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Block 1 Week 3 > MOL BIOL (Singer): Gene Expression > Flashcards

MOL BIOL (Singer): Gene Expression Flashcards

1
Q

What two factors play a role in mRNA stability and degradation?

A

5 prime cap and poly A tail

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2
Q

What does DAN, deadenylation nuclease do?

A

It docks on the 5 PRIME CAP of mRNA BUT it shortens the poly A tail in the 3’ to 5’ direction. so it degrades mRNA

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3
Q

Describe pri-miRNA structure

A

ssRNA sequence….. dsRNA hairpin…… ssrRNA sequence……. dsRNA hairpin……. ssRNA sequence……and so forth

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4
Q

describe pre-miRNA structure

A

dsRNA hairpin

but no ssRNA, except in the hairpin loop region

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5
Q

Summarize the steps in miRNA mediated gene silencing

A

[1] in nucleus Drosha cleaves pri-miRNA to just leave the hairpin miRNA (pre miRNA)
[2] in CYTOPLASM now, dicer cuts off the hairpin loop, leaving ds miRNA
[3] miRNA is now said to be pre-mature miRNA. and goes to the RISC complex.
[4] RISC complex assembles (includes argonaute) with RNA and associates miRNA with its complementary RNA.
[5] mRNA is degraded or repressed

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6
Q

What happens in cases of 100% mature miRNA to mRNA complementation?

A

Argonaute, part of the RISC complex, slices the mRNA to promote quick and efficient mRNA degradation

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7
Q

What happens if the mature miRNA and mRNA are an imperfect match?

A

Translation is repressed.

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8
Q

Why do miRNAs have good potential in therapeutics?

A

They function as oncogens and tumor suppressors in the heart, have no immune.
they are also able to target disease tissue in mouse and primate models of cancer and cholesterol

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9
Q

Three steps in translation>?

A

Initiation
elongation
termination

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10
Q

describe structure of ribosome and where they’re located in EUK

A

they have two subunits.
the big subunit is 60s. the small 40s. 90s the total of the two subunits.
they’re sedimentation rates

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11
Q

What are the 4 major sties on ribosome?

A

a. mRNA bidning site
b. P (peptidyl) site
c. A (amino acyl tRNA) site
d. E (exiting) site

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12
Q

Describe degeneracy

A

If a mutation occurs at the third site, it’s whatever coz the mutation is in the wobble position and may not have any effect

64 codons but only 20 AA

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13
Q

How many reading frames are possible? and why don’t we do random reading frame iterations?

A

three possible reading frames

we start at the AUG, methionine, site to keep things consistent

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14
Q

What do tRNA do?

A

They’re adapter molecules that link codon on mRNA to a specific AA

have atnicodon and AA attachment site

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15
Q

What’s the point of the regions of the tRNA that are not attachment sites?

A

they help associate with the rest of the ribosome

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16
Q

define wobble base.

A

3rd position in codon; it’s not tally require to match all tRNAs correctly. think degeneracy

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17
Q

What does aminoacyl-tRNA synthase enzyme do?

A

it links SPECIFIC tRNA with a SPECIFIC AA

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18
Q

describe tRNA synthase linking process?

A

both AA and tRNA dock onto tRNA synthase (a different synthase for every AA). paring is correct, then ATP is converted to ADP + PP., connecting the -OH on the carboxylic side of the amino acid to the tRNA for that amino acid.

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19
Q

Hydrolytic editing

A

correct pairing by literally cleaving out incorrect AA

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20
Q

Kozak sequence is usually first AUG from 5’ cap site. how would it look like if you drew it out?

A

GGGGG XXAUGXXXXX

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21
Q

Translation initiation can be blocked by what?

A

repressor proteins blocking the kozak sequence or miRNA

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22
Q

what are the initiation factors most important for initiation?

A

eiF2 and eiF4.

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23
Q

WHat does eiF4 do?

A

it binds with the mRNA at the 5’ cap and poly A tail, so it forms a CIRCULAR loop of mRNA with the ends (connected to eif4) serving as linking regions

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24
Q

What does eiF2 do?

A

it comes bound to GTP and recruits the Met, the start AA. to the small ribosomal subunit.

25
Q

What happens when eif2-small ribosomal subunit-met come together with eif4-mRNA complex?

A

The first complex docks, along with additional intiation factors, docks onto the mRNA.

26
Q

What happens after Met (bound to small Rsub and eif2GTP) finds the AUG) finds the AUG sequence?

A

GTP is hydrolyzed, so eif2 now pops out along with GD, and this is a CRITICAL stop coz now the large ribosomal subunit can bind onto the small one and the small ribosomal subunit.

INITIATION COMPLETE

27
Q

Describe elongation

A

E P A
1. start: polypeptide on P; new aminoacyl tRNA on A site. E site is vacant.

