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Genetics - Lecture > 2.3. Transcription > Flashcards

2.3. Transcription Flashcards

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1
Q

DNA-dependent synthesis of RNA wherein the information in a DNA strand is copied into a new molecule of RNA

A

transcription

transcription is important as it is the** initial step** in the process of information flow within the cell

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2
Q

transcription regulation

transcription is highly regulated

A

(1)** protein demand-dependent** : cells adjust transcription based on their immediate needs, e.g., response to stress
(2) allow conservation of cell resources : this regulation allows energy and resource conservation in cells
(3) allows enhanced cell fitness : also helps cells to quickly adapt to new conditions and thrive

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3
Q

evidences of RNA as an intermediate molecule in the genetic information flow

A

(1) DNA does not appear to participate directly in protein synthesis : DNA is associated with the chromosomes in the nucleus; however, protein synthesis occurs in ribosomes located outside the nucleus
(2) RNA is synthesized in the nucleus or nuclear region : RNA acts as a messenger, carrying the genetic code transcribed from DNA
(3) RNA migrates to the cytoplasm where protein synthesis occurs : shows RNA’s role as intermediary
(4) RNA is chemically similar to DNA : allows RNA to effectively copy and transport genetic instructions

these observations suggested that genetic information, stored in DNA, is transferred to an RNA intermediate, which directs the synthesis of proteins

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4
Q

what are the different transcription components?

A

(1) RNA polymerase core enzyme
(2) σ factor
(3) nucleoside triphosphates (NTPs)
(4) promoters

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5
Q

catalyzes polymerization of RNA molecule in a 5’ to 3’ direction; can inititate new RNA on its own (primer is not needed)

A

RNA polymerase

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6
Q

how many types of RNA polymerase do eukaryotes and prokaryotes have?

A

eukaryotes : three (RNA Pols I, II, and III)
prokaryotes : one

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7
Q

products and locations of RNA Pols I, II, III

A

RNA pol I : produces rRNA in nucleolus
RNA pol II : produces mRNA and snRNA (small nuclear) in the nucleoplasm
RNA pol III : produces 5SrRNA, tRNA (transfer) in the nucleoplasm

RNAP II also synthesizes a variety of other RNAs, such as snRNA, miRNAs (micro), and IncRNAS (long non-coding)

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8
Q

transcription component that provides catalytic basis and active site for transcription

A

RNA polymerase core enzyme

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9
Q

transcription component that (1) regulates initiation of transcription and (2) recognizes the appropriate site on the DNA to initiate transcription

A

sigma (σ) factor

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10
Q

true or false : similar to other subunits, sigma σ factor is tightly bound to the core enzyme.

A

false. sigma factor is not as tightly bound as the other subunits in order to easily dissociate to yield the RNA polymerase core enzyme

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11
Q

how is RNA polymerase core enzyme different from RNAP holoenzyme?

A

RNAP holoenzyme has sigma factor + core enzyme

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12
Q

transcription component recognized by the sigma factor; a cis-acting DNA element

A

promoter

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13
Q

where is the promoter located?

A

upstream of the gene

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14
Q

true or false : the promoter is not transcribed.

A

true

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15
Q

template strand vs coding strand

A

template strand : DNA strand that serves as the template for RNAP
coding strand : complementary DNA strand

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16
Q

the template strand runs in what direction? the direction of RNA synthesis follows what direction?

