Biochemistry > Transcription > Flashcards

Transcription Flashcards

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1
Q

Summarise transcription

A

Synthesis of RNA from DNA

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2
Q

Role of the coding (sense) strand in transcription

A

Storage of genetic information

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3
Q

Role of the non-coding (antisense, template) strand in transcription

A
  • Compliments the coding strand
  • Template for transcription
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4
Q

The functional unit of DNA during transcription

A

Transcription unit (TU)

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5
Q

The regions of the transcription unit

A
  • Promoter region
  • RNA coding region
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6
Q

Promoter region

A
  • Responsible for regulation of transcription
  • Consensus sequences:
    • TATA-box
    • GC-box
    • CAP-cAMP binding site
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7
Q

TATA-box

A
  • Prokaryotes → Called Pribnow-box
  • Right in Thymine and Adenosine
  • RNA polymerase binds tightly to this box
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8
Q

GC-box

A
  • Right in Guanine and Cytosine
  • RNA polymerase binds loosely to this box
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9
Q

CAP-cAMP binding site

A
  • Only found in prokaryotes
  • Binding of CAP-cAMP complex
    • ​​(Required for transcription)
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10
Q

Location of the transcription start site

A

Between promotor and RNA coding region

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11
Q

‘Upstream’ direction

A

From the start site → Promoter region

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12
Q

‘Downstream’ direction

A

From start site → RNA coding region

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13
Q

Untranslated region

A

DNA sequence which is transcribed but doesn’t code for an amino acid

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14
Q

The composition of 1 transcription unit in prokaryotes

A
  • Several genes
  • TU is polycistronic
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15
Q

The composition of 1 transcription unit in eukaryotes

A
  • One gene
  • TU is monocistronic
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16
Q

Introns and exons are found in…

A

Eukaryotes

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17
Q

Intron

A
  • Found in pre-mRNA only
  • Cut out of the sequence
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18
Q

Exons are found only in…

A

Mature mRNA

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19
Q

At what point does transcription finish

A

At the termination signal

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20
Q

Genetic information is transferred from DNA to protein synthesis via…

A

mRNA

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21
Q

3 phases of mRNA transcription in eukaryote and prokaryotes

A
  1. Initiation
  2. Elongation
  3. Termination
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22
Q

Initiation of transcription of prokaryotes

A
  • RNA polymerase → Transcription of RNA
  • Binding of CAP-cAMP complex
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23
Q

RNA polymerase holoenzyme composition

A
  • RNA polymerase
  • Sigma (σ) factor
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24
Q