  1. polypeptide (previously at P site) binds to elongate the A site aminoacyl tRNA; the P site now has empty tRNA.
  2. mRNA doves down three positions through the E site. now the polypeptide (previously on the A site) goes to P site. and the empty tRNA goes to E site; A site is currently totally empty.
  3. a new aminoacyl tRNA docks onto the A site; the E site empty tRNA pops out now; the growing polypeptide is still on the P site. PROCESS REPEATS AGAIN
28
Q

What do elongation factos do?

A

EF 1 and EF two enhance translation accuracy

29
Q

EF1 does what?

A

EF1 brings in aminoacyl to P site

30
Q

EF2 does what?

A

pushes PA (when polypeptide is on A) down into the EP

31
Q

What causes termination?

A

UAG goes onto the A site, which causes binding of RELEASE FACTOR to A site.

32
Q

What happens after the release factor binds to the A site?

A

The aminoacyl bond between the polypeptide and the tRNA on the P site are HYDROLYZED, cleaving the polypetide from the tRNA.

33
Q

What is the termination step?

A

basically the cleaving of the aminoacyl bond between the peptide and tRNA!!!

34
Q

What happens immediately after the polypeptide gets cleaved from the P site tRNA?

A

the tRNA moves from P to E; then the release factor from A to P. After this, the large and small subunits DISSOCIATE

35
Q

tatracycline mechanism

A

ACTS ONLY ON BACTERIA.

blocks binding of aminoacyl-tRNA to A site of ribosomes

36
Q

Actinomycin mechnaism

A

ACTS ON BOTH PROK AND EUK.

binds to DNA nd blocks the movement of RNA pol (so no RNA synthesis)

37
Q

Cyclohexamide mechanism

A

ACT ONLY ON EUK.

Blocks the translocation RXN on ribosomes (so moving from PA to EP)

38
Q

are folding/structural changes/processing problems reversible or irreversible post translational events?

A

They’re reversible

39
Q

Is adding or removing functional groups (such as methionine) reversible or irreversible post translational events?

A

They’re reversible!!!

40
Q

What’s an IRREVERSIBLE event?

A

proteolysis

41
Q

Some molecular chaperones are also known as?

A

Heat shock proteins

42
Q

Hsp60 mechanism

A

Structure looks like a dimeric “|=|” (presuming there is a top and bottom subunit). the incorrectly folded protein will dock INSIDE the subutin. a GRO ES cap will bind with the help of ATP; then the badly folded protein will fold into shape., and then ATP hydrolysis will remove cap and release a correctly folded protein

43
Q

Mono ubiquitylation signals for what?

A

histone regulation

44
Q

multi ubiquitylation signals for what?

A

endocytosis

45
Q

polyubiquitylation signals for what TWO things?

A

proteasomal degradation

AND DNA repair

46
Q

Compartmentalization?

A

term used to describe preferentially localized protein assembly

47
Q

Translocation, in respect to protein position rather than translocation in elongation?

A

Movement of proteins to specific regions of the cell

48
Q

In a generalized sense, what do histone modifications do?

A

they transcriptionally activate or downregulate them

49
Q

How do histone modifications help in stem cell differentiation?

A

These modifications stay conserved and allow cells to continue to proliferate along certain lineages

50
Q

When do most epigenetic changes occur? Within the course of one’s life, or are they inherited from one generation to the next?

A

Across the course of one’s life.

BUT they DEFINITELY OCCUR accorss generations

51
Q

DNA methylation is paternally inherited, T/F?

A

TRUE

52
Q

What are DNMTs?

A

DNA methyltransfreases; they add methyl groups to DNA

53
Q

What do maintence methylases do?

A

they add conserve methylation patterns through DNA replication

54
Q

What are some fxns of DMNT-1? (2)

A
  1. It localizes to rep forx where it transfers patterns of methylation to newly synthesized DNA.
  2. it’s essential for proper embryonic development, imprinting, and X-inactivation
55
Q

How devastating can any DMNT loss be?

A

In mice studies, it has proven to be lethal

56
Q

How does genomic imprinting get passed down?

A

Upon gametogensis, the female passes down the imprint from its MATERNALLy derived genes.
upon gametogenesis, the male passes down the imprint from its PATERNALLY derived imprint.

the end result is that the offspring differ in the allele of a gene that is expressed

57
Q

X-chromosome inactivation

A

the choice of which X to be deactivated happens randomly and then each subsequent division continues with that choice–clonal propagation.

58
Q

XIC

A

X-inactivation center, a place in the middle of the chromosome that encodes XIST-RNA molecule

59
Q

XIST-RNA

A

XIST-RNA coats the rest of the chromosome. It starts at the XIC and then goes outward toward both ends. It makes the DNA transcriptionally inactive and promotes heterochromatin formation.

Block 1 Week 3 (10 decks)

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