T.14 TRANSCRIPTION Flashcards

(87 cards)

1
Q

What does the central dogma of biology describe?

A

It describes the flow of genetic information: DNA is transcribed into RNA, which is translated into proteins.

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2
Q

What happens to non-coding RNA fragments like miRNA?

A

They are not translated and function to regulate gene transcription and chromatin packaging.

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3
Q

What determines the functions of synthesized proteins?

A

Posttranslational modifications determine the functions of synthesized proteins.

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4
Q

How are DNA sequences passed to daughter cells?

A

Through replication, including modifications.

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5
Q

Is the DNA–RNA–protein system reversible or fixed?

A

It is relatively reversible and highly coordinated and regulated.

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6
Q

What is transcription?

A

The process where double-stranded DNA is used to produce single-stranded RNA using one of the DNA strands.

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7
Q

What is a gene?

A

A fragment of DNA that differs from others in length and sequence.

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8
Q

What regions can prokaryotic genes have?

A

Coding and non-coding regions.

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9
Q

What happens in the coding region of prokaryotic genes?

A

It is transcribed and translated into proteins.

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10
Q

What is the role of the non-coding region in prokaryotic genes?

A

It acts as a regulatory region (e.g., promoters).

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11
Q

What is a polycistronic gene?

A

A gene with coding information for more than one protein.

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12
Q

What is characteristic of the promoter in eukaryotic genes?

A

It is longer due to more complex regulation.

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13
Q

What follows the promoter in eukaryotic genes?

A

A coding region divided into exons and introns.

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14
Q

What happens to the exons and introns during transcription in eukaryotes?

A

Both are transcribed.

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15
Q

What happens to introns during maturation?

A

They are removed; only exons are translated into proteins.

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16
Q

What is the function of non-coding regions in eukaryotic genes?

A

They serve as regulatory structures.

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17
Q

Are all parts of the genome transcribed during transcription?

A

No, only specific genes are transcribed.

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18
Q

How are DNA strands characterized in transcription?

A

They are complementary but encode different genes; only one is transcribed.

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19
Q

In which direction does transcription occur?

A

5’ to 3’, opposite to replication.

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20
Q

How many times is each gene transcribed?

A

Many times, to produce many RNA/protein copies.

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21
Q

What are the template and non-template strands?

A

Template strand is transcribed; non-template is not.

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22
Q

In which orientation should the template strand be written?

A

5’ to 3’, to reflect transcription direction.

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23
Q

What is TSS?

A

Transcription Start Site, also called +1, the nucleotide where transcription begins.

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24
Q

What does “downstream” mean in transcription?

A

Positions with positive values after +1, toward gene end.

