transcriptional circuits Flashcards
(38 cards)
define transcriptome
The segment that is transcribed
what are the 4 levels of gene transcription
- abundant transcript ( gene gives rise to many mRNA transcripts). If one in every cell this is called a housekeeping gene ( e.g glycolytic enzymes ) - genes that are required for the functioning of all cell types
- no transcript - not expressed or expressed in low levels.
- • Rare transcript -may not be expressed in one cell type, however it can be highly expressed in another tissue
• Rare or no transcript - stimulus - abundant transcript.
what is an inducible gene
gene that becomes abundantly expressed in response to a stimulus such as hormones or viruses.
what is a promotor
The sequence immediately 5’ to the region to be transcribed is called a “promoter”
•Promoters recruit RNA polymerase to a DNA template
what is an enhancer
- Sequences of DNA that are not immediately adjacent to where transcription starts that act to enhance the recruitment of RNA polymerase to a promoter
- Enhancers can reside 5’ or 3’ to a transcription unit, and can even be located within an intron
- Like promoters, enhancers contain DNA sequences that are very strong binding sites for specificity factors or “transcription factors”
what happens when RNA is recruited.
- Neither prokaryotic nor eukaryotic RNA polymerases make stable contacts with DNA – they slide along the duplex without being able to efficiently recognise promoters
- Once stably recruited to DNA, RNA polymerase is able to convert the DNA from a closed to an open complex
describe the prokaryotic promotors
- Sigma factor recognises the -35 and -10 motifs common to prokaryotic promoters and enables RNA polymerase to make stable contacts with DNA.
- The region at -10bp called the pribnow box, there is also a region at -35 base pairs.
- The first nucleotide that is copied and transcribed into an RNA molecule will be +1. Nucleotides upstream of +1 will have a negative number.
– Binding of the sigma factor to the part of the promotor that will then recruit the RNA polymerase to the region of the promotor and start site of transcription.
what is a consensus sequence
the sequence that you are most likely to find if you are studying a new promotor. It is the calculated order of most frequent residues found at each position in a sequence alignment.
what is meant by the ability of the sigma factor and tfII to recruit RNA polymerase is generic
- it occurs at every promotor
- it does not account for the ability to vary the level of transcription
what are regulatory transcription factors
- regulatory changes are mediated by regulatory TFs.
- •In both prokaryotes and eukaryotes they function to dramatically alter the level of recruitment of RNA polymerase and/or its ability to initiate transcription
•Additionally, in eukaryotes they can influence local chromatin structure - they recognise and binds to specific DNA target sequences, and do not need to unwind the DNA to see their target.
what is a prokaryotic transcriptional switch
The lac operon
give 3 examples of a eukaryotic transcriptional switch
–Oestrogen-responsive transcription
–Tissue-specific transcription (b-globin)
–A complex regulatory circuit (cell cycle)
define an operon
clusters of genes that share the same promotor and are transcribed as a single large mRNA that contains multiple structural genes. a genetic regulatory system
what is the on/off switch in a lac operon and what tf binds to it
operator - repressor.
what is the lac operon in ecoli designed to do ?
breakdown lactose.
what is the function of the lac operon
In bacteria, when there is a glucose and lactose, they always prefer to utilise glucose as a source of energy, as it has more energy. so therefore, if cells are in the presence of both glucose and lactose, the lac operon would be silenced and will not utilise lactose.
what happens if there are low levels of glucose
if there are low levels of glucose, bacteria will try to utilise lactose if it is present in the media. In response to the absence of glucose/ low glucose levels, the CAP protein becomes active and binds to the promotor of the lac operon.
what happens in the absence of lactose and low glucose levels
The lac repressor is another transcription factor that binds to this DNA sequence in the promotor. This gene is not expressed because it would be a waste of energy to express these enzymes if there is no lactose available. It is silenced as the cap protein which intends to recruit the sigma factor and RNA pol II but cannot transcribe the RNA molecule because of the lap repressor.
what happens in the presence of lactose
In the presence of lactose, the lactose can bind to the protein and as a result the lac repressor is released from binding the DNA. This allows the cap to recruit the RNA polymerase and express the genes which will utilise the lactose as a source of energy.
when is the cap protein active
low glucose concentrations
+ Glucose, +lactose –>
OPERON OFF because CAP not bound
+glucose, -lactose –>
OPERON OFF both because lac repressor bound and because CAP not bound.
-Glucose, -lactose –>
OPERON OFF because lac repressor bound.
-Glucose, +lactose –>
operon on – RNA is transcribed.
