RNA Structure And Synthesis Flashcards
Amount of RNA in cell vs DNA
40x more RNA than DNA in the cell
DNA vs RNA
DNA
- master copy
- carefully reproduced
- stable
- nucleus
RNA
- working copy
- so tangly synthesized, used and degraded
- cytoplasm
Which is larger: eukaryotic cell or bacterial cell?
Eukaryotic cell
Which is larger: mRNA or primary transcript?
Primary transcript
Similarities between DNA and RNA structures
- long unbranched polymers of nucleotides linked by 3’-5’ phosphodiester bonds
- sugar phosphate backbone
- 3 common bases: adenine, guanine, cytosine
Difference in DNA and RNA structures
- sugar in RNA is ribose
- RNA contains uracil instead of thymine
- RNA is shorter than DNA
- always single stranded
- RNA can form secondary loop and stem structures (i.e. tRNA)
Sort types of RNA from most abundant to least
rRNA –> tRNA –> mRNA
Basics of Transcription
Sequence dependent
Anti-parallel direction for DNA and RNA
- DNA read 3’ –> 5’
- RNA synthesized 5’ –> 3’
Asymmetrical: only one strand is transcribed
Does not require a primer
Coding (sense) strand
the DNA strand that goes 5’ –> 3’
The sequence that correlates with the mRNA
Template (non-coding) strand
DNA strand that goes 3’ –> 5’
Strand that is copied during RNA synthesis
Beta subunit on RNA polymerase
Contains the catalytic site- catalyzes 3’ –> 5’ phosphodiester bonds
Alpha subunit on bacterial RNA polymerase
Recognizes promoter regions, which is required for appropriate initiation of transcription
Does RNA polymerase transcribe the entire genome?
Nope
Subunits of the core enzyme
Alpha (2) (interacts with proteins)
Beta
Beta’ (binds DNA template)
Subunits of the holoenzyme
Same as core + sigma
Is transcription discontinuous or continuous?
It’s discontinuous –> different start/stop signals
Either strand can be a coding template
Prokaryotic Promoter Region
Upstream of the start site of transcription initiation (++1)
Written on the sense strand
Specifically recognized by sigma subunit
Pribnow sequence and -35 region : signals RNA polymerase to come and start transcription
What is important for efficient initiation of transcription?
The distance between pribnow box and the -35 region
Not every gene has the same Pribnow and -35 sequence
Transcription: Initiation
Sigma binds to specific promoter regions of DNA (-35 and -10)
These regions correspond with DNA sequence…if there was a different sequence in between, sigma would not bind
Steps in transcription initiation
1) RNA pol binds to DNA- RNA pol for enzyme is always bound to DNA in a non-specific manner
2) when sigma subunit binds to core enzyme at promoter site, a conformational change occurs and binding is stabilized (closed promoter complex)
3) After formation of the closed promoter complex, the 2 strands of the DNA template unwind to produce and unpaired region containing approximately 12 bases (open promoter complex)
4) 1st base in RNA chain is added complementary to the base at +1 of the template strand
5) After 8-10 bases are added, the sigma subunit leaves the complex and only the core enzyme remains
Role of beta subunit of RNA polymerase in initiation
Beta subunit has 2 nucleotide binding sites
1) for 5’ purine (therefore first base is a 5’ purine)
2) for subsequent NTPs
Also synthesized the phosphodiester 3’–5’ bond between NTPs
Transcription Elongation
RNA-DNA hybrid about 8 bases long
Transcription bubble always 12 bases
As the enzyme moves to the region in front, creates + super coils and the region behind it re-winds creating negative supercoils
Hairpin formation in transcription termination
Must be a GC rich palindrome (very stable)
Must be followed by UUUs
Rho-independent termination of transcription
Pol slows down at GC rich region
Hairpin forms
Weak A/U bonds
