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Biochem > Transcription > Flashcards

Transcription Flashcards

1
Q

What is transcription?

A

Synthesis of RNA from DNA

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2
Q

What stores the genetic information?

A

Coding (sense) strand

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3
Q

What is a Antisense strand?

A

Non Coding (antisense) strand - template

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4
Q

RNA is synthesised from?

A

the Antisense strand

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5
Q

Is primer needed in transcription?

A

no

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6
Q

What is the functional unit of DNA?

A

The transcription unit (TU)

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7
Q

What regions does the Transcription Unit (TU) compose of?

A
  • (1) promoter: regulatory function

- (2) RNA coding region

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8
Q

Where is the Transcription start site?

A

Located between promoter and RNA coding region -> transcription starts form this point

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9
Q

What is the “Upstream” direction?

A

= from the start site towards promoter (“left”), bases found here get numbers minus 1,2 etc. when moving away from the start site.

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10
Q

What is the “Downstream” direction?

A

= from the start site towards RNA coding region (“right”), bases found here get numbers flus 1, 2 etc. whn moving away from start site.

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11
Q

What main things does the transcritpion unit compose of?

A
  • Transcription start site
  • upstream
  • downstream
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12
Q

What is responsible for the regulation of transcription?

A

the Promoter

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13
Q

What are the most important consensus sequences of promoter regions?

A
  • TATA-box
  • GC-box
  • CAP - cAMP binding site
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14
Q

What is TATA-box?

A

It is an important consensys sequence of the promoter region.

  • Called Pribnow-box in Prokaryotes
  • Rich in T and A bases
  • RNA polymerase binds tightly to this box
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15
Q

What is GC-box?

A

It is an important consensys sequence of the promoter region.

  • Rich in G and C bases
  • RNA polymerase binds loosely to this box
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16
Q

What is CAP-cAMP binding site?

A

It is an important consensys sequence of the promoter region.

  • Only in prokaryotes
  • Binding of CAP-cAMP-complex -> one of the prerequisites of transcritpion
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17
Q

Such DNa sequence which is coding one functional unit?

A

Gene,/structure gene

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18
Q

What is polycistronic transcription unit?

A

One transcription is composed of several genes (only in prkaryotes)

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19
Q

What is monocistrnic transcription unit?

A

One transcription unit is composed of one gene (only in eukaryotes)

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20
Q

What can be found inside the genes of Eukaryotes?

A

Introns and exons

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21
Q

What is Introns?

A

can be found in pre-mRNA (primary transcript) only -> they are cut out -> Mature mRNA contains no intron

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22
Q

What are Exons?

A

mature mRNA contains exons only

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23
Q

What is the termination signal?

A

transcription finishes here

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24
Q

What is translation?

A

mRNA transports genetc information from DNA to the protein synthesis

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25
Q

What are the phases of transcription of mRNA of prokaryotes?

A
  • Initiation
  • Elongation
  • Termination
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26
Q

What is the function of the RNA polymerase in Prokaryotes?

A

Catalyses transcription of all types of RNA

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27
Q

RNA polymerase + sigma factor =

A

RNA polymerase holoenzyme -> specific affinity of the enzyme to the promoter -> holoenzyme binds tightly to TATA (pribnow) and loosely to GC-box of promoter

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28
Q

What is RNA polymerase holoenzyme?

A

specific affinity of the enzyme to the promoter -> holoenzyme binds tightly to TATA (pribnow) and loosely to GC-box of promoter

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29
Q

What is necessary for the initiation of transcription in Prokaryotes?

A

Binding of CAP- cAMP complex to the binding site on the promoter

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30
Q

Elongation of transcription of Prokaryotes happens when?

A

Signa factor is released from RNA polymerase

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31
Q

The RNA polymerase builds nucleotides into?

A

mRNA chain -> mRNA is being synthesised in the 5´to 3´direction

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32
Q

What are the possibilites of termination in Prokaryotes?