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25
What does "upstream" mean in transcription?
Positions with negative values before +1, toward promoter.
26
How are template and non-template strands labeled?
Template is (+), non-template is (−).
27
How many types of RNA polymerase exist in prokaryotes?
Only one type.
28
How many RNA polymerases do eukaryotes have?
Three types: RNA pol I, II, and III.
29
Which RNA polymerase is involved in eukaryotic transcription?
RNA polymerase II.
30
What is the composition of prokaryotic RNA polymerase?
A holoenzyme with core (2α, β, β′, ω) and σ subunit.
31
What is the function of β and β′ subunits in RNA polymerase?
They have catalytic activity.
32
Does RNA polymerase require a primer?
No, it does not need a primer.
33
What proofreading activity does RNA polymerase have?
3′ to 5′ exonuclease activity to repair errors.
34
Why don't prokaryotes need a repair system for RNA polymerase errors?
Because errors are not passed to offspring.
35
What bonds does RNA polymerase form in transcription?
Phosphodiester bonds between ribonucleotides.
36
What is released during bond formation by RNA polymerase?
Pyrophosphate, which is then hydrolyzed to 2 Pi.
37
What sequences define a prokaryotic promoter?
Consensus -10 (TATAAT) and -35 sequences.
38
What binds to the -10 and -35 promoter regions in prokaryotes?
The σ (sigma) subunit of RNA polymerase.
39
What does the sigma factor do after binding the promoter?
It unwinds the -10 region to create a transcription bubble.
40
Why is the -10 region easier to unwind?
Because it is AT-rich, forming weaker double bonds.
41
What happens during the initiation phase of transcription?
RNA pol moves over the first 8 nucleotides to ensure correct start from +1.
42
What triggers the start of elongation?
Release of the sigma factor and conformational change in RNA polymerase.
43
In which direction is RNA synthesized during elongation?
From 5′ to 3′, adding nucleotides to the 3′ end.
44
How does RNA polymerase maintain the transcription bubble?
By separating strands and allowing one to pass over and one inside the enzyme.
45
How is hybridization of RNA and DNA avoided?
RNA exits through a separate channel in RNA polymerase.
46
What happens around the transcription bubble?
Supercoils form and are relaxed by topoisomerases.
47
What is factor-independent termination in prokaryotes?
Termination without protein factors, using specific sequences.
48
What sequence causes factor-independent termination?
GC-rich sequence followed by adenines.
49
What structure forms in RNA during factor-independent termination?
A hairpin loop due to complementary GC sequences.
50
What follows the RNA hairpin that leads to termination?
An AU-rich region that destabilizes RNA polymerase binding.
51
Why does the AU region cause termination?
AU bonds are weak, causing RNA polymerase to detach and end transcription.
52
What is factor-dependent termination in transcription?
It occurs when the gene lacks a termination sequence and requires additional proteins to end transcription.
53
What is the RUT sequence?
A codification sequence in the RNA that is recognized by the helicase protein ρ (rho) after transcription.
54
What is the role of the ρ protein in factor-dependent termination?
ρ binds to the RUT sequence on the RNA, then moves to the RNA/DNA hybrid and unrolls it, separating RNA and DNA and releasing RNA polymerase.
55
What is transcriptional plasticity?
The ability of the cell to adapt to environmental changes via transcriptional responses.
56
What are conserved proteins?
Proteins that perform basic functions, are not regulatory, and are conserved across generations.
57
What are inducible proteins?
Proteins involved in homeostasis and regulation, varying between genes and acting as regulators.
58
Where does transcription occur in eukaryotes?
In the nucleus; translation occurs in the cytoplasm, so the processes are not simultaneous.
59
Where does transcription occur in prokaryotes?
In the cytoplasm, and it occurs simultaneously with translation.
60
How is DNA packaged in eukaryotes?
Condensed and involves chromatin (heterochromatin and euchromatin states).
61
How is DNA packaged in prokaryotes?
As a supercoiled circular molecule, with no chromatin.
62
What percent of eukaryotic genome is coding?
30% codes for proteins (genes), 70% has regulatory functions.
63
What percent of prokaryotic genome is coding?
90% codes for proteins, 10% has regulatory roles.
64
What RNA polymerases are found in eukaryotes and what do they synthesize?
RNA pol I: rRNA (nucleus); RNA pol II: mRNA (nucleoplasm); RNA pol III: tRNA (nucleoplasm).
65
What RNA polymerase is found in prokaryotes?
A single RNA polymerase synthesizes all RNAs.
66
Compare promoters in eukaryotes and prokaryotes.
Eukaryotic promoters are long and complex; prokaryotic promoters are short and simple.
67
Compare regulatory sequences in eukaryotes and prokaryotes.
Eukaryotes have more and repeated regulatory sequences; prokaryotes have fewer.
68
Compare transcription factors in eukaryotes and prokaryotes.
Eukaryotes have around 2,000 different transcription factors; prokaryotes have few.
69
Is RNA maturation needed in eukaryotes?
Yes, eukaryotic pre-RNA must be matured before functioning as mRNA.
70
Is RNA maturation needed in prokaryotes?
No, maturation does not occur.
71
What are functions of RNA transcription in eukaryotes?
Transfers information, enables plasticity, maintains homeostasis, provides tissue specificity, and has therapeutic relevance.
72
What is capping in RNA maturation?
Addition of a methylated guanine cap to the 5' end of RNA, protecting it and aiding ribosome recognition.
73
What is splicing in RNA maturation?
Removal of introns and joining of exons by the spliceosome.
74
What is polyadenylation in RNA maturation?
Addition of a poly(A) tail (~200 adenines) to the 3' end for RNA stability and transport to cytoplasm.
75
What are eukaryotic promoters?
Non-coding DNA sequences with regulatory functions, including proximal and distal elements.
76
What is the proximal promoter?
The region closest to the TSS where RNA pol II binds, with variable regulatory sequences for transcription factor binding.
77
What is the role of the TATA box?
Present in most genes, helps form the basal transcription machinery and facilitates RNA pol II binding.
78
What forms the basal transcription machinery in prokaryotes?
Promoter (-10, -35 + DNA), RNA polymerase, and σ factor for binding site recognition.
79
What forms the basal transcription machinery in eukaryotes?
TATA box promoter, RNA polymerase II, and General Transcription Factors (GTFs).
80
What is the structure and role of RNA polymerase II?
Multisubunit enzyme in eukaryotes that synthesizes mRNA and interacts with GTFs and the mediator complex.
81
What is the function of the CTD of RNA polymerase II?
Regulates transcription and maturation via its multiple binding sites for regulatory enzymes.
82
What are the three main functions of the CTD in RNA polymerase II?
Interaction with mediator, interaction with GTFs, and proofreading activity.
83
What are General Transcription Factors (GTFs)?
Conserved proteins that bind to the promoter and form the basal transcription machinery; named TFII + letter.
84
What is TFIID and its role?
First GTF to bind DNA; a large multimeric protein complex containing TBP and TAFs.
85
What is TBP (TATA-binding protein)?
The only GTF that directly binds DNA; recognizes TATA box and recruits other GTFs and RNA pol II.
86
What is TAF (TBP-associated factors)?
Multisubunit complex that acts as coactivator and stabilizes binding between TFIID and DNA.
87
What are the steps in PIC assembly (eukaryotic transcription initiation)?
1. TFIID binds DNA via TBP. 2. TBP recruits TFIIA, TFIIB, and TFIIH. 3. RNA pol II binds with TFIIE and TFIIF. 4. TFIIH phosphorylates CTD to start transcription.