RNA polymerase holoenzyme binds tightly to…

A

TATA-box of the promotor region

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25
RNA polymerase enzyme binds loosely to...
GC-box of the promotor region
26
_Elongation_ of _transcription_ of _prokaryotes_
* RNA polymerase builds nucleotides into mRNA chain * (mRNA is synthesised)
27
RNA polymerase use...to build the mRNA chain
* _Nucleoside triphosphates_ * Converted to _nucleoside monophosphates_ * *(e.g ATP → AMP)*
28
_Termination_ of _transcription_ of _prokaryotes_
* Starts at the termination signal * Rho-factor independent termination * Rho-factor dependent termination
29
Rho-factor _independent_ termination
* Guanine and Cytosine bases on mRNA termination signal * H-bonds form between Guanine and Cytosine bases * Destabilise DNA-RNA complex * Dissociation
30
Rho-factor _dependent_ termination
* Guanine and Cytosine rich regions slow mRNA synthesis * Rho-factor allows RNA-polymerase enzyme activity * Catalyses dissociation
31
Termination involves dissociation of...
* DNA chain * mRNA polymerase * RNA polymerase
32
Structure of prokaryote mRNA
* Polycistronic (Several genes) * Triplets of mRNA: Codons * Shine-Dalgarno-sequences * Untranslated regions (UTR)
33
Site of ribosome binding on mRNA
Shine-Dalgarno-sequence
34
Which model regulates prokaryote transcription
Operon model
35
Operator region
_The binding site for repressor protein inhibition_ of transcription ## Footnote *(Found on the DNA sequence)*
36
Two requirements for prokaryotic transcription
* No repressor bound to the operator region * CAP-cAMP complex must be bound to its binding site
37
CAP
Catabolite Activator Protein
38
cAMP
Cyclic Adenosine Monophosphate
39
What are the two examples of the operon model
* Lactose Operon * Tryptophan Operon
40
Lactose operon
* Codes lactose degrading enzymes (Lactase) * Lactose binds to and removes the repressor * Genes only transcribed when lactose is present
41
Lactose operon in the presence of glucose
* [cAMP] decrease * No CAP-cAMP complex formation * No transcription ## Footnote *Bacteria degrade glucose instead of lactose*
42
Lactose operon: * Glucose present * Lactose present
No transcription
43
Lactose operon: * Glucose present * Lactose not present
No transcription
44
Lactose operon: * Glucose not present * Lactose not present
No transcription
45
Lactose operon: * Glucose not present * Lactose present
Transcription occurs
46
Tryptophan operon is responsible for
Tryptophan enzyme synthesis
47
Role of Tryptophan
Corepressor
48
Tryptophan operon in the presence of Tryptophan
* Repressor is activated * Transcription is inhibited
49
Tryptophan operon without the presence of Tryptophan
* Repressor is inactive * Transcription happens ## Footnote *Bacteria synthesise Tryptophan*
50
List the stages of pre-mRNA transformation in Eukaryotes
1. pre-mRNA synthesis 2. Post-transcriptional modification 3. mRNA maturation
51
Name the RNA polymerases involved in eukaryotic mRNA transcription
* RNA polymerase I * RNA polymerase II * RNA polymerase III
52
What characterises an RNA polymerase enzyme?
The ability to be inhibited by _α-amanitin_
53
Where is α-amanitin found?
In the 'death cap' fungus
54
Inhibition ability of RNA polymerase I
Cannot be inhibited
55
Inhibition ability of RNA polymerase II
Inhibition at low concentrations of toxin
56
Inhibition ability of RNA polymerase III
Inhibition at high concentrations of toxin
57
Which kind of protein is needed in order for the initiation stage of eukaryotes
'Basal'/'General' transcription factors
58
List the stages of Pre-initiation complex formation in eukaryotes
1. Binding of TFIID to TATA-box 2. Binding of TFIIA to TFIIB 3. Binding of TFIIE to TFIIH 4. _Pre-initiation complex_ formed
59
TFIID is composed of:
* TBP * TAF
60
TFIIH is composed of:
* Helicase * Protein kinase
61
List the stages following on from pre-initiation complex formation
* Helicase uncoils → 2x DNA strands * Initial nucleotides are built in the mRNA chain * Protein kinase phosphorylases C-terminal of RNA * Enzyme activated * Transcription factors dissociate * Elongation
62
Elongation stage of eukaryotic transcription
* RNA polymerase II constructs nucleotides in the new mRNA chain * Substrates produced → Nucleoside triphosphates (NTPs) * NTPs → NMPs * NMPs built into the new mRNA strand
63
Termination stage of eukaryotic transcription is caused by...
The cleavage sequence
64
Post-transcriptional modification
Maturation and Splicing of mRNA
65
Give the types of post-transcriptional modification of mRNA
* (5'-) capping → During elongation * (3'-) tailing → During termination * Splicing → During termination
66
(5')capping
_7-methyl-GTP_ bound to _5'-end of pre mRNA_
67
(3'-)tailing
* _Polyadenylation_ * _Poly-A-tail_ bound to _3' end of pre mRNA_ * Poly-A-tail synthesised by _poly-A-polymerase_
68
Splicing
* Removal of introns, exons are reunited * Catalysed by _small nuclear RNA_s (ribosymes) * Work with _small nuclear ribonucleoproteins_ (snRNP) * Form _spliceosome_
69
Examples of snRNAs
* U1 * U2 * U4 * U5 * U6
70
U1 snRNA binds to...
5'-end of intron
71
U2 snRNA binds to...
AMP
72
U5 snRNA binds to...
* 3'-end of intron * Intron removed
73
Excised introns form which structure?
Intron loop / Intron lariat
74
How is eukaryotic transcription regulated?
* Modification of chromatin structure * Histone modification * DNA modification * Regulation with transcription factors * Altering gene expression
75
Gene expression
Information from a gene is used in the synthesis of a gene product _(protein)_
76
Gene expression can be influenced and regulated on the level of...
* Transcription * Translation * Post-translation
77
_Epigenetic regulation_ of transcription
* Changing chromatin structure
78
Histone modifications
* _Covalent_ modification → Nucleosome structure change * Transcription intensity influenced
79
Histone acetyltransferase
* Binds acetyl group * Less positive charge * Transcriptionally more active
80
Histone deacetylase
* Removes acetyl group * Positive charge * Transcriptionally inactive
81
HDAC inhibitors
* Histones hyperacetylated * Gene expression stimulated
82
Compunds of histone acetylation
* Histone acetyltransferase * Histon deacetylase * HDAC inhibitors
83
DNA methylation
DNA methyltransferase * Binds methyl group to cytosine * Gene inactivated * Gene silencing
84
Transcription factors used in transcription regulation
* Cis-regulatory elements * Trans-regulatory elements
85
Types of Cis-regulatory elements
* Promoter * Enhancer * Silencer
86
Types of trans-regulatory elements
* Basal transcription factors * Activators → Bind to enhancer * Repressors → Bind to silencer
87
How many binding domains do transcription factors have?
At least 1
88
Motifs of DNA binding domains
* Helix-turn-helix * Helis-loop-helix * Zinc finger * Leucine zipper
89
Helix-turn-helix
Regulates animal development
90
Zinc finger
Act as nuclear receptors
91
Leucine zipper
Oncogenes
92
Helix-loop-helix
Oncogenes
93
Nuclear receptors
1. Bind to ligand (e.g steroid hormone) → activate 2. Activated receptor enters the nucleus (internalisation) 3. Receptor acts a transcription factor
Biochemistry
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