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BMSC 220 > Chapter 6 (FUCK THIS CHAPTER) > Flashcards

Chapter 6 (FUCK THIS CHAPTER) Flashcards

1
Q

When is gene expression changed?

A

Responding to environment, regulating cell cycle, activity of differentiated cells, cell differentiation and development

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2
Q

Leg-eyeball fly:

A

Homeobox mutation. A single mutation in a regulatory protein changes the fate of embryonic cells. The protein is wrong and no activated at the right time.

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3
Q

RNA polymerases:

A

Enzymes responsible for RNA synthesis. Do not need primer to initiate.

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4
Q

Promoters:

A

“Dimmers”. Interacts with RNA pmase and other proteins to initiate and regulate transcription.

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5
Q

Transcription vs translation:

A

RNA synthesis using DNA template; protein synthesis using mRNA template.
Transcribing is making a copy. Translating is turning from one language to another.

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6
Q

RNA pmase:

A

Enzyme that catalyzes RNA synthesis from DNA template.

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7
Q

Kinds of RNA pmase:

A

mRNA (II): protein synthesis template
rRNA (I and kind of III): component of ribosomes
tRNA (III): adaptor molecules to align amino acids on the mRNA template

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8
Q

rRNA and tRNA:

A

Make up 90% of total RNA by mass. Small number of genes transcribed at very high levels.

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9
Q

mRNA:

A

Smaller proportion of RNA by mass than t- and r-. Complex regulatory mechanisms to ensure the correct gene is transcribed by the correct cell type at the correct time and in the correct amount.

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10
Q

Steps of transcription (scary blue boxes):

A

Zero, start of transcription. mRNA processing (G-cap addition, polyadenylation, splicing). Now you’re mature! Translocation from nucleus to cytoplasm. Translation. Post translational processing. Transport to final destination.

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11
Q

Define: DNA sequence element

A

A specific short sequence of DNA BPs within a gene promoter with a specific functional property with respect to reg and transcription.

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12
Q

Define: cis-acting DNA sequences

A

Promoters/enhancers - regulate gene expression.

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13
Q

Examples of basal/core promoters:

A

TATA box and initiator sequences

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14
Q

Reporter gene:

A

Gene that can be placed after a promoter to report the promoter’s activity.

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15
Q

Tell me some stuff about Hsp70 and GFP.

A

Exposed larvae to toxic cadmium. Showed up in gills and skin, then nose, then liver and kidneys.

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16
Q

Define: transcription factor

A

Proteins required for RNA pmase II to initiate transcription. Gas pedal.

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17
Q

Two kinds of transcription factors:

A

General/basal: involved in transcription from ALL pmase II promoters. Part of basic transcription machinery. Involved in formation of transcription initiation complex.
Gene-specific: bind to promoters/enhancers of specific genes and direct activity of general transcription factors.

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18
Q

Preinitiation complex:

A

General transcription factors and RNA pmase II surround basal promoter region. This is the engine - it needs gas.

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19
Q

Tell me the story of the TATA box.

A

It’s a regulatory DNA sequence found in promoters. TBP binds to TATA box. TAF are proteins that associate with TBP. It’s now called TFIID. Then TFIIB joins the party. Then TFIIF. RNA pmase II comes to hang out. TFIIE and TFIIH complete the hangout sesh.

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20
Q

How gene-specific transcription factors work:

A

Modify rate of initiation and/or the rate of assembly of the transcription complex.

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21
Q

Transcription factor binding sites:

A

Short DNA sequences 6-10 BPs.

22
Q

DNA affinity chromatography:

A

Method of isolating transcription factors based on binding to specific DNA sequences. Attach sequence to agarose bead. Desired proteins get stuck. High salt buffer washes them out, purified.

23
Q

Examples of DNA binding domains:

A

Zinc fingers, helix-turn-helix, leucine zipper, helix-loop-helix.

24
Q

Steroid hormone receptors:

A

Contain zinc fingers. Regulate gene transcription in response to hormones like estrogen and testosterone.

25
Q

Homeodomain proteins:

A

Contain helix-turn-helix. Roles in gene expression regulation during embryonic development.

26
Q

Transcriptional activators:

A

Activators either interact with mediators and factors or with coactivators (which modify chromatin structure).

27
Q

Here is the hierarchy of transcription initiation:

A

Activator tells mediator to tell transcription machinery to make stuff.

