RNA structure and transcription Flashcards
what’s the The Central Dogma of Molecular Biology
-genetic information in DNA molecules is read to generate RNA, this RNA is then decoded into protein molecules
-DNA replication-> transcription-> RNA-> translation-> protein
-reverse transcription can happen between RNA and DNA replication- this is the exception
-DNA is copied into RNA by a template-directed polymerisation reaction known as transcription.
-RNA transcripts can be decoded to generate cellular proteins in a process called translation.
RNA is a linear polymer of nucleotides
-RNA is more unstable than DNA- contains 2 hydroxyl groups meaning more easy to be hydrolysed
-RNA has a very similar structure to DNA
-contains uracil instead of thymine
-phosphate groups attach nucleotide groups together
-nucleotide contains: sugar (5 carbon ribose), base, phosphate (up to 3)
what’s a nucleoside
just a base and sugar- no phosphate
what’s a heterocyclic base
-base contains N and C atoms
RNA: bases and their nucleosides
-uracil- uridine
-adenine- adenosine
-guanine- guanosine
-cytosine- cytidine
what’s the Stem-loop structures in RNA
-Cellular RNAs typically have a 5’ phosphate group and a 3’ hydroxyl group.
-Intramolecular base-pairing within RNA allows short helices, many of which are stem-loops. RNA helices are normally irregular.
-Stem-loops (RNA folding to form short helical structures) are secondary structural elements within RNA.
-The major groove of RNA is narrow. Many interactions with RNA involve the minor groove- so the helix isn’t fully similar
-they do have base pair interactions however its intramolecular reactions (within molecule)
-RNA typically is imperfect- kinked or warped
what are the 2 different types of base pairing in RNA
-Watson/Crick canonical base-pairing: 3 H bonds(C and G) more stable than 2 H bonds(U and A)
-Non-canonical base-pairing (G:U wobble base-pair, has an important role in reading genetic code, neutral in helix)- H bonding not the same
what’s the secondary and tertiary structure of RNA
-The secondary structure of an RNA is the two-dimensional “map” that is defined through localised intramolecular base-pairing.
-Tertiary structure interactions connect regions of RNA that are separated in the secondary structure. -These can be canonical base-pair interactions ( to form parts of the 3D structure )
-The A minor motif (of DNA) consists of two adjacent A residues that interact with the edge of a G:C base pair- A is forming chemical interactions with G:C bases and ribose, formed between nucleotides in a loop and else where in the molecule
-pseudoknot formed
what occurs during RNA transcription
-RNA is made by (DNA-dependent) RNA polymerases (RNAPs)- proteins that interact with double stranded DNA
-The genetic sequence information in the coding (sense) strand is transcribed into RNA.
-Nucleotide triphosphates (NTPs) are selected by base-pairing with the template strand and added to the 3’ end of the extending RNA strand- double stranded DNA is pulled apart here called the transcription bubble
-The RNAP active site contains a short RNA/DNA heteroduplex (involved both RNA and DNA where RNA product is paired with the DNA)
what’s the structure of transcription units
-cells only want to express DNA from genes
-Transcription has defined “start” and “stop” positions in the genome.
-RNA polymerase is targeted to promoter regions of genes.
-Transcription occurs until the polymerase reaches the terminator region, where it is released from the DNA.
what’s the Structure of the core RNAP of E. coli
-RNAPs need a DNA template (other enzymes can make RNA in the absence of DNA.)
-The E. coli RNA polymerase core enzyme is a protein complex containing 5 subunits (a,a,b,b’,w).
-b,b’= catalytic
-a,a= binds to transcription factors
-w= assembly and stability
whats happens when Prokaryotic Sigma factors target RNAP to genes
-facilitates targeting the RNAP enabling it to find he promoter region
-In prokaryotes, sigma (s) factors provide specificity to the RNAP for the gene promoter.
-RNAPs can initiate transcription without an additional primase activity.
-delta factor is released from RNAP as it moves away from the promoter.
what are the 3 nuclear RNA polymerases in eukaryotic cells
-RNA polymerase I
-RNA polymerase II
-RNA polymerase III
-The eukaryotic RNAPs have a conserved core structure homologous to the bacterial enzyme
how does RNA polymerase I work
-processed to gene rate
-large ribosomal RNA
how does RNA polymerase II work
-transcription of all protein coding gene
-transcribes other RNA in splicing
-this is for mRNA, and non-coding RNA’s
how does RNA polymerase III work
-involved in the production of RNA molecules and 5s rRNA
-uses tRNA, and 5 rRNA
how do gTFs assemble RNAPII at eukaryotic gene promoters
-Eukaryotic cells do not express delta factors.
-Multiple general transcription factor (gTF) complexes are required for the assembly of -RNAP II onto gene promoters in eukaryotic cells. These are called TFIIA, TFIIB etc.
-gTFs are required for the recruitment of RNAP II to all its promoters. Assembly of the preinitiation complex (PIC) involves a multi-step pathway.
-The assembled PIC initiates transcription upon activation through specific signals.
