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biochem > eukaryotic transcription > Flashcards

eukaryotic transcription Flashcards

1
Q

messenger RNA (mRNA)

A

encodes the AA sequence for a protein; primary transcript of a gene undergoes RNA processing to generate a mature mRNA that can be used by the ribosome

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2
Q

transfer RNA (tRNA)

A

delivers an amino acid to the ribosome

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3
Q

ribosomal RNAs (rRNA)

A

components of a ribosome

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4
Q

small nuclear RNA (snRNA)

A

components of the spliceosome, the enzyme that catalyzes removal of introns during RNA processing

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5
Q

microRNA (miRNA) and small interfering (siRNA)

A

act on mature mRNAs to decrease translation of the mRNA

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6
Q

small nucleolar RNAs (snoRNA)

A

small RNA molecules that guide posttranscriptional base modifications in tRNAs, rRNAs, and snRNAs

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7
Q

long non-coding RNA (lncRNA)

A

RNA molecules that do not encode protein; some lncRNAs influence gene expression

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8
Q

eukaryotic genes stand alone in single transcription units. each gene has its own ___________ and __________

A

promoters and terminators

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9
Q

the genes are organized with ___________ structure
- _____ code for sequence that will be included in a mature mRNA
- ______ sequences will be eliminated during RNA processing
- a _______________ includes both introns and exon sequences

A

intro-exon; exons; introns; primary transcript

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10
Q

___________ is a light staining material
- the level of staining suggests a more open chromatin structure
- the genes in _______ are available for transcription

A

euchromatin

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11
Q

___________ is the dark staining matter in a nucleus
- the level of staining reflects a condensed chromatin structure
- the DNA contains silenced genes and many types of repetitive DNA

A

heterchromatin

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12
Q

constitutive heterchromatin

A

always in heterochromatin state; telomeres (no genes so nothing to express

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13
Q

facultative heterchromatin

A

differs between cell types; can revert to euchromatin under certain stimuli

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14
Q

the ___________ is the basic unit of chromatin

A

nucleosome

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15
Q

DNA-histone core contacts are ___________________
- ______________ and ___________ occur between the positively charged ______________ and the negatively charged ________________ of DNA

A

sequence independent; electrostatic interactions and H-bonds; histone proteins; sugar-phosphate backbone of DNA

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16
Q

a _______________ contains two copies each of histones ____, _____, ___, and ____
- disordered histone tails interact with other nucleosomes

A

histone core; H2A, H2B, H3, and H4

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17
Q

_____________ locks DNA to the nucleosome

A

Histone H1

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18
Q

chromatin structure is a product of the combined actions of _____________, such as _________________ and _____________, and trans-acting _____________________ that bind to epigenetic marks or to DNA

A

epigenetic marks; histone modifications; DNA methylation; transcription factors

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19
Q

condensed chromatin is “closed” and viewed as transcriptionally silent
- inaccessible to most activators and chromatin remodeling complexes
- accessible only by ___________________________

A

pioneering transcription factors

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20
Q

____________ means above genetics. the mediators of epigenetics are covalent modifications of the chromatin or DNA that do NOT affect the DNA sequence of bases (just affects access)

A

epigenetics

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21
Q

the ___________ provide areas for interaction between ______________

A

histone tails; nucleosomes

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22
Q

hypermethylation

A

often associated with closed chromatin (heterochromatin)

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23
Q

histone acetylation

A

is found in areas of open chromatin (euchromatin)

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24
Q

the histone tails include the N termini of histones ___ and ____, plus both the N and C termini of ____ and ____.

A

H3 and H4; H2A and H2B

25
Q

histone acetyltransferase (HAT)

A

acetylates lysine in the histone tails (euchromatin region)

26
Q

histone deacetylase (HDAC)

A

removes acetyl groups from the histone tails (not as accessible so transcription turns off; in euchromatin region)

27
Q

histone methyltransferase (HMT)

A

methylates lysine and arginine (lot harder to reverse; heterochromatin regions)

28
Q

the actions of HATs and HDACs oppose each other so acetylation of histone tails is _____________

A

readily reversible

29
Q

acetylation…
- reduces the electrostatic attraction between nucleosomes and with DNA
- favors recruitment of a _______________
- highly associated with transcriptional activation

A

neutralizes the positive charge on lysine in histone tails
chromatin remodeling complex

30
Q

methylation …
- effect on transcription depends on location of amino acid and # of methyl groups
- H3K4/H3K36/H3K79 (activation)
- H3K9/H3K27/H4K20 (silencing)

A

retains the positive charge on lysine/arginine in histone tails

31
Q

hypermethylation (DNA) of a CpG island near a promoter ______________________

A

silences that promoter

32
Q

cytosine in the sequence CG is called a “CpG” and can be methylated by ______________________ at many sites within the genome
- some promoter proximal regions of genes have a cluster of CG’s in the sequence called a __________

