Gene Expression - Transcription Flashcards
Transcription Definition
- Coding vs Template strand
- Promoter region
- Process whereby DNA is copied to RNA
- RNA always synthesised in a 5’ to 3’ direction (RNA polymerase adds bases to 3’ end)
Template strand: RNA polymerase uses this strand as a template to build the mRNA transcript
Coding strand: Has same sequence as RNA (but with T’s instead of U’s)
Promoter region = -10 and -35 bases from gene (upstream)
2 ways transcription is terminated
- Rho Dependent termination: Protein called Rho (hexose) binds at Rut site and pulls RNA from RNA polymerase
- energy gotten from ATP hydrolysis
- is a well defined process - there is a specific place that Rho protein can bind - Rho independent termination: termination by hairpin loop formation (due to inverted repeats)
- U’s at end of hairpin (serve as signal for RNA polymerase release)
- causes a decrease in the affinity between RNA polymerase and the DNA (lots of U’s mean only A-U bonds holding them together = weak (has only 2 H bonds))
Numbers of RNA polymerases in Bacteria, Plants & Eukaryotes
Bacteria; 1 type of RNA polymerase
Plants; 5 types of RNA polymerase
Eukaryotes; 3 Types of RNA polymerase
-these have divided the jobs
rRNA = RNA polymerase 1
pre-mRNA = RNA polymerase 2
small RNA = RNA polymerase 3
RNA polymerase 1 - UPE, UPF & core element
- RNApolymerase 1 transcribes rRNA precursor gene
- core element -45 to +20
- upstream promoter element (UPE) = -180 to -107
- gene present in 100s of copies in cell
- rRNA make ribosomes
- Upstream promoting factor (UPF) binds to UPE to increase ability of core binding actor to bind to core promoter
- for core promoter to bind, need protein to bind upstream
-Core binding factor consists of 4 proteins including Tata box binding protein) - required for initiation by RNA plymerase 2 & 3 also
RNA polymerase 3
- exception to rule that promoter region is upstream of gene
- has promoters w/in genes (2 out of 3 types do)
- all transcribe small RNAs (i.e. tRNA, small nuclear RNA)
RNA polymerase 2
- Is the main one - transcribes genes that get translated later
- many different types of promoters - have different types of control mechanisms (i.e. TATA box, GC box)
Gene Expression
Gene
*Important note about reading nucleic acids
Gene expression: is the flow of genetic information from DNA via RNA (transcription) to protein (translation)
Gene: Part of DNA that gets transcribed into an RNA
*A nucleic acid only makes sense if read in 5’ to 3’ direction
2 types of RNAs produced (classification)
-enzyme that synthesizes RNAs
- Informational RNAs - contain messages of amino acid sequence of proteins (get translated into proteins)
- rRNAs, tRNAs, snRNAs, scRNAs - are not translated into proteins - are functional
Enzyme that sysnthesises RNAs = RNA polymerase
2 ways transcription is terminated
- Rho Dependent termination: Protein called Rho (hexamer - 6 subunits) binds at Rut site and pulls RNA from RNA polymerase
- energy gotten from ATP hydrolysis
- is a well defined process - there is a specific place that Rho protein can bind - Rho independent termination: termination by hairpin loop formation (due to inverted repeats)
- U’s at end of hairpin (serve as signal for RNA polymerase release)
- causes a decrease in the affinity between RNA polymerase and the DNA (lots of U’s mean only A-U bonds holding them together = weak (has only 2 H bonds))
Bacterial RNA polymerase
- Core element (5 subunits & function)
- Holoenzyme - what factor joins
-Bacteria possess only 1 type of RNA polymerase that catalyses all classes of RNA
Core element (5 subunits):
-2 x alpha (enzyme assembly, promoter recog.)
-beta (Catalytic centre)
-beta prime (Catalytic centre)
-omega (provides stability of enzyme)
*Sigma factor joins to core to form holoenzyme (promoter specificity)
Transcription Unit
-composition (3)
Transcription unit: stretch of DNA that encodes an RNA molecule & sequence necessary for its transcription
Composed of; -
- Promoter
- RNA coding sequence
- Terminator
Promoter Region
- 3 parts
- Consensus sequence (definition)
[Bacteria]
-Typical promoter has 3 components; consensus sequences at -35 and -10 and the start point (which is a purine 90% of time)
- 10 sequence = TATAAT
- 35 sequence + TTGACA
Consensus sequences: consists of most commonly encountered bases at each position in a group of related sequences
Stages of Transcription
Initiation -> Elongation -> Trmination
RNA polymerase Action during stages of transcription
- RNA polymerase binds to promoter and melts DNA, remains stationary during initiation
- Moves along template during elongation
- Dissociates at termination
Eukaryotic RNA polymerases - number
-Eukaryotic cells contain 5 types of RNA polymerases - 4th and 5th found in plants
RNA polymerase 1 (eukaryotes)
- 2 critical regions in promoter
- what it transcribes
- Transcribes the rRNA precursor gene (hundreds of copies in each cell)
- promoter has 2 critical regions: core element (located -45 to +20) and Upstream promoter element (-180 to -107)
- transcription units for RNA polymerase 1 have a core promoter separated by approx 70 bp from the upstream promoter element
- space between these two elements crucial for proper transcription
- Upstream binding factors bind to Upstream promoter element to increase the ability of core-binding factor to bind to core promoter (consists of 4 proteins)
RNA polymerase 2 (Eukaryotes)
- what it transcribes
- what the genes have
- Transcribes pre-mRNA, snoRNAs, some miRNA 7 some snRNAs
- Genes transcribed have core promoter region and regulatory promoter w/ conserved sequences
- Minimal pol 2 Promoter has a TATA box approx 25 bp upstream of InR
- TATA box has consensus seq. of TATAAA
- promoters also contain short sequences where regulatory protein bind and control gene expression
RNA Polymerase 3 (Eukaryotes)
-Transcribes tRNA and other small rRNA
Termination of Transcription (in eukaryotes) for different polymerases
- RNA polymerase 1: 18 bases terminator sequence 1kb downstream - accessory factor required
- RNA polymerase 2: polyadylation of mRNA
- RNA polymerase 3: Terminator region similar to prokaryotic terminator - termination occurs at a run of 4Us locatd w/in rich GC region
*hairpin structures do not appear to be involved in termination of RNA polymerases 1 or 3
