individual

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12
Q

FGF9

A

boy
-production is stimulated by SOX9 and when FGF9 is produced it will inhibit WNT4

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13
Q

WNT4

A

girl
-inhibits FGF9 and then the female cascade begins
-typically wins

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14
Q

FGF9 and WNT4

A

-protein hormones

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15
Q

SOX 9

A

promotes by SRY to make FGF9 and inhibit WNT4

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16
Q

no SRY

A

WNT4 will win bc there is no FGF9 to inhibit itself

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17
Q

what happens when we block SRY

A

we get an XY female bc we cant inhibit WNT4

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18
Q

block WNT4

A

XX male bc female cant win

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19
Q

steroid hormones

A

activate nuclear hormone receptor transcription factors
-testosterone and estradiol (ovaries)
-a recceptor in cytoplasm will change to let it into the nucleaus where the transcription factors are

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20
Q

sex hormone

A

ligand binding to the transcription factors (like CAP or LUX R)

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21
Q

is the eukaryotic coding region continuous?

A

no
-it has introns and exons

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22
Q

non coding regions

A

-introns
-removed with splice
-NOT IN BACTERIA
-not in mRNA

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23
Q

splicesome

A

catalyze splice
-small ribonucleoprotein particles (snRNPs)
-form the lariat loop
-DONT CUT just hold the lariat folded

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24
Q

A in the splice

A

makes 3 bonds bc RNA has a 2 prime hydroxyl this is why DNA cant do the splice
-forms the lariat

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25
Q

splice

A

the lariat is removed and degrades and the 3 prime (donor) and 5 prime (acceptor) ends connect to make a continuous coding sequence

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26
Q

self splicing

A

-can self fold without proteins and use ribozymes which are RNA molecules that act like enzymes
-cuts lariant out itself

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27
Q

life theory

A

begain with catayltic RNA

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28
Q

splicing different exons determines?

A

the gene we encode
-ALTERNATIVE SPLICING
-one gene can encode many proteins depending on what we express

29
Q

isoform

A

splice variant
-lets us make antibodies and recognize infection

30
Q

DSCAM

A

how neurons detect each other and synapse

31
Q

DOWNS

A

extra DSCAm which leads to neuro issues
-too many synapses
-neurons bump into each other

32
Q

no DSCAM

A

neurons self synapse

33
Q

why is each neuron different?

A

bc they are isoforms and all express different isoforms
-it knows its own DSCAM so it can detect others

34
Q

mutant slicing machinery

A

retain introns, convert exons to introns, delete the wrong exons

35
Q

treating DMD

A

-splice nucleic acid drug that will block 51 so 47 shifts to 52 and keeps translating
-results in a dystrophin protein missing an amino acid but it is still a funcitonal protein

36
Q

DMD

A

deletion of exons 48- 50 which causes a framshift putting 47 next to 52 this causes a stop resulting in a useless truncated protein

37
Q

what happens to the ends of premRNA

A

they get modified by hydrolytic enzymes
-also helps ribosome attach at 5 prime end
-this helps export mRNA and protect it

38
Q

5 prime end

A

gets a guanine methyl cap

39
Q

3 prime end

A

gets a poly A tail when polyadenylation signal is reached
-the cleave is after AAUAAA
-cleaved by an enzyme

40
Q

translation initiation factor 4 (ELF4)

A

binds at 5 prime cap and gets the ribosome to the mRNA
-makes a complex with poly A binding protein which will make a loop that attracts the small ribosomal subunit

41
Q

what does a cell do when it is starving?

A

4E-BP1 blocks the elf 4 from binding to PABP so we dont do translation and conserve energy

42
Q

what happens when starved cell receives nutrients again

A

4e-bp1 is phosphorylated and translation can happen

43
Q

3 prime UTR

A

determines the life span of mRNA bc of the nucleotides here
-can be transferred

44
Q

eukaryotic mRNA lifespan. longer or shorter than prokaryot?

A

longer

45
Q

transfer of long life UTR

A

-can transfer to short life mRNA to extend their lives

46
Q

antisense mRNA

A

prevent translation by sending RNA that is complementary to the sequence being expressed so the ribosome cant access that sequence
-doesnt always work
-doesnt affect DNA

47
Q

RNAi

A

-rna interference
-injecting dsRNA which stops translation
-ex: c elegan eating transgenic bacteria with dsRNA
-siRNA in mammal
-regulate lifespan

48
Q

dsRNA in mammals

A

-dsRNA short hairpins (siRNA)
-short 22 nucleotide hairpins knock out translation of the gene and leave the rest unaffected
-only in mammals

49
Q

does RNAi increase or decrease mRNA lifespan

A

decrease
-promotes RNA degradation

50
Q

evolution of RNA

A

many viruses are dsRNA so maybe organisms developed to shut down at dsRNA so they dont get infected

51
Q

c elegans have

A

4 larval stages
-L1-4

52
Q

retarded

A

2 L1 phases
-lin mutant
-has lin 14 in the 3 prime UTR

53
Q

precocious

A

skip L1
-lin mutant

54
Q

lin 14 lf

A

mutant causing precosious
-recessive
-in coding region

55
Q

lin 14 dominant

A

retared
- in untranslated region
-lin 14/ clock stays elevated for two long so organism doesnt move on
-also happens when there is no lin 4 present

56
Q

lin 4

A

causes retarded
-encodes RNA sequence that is complementary to lin 14 in UTR (dominant)
-micro RNA/ miRNA
-inhibit/ reduce lin 14 that cuases retardation

57
Q

double mutants

A

lin 14 and lin 4
-precocious
-therefore lin 4 effect is acting through lin 14 therefore retarded growth has to have normal lin 14

58
Q

lin 14 gene

A

encodes a protein
-loss of function mutations are in the coding regions

59
Q

clock

A

lin 14
-protein decreases as animal develops

60
Q

lin 4 level

A

increases as animal develops

61
Q

lin 4 miRNA model

A

-lin 4 makes 70 nucleotide precurser in hairpin that will unwind and bind to lin 14 which stops the translation of the lin 14 protein
-this is the mechanism of the dsRNA shutting down translation

62
Q

miRNA

A

-hairpins that get processed and create dsRNA
-dicer
-RISC

63
Q

dicer enzymes

A

cut dsRNA into 22 nucleotide pieces
-dsRNA is from the miRNA

64
Q

why does 22 nt work better in mammals

A

skipping the first step
-we dont need dicer to work

65
Q

RISC

A

-22 nt bind to RISC complex
-takes on strand from dsRNA and then guides remaining strand to the ssRNA that we want to shut down
-cuts that mRNA shutting it down
-no protein made

66
Q

RNA dependant RNA pol

A

amplifies response of RNAi
-dont attach to RISC instead RdRP extends as a primer which makes a longer dsRNA for dicer to cut
-destroys mRNA but leaves 22 nt that can create a feedback loop and further shut down protein production
-can be started by a parent, some of the nt can be passed down to the offspring and retain the ability to shut down this protein

67
Q

how to pass on change without changing DNA

A

recycle ds mRNA fragments/ 22 nt to offspring
-from RdRP loop

68
Q
A

genetics (16 decks)

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