Gene Structure and Bacterial Transcription Flashcards
General gene structure but specifics usually about prokaryotes/bacteria
Intron vs exon?
Intron = non coding sequence and allows for alternative splicing.
Exon = protein coding region
What defines a gene?
A DNA sequence that is the template that encodes information for a functional product made of RNA or protein.
Only 25% of the genome meets this criteria.
Is non coding RNA still a gene?
Yes: for example tRNAs and rRNAs still have vital functions
Why must gene expression be highly controlled?
Gene expression control is essential for
-cells being able to move through the cell cycle
-cells responding to the external environment
-cells differentiating into different cells.
Not all genes need to be expressed at the same time or to the same degree -> gene expression is highly regulated from transcription through to translation.
As a general rule the amount of RNA transcripts is proportional to the number of proteins.
How is transcription regulated?(eukaryotes)
Segments of DNA around a gene regulate gene expression via regulating the activity of RNA polymerase II which is responsible for creating the RNA molecule
In bacteria: what are the main regulatory structures of the gene.
Promoter region
Transcriptional start site
Transcriptional terminator site
Note that these are different to start/stop codons involved in protein synthesis / translation.
What does the promoter region do? How?
Sequence of DNA where RNA polymerase binds to synthesize the RNA transcript. These sequences are found before the gene and also direct the RNA polymerase to which DNA strand is to be used as a template.
What are consensus sequences in a promoter region.
Consensus sequences in a promoter region of DNA refer to the specific nucleotide sequences that are recognized by transcription factors and RNA polymerase during the initiation of transcription. These sequences are found upstream of the transcription start site and play a crucial role in regulating gene expression by facilitating the binding of transcriptional machinery.
Where are bacterial consensus sequences found and what are they?
TTGACA found at -35 and TATATT (Prinbow box) found at -10. These sequences have been shown to be conserved (in E.coli at least).
What is a UP element?
Also known as an up stream element, UP elements are sequences rich in thymine and help strengthen the promoter region (can be found upstream of promoter region). These are not common to all promoter regions.
What can deviations from consensus sequences cause?
Impaired binding of RNA polymerase to the promoter and affected gene expression.
What are operator sequences and activator sequences
Operator sequences are specific to prokaryotes and are found either within the promoter regions (e.g. between the consensus sequences) or between the promoter region and the gene. They are binding sequences on which repressor proteins can bind and physically stop RNA polymerase from binding.
Activator sequences bind proteins that increase the efficiency of RNA polymerase binding to DNA by stabilising RNA polymerase. Activator sequences are especially important if there are mutations in the promoter region which make it hard for RNA polymerase to bind.
What does a terminator sequence do and how? (prokaryote)
Stops the RNA from transcribing. This consists of consensus sequences cause the formation of a hairpin stalling the RNA polymerase. Hairpin: two nearby consensus sequences on the same strand that are complementary to each (e.g. TATA-> ATAT) bind to each other
What is different about bacterial genes?
They are distinct and don’t overlap with one another
They can be polycistronic
They don’t have introns and exons
What does monocistronic and polycistronic mean?
Monocistronic: 1 gene between a promoter and terminator sequence -> makes one mRNA transcript and protein
Polycistronic: multiple genes between a promoter and terminator sequence -> makes one mRNA transcript but can be used to make multiple proteins.
How are polycistronic genes expressed?
A coordinated expression of genes in one pathway and often occurs by enzymatic pathways. All the different genes within the produced mRNA are regulated by the same promoter.
What is the TATA box?
(TATAAAA - eukaryotic equivalent of the prinbow box) This is found in the promoter region of eukaryotes and is a common consensus sequence of type II genes and is where the TATA protein binds which helps RNA polymerase II bind to initiate transcription. Typically found 25 base pairs from the start site. RNA polymerase II is the polymerase used in eukaryotes for coding mRNA transcripts, I and III do other stuff.
What are the common upstream elements that can be found in eukaryotes? Where are they found and what do they do?
CAAT box (GGCCAATCT) and GC box (GGGCGG)
These consensus sequences can be found 50 to 200 base pairs from the start site.
Most eukaryotes have one of these and they are binding sites for transcription factors (proteins that help RNA polymerase bind). These are found upstream from the TATA box btw.
What are regulators and what is their role?
The eukaryotic equivalent of operators. They can either act as enhancers or silencers of gene expression. This is crucial for ensuring the right genes are expressed when needed in the appropriate cells. Silencers and enhancers can sometimes occupy the same space competing with one another to regulate gene expression.
How do regulators affect gene expression over long distances?
Eukaryotic equivalent of operators/activators but are called enhancers or silencers and they can compete with each to affect gene expression and are sometimes in the same location. The upstream control elements bind general transcription factors which recruit the mediator complex which can then interact with the proteins binding to the regulators significantly further upstream along the DNA. Unlike prokaryotic operators, regulators can be very far from the start site. This works as DNA can be orientated in such away that distant sequences can come into close proximity to each other by the function of specialized proteins that can hold eukaryotic chromosomal DNA in loops, which increases the association of a gene with a regulator like an enhancer or repressor.
Where generally on a chromosome do you find heterochromatin and euchromatin. What does this imply?
Heterochromatin: telomere and centrosome as there is high quantity of chromatin and must be condensed.
Euchromatin: everywhere else.
Genes are found in the euchromatic region as it would inefficient/damaging to condense and decondense the heterochromatic areas for gene expression.
What do insulators do?
They have a barrier function stopping the spread of heterochromatin into euchromatic regions and stop other genes/chromatin structures interfering with another gene being expressed.
Insulators stop enhancers from interacting with the promoter regions of neighbouring genes ensuring they act on the promoter regions within their regulatory domain.
Explain introns.
Intros are the non coding region between introns. These regions play important regulatory roles.
What do eukaryotic regulations ensure?
Genes are expressed:
-at the right level
-in the right cell
-in response to the right conditions
-at the right time.