A

3’ to 5’: template strand
5’ to 3’ : direction of synthesis

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17
Q

segment of DNA that gets transcribed into RNA, along with the sequences necessary for its transcription

def not in the ppt

A

transcriptional unit : composed of (1) promoter, (2) initiation site also known as transcription start site or TSS (+1), (3) transcribed region, and (4) termination site

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18
Q

cluster of genes under a single promoter that are transcribed as a group

A

operons

not from ppt

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19
Q

actual genes transcribed into mRNA and subsequently translated into proteins

A

structural genes

when these genes are part of an operon in prokaryotes, they are transcribed together into a single polycistronic mRNA; not in ppt

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20
Q

describe the promoter consensus sequences in bacteria. what are some examples of this?

promoter consensus sequences are specific DNA sequences found in the promoter region of genes that are highly conserved across different genes within the same or related organisms

A

(1) sequences are similar (homologous) in different genes of the same organism
(2) sequences are similar (homologous) in one or more genes of related organisms
(3) degree of RNAP binding influences strength of promoters : RNAP attaches to specific promoter sequences; the efficiency of this binding affects how strongly the promoter initiates transcription. the better RNA polymerase binds to the promoter, the more likely it is that the gene will be transcribed regularly.

examples : -35 region and pribnow box

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21
Q

describe the (1) structure of promoter and (2) recognition sequences in the promoter in bacteria and in archaea

A

structure of promoter
🔸for bacteria, it does not resemble eukarya
🔸archaea resembles eukarya
recognition sequences in the promoter
🔸bacteria : TTGACA (-35) and TATAAT or pribnow box (-10)
🔸archaea : TATA (-18 to -27)

22
Q

recognition sequences in the promoter region of eukaryotic genes

A

(1) TATA (-30) or Goldberg-Hogness box
(2) CAAT/CCAAT box (-50 to -200)
(3) GC

23
Q

different types of cis-acting DNA elements in eukaryotes

cis-acting DNA elements are adjacent parts of the same DNA molecules

A

(1) core promoter
(2) proximal-promoter element
(3) enhancers and silencers

24
Q

a cis-acting DNA element in eukaryotes that determines the binding site of RNAP II; includes the TSS (transcription start site)

A

core promoter

25
Q

a cis-acting DNA element in eukaryotes that helps modulate the level of transcription; located upstream of the start site

A

proximal-promoter element

26
Q

a cis-acting DNA element in eukaryotes that influence the efficiency or the rate of transcription initiation by RNAP II from the core-promoter element

A

enhancers and silencers

27
Q

proteins that facilitate RNAP II binding and thus the initiation of transcription

A

trans-acting / transcription factors

trans-acting factors bind to cis-acting DNA elements to influence gene expression

28
Q

type of transcription factor in eukaryotes that are required for RNAP II-mediated transcription

A

general transcription factors (GTFs)
examples: TFIIA, TFIIB, TFIID

29
Q

type of transcription factors in eukaryotes that influence the efficiency or rate of RNAP II transcription initiation as they bind to enhancer and silencer elements

A

transcriptional activators and repressors

30
Q

stages of transcription

A

(1) promoter recognition
(2) local unwinding
(3) chain initiation
(4) chain elongation
(5) chain termination

31
Q

what happens in the first stage: promoter recognition?

A

sigma factor recognizes promoter and initiation site

32
Q

what happens in second stage: local unwinding?

A

🔸RNA pol begins to unwind the DNA double helix at the promoter region
🔸this unwinding creates an open promoter complex where the DNA strands are separated which exposes the template strand
🔸RNA pol then locates and recognizes the transcription start site (TSS) which is close to the initial binding site

33
Q

what happens in the third stage: chain initiation?

A

🔸RNAP begins reading the DNA template strand
🔸using free nucleoside triphosphates (NTPs), RNAP starts synthesizing a complementary RNA strand

34
Q

what happens to the sigma factor once a short sequence of RNA has been formed during chain initiation?

A

dissociates from the holoenzyme; RNA chain continues to grow

35
Q

how does initiation of transcription go about in eukaryotes?

A

requires chromatin remodelling, which involves the use of ATP-dependent chromatin remodelers and histone-modifying enzymes to uncoil compact chromatin fibers and make the DNA helix accessible to RNA polymerase and other regulatory proteins

36
Q

what happens in the fourth stage: chain elongation?