A
  • Pho(p) factor independent termination

- Pho(p) factor dependent termination

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33
Q

What is Pho(p) factor independent termination?

A
  • A region rich in G anc C bases can be found on the mRNA at the region of termination signal.
  • H-bonds formed between the G and C bases destabilise DNA-RNA complex -> DNa chain, mRNA and RNA polymerase dissociate
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34
Q

What is Pho(p) factor dependent termination?

A
  • G-C rich region slows down mRNa synthesis
  • The so called rho(p) factor follows RNa polymerase enzyme during transcription
  • Pho-p factor reaches RNA polymerase when it is slowed down and catalyses dissociaten of DNA chain, mRNA and RNa polymerase
  • ATP is needed
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35
Q

What is a Codon?

A

Base triplets found on mRNA

36
Q

Prokaryotic mRNA is?

A

polycistronic: containes transcript of several genes

37
Q

What are located between transcripts of genes in Prokaryotes?

A

Shine-Dalgarno-Sequences (RBS = ribosome binding site).

- during translation, mRNA binds to ribosomes by these sites.

38
Q

Transcription of Prokaryotes is regulated by?

A

Operon model

39
Q

What is a Operator region?

A

a DNA-sequence on the promoter or between transcription start site and UTR -> binding site for repressor protein -> inhibition of transcription

40
Q

What happens if there are no repressor bound on the operator region?

A

No inhibition

41
Q

How does transcription start?

A

CAP -cAMP complex must be bound to CAP-cAMP binding site of promoter.

42
Q

Two examples for operon model:

A
  • Lactose operon

- Tryptophan operon

43
Q

What is a Lactose operon?

A

Regulates transcription og genes of lactose degrading enzymes

44
Q

What is a Tryptophan operon?

A

Regulates transcription of genes of tryptophan syntehsising enzymes.

45
Q

phases of Transcription of mRNA of Eukaryotes?

A
  • initiation
  • elongation
  • termination

(same as in prokaryotes)

46
Q

What is synthesised first in transcription of Eukaryotes?

A

pre-mRNA is synthesised first -> cotranscriptional processing of mRNA is needed = maturation of mRNA (pre-mRNa -> mRNA transformation)

47
Q

RNA polymerases can be characterised according to the ability of inhibition with?

A

alpha-amantin

48
Q

Can not be inhibited?

A

RNA polymerase I

49
Q

Inhibition happens at low concentrations of toxins?

enzyme is very sensitive

A

RNA polymerase II

50
Q

Inhibition happens at higher concentrations of toxins?

enzyme is less sensitive

A

RNA polymerase III

51
Q

Factors needed for initiation of transcription in Eukaryotes?

A
  1. Binding of TFIID (= transcription factor IID) to TATA-box
  2. Binding of TFIIA to TFIIB
  3. Binding of RNA polymerase II and TFIIF
  4. Binding of TFIIE and TFIIH

-> pre-initiation complex is formed

  1. Helicase subunit of TFIIH uncoils the two DNA strands.
  2. The first few nucleotides are built in the new mRNA chain
  3. Protein kinase subunit of TFIIH phosphorylises C-terminal domain of RNA polymerase II.
  4. Basal transcription factors diccociate
    - > elongation starts.
52
Q

TFIID is composed of?

A

two subunits:

  • TBP = TATA-binding protein (recognices TATA-box)
  • TAF = TBP-associated factors.
53
Q

What is TFIIH composed of?

A

two subunits:

  • Helicase
  • Protein kinase
54
Q

Substrates of RNA polymerase II are?

A

Nucleoside-triphosphates (NTP´s: ATP, GTP, UTP, CTP)

55
Q

Termiantion happens when?

A

Synthesis of new mRNA stops at the end of transcription unit, at cleavage sequence

56
Q

5´-capping happens during?

eukaryotes

A

elongation

57
Q

3´-capping happens during?

eukaryotes

A

= polyadenylation -> happens during termination

58
Q

Splicing happens during?

