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BMSC 220 > Lecture #17 > Flashcards

Lecture #17 Flashcards

1
Q

RNAs have ______ folding, and the _____ functions depending on the folding.

A

specific, diverse

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2
Q

RNA folding is driven by the formation of regions having _______ base pairs

A

complementary

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3
Q

Base paired regions form double stranded stems connected by _____

A

loops

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4
Q

Transcription enzymes - in both prokaryotic and eukaryotic cells are called DNA‐dependent RNA _________

A

polymerases

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5
Q

Incorporate nucleotides into an RNA strand complementary to the ____ template strand

A

DNA

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6
Q

RNA polymerase moves in a ___ to ___ direction; the DNA is unwound, and the polymerase assembles a complementary strand of RNA at 20–50 nucleotides molecule per second

A

3’, 5’

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7
Q

The frequency at which a gene is transcribed is tightly ______ and ________ function observed

A

regulated, proofreading

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8
Q

_______ have no nuclei

A

Bacteria

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9
Q

In bacteria, there is no physical ________ of DNA/RNA and ribosomes

A

separation

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10
Q

In bacteria, there is translation of the mRNA while its _______ is in progress.

A

transcription

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11
Q

Genes are organized in clusters that are transcribed together as a single mRNA molecule encoding for multiple proteins. These clusters are called ________

A

operons

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12
Q

Bacteria have 1 RNA _______, which is composed of __ subunits tightly associated to form a core enzyme.

A

polymerase, 5

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13
Q

_______: a region of DNA upstream of a gene where relevant proteins bind to initiate transcription of that gene.

A

Promoter

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14
Q

__ factor binds promoter

A

σ

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15
Q

Once about 10 nucleotides have been incorporated, the enzyme undergoes a _________ change. σ factor is loss. It becomes a transcriptional elongation _______

A

conformational, complex

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16
Q

The polymerase stops transcription when it reaches a __________ sequence and releases the completed RNA

A

terminator

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17
Q

In the absence of the sigma (σ) factor, the _____ _______ cannot interact with the DNA at specific initiation sites

A

core enzyme

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18
Q

_________ cells have nuclei

A

Eukaryotic

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19
Q

In ________ cells, there is physical separation of DNA/RNA and ribosomes.

A

eukaryotic

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20
Q

In eukaryotic cells, transcription and RNA processing steps happens in the _______

A

nucleus

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21
Q

In eukaryotic cells, the mRNA needs to be exported to the ________.

A

cytoplasm

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22
Q

In eukaryotic cells, translation happens in the ________

A

cytoplasm

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23
Q

There are _____ types of RNA polymerases in eukaryotes

A

three

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24
Q

Most rRNAs are transcribed by RNA polymerase ___

A

I

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25
Q

mRNAs are transcribed by RNA polymerase ___

A

II

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26
Q

tRNAs are transcribed by RNA polymerase ___

A

III

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27
Q

RNA polymerases have been characterized from each of the three domains of life: ?

A

archaea, bacteria, and eukaryotes

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28
Q

The ______ and eukaryotic enzymes are more similar in structure to one another than are the ______ and archaeal enzymes

A

archaeal, bacterial

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29
Q

What are the 3 transcription steps?

A
  1. Initiation
  2. Elongation
  3. Termination
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30
Q
  • Transcription bubble around 35nt of _______-stranded DNA (melted DNA)
  • Polymerase incorporates nucleotides (nt) into transcript in __-__ direction.
  • About 9 nt DNA-RNA transient ______.
  • Generation of ________ (positively supercoiled) DNA ahead and _______ (negatively supercoiled) DNA behind.
A

single
5’, 3’
hybrid
overwound, underwound

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31
Q

RNA Pol is a ________ complex. It forms a ______ for the DNA template. The RNA transcript exit through a _______

A

multisubunit, groove, channel

32
Q

RNA polymerase II is assisted by general transcription factors (GTFs) to form the _______ _______ (PIC)

A

preinitiation complex

33
Q

Transcription factors are proteins that bind _____. Each of them recognize different DNA sequences. They control the rate of _________

A

DNA, transcription

34
Q

The critical portion of the promoter lies 24–32 bases _______ from the initiation site and contains the _____ box

A

upstream, TATA

35
Q

BRE: ?

A

B recognition element

36
Q

INR: _____

A

Initiator

37
Q

DPE: ?

A

Downstream Promoter Element

38
Q

For most RNA polymerase ___ transcription start points, only 2 or 3 of the 4 sequences are present

A

II

39
Q

What is the general transcription factor for BRE?

A

TFIIB

40
Q

What is the general transcription factor for TATA?

A

TBP (subunit of TFIID)

41
Q

What is the general transcription factor for INR?

