Transcription Flashcards
Summarise transcription
Synthesis of RNA from DNA
Role of the coding (sense) strand in transcription
Storage of genetic information
Role of the non-coding (antisense, template) strand in transcription
- Compliments the coding strand
- Template for transcription
The functional unit of DNA during transcription
Transcription unit (TU)
The regions of the transcription unit
- Promoter region
- RNA coding region
Promoter region
- Responsible for regulation of transcription
- Consensus sequences:
- TATA-box
- GC-box
- CAP-cAMP binding site
TATA-box
- Prokaryotes → Called Pribnow-box
- Right in Thymine and Adenosine
- RNA polymerase binds tightly to this box
GC-box
- Right in Guanine and Cytosine
- RNA polymerase binds loosely to this box
CAP-cAMP binding site
- Only found in prokaryotes
- Binding of CAP-cAMP complex
- (Required for transcription)
Location of the transcription start site
Between promotor and RNA coding region
‘Upstream’ direction
From the start site → Promoter region
‘Downstream’ direction
From start site → RNA coding region
Untranslated region
DNA sequence which is transcribed but doesn’t code for an amino acid
The composition of 1 transcription unit in prokaryotes
- Several genes
- TU is polycistronic
The composition of 1 transcription unit in eukaryotes
- One gene
- TU is monocistronic
Introns and exons are found in…
Eukaryotes
Intron
- Found in pre-mRNA only
- Cut out of the sequence
Exons are found only in…
Mature mRNA
At what point does transcription finish
At the termination signal
Genetic information is transferred from DNA to protein synthesis via…
mRNA
3 phases of mRNA transcription in eukaryote and prokaryotes
- Initiation
- Elongation
- Termination
Initiation of transcription of prokaryotes
- RNA polymerase → Transcription of RNA
- Binding of CAP-cAMP complex
RNA polymerase holoenzyme composition
- RNA polymerase
- Sigma (σ) factor
RNA polymerase holoenzyme binds tightly to…
TATA-box of the promotor region
RNA polymerase enzyme binds loosely to…
GC-box of the promotor region
Elongation of transcription of prokaryotes
- RNA polymerase builds nucleotides into mRNA chain
- (mRNA is synthesised)
RNA polymerase use…to build the mRNA chain
- Nucleoside triphosphates
- Converted to nucleoside monophosphates
- (e.g ATP → AMP)
Termination of transcription of prokaryotes
- Starts at the termination signal
- Rho-factor independent termination
- Rho-factor dependent termination
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

Rho-factor dependent termination
- Guanine and Cytosine rich regions slow mRNA synthesis
- Rho-factor allows RNA-polymerase enzyme activity
- Catalyses dissociation

Termination involves dissociation of…
- DNA chain
- mRNA polymerase
- RNA polymerase
Structure of prokaryote mRNA
- Polycistronic (Several genes)
- Triplets of mRNA: Codons
- Shine-Dalgarno-sequences
- Untranslated regions (UTR)
Site of ribosome binding on mRNA
Shine-Dalgarno-sequence
Which model regulates prokaryote transcription
Operon model
Operator region
The binding site for repressor protein inhibition of transcription

(Found on the DNA sequence)
Two requirements for prokaryotic transcription
- No repressor bound to the operator region
- CAP-cAMP complex must be bound to its binding site
CAP
Catabolite Activator Protein
cAMP
Cyclic Adenosine Monophosphate
What are the two examples of the operon model
- Lactose Operon
- Tryptophan Operon
Lactose operon
- Codes lactose degrading enzymes (Lactase)
- Lactose binds to and removes the repressor
- Genes only transcribed when lactose is present
Lactose operon in the presence of glucose
- [cAMP] decrease
- No CAP-cAMP complex formation
- No transcription
Bacteria degrade glucose instead of lactose
Lactose operon:
- Glucose present
- Lactose present

No transcription
Lactose operon:
- Glucose present
- Lactose not present
No transcription

Lactose operon:
- Glucose not present
- Lactose not present
No transcription

Lactose operon:
- Glucose not present
- Lactose present
Transcription occurs

Tryptophan operon is responsible for
Tryptophan enzyme synthesis
Role of Tryptophan
Corepressor
Tryptophan operon in the presence of Tryptophan
- Repressor is activated
- Transcription is inhibited

