Transcription Flashcards
What is transcription?
Synthesis of RNA from DNA
What stores the genetic information?
Coding (sense) strand
What is a Antisense strand?
Non Coding (antisense) strand - template
RNA is synthesised from?
the Antisense strand
Is primer needed in transcription?
no
What is the functional unit of DNA?
The transcription unit (TU)
What regions does the Transcription Unit (TU) compose of?
- (1) promoter: regulatory function
- (2) RNA coding region
Where is the Transcription start site?
Located between promoter and RNA coding region -> transcription starts form this point
What is the “Upstream” direction?
= from the start site towards promoter (“left”), bases found here get numbers minus 1,2 etc. when moving away from the start site.
What is the “Downstream” direction?
= from the start site towards RNA coding region (“right”), bases found here get numbers flus 1, 2 etc. whn moving away from start site.
What main things does the transcritpion unit compose of?
- Transcription start site
- upstream
- downstream
What is responsible for the regulation of transcription?
the Promoter
What are the most important consensus sequences of promoter regions?
- TATA-box
- GC-box
- CAP - cAMP binding site
What is TATA-box?
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
What is GC-box?
It is an important consensys sequence of the promoter region.
- Rich in G and C bases
- RNA polymerase binds loosely to this box
What is CAP-cAMP binding site?
It is an important consensys sequence of the promoter region.
- Only in prokaryotes
- Binding of CAP-cAMP-complex -> one of the prerequisites of transcritpion
Such DNa sequence which is coding one functional unit?
Gene,/structure gene
What is polycistronic transcription unit?
One transcription is composed of several genes (only in prkaryotes)
What is monocistrnic transcription unit?
One transcription unit is composed of one gene (only in eukaryotes)
What can be found inside the genes of Eukaryotes?
Introns and exons
What is Introns?
can be found in pre-mRNA (primary transcript) only -> they are cut out -> Mature mRNA contains no intron
What are Exons?
mature mRNA contains exons only
What is the termination signal?
transcription finishes here
What is translation?
mRNA transports genetc information from DNA to the protein synthesis
What are the phases of transcription of mRNA of prokaryotes?
- Initiation
- Elongation
- Termination
What is the function of the RNA polymerase in Prokaryotes?
Catalyses transcription of all types of RNA
RNA polymerase + sigma factor =
RNA polymerase holoenzyme -> specific affinity of the enzyme to the promoter -> holoenzyme binds tightly to TATA (pribnow) and loosely to GC-box of promoter
What is RNA polymerase holoenzyme?
specific affinity of the enzyme to the promoter -> holoenzyme binds tightly to TATA (pribnow) and loosely to GC-box of promoter
What is necessary for the initiation of transcription in Prokaryotes?
Binding of CAP- cAMP complex to the binding site on the promoter
Elongation of transcription of Prokaryotes happens when?
Signa factor is released from RNA polymerase
The RNA polymerase builds nucleotides into?
mRNA chain -> mRNA is being synthesised in the 5´to 3´direction
What are the possibilites of termination in Prokaryotes?
- Pho(p) factor independent termination
- Pho(p) factor dependent termination
What is Pho(p) factor independent termination?
- 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
What is Pho(p) factor dependent termination?
- 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
What is a Codon?
Base triplets found on mRNA
Prokaryotic mRNA is?
polycistronic: containes transcript of several genes
What are located between transcripts of genes in Prokaryotes?
Shine-Dalgarno-Sequences (RBS = ribosome binding site).
- during translation, mRNA binds to ribosomes by these sites.
Transcription of Prokaryotes is regulated by?
Operon model
What is a Operator region?
a DNA-sequence on the promoter or between transcription start site and UTR -> binding site for repressor protein -> inhibition of transcription
What happens if there are no repressor bound on the operator region?
No inhibition
How does transcription start?
CAP -cAMP complex must be bound to CAP-cAMP binding site of promoter.
Two examples for operon model:
- Lactose operon
- Tryptophan operon
What is a Lactose operon?
Regulates transcription og genes of lactose degrading enzymes
What is a Tryptophan operon?
Regulates transcription of genes of tryptophan syntehsising enzymes.
phases of Transcription of mRNA of Eukaryotes?