28
Q

RNA pmase has to run away.

A

RNA pmase is released from the basal complex to initiate transcription. It needs TFIIH to help it get away, with its phosphorylation/helicase powers.

29
Q

Transcriptional repressors:

A

Functions by competing for binding to DNA sequence element. Often depends on mediator activity. Interact with co-repressors (which modify chromatin in a bad way).

30
Q

Chromatin structure and transcription:

A

Held in decondensed form when it’s being transcribed. Histone code modification or chromatin remodelling.

31
Q

Histone de/acetylation:

A

Adding/removing acetyl groups from lysine residues. Adding (HAT) = permissive chromatin; removing (HDAC) = non-permissive chromatin.

32
Q

Chromatin remodelling:

A

Chromatin remodelling factor binds to activator. Displaces a nucleosome. WHAT DOES THIS MEAN??!?!?!?!?

33
Q

Processing mRNA:

A

Raw product of transcription is pre-mRNA. 5’ capping -> 3’ polyadenylation -> splicing.

34
Q

G-cap:

A

7-methylguanosine cap is added to the 5’ end immediately after transcription begins.

35
Q

Poly-A tail:

A

Tract of 200 As added to 3’ end of mRNA. It was easy to isolate with T residues because all the As would stick.

36
Q

Polyadenylation signal:

A

AAUAAA

37
Q

Two steps of splicing:

A 
Cleavage at 5' splice site. 
->
Lariat forms at branch point. 
->
Cleavage at 3' splice site. RNA ligates exons and lariat goes away.
38
Q

snRNA:

A

Small nuclear RNAs. 50-200 bases. RNA component of spliceosome.
U1, U2, U4, U5, U6.

39
Q

snRNP:

A

Small nuclear ribonucleoprotein particles. Complexes of snRNAs with proteins.
U1, U2, U5, U4/U6.

40
Q

Splicing. STEP ONE: FORMATION OF SPLICEOSOME.

A

U1 binds to 5’ splice site. U2 grabs U1 and the branch point and pulls them together. U4/U6 and U5 join the party.

41
Q

Splicing. STEP TWO: THE ACTUAL SPLICING.

A

Cleavage at U1 splicing site. U1 and U4 fuck off. Cowboy party - lariat forms. U2 joins the 5’ SS and the branch point in holy matrimony then fucks off with U6. U5 grabs the exons and splices at 3’ SS. End up with a lariat and the ligated exons.

42
Q

snRNA function: (2)

A

Help guide snRNPs to splice junctions. Catalyze and carry out steps in splicing reaction.

43
Q

Tell me more about U1 and its structure.

A

U1 snRNA is a complicated hairpin structure. A small part of it is complementary to the strand that it wants to cut. The snRNA brings the snRNP to the right place.

44
Q

Why does alternative splicing happen?

A

Because transcription and translation are separate processes! This is an evolutionary advantage, dude. yeeeee

45
Q

What determines drosophila sex?

A

Alternative splicing of the same pre-mRNA.

46
Q

SR factors: (SR doesn’t stand for anything)

A

Bind to exon sequences to tell spliceosomes where to party. The proteins differ for alternative splicing. Like the bitchy house owner at the splicing party. The SR factor decides if you stay or go.

47
Q

Dscam:

A

XTREME SPLICING. A gene with four sets of alternative exons, with one exon from each set being incorporated into the final mRNA. Dscam itself is the CAM that allows neurons to find their target muscle cell. (nope nope nope yeah)

48
Q

The rRNA family:

A

45S rRNA gene is mom. 5.8S, 18S, and 28S are the children. 45S is processed (cutting out spacers) to produce the children.

49
Q

How much of cellular RNA is 45S rRNA’s babies?

A

80%

50
Q

The rRNA family never rests.

A

This party occurs in the nucleolus. It’s a fucking huge party. SO many of these have to be produced. Pmase I doesn’t rest. Turn down for what. Keep transcribing.

51
Q

rRNA christmas tree:

A

A THOUSAND 45S squigglies make a tree. One pmase I starts and another one comes in immediately. THERE ARE A LOT. THEY JUST DO THE SAME THING FOREVER.

52
Q

Processing tRNAs:

A

tRNAs form weird hairpins through complementary base pairing. The tRNA is cleaved from the 45S mom. CCA is added to 3’. Covalent modification of bases.

BMSC 220 (2 decks)

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