Transcription Flashcards

1
Q

The synthesis of RNA molecules using DNA strands as the templates so that the genetic information can be transferred from DNA to RNA.

A

Transcription

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2
Q

code for proteins

A

mRNAs

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3
Q

form the basic structure of the ribosome and catalyze protein synthesis

A

rRNAs

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4
Q

central to protein synthesis as the adaptors between mRNA and amino acids

A

tRNAs

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5
Q

Serves as the template for the telomerase enzyme that extends the ends of chromosomes

A

Telomerase RNA

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6
Q

Function in a variety of nuclear processes including the splicing of pre-mRNA

A

snRNAs (small nuclear RNAs)

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7
Q

Help to process and chemically modify rRNAs

A

snoRNAs (small nucleolar RNAs)

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8
Q

________________, not all of which appear to have a function; some serve as scaffolds and regulate diverse cell processes, including X-chromosome inactivation

A

lncRNAs (long noncoding RNAs)

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9
Q

Regulate gene expression by blocking expression of specific mRNAs and causing their degradation

A

miRNAs (microRNAs)

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10
Q

Turn off gene expression by directing the degradation of selective mRNAs and helping to establish repressive chromatin structures

A

siRNAs (small interfering RNAs)

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11
Q

Bind to piwi proteins and protect the germ line from transposable elements

A

piRNAs (Piwi-interacting RNAs)

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12
Q

DNA regions that can be transcribed (includes promoter, operator, and structural genes)

A

Operon

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13
Q

Is the strand from which the RNA is actually transcribed

A

Template strand (antisense strand)

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14
Q

Is the strand whose base sequence specifies the amino acid sequence of the encoded protein.

A

Coding strand (sense strand)

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15
Q

*The enzyme responsible for the RNA synthesis

A

RNA Polymerase

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16
Q

What factor binds to the core RNA polymerase to become an RNA polymerase holoenzyme

A

Sigma factor (σ)

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17
Q

In E. coli is consists of 5 different subunits:

A

α2 = Determine the DNA to be transcribed
β = Catalyze polymerization
β’ = Bind & open DNA template
ω = Non-essential smallest subunit that facilitates the assembly of RNA polymerase
σ = Recognize the promoter for synthesis initiation

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18
Q

*Drug for tuberculosis, can bind specifically to the β subunit of RNA-pol and inhibit the RNA synthesis.

A

Rifampicin

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19
Q

Each transcriptable region is called

A

Structural gene

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20
Q

*Is the DNA sequence that RNA-pol can bind.

*Is a region of DNA where transcription of a gene is initiated.

A

promoter

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21
Q

Repressor protein binding site

A

Operator

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22
Q

In a bacterial promoter, the TTGACG region is at __________ and the Pribnow region is at _________

A

-35 element
-10 element

Note: *Promoter + 1 is the transcription start site

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23
Q

Eukaryotic promoter

A

TATA box

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24
Q

Transcription of Prokaryotes:

A

*Initiation phase: RNA-pol recognizes the promoter and starts the transcription.

*Elongation phase: the RNA strand is continuously growing.

*Termination phase: the RNA-pol stops synthesis, and the nascent RNA is separated from the DNA template.

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25
Q

a. Initiation
* The first nucleotide on RNA transcript is always _______.

A

purine triphosphate

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26
Q

(GTP, ATP) is more often than (GTP, ATP).

A

GTP; ATP

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27
Q

In which phase of transcription is the sigma factor released

A

Elongation phase

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28
Q

Which factor enters during termination phase

A

rho factor

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29
Q

Which phase?
Free nucleotide triphosphates are added sequentially to the 3’OH of the nascent RNA strand.

A

Elongation phase

30
Q

Two types of termination in bacteria:

A
  1. intrinsic (determined by specific sequences (termination sites)
  2. rho-dependent (no formation of hairpin structure)
31
Q

______ is a protein that binds to nascent RNA and tracks along the RNA to interact with RNA polymerase and release it from the elongation complex.

A

Rho factor

32
Q

____ is a hexameric and ATP-dependent RNA translocase, that terminates transcription at certain specific genomic sites called a _____.

A

Rho; rut (rho utilization)

33
Q

r-independent termination

Termination sites consist of 3
features:

A
  • Inverted repeats, rich in G:C which form a stem-loop structure (hairpin) in RNA transcript
  • Series of 7 U residues following the hairpin stem
34
Q

In rho-independent termination, which structure causes the RNA polymerase to pause

35
Q

While RNA polymerase pauses, the U-rich sequence in the open complex is unable to hold the RNA-DNA hybrid together. Termination occurs

36
Q

The 3 RNA Polymerases in Eukaryotic Cells

A

Types of polymerase and the genes they transcribe

  1. RNA polymerase I = 5.8S, 18S, and 28S genes
  2. RNA polymerase II = All protein-coding genes, plus snoRNA genes, miRNA genes, siRNA genes, lncRNA genes, and most snRNA genes
  3. RNA polymerase III = tRNA genes, 5S rRNA genes, some snRNA genes, and genes for other small RNAs
37
Q

The rRNAs were named according to their “S” values, which refer to their _________. The larger the S value, the larger the rRNA.

