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Biochemistry > Transcription > Flashcards

Transcription Flashcards

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
Q

RNA polymerase enzyme binds loosely to…

A

GC-box of the promotor region

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26
Q

Elongation of transcription of prokaryotes

A
  • RNA polymerase builds nucleotides into mRNA chain
    • (mRNA is synthesised)
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27
Q

RNA polymerase use…to build the mRNA chain

A
  • Nucleoside triphosphates
  • Converted to nucleoside monophosphates
  • (e.g ATP → AMP)
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28
Q

Termination of transcription of prokaryotes

A
  • Starts at the termination signal
  • Rho-factor independent termination
  • Rho-factor dependent termination
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29
Q

Rho-factor independent termination

A
  • Guanine and Cytosine bases on mRNA termination signal
  • H-bonds form between Guanine and Cytosine bases
  • Destabilise DNA-RNA complex
  • Dissociation
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30
Q

Rho-factor dependent termination

A
  • Guanine and Cytosine rich regions slow mRNA synthesis
  • Rho-factor allows RNA-polymerase enzyme activity
  • Catalyses dissociation
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31
Q

Termination involves dissociation of…

A
  • DNA chain
  • mRNA polymerase
  • RNA polymerase
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32
Q

Structure of prokaryote mRNA

A
  • Polycistronic (Several genes)
  • Triplets of mRNA: Codons
  • Shine-Dalgarno-sequences
  • Untranslated regions (UTR)
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33
Q

Site of ribosome binding on mRNA

A

Shine-Dalgarno-sequence

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34
Q

Which model regulates prokaryote transcription

A

Operon model

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35
Q

Operator region

A

The binding site for repressor protein inhibition of transcription

(Found on the DNA sequence)

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36
Q

Two requirements for prokaryotic transcription

A
  • No repressor bound to the operator region
  • CAP-cAMP complex must be bound to its binding site
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37
Q

CAP

A

Catabolite Activator Protein

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38
Q

cAMP

A

Cyclic Adenosine Monophosphate

39
Q

What are the two examples of the operon model

A
  • Lactose Operon
  • Tryptophan Operon
40
Q

Lactose operon

A
  • Codes lactose degrading enzymes (Lactase)
  • Lactose binds to and removes the repressor
  • Genes only transcribed when lactose is present
41
Q

Lactose operon in the presence of glucose

A
  • [cAMP] decrease
  • No CAP-cAMP complex formation
  • No transcription

Bacteria degrade glucose instead of lactose

42
Q

Lactose operon:

  • Glucose present
  • Lactose present
A

No transcription

43
Q

Lactose operon:

  • Glucose present
  • Lactose not present
A

No transcription

44
Q

Lactose operon:

  • Glucose not present
  • Lactose not present
A

No transcription

45
Q

Lactose operon:

  • Glucose not present
  • Lactose present
A

Transcription occurs

46
Q

Tryptophan operon is responsible for

A

Tryptophan enzyme synthesis

47
Q

Role of Tryptophan

A

Corepressor

48
Q

Tryptophan operon in the presence of Tryptophan

A
  • Repressor is activated
  • Transcription is inhibited
49
Q

Tryptophan operon without the presence of Tryptophan

A
  • Repressor is inactive
  • Transcription happens

Bacteria synthesise Tryptophan

50
Q

List the stages of pre-mRNA transformation in Eukaryotes

A
  1. pre-mRNA synthesis
  2. Post-transcriptional modification
  3. mRNA maturation
51
Q

Name the RNA polymerases involved in eukaryotic mRNA transcription

A
  • RNA polymerase I
  • RNA polymerase II
  • RNA polymerase III
52
Q

What characterises an RNA polymerase enzyme?

A

The ability to be inhibited by α-amanitin

53
Q

Where is α-amanitin found?

