Overview of the process of converting DNA to RNA.
Transcription involves copying a short region of DNA into RNA across all organisms.
Types of RNA:
mRNA or pre-mRNA
rRNA
tRNA
Specific to organisms:
Archaea and Eukaryotes:
snRNA, snoRNA
siRNA, miRNA, piRNA, lncRNA
Bacteria and Archaea:
crRNA (CRISPR—clustered regularly interspaced short palindromic repeats)
Gene Definition: Copied portion of DNA.
RNA Properties:
Contains ribose, uracil, and is single-stranded, allowing tertiary structure formation.
RNA can fold into complex tertiary structures that are critical for function.
Introduction to the transcription mechanism in prokaryotic organisms.
σ Factor Role:
Binds to RNA polymerase and slides along DNA to find promoter.
Binds to promoter and causes double helix opening.
Dissociates, allowing elongation to occur.
After σ factor dissociation:
A jaw-like structure forms, holding DNA in place.
rNTP uptake and RNA exit channels are formed.
Rudder-like protrusion pries apart the DNA-RNA double helix, allowing single strands to re-anneal.
Polarity termination sequence is reached:
A special RNA sequence gets transcribed, folding into a hairpin structure, forcing the jaw to open and releasing the transcript.
RNA polymerase dissociates from the DNA.
Introduction to eukaryotic transcription with a focus on complexity and variety of polymerases.
There are three eukaryotic polymerases:
POL I: Transcribes rRNA.
POL II: Transcribes pre-mRNA.
POL III: Transcribes tRNA and other small RNAs.
Functionally similar to bacterial polymerase.
Involves general transcription factors (TFs).
Multi-subunit protein family.
Some TFs bind to the double helix before polymerase binding, others bind to polymerase first.
Promoter sequence located ~25 bp upstream of transcription start; typically involves a TATA box.
TFIID binds to the promoter and distorts the double helix, which attracts other transcription factors to initiate transcription complex formation.
Sequence of steps involved in TBP and associated factors binding is detailed.
Involves assembling a complex of various transcription factors with RNA polymerase II.
TFIIH Role:
Contains DNA helicase, accessing the template strand.
Synthesizes a short pre-mRNA strand.
Phosphorylates POL II's C-terminus, transitioning it out of the initiation phase.
The depicted steps summarize the initiation process, including the involvement of multiple transcription factors.
Detailed structure of the C-terminal domain (CTD) of RNA Polymerase II showing heptapeptide repeats.
Role of phosphorylation in regulating transcription initiation and elongation.
Activators, repressors, mediators, and chromatin-remodeling enzymes are part of the initiation control.
Bacterial mRNA is directly translated, while eukaryotic pre-mRNA undergoes significant modifications.
Key Modifications Include:
Capping of the 5' end.
Splicing: Removing introns and ligating exons.
Polyadenylation of the 3' end.
POL II’s C-terminal phosphorylation couples transcription and mRNA processing, facilitating the binding of processing proteins to emerging mRNA.
Various proteins associated with the processing of pre-mRNA are highlighted, including those responsible for capping, splicing, and polyadenylation.
Added by a complex of enzymes, serves to mark the mRNA for nuclear export and plays a role in translation regulation.
Three Steps to 5’ Cap Addition:
Phosphatase removes a phosphate from the 5' end.
Guanyl transferase adds GMP to the 5' end.
Methyl transferase adds a methyl group to the guanosine.
Splicing removes introns while retaining exons; alternative splicing allows different protein forms to be produced from a single gene.
The a-tropomyosin gene serves as an example of alternative splicing resulting in varied mRNA for different tissues.
The spliceosome includes a core of snRNA-protein complexes that undergo dynamic rearrangements using ATP hydrolysis to facilitate splicing reactions.
Detailed steps of intron removal and exon ligation in the splicing process are described, including the formation of a lariat structure.
Importance of ensuring that splice sites are correctly identified through RNA-RNA interactions.
Discussion of how poly-A signals lead to cleavage and the addition of poly-A tails to mRNA for stability and regulation.
Only a few mRNA copies are needed for protein production, while non-coding RNAs need many copies, often encoded across multiple chromosomes.
Synthesized by POL I, characterized by modifications such as methylation and isomerization for proper function.
The nucleolus is a key site within the eukaryotic nucleus where ribonucleoprotein assembly occurs.