- initiation
- elongation
- termination
(same as in prokaryotes)
What is synthesised first in transcription of Eukaryotes?
pre-mRNA is synthesised first -> cotranscriptional processing of mRNA is needed = maturation of mRNA (pre-mRNa -> mRNA transformation)
RNA polymerases can be characterised according to the ability of inhibition with?
alpha-amantin
Can not be inhibited?
RNA polymerase I
Inhibition happens at low concentrations of toxins?
enzyme is very sensitive
RNA polymerase II
Inhibition happens at higher concentrations of toxins?
enzyme is less sensitive
RNA polymerase III
Factors needed for initiation of transcription in Eukaryotes?
- Binding of TFIID (= transcription factor IID) to TATA-box
- Binding of TFIIA to TFIIB
- Binding of RNA polymerase II and TFIIF
- Binding of TFIIE and TFIIH
-> pre-initiation complex is formed
- Helicase subunit of TFIIH uncoils the two DNA strands.
- The first few nucleotides are built in the new mRNA chain
- Protein kinase subunit of TFIIH phosphorylises C-terminal domain of RNA polymerase II.
- Basal transcription factors diccociate
- > elongation starts.
TFIID is composed of?
two subunits:
- TBP = TATA-binding protein (recognices TATA-box)
- TAF = TBP-associated factors.
What is TFIIH composed of?
two subunits:
- Helicase
- Protein kinase
Substrates of RNA polymerase II are?
Nucleoside-triphosphates (NTP´s: ATP, GTP, UTP, CTP)
Termiantion happens when?
Synthesis of new mRNA stops at the end of transcription unit, at cleavage sequence
5´-capping happens during?
eukaryotes
elongation
3´-capping happens during?
eukaryotes
= polyadenylation -> happens during termination
Splicing happens during?
termination
What is splicing?
That process in the cell nucleus where introns are removed (cut out) and exons are reunited.
Processes are catalysed by?
snRNA´s (smal nuclear RNAs). They are ribosymes (RNA molecule with enzymatid property)
snRNA works with?
proteins called snRNPs (= small nuclear ribonucleoproteins)
What happens when U1 snRNA binds to 5énd of intron?
phosphodiester bond is split between intron and exon
What happens when U2 snRNA binds to one AMP?
a consensus sequence, inside the intron
what happens when 5-end of intron binds to the AMP?
Intron loop or intron-lariat is formed (inside the intron)
What happens when U5 snRNA binds to the 3´-end of intron?
phosphodiester bond is split between intron and exons -> intron is removed
Function of U4 and U6?
they help the work of the other snRNA molecules
when are the neighbour exons reunited?
after removal of intron
What is Gene expression?
The process where information from a gene is used in the synthesis of a functional gene product (usually protein)
Gene expression can be influenced and regulated on the level of?
- Transcription: How many mRNA are produced?
- Translation: How may proteins are produced?
- Post-translation: How many active proteins are produced?
What are the most important ways of regulation of eukaryotic transcription?
- Modification of structure of chromatins
2. Regulation with transcription factors
What is modification of structure of chromatins?
- Modification of histones (acetylation, methylation, phosphorylation, ubiquitinylation, SUMOylation)
- Modification of DNA (methuylation)
What happens during Regulation with transcription factors?
gene expression can be altered
Epigenetically active molecules (from feed or the environment) are able to influence?
gene expression via epigenetic regulation
What happens when the strucutre of histone protein is covalently modified?
leading to the change of structure of the whole nucleosome, influencing the intensity of transcription (RNA synthesis)
What is gene silencing?
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
What is Cis-regulatory elements?
= such region of the DNA, to where binding of transregulatory element regulates/influences transcription
Types of Cis-regulatory elements?
- Promoter: central roe in the regualation of transcription
- Enhancer region: stimulation of transcription
- Silencer region: inhibition of transcription
What is trans-regulatory elements?
= transcription factors:
= proteins which binds to the appropriate cis-regulatory element
Types of Trans-regulatory elements (transcription factors)
- 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
Function of Helix-turn-helix?
uslually regulates development of animals
Function of Zinc finger?
Functions usually as nuclear receptors
Function of Leucin zipper?
usually proto-onco-genes -> tumorigenic
Function of Helix-loop-helix?
usually proto-onco-genes -Z tumorigenic
What are typical motifs of DNa binding domains?
- helix-turn-helix
- zinc finger
- leucine zipper
- helix-loop-helix
Nuclear receptors bind to..?
- 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
Ligand is?
usually a hormone, eg steroid or thyroid.