A

🔸during elongation, RNAP moves along the 3’ to 5’ template strand in 5’ to 3’ direction by adding nucleotides to the 3’ OH of the growing RNA chain

37
Q

what happens in the fifth stage: chain termination?

A

🔸when the termination site is reached, chain growth stops.
🔸polymerase and RNA are released
🔸governed by specific base sequences on the DNA

38
Q

mechanisms of termination in bacteria

A

(1) rho-dependent termination
(2) rho-independent termination

39
Q

explain rho-dependent termination

A

(1) rho (ρ) protein recognizes and binds to a rho dependent termination site, called rho utilization or rut site, on the mRNA
(2) after binding, rho moves down the chain in the 3’ direction chasing after the RNA polymerase-DNA complex
(3) RNA polymerase pauses at a specific sequence in the DNA which allows rho to catch up
(4) once rho catches up, it uses its helicase activity to unwind the RNA-DNA hybrid, causing both the RNA transcript and RNA polymerase to be released from the DNA
(5) transcriptions is terminated

rho protein is a large hexameric protein with RNA helicase activity–it can dissociate RNA hairpins and DNA-RNA interactions

40
Q

explain rho-independent termination

A

(1) the DNA template has G-C rich sequence with inverted repeats and a central nonrepeating segment
(2) inverted repeats cause the newly formed RNA to fold into a stem-loop structure via intra-strand base pairing
(3) after the hairpin, the DNA template has a sequence of adenines, resulting in uracils in the RNA
(4) RNA forms weak U-A base pairs with the DNA
(5) hairpin causes the RNAP to pause
(6) the weak U-A bonds allow the RNA to dissociate from the DNA, terminating transcription

41
Q

true or false : unlike prokaryotes, eukaryotes do not have a single and specific sequence that signals transcription termination.

A

true

42
Q

how does transcription termination occur in eukaryotes?

A

involves sequence-specific cleavage fo the transcript
🔸incorporation of polyadenylation signal sequence AAUAAA
🔸cleavage roughly 10 - 35 bases downstream in the 3’ direction
🔸leads to eventual dissociation of RNA polymerase from the DNA template

cleavage of the transcript destabilizes RNAP II which leads to dissociation of both dna and rna

43
Q

initial or primary transcripts of protein-coding mRNA found in eukaryotes that undergo “processing” to produce a mature RNA; post-transcriptional modification

A

pre-mRNA

44
Q

post-transcriptional modifications

A

(1) addition of 7-methylguanosine cap
(2) poly-A tailing
(3) RNA splicing

45
Q

explain the addition of 7-methylguanosine cap at 5’end. when is it added? what is/are its significance?

A

🔸cap is added shortly after synthesis of the initial RNA transcript has begun
🔸cap stabilizes the mRNA by protecting the 5’ end of the molecule from nuclease attack
🔸facilitates transport of mRNAs across nuclear membrane
🔸facilitates initiation of translation

46
Q

a post-transcriptional modification that involves the addition of 250 adenylic acid residues at the 3’ end’ contributes to mRNA stability

A

poly-A tailing

47
Q

what enzyme facilitate poly-A tailing?

A

poly-A polymerase

this enzyme catalyzes the addition of a poly-A tail to the free 3’ OH group at the end of the transcript

48
Q

what proteins bind to poly-A tails, preventing the mRNA to be degraded?

A

poly-A binding protein

they bind to poly-A tails and prevent nucleases from degrading the 3’ end of the mRNA

49
Q

removal of intervening sequences

A

RNA splicing

introns are removed from a pre-mRNA; exons are joined together

50
Q

true or false : introns are non-coding.

A

true

51
Q

what type of introns are capable of self-splicing?

A

group I introns (rRNA) and
group II introns (organelle mRNA and tRNA)

group I introns are found in rRNA; group II are found in organelle mRNA and tRNA

52
Q

the removal of introns in nuclear-derived eukaryotic pre-mRNA are mediated by ___.

A

spliceosome

Genetics - Lecture (12 decks)

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