A

termination

59
Q

What is splicing?

A

That process in the cell nucleus where introns are removed (cut out) and exons are reunited.

60
Q

Processes are catalysed by?

A

snRNA´s (smal nuclear RNAs). They are ribosymes (RNA molecule with enzymatid property)

61
Q

snRNA works with?

A

proteins called snRNPs (= small nuclear ribonucleoproteins)

62
Q

What happens when U1 snRNA binds to 5énd of intron?

A

phosphodiester bond is split between intron and exon

63
Q

What happens when U2 snRNA binds to one AMP?

A

a consensus sequence, inside the intron

64
Q

what happens when 5-end of intron binds to the AMP?

A

Intron loop or intron-lariat is formed (inside the intron)

65
Q

What happens when U5 snRNA binds to the 3´-end of intron?

A

phosphodiester bond is split between intron and exons -> intron is removed

66
Q

Function of U4 and U6?

A

they help the work of the other snRNA molecules

67
Q

when are the neighbour exons reunited?

A

after removal of intron

68
Q

What is Gene expression?

A

The process where information from a gene is used in the synthesis of a functional gene product (usually protein)

69
Q

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

A
  • Transcription: How many mRNA are produced?
  • Translation: How may proteins are produced?
  • Post-translation: How many active proteins are produced?
70
Q

What are the most important ways of regulation of eukaryotic transcription?

A
  1. Modification of structure of chromatins

2. Regulation with transcription factors

71
Q

What is modification of structure of chromatins?

A
  • Modification of histones (acetylation, methylation, phosphorylation, ubiquitinylation, SUMOylation)
  • Modification of DNA (methuylation)
72
Q

What happens during Regulation with transcription factors?

A

gene expression can be altered

73
Q

Epigenetically active molecules (from feed or the environment) are able to influence?

A

gene expression via epigenetic regulation

74
Q

What happens when the strucutre of histone protein is covalently modified?

A

leading to the change of structure of the whole nucleosome, influencing the intensity of transcription (RNA synthesis)

75
Q

What is gene silencing?

A

DNA methyltransferase binds methyl group to a cytosine on the promoter region of DNA -> transcription is blocked, the affected gene gets inactivated -> gene expression is decreased

76
Q

What is Cis-regulatory elements?

A

= such region of the DNA, to where binding of transregulatory element regulates/influences transcription

77
Q

Types of Cis-regulatory elements?

A
  • Promoter: central roe in the regualation of transcription
  • Enhancer region: stimulation of transcription
  • Silencer region: inhibition of transcription
78
Q

What is trans-regulatory elements?

A

= transcription factors:

= proteins which binds to the appropriate cis-regulatory element

79
Q

Types of Trans-regulatory elements (transcription factors)

A
  • Basal (general) transcription factors: binding to the promoter -> prerequisite of transcription
  • Activators: binding to an enhancer region stimulates transcription
  • Receptors: binding to a silencer region inhibits transcription
80
Q

Function of Helix-turn-helix?

A

uslually regulates development of animals

81
Q

Function of Zinc finger?

A

Functions usually as nuclear receptors

82
Q

Function of Leucin zipper?

A

usually proto-onco-genes -> tumorigenic

83
Q

Function of Helix-loop-helix?

A

usually proto-onco-genes -Z tumorigenic

84
Q

What are typical motifs of DNa binding domains?

A
  • helix-turn-helix
  • zinc finger
  • leucine zipper
  • helix-loop-helix
85
Q

Nuclear receptors bind to..?

A
  • the appropriate ligand and get activated.
  • > the activated receptor enters the nucleus (internalisation)
  • > in the nucleus, receptor acts as transcription factor which has impact on transcription
86
Q

Ligand is?

A

usually a hormone, eg steroid or thyroid.

Biochem (14 decks)

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