A

In the ‘death cap’ fungus

54
Q

Inhibition ability of RNA polymerase I

A

Cannot be inhibited

55
Q

Inhibition ability of RNA polymerase II

A

Inhibition at low concentrations of toxin

56
Q

Inhibition ability of RNA polymerase III

A

Inhibition at high concentrations of toxin

57
Q

Which kind of protein is needed in order for the initiation stage of eukaryotes

A

‘Basal’/’General’ transcription factors

58
Q

List the stages of Pre-initiation complex formation in eukaryotes

A
  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
Q

TFIID is composed of:

A
  • TBP
  • TAF
60
Q

TFIIH is composed of:

A
  • Helicase
  • Protein kinase
61
Q

List the stages following on from pre-initiation complex formation

A
  • 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
Q

Elongation stage of eukaryotic transcription

A
  • 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
Q

Termination stage of eukaryotic transcription is caused by…

A

The cleavage sequence

64
Q

Post-transcriptional modification

A

Maturation and Splicing of mRNA

65
Q

Give the types of post-transcriptional modification of mRNA

A
  • (5’-) capping → During elongation
  • (3’-) tailing → During termination
  • Splicing → During termination
66
Q

(5’)capping

A

7-methyl-GTP bound to 5’-end of pre mRNA

67
Q

(3’-)tailing

A
  • Polyadenylation
  • Poly-A-tail bound to 3’ end of pre mRNA
  • Poly-A-tail synthesised by poly-A-polymerase
68
Q

Splicing

A
  • Removal of introns, exons are reunited
  • Catalysed by _small nuclear RNA_s (ribosymes)
  • Work with small nuclear ribonucleoproteins (snRNP)
  • Form spliceosome
69
Q

Examples of snRNAs

A
  • U1
  • U2
  • U4
  • U5
  • U6
70
Q

U1 snRNA binds to…

A

5’-end of intron

71
Q

U2 snRNA binds to…

A

AMP

72
Q

U5 snRNA binds to…

A
  • 3’-end of intron
  • Intron removed
73
Q

Excised introns form which structure?

A

Intron loop / Intron lariat

74
Q

How is eukaryotic transcription regulated?

A
  • Modification of chromatin structure
    • Histone modification
    • DNA modification
  • Regulation with transcription factors
    • Altering gene expression
75
Q

Gene expression

A

Information from a gene is used in the synthesis of a gene product (protein)

76
Q

Gene expression can be influenced and regulated on the level of…

A
  • Transcription
  • Translation
  • Post-translation
77
Q

Epigenetic regulation of transcription

A
  • Changing chromatin structure
78
Q

Histone modifications

A
  • Covalent modification → Nucleosome structure change
  • Transcription intensity influenced
79
Q

Histone acetyltransferase

A
  • Binds acetyl group
  • Less positive charge
  • Transcriptionally more active
80
Q

Histone deacetylase

A
  • Removes acetyl group
  • Positive charge
  • Transcriptionally inactive
81
Q

HDAC inhibitors

A
  • Histones hyperacetylated
  • Gene expression stimulated
82
Q

Compunds of histone acetylation

A
  • Histone acetyltransferase
  • Histon deacetylase
  • HDAC inhibitors
83
Q

DNA methylation

A

DNA methyltransferase

  • Binds methyl group to cytosine
  • Gene inactivated
  • Gene silencing
84
Q

Transcription factors used in transcription regulation

A
  • Cis-regulatory elements
  • Trans-regulatory elements
85
Q

Types of Cis-regulatory elements

A
  • Promoter
  • Enhancer
  • Silencer
86
Q

Types of trans-regulatory elements

A
  • Basal transcription factors
  • Activators → Bind to enhancer
  • Repressors → Bind to silencer
87
Q

How many binding domains do transcription factors have?

A

At least 1

88
Q

Motifs of DNA binding domains

A
  • Helix-turn-helix
  • Helis-loop-helix
  • Zinc finger
  • Leucine zipper
89
Q

Helix-turn-helix

A

Regulates animal development

90
Q

Zinc finger

A

Act as nuclear receptors

91
Q

Leucine zipper

A

Oncogenes

92
Q

Helix-loop-helix

A

Oncogenes

93
Q

Nuclear receptors

A
  1. Bind to ligand (e.g steroid hormone) → activate
  2. Activated receptor enters the nucleus (internalisation)
  3. Receptor acts a transcription factor

Biochemistry (21 decks)

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