Tryptophan operon without the presence of Tryptophan
- Repressor is inactive
- Transcription happens

Bacteria synthesise Tryptophan
List the stages of pre-mRNA transformation in Eukaryotes
- pre-mRNA synthesis
- Post-transcriptional modification
- mRNA maturation
Name the RNA polymerases involved in eukaryotic mRNA transcription
- RNA polymerase I
- RNA polymerase II
- RNA polymerase III
What characterises an RNA polymerase enzyme?
The ability to be inhibited by α-amanitin
Where is α-amanitin found?
In the ‘death cap’ fungus
Inhibition ability of RNA polymerase I
Cannot be inhibited
Inhibition ability of RNA polymerase II
Inhibition at low concentrations of toxin
Inhibition ability of RNA polymerase III
Inhibition at high concentrations of toxin
Which kind of protein is needed in order for the initiation stage of eukaryotes
‘Basal’/’General’ transcription factors
List the stages of Pre-initiation complex formation in eukaryotes
- Binding of TFIID to TATA-box
- Binding of TFIIA to TFIIB
- Binding of TFIIE to TFIIH
- Pre-initiation complex formed

TFIID is composed of:
- TBP
- TAF
TFIIH is composed of:
- Helicase
- Protein kinase
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

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
Termination stage of eukaryotic transcription is caused by…
The cleavage sequence
Post-transcriptional modification
Maturation and Splicing of mRNA
Give the types of post-transcriptional modification of mRNA
- (5’-) capping → During elongation
- (3’-) tailing → During termination
- Splicing → During termination
(5’)capping
7-methyl-GTP bound to 5’-end of pre mRNA
(3’-)tailing
- Polyadenylation
- Poly-A-tail bound to 3’ end of pre mRNA
- Poly-A-tail synthesised by poly-A-polymerase
Splicing
- Removal of introns, exons are reunited
- Catalysed by _small nuclear RNA_s (ribosymes)
- Work with small nuclear ribonucleoproteins (snRNP)
- Form spliceosome
Examples of snRNAs
- U1
- U2
- U4
- U5
- U6
U1 snRNA binds to…
5’-end of intron
U2 snRNA binds to…
AMP
U5 snRNA binds to…
- 3’-end of intron
- Intron removed
Excised introns form which structure?
Intron loop / Intron lariat

How is eukaryotic transcription regulated?
- Modification of chromatin structure
- Histone modification
- DNA modification
- Regulation with transcription factors
- Altering gene expression
Gene expression
Information from a gene is used in the synthesis of a gene product (protein)
Gene expression can be influenced and regulated on the level of…
- Transcription
- Translation
- Post-translation
Epigenetic regulation of transcription
- Changing chromatin structure
Histone modifications
- Covalent modification → Nucleosome structure change
- Transcription intensity influenced
Histone acetyltransferase
- Binds acetyl group
- Less positive charge
- Transcriptionally more active
Histone deacetylase
- Removes acetyl group
- Positive charge
- Transcriptionally inactive
HDAC inhibitors
- Histones hyperacetylated
- Gene expression stimulated
Compunds of histone acetylation
- Histone acetyltransferase
- Histon deacetylase
- HDAC inhibitors
DNA methylation
DNA methyltransferase
- Binds methyl group to cytosine
- Gene inactivated
- Gene silencing
Transcription factors used in transcription regulation
- Cis-regulatory elements
- Trans-regulatory elements
Types of Cis-regulatory elements
- Promoter
- Enhancer
- Silencer
Types of trans-regulatory elements
- Basal transcription factors
- Activators → Bind to enhancer
- Repressors → Bind to silencer
How many binding domains do transcription factors have?
At least 1
Motifs of DNA binding domains
- Helix-turn-helix
- Helis-loop-helix
- Zinc finger
- Leucine zipper
Helix-turn-helix
Regulates animal development
Zinc finger
Act as nuclear receptors
Leucine zipper
Oncogenes
Helix-loop-helix
Oncogenes
Nuclear receptors
- Bind to ligand (e.g steroid hormone) → activate
- Activated receptor enters the nucleus (internalisation)
- Receptor acts a transcription factor