A

rate of sedimentation in an ultracentrifuge

38
Q

a specific inhibitor of RNA-pol found in mushroom

39
Q

RNA-pol of Eukaryotes sensitivity to Amanitin

A

RNA-pol I = No
RNA-pol II = High
RNA-pol III = Moderate

40
Q

are the specific sequences on the DNA template that regulate the transcription of one or more genes.

A

Cis-acting element

41
Q

Cis-acting element includes…

A

Enhancer
GC box
CAAT box (-75)
TATA box (Hogness box) (-25)

42
Q

Transcription Factor:

Recognizes TATA box and other DNA sequences near the transcription start point

43
Q

Transcription Factor:

Recognizes BRE element in promoters; accurately positions RNA polymerase at the start site of transcription

44
Q

Transcription Factor:

Not required in all promoters; stabilizes binding of TFIID

45
Q

Stabilizes RNA polymerase interaction with TFIIB; helps attract TFIIE and TFIIH

46
Q

Transcription Factor:

Attracts and regulates TFIIH

47
Q

Transcription Factor:

Unwinds DNA at the transcription start point, phosphorylates Ser5 of the RNA polymerase C-terminal domain (CTD); releases RNA polymerase from the promoter

48
Q

Pre-initiation complex (PIC)

A
  • TBP (TATA binding proteins) of TFIID binds TATA
  • TFII A and TFII B bind TFII D
  • TFII F-RNA-pol complex binds TFIIB
  • TFII F and TFII E open the dsDNA (helicase and ATPase)
  • TFII H: completion of PIC
49
Q

Gene regulatory proteins that help RNA pol, the general factors, and the mediator all to assemble at the promoter

A

Activators

50
Q

Binding site for activator protein

51
Q

*Allows the activator proteins to communicate properly with the Pol II and with the general transcription factors.

52
Q

Elongation factors in eukaryotes (___, ____, and ____) that stabilizes RNA pol

A

Spt4; Spt5; Elf

53
Q
  • Enzymes that rapidly remove superhelical tension in DNA
A

DNA topoisomerase

54
Q

*A specialized topoisomerase in bacteria that Uses the energy of ATP hydrolysis to pump supercoils continuously into the DNA, thereby maintaining the DNA under constant tension

A

DNA gyrase

55
Q

In eukaryotic transcription, the termination sequence is _________ followed by ____ repeats

A

AATAAA; GT

56
Q

Post-transcriptional modifications in the nucleus

A

5’ capping
RNA splicing
3’ polyadenylation

57
Q
  • Primary transcripts of mRNA are called as ______
A

heteronuclear RNA (hnRNA)

58
Q

The capping occurs before the splicing.

59
Q

A gene consisting of introns and exons.

A

Split gene

60
Q

are the coding sequences that appear on split genes and primary transcripts, and will be expressed to matured mRNA.

61
Q

are the non-coding sequences that are transcripted into primary mRNAs, and will be cleaved out in the later splicing process.

62
Q

the large assembly of small nuclear RNA (snRNAs) and protein molecules that performs pre-mRNA splicing in the cell.

A

Spliceosome

63
Q

Changes (insertion, deletion, base substitution) to specific nucleotide sequences within an RNA molecule after it has been generated.

A

RNA editing

64
Q

Significance of RNA editing

A

multiple functions of gene, localization and stability of RNAs has been linked to human diseases

65
Q

Excised intron is in the shape of ________

66
Q

post-transcriptional modifications

A

5 methyl capping
poly-A tail
splicing in the nucleoplasm

67
Q

What factor?
Delivers aa-tRNAs to the A-site of the ribosomes

A

EF-Tu (elongation factor thermos unstable)

68
Q

The enzyme ___________ catalyzes the conversion of cytidine (C) to uridine (U) in RNA

A

APOBEC1 (Apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 1)

69
Q

C to U
APOBEC1
Glutamine to Stop Codon

Unedited RNA: Produces the full-length Apo-B100 protein, primarily found in the liver (hepatic form).

Edited RNA: Generates a truncated protein called Apo-B48, found in the intestines (intestinal form).

70
Q

The enzyme _____________ catalyzes the A-to-I (adenosine to inosine) conversion in double-stranded RNA regions.

A

ADAR2 (Adenosine Deaminase Acting on RNA 2)

71
Q

A to I
ADAR2
Glutamine to Arginine

Unedited GluR2 (Q form): Permits Ca²⁺ permeability, which is crucial for neuronal excitability.
Edited GluR2 (R form): Becomes impermeable to Ca²⁺, stabilizing neuronal function and preventing excessive excitability.