A

TFIID

42
Q

What is the general transcription factor for DPE?

A

TFIID

43
Q

The RNA Polymerase II Requires a Set of ________ Transcription Factors

A

General

44
Q

General Transcription factors (GTFs) assemble at the Pre-Intitiation complex just upstream of the transcriptional start site to recruit and modify ?

A

RNA-Pol II

45
Q

First step is binding of the TBP (TATA-binding protein) which is a component of ______ which is composed of proteins called _____ (TFIID Associated Factors)

A

TFIID, TAFs

46
Q

There is a ______ recruitment of TFIIA & TFIIB. This serves as a platform for _______ (a huge multiprotein complex) and bound TFIIF. TFIIE and TFIIH are then recruited.

A

stepwise, RNA-Pol II

47
Q

TFIIH complex has a subunit that is a _______ that phosphorylates the C-term tail of Polymerase, and it also has helicase activity to _____ the DNA duplex

A

kinase, unwind

48
Q

This is the _____ _______. The rate of initiation is affected by Transcription Factors that bind to DNA elements in upstream regulatory regions within a few hundred bp upstream (promoters) as well as enhancers (at a distance)

A

basal promoter

49
Q

The structure of mRNAs have a ______ coding sequence.; have a ______ location; and are translated on ________.

A

continuous, cytoplasmic, ribosomes

50
Q

The structure of mRNAs have ________ regulatory terminals; a ___ Poly A tail (50-250 adenosine); and a ___ Methylated guanosine cap.

A

noncoding, 3’, 5’

51
Q

In the structure of mRNAs, the tail and cap protect from _______, help the export outside the nucleus, and the ________ process

A

degradation, translation

52
Q

The difference between heterogeneous nuclear RNA (hnRNA) and mRNA provided early clues about RNA ________

A

processing

53
Q

Eukaryotic genes contain intervening sequences which are missing from _____ mRNAs

A

mature

54
Q

The presence of genes with intervening sequences are called _____ genes

A

split

55
Q

The parts of the split gene that contribute to the mature mRNA are called ______

A

exons

56
Q

The intervening sequences are called ______

A

introns

57
Q

______ are nucleotide sequences that carry information for protein synthesis, whereas ______ are interrupting sequences that do not code for any protein but are found between exons

A

Exons, introns

58
Q

Because the ______ are removed during the hnRNA-to-mRNA conversion process, the mature mRNA contains only _____

A

introns, exons

59
Q

The ________ DNA and mRNA hybrid contains seven distinct loops corresponding to seven introns

A

ovalbumin

60
Q

The _______ account for about three times as much DNA as that present in the eight combined coding portions (_____)

A

introns, exons

61
Q

RNA transcripts are associated with _____________ as soon as they are synthesized

A

ribonucleoproteins

62
Q

Once processing is completed, the mRNP, which consists of mRNA and associated proteins, is ready for export from the _______

A

nucleus

63
Q

Pre-mRNA transcripts are processed ____________

A

cotranscriptionally

64
Q

RNA ________: Removal of Introns from a Pre-RNA

A

Splicing

65
Q

Since most genes contain a number of introns, the splicing reactions must occur repeatedly on a single primary _______. Evidence suggests that introns are removed in a ________ order

A

transcript, preferred

66
Q

RNA Splicing Increases _______ diversity from a single gene

A

protein

67
Q

Transcription factors:
1. bind at ______ _____ sites in association with RNA pol
2. bind to various _________ sites of particular genes (can act as transcription activators or inhibitors)

A

core promoter
regulatory

68
Q

A single gene can be controlled by ______ regulatory proteins; while a single DNA-binding protein may control the expression of many ______ genes.

A

different, different

69
Q

The extent to which a given gene is transcribed depends on the particular combination of __________ ________ bound to upstream regulatory elements

A

transcription factors

70
Q

Roughly 5–10% of genes encode transcription factors, which gives a nearly ________ number of possible combinations of interactions among these proteins

A

unlimited

71
Q

Gene expression gives rise to _______ within cells and tissues of an organism

A

phenotypes

72
Q

______ or forced gene expression can alter the phenotype

A

Ectopic

73
Q

__________ _____ (ES) cells are capable of indefinite self-renewal, and pluripotent, capable of differentiating into all of the different types of cells

A

Embryonic stem

74
Q

The importance of transcription factors in ES cells was demonstrated when these factors were introduced and shown to ________ these cells

A

reprogram

75
Q

Transcription factors contain a DNA-binding domain and an _______ domain

A

activation

76
Q

Many transcription factors can bind a protein of identical or similar structure to form a ______

A

dimer

77
Q

The DNA-binding domains of most transcription factors have related structures (______) that interact with DNA sequences

A

motifs

BMSC 220 (22 decks)

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