RNA Flashcards
ribosomal RNA
pair with ribosomal proteins to form ribosomes
messenger RNA
encode a gene to be translated
transfer RNA
Adapter molecule that links AA to RNA codons
Non-coding RNA: sense
same region as gene, same direction
Non-coding RNA: antisense
DNA strand that is template, not coding strand
same region as gene
.
noncoding strand, not in area of gene
Non-coding RNA: interonic
non-coding RNA within intron
Non-coding RNA: intergenic
non-coding RNA between genes
Roles in NC RNA
anneal to DNA/mRNA to regulate gene expression
recruit factors to mRNA
directly bind to proteins
conformational switches that alter RNA function
sigma factor
protein that binds to promoter region; RNA polymerase binds sigma factor
-35 prime box and -10 prime box help bind sigma factor, prokaryotic
RNA Pol 1 promoter region
eukaryotic, transcribes rRNA, upstream control element where pol 1 binds, core promoter with start site follows
RNA pol 2 promoter region
eukaryotic, transcribes protein coding region: TATA box, Inr start site, downstream promoter
RNA Pol 3 promoter region
eukaryotic, transcribes tRNA:
start site, Box A, Box B
start site, Box A, Box C
TBP binds DNA through intercalation and salt bridges
TFIID
transcription factor for Pol 2
TFIID is itself composed of TBP and several subunits called TATA-binding protein Associated Factors (TBP-associated factors
TBP binds to TATA box and recruits promotors
Rho dependent termination
Rho helicase protein indicates termination; disrupts DNA/RNA interaction
Rho independent termination
RNA structure indicates termination
formation of GC rich stem loop with strong base interactions and hydrogen bonding
causes melting of RNA/DNA duplex: RNA dissociates
ribozymes (R splicesome)
Base pair with target RNA and cleaves RNA
divalent metals are required cofactors for ribozymes
Group 1 introns
self-splicing intron sequence, rybozyme
exogenous G fits into binding pocket- not part of RNA transcript, G covalently linked to intron
G attacks phosphodiester bond at 5’ splice site
5’ exon attacks 3’ splice site
intron is linear
exon ligated together
group 2 introns
endogenous A attacks phosphodiester bond
intron is cyclic “lariat” structure
snRNP
small nuclear ribonucleoprotein
RNA protein complex acts as spliceosome: a large RNA-protein molecular complex upon which splicing of pre-mRNA occurs
spliceosome assembly
snRNA transcribed and exported out of nucleus
snRNA is methylated and forms complex with sm proteins
spliceosome assembly
snRNA transcribed and exported out of nucleus
snRNA is methylated and forms complex with sm proteins
snRNA enters nucleus and forms spliceosome
snRNP forms complex to perform cleavage and ligation by endogenous A
intermolecular and intramolecular base pairing stabilize spliceosome
spliceosome mediated splicing has 2 transesterification steps
CTD
carboxyterminal domain
CTD gets hyper phosphorylated
polyA tail added to 5’ end
snoRNA
pre-rRNA is processed in nucleolus by snoRNA ribonucleoprotein complexes
snoRNA: small nucleolar RNA
rRNA maturation process
pre-rRNA is chemically modified
U is modified to pesudoouridine
2’ O methlylation
5’ capping mechanism
5’ m7G cap protects mRNA from 5’ to 3’ endonucleases
a cap binding complex binds to 7-methylguanoside and initiates splicing of the first intron by stabilizing the interaction of the spliceosome complex
Mechanism:
GTP comes in
monophosphorylated
energy released to add G to the end of the RNA transcript
7-methylguanosine
methionine donates methyl group to carbon 7 of g
polyadenylation of eukaryotic mRNA
signal indicates formation of polyA tail
signal causes CPSF to bind to binding cite, other factors recruited
polyA polymerase synthesizes polyA tail
canonical isoform
all introns removed, all exones present
alternative promoters
mRNA synthesis starts after first one or few exons
alternative polyadenylation
polyadenylation occurs after inner exon
alternative splice cites
inner exon not included
intron retention
intron remains in mRNA transcript
alternative 5’ splicing cites
portion of intron in mRNA transcript
5’ end of intron
alternative 3’ splice cites
portion of intron in mRNA transcript
3’ end of intron
mutually exclusive exon
one exon or another exon included in transcript
cis-effect
mutation in gene causes improper splicing and improper protein formation
trans effect
gene is not mutated-spliceosome protein complexes are defective which causes improper splicing
siRNA
small interfering RNA that directly inhibits translation
miRNA
microRNA
directly inhibits gene expression
RNAi pathway
dicer cleaves dsRNA producing siRNA that is assembled onto RISC
RISC (RNA-induced silencing complexes): mediates interaction between siRNA and the target mRNA
mRNA cleaved and degraded
miRNA pathway
primary mRNA is modified by drosha to make precursor miRNA
precursor mRNA leaves nucleus
dicer complex forms mature miRNA
RISC binds to miRNA and blocks translation or cleaves mRNA