A

DNA methyltransferase (DNMT); CpG island

33
Q

once chromatin structure is open, transcription factors (___________) bind specifically to sites in DNA to facilitate transcription. In eukaryotes, most gene regulation is positive, because activators are required to recruit ___________________ to a _____________

A

activators; RNA polymerase II; promoter

34
Q

_____________________ is recruited to a gene locus by a transcription factor and then acetylates surrounding histones.

A

histone acetyltransferase (HAT) -> favors DNA accessibility

35
Q

__________________ like _______ manipulate nucleosomes.

A

chromatin remodeling complexes; SWI/SNF

36
Q

______ is recruited to local sites in the genome
- ______ either binds to acetylated histone or is recruited to a gene by protein-protein interactions with a _____________________

A

SWI/SNF; SWI/SNF; pioneering transcription factor

37
Q

chromatin remodeling complexes alter chromatin structure by:
- chromatin remodeling “spreads” to surrounding area of the genome changing the accessibility of the DNA for activator proteins

A

unwrapping DNA from nucleosomes
repositioning nucleosomes
evicting nucleosomes

38
Q

the combined actions of _______ and ______________________ together lead to open chromatin structure

A

HATs and chromatin remodeling complexes

39
Q

the transcription start site is devoid of _________________ to make room for assembly of the _____________________________.
- ______ bind near promoters and act to maintain open chromatin structure

A

nucleosomes; transcription preinitiation complex; HATS

40
Q

RNA polymerase II

A

makes mRNA and some small RNAs

41
Q

RNA polymerase I

A

synthesizes ribosomal rRNA

42
Q

RNA polymerase III

A

generates tRNA and other small RNAs

43
Q

if there is no _______ subunit, then it cannot locate and bind to promoters

A

sigma

44
Q

mammalian genes have ______________ elements, but also ____________ at distant locations along the chromosome. they are binding sites for transcription factors.

A

promoter proximal; enhancers

45
Q

______________ are sequence specific DNA binding proteins. These proteins typically have a modular design with a ________________ and _______________

A

transcription factors; DNA binding domain (DBD); activation domain (AD)

46
Q

the DBD is designed to position a _____________ into the major groove forming chemical bonds with the base pairs.

A

recognition helix

47
Q

recognition helix

A

amino acids that interact with base pairs

48
Q

_____________
major structural features: two anti-parallel B strands and an a helix; Zn coordinated by 2 cys and 2 his; a conserved phe/tyr and leu
- _________ can be used to recognize many different DNA sequences

A

classical zinc-finger motif; Zn fingers

49
Q

the recognition helix AAs facing the DNA major groove can be different for each of the Zn fingers. therefore…

A

each Zn finger recognizes a different sequence of bases

50
Q

nuclear receptor transcription factors bind DNA as _________
- both subunits contribute one recognition helix
- each subunit has two Zn fingers: only the first Zn finger has a recognition helix and the second is a structural feature that supports the recognition helix

A

dimers

51
Q

the level of transcription of a gene depends on the occupancy of its ____________ regulatory elements by _______________. Binding of several activators to a gene is required. The coordinate action between factors is referred to as __________________. The same gene may be subject to different regulatory mechanisms in different cell types.

A

cis-acting; transcription factors; combinatorial control

52
Q

before initiation of transcription, what must happen?

A

a very large protein complex must be assembled on the cis-acting regulatory elements of a gene

53
Q

transcription factor GR is a nuclear receptor that acts as an ____________ for many mammalian genes
- GR binds to _________________ located at promoter-proximal sites or in enhancers

A

activator; hormone response element

54
Q

_____________ contain clusters of the recognition sequences for several different transcription factors; together these transcription factors account for ____________ function
- also relies on DNA bending by ____________________ proteins

A

enhancers; enhancer; high mobility group (HMG)

55
Q

although some transcription factors directly interact with the preinitiation complex, __________ provides the primary means of communication between ___________ and the ____________________

A

mediator; activators; preinitiation complex

56
Q

transcription preinitation complex
- ______ (complex) binds at the promoter
- _______ may join the complex (creates docking site)
- _______ binds to DNA and TBP (creates docking site)
- _____________ joins the complex by binding to TFIIB
- ____ and _____ enter the complex in succession
- ______ is a complex with two distinct functions: _________________________________ & _____________________________________

A

TFIID; TFIIA; TFIIB; TFIIF/RNA pol II; TFIIE and TFIIH; TFIIH; DNA helicase to generate transcription bubble and protein kinase that phosphorylated the RNA pol II CTD to initiate transcription

57
Q

________ is a complex made up of _______ and many _____ proteins

A

TFIID; TBP; TAF

58
Q

_______________ locates and binds to TATA boxes in eukaryotic promoters
- TATA boxes are present in only about 10% of promoters
- TBP is an example of a minor groove DNA binding protein

A

TATA binding protein (TBP)

59
Q

________________ methylates H3K9->H3K9me3
- provides a docking site for _________________

A

histone methyltransferase (HMT); heterochromatin protein (HP1)

biochem (37 decks)

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