lecture 15, 16 Flashcards
what does RNA stand for
ribonucleic acid
what is RNA made from?
a DNA template
trasncription
the process of making RNA using DNA template
what are the four ribonucleotides found in RNA?
adenine, guanine, cytosine, and uracil
what are the ribonucleotides that pair with each other?
A to U, G to C
what is different about the structure of RNA vs DNA?
RNA has an OH group instead of H in DNA, making it less stable
what about RNA makes base-pairing slightly different?
when RNA folds, U can pair with A or G
what is the benefit behind U being able to bind with A or G?
more options in forming secondary structures
is RNA single or double stranded?
single stranded
what benefit comes out of RNA being single-stranded?
it is able to fold on itself to form secondary structures
ribozyme
RNA that can catalyze reactions
mRNA
encodes for proteins
functional RNA
involved in regulating gene function
can functional RNA encode for proteins?
no
which strand is RNA complementary to?
the template strand
which strand is RNA identical to with the exception of U swapped with T?
non-template strand
what is another name for the non-template strand?
coding strand
where does transcription start on the gene?
between the promoter and the first codon in a (+1) region
what RNA regions do not code/are considered untranslated regions?
5’ UTR and 3’ UTR
Where is the 5’ UTR located?
just before the first/start codon
where is the 3’UTR located?
after the stop codon
promoter
a region of DNA where RNA polymerase holoenzyme binds to initiate transcription for the gene
how far is the promoter from the (+1) site?
50-100 bps
when is a promoter considered active?
when the promote binds the RNA polymerase holoenzyme/when transcription occurs
when is the promoter considered inactive?
when there is no transcription
what is the purpose of the -35 consensus sequence?
its a site that recognizes RNA pol
what is the purpose of the -10 consensus sequence?
to help RNA pol open DNA
What binds to the -35 and -10 consensus sites?
RNA pol sigma factor
What does the beta subunit do?
Harbors the catalytic site
what does beta prime subunit do?
assists in catalysis
what do alpha and omega factor subunits do?
regulation and assembly
transcription bubble
the single strand DNA region formed during transcription inside RNA pol
in prokaryotes, what are the two main termination mechanisms in prokaryotes
intrinsic and rho-dependent termination
intrinsic termination
occurs through RNA pol activity with the formation of a loop structure in the RNA that is rich in GC, followed by an upstream poly-U sequence
rho-dependent termination
RNA pol encounters a C-rich region and signals a pause in transcription, and the protein rho binds to the RNA to find the rut region and terminates transcription
in prokaryotes, where do transcription and translation occur?
In the cytoplasm
in eukaryotes, where do transcription and translation occur?
in the nucleus and cytoplasm respectively
how many RNA pol do prokaryotes have?
one
how many RNA pol do eukaryotes have?
three
what does eukaryotic DNA wrap around?
proteins (histones)
what needs to be removed/moved in eukaryotes for transcription to occur?
histones
what is the equivalent of mRNA in eukaryotes?
RNA pol II
what is the purpose of RNA pol I and RNA pol III?
to make functional RNA
RNA pol II
transcribes mRNA and some functional RNA
general transcription factors
protein complexes that help RNA pol II recognize and initiate transcription at the promoter
what do many RNA pol promoters use as a binding site for transcription?
a TATA box or an INR (in pol II)
what general transcription factor does RNA pol II mostly rely on?
TFIID
what does TFIID do?
binds the promoter at the TATA box via TBP
describe a summary of transcription initiation in eukaryotes
binding of TBP and TFIID -> formation of preinitiation complex- > RNA pol II begins elongation
what happens after RNA pol II synthesizes the RNA
It leaves the promoter and TFIID behind
what are the major transcriptional processes in eukaryotes?
(1) 5’ Cap
(2) splicing
(3) polyadenylation
5’ Capping process
7-methylguanosine attaches to the 5’ UTR end with three phosphate groups
what is the purpose of the 5’ capping process?
to protect the RNA from degradation and provides binding sites for proteins that assist in translation
splicing
an RNA transcription process that removes introns
what is the purpose of splicing?
to remove non-coding sequences from the pre-mRNA to make a “proper” mRNA for protein translation
polyadenylation
An RNA transcription process that adds a poly-A tail to the end of mRNA
what is the purpose of polyadenylation?
to protect the RNA from degradation and stimulates translation by interacting with translation machinery
open reading frame (ORF)
the nucleotide sequence from start to stop but does not include stop
coding sequence (CDS)
the nucleotide sequence from start to stop that will appear in the mRNA that will appear in the mRNA
in prokaryotes, what is ORF equal to?
CDS
in eukaryotes, what is ORF equal to?
CDS + introns
pre-mRNA
RNA that has not been processed yet
What do all introns require?
GU at the 5’, AG at the 3’, and an A in between, but closer to 3’
snRNPs
small protein complexes involved in splicing
describe how a spliceosome is constructed
U1 and U2 SNPs bind to the 5’ splice site (U1) and internal A (U2) , then U4-5-6 complex joins to complete the full spliceosome
describe how the spliceosome functions following assembly
some U SNPs are displaced followed by the formation of a Lariat structure, where 1 end of the intron attaches to the internal A while the other is cleaved, concluded by the joining of the exons
list the different types of functional RNA
tRNA, rRNA, snRNA, miRNA, siRNA, piRNA
tRNA
transfer RNA; carries amino acids to the ribosome for protein synthesis
Which RNA polymerase transcribes tRNA?
RNA pol III
rRNA
ribosomal RNA; RNA components of the ribosome that have structural and enzymatic activities
Which RNA polymerase transcribes rRNA?
RNA pol I except 5S rRNA (transcribed by RNA pol III)
snRNA
small nuclear RNA; involved in the splicing of eukaryotic RNAs into mRNA
Which RNA polymerase transcribes snRNA?
RNA pol II and RNA pol III
miRNA
micro RNA; regulates translation and infection via regulating RNA stability
siRNA
small interfering RNA; help prevent mobilization of transposons and viruses
piRNA
piwi-interacting RNA; control transposition (jumping genes that could be harmful)
how is siRNA formed?
using the enzyme DICER
DICER
an enzyme that chops up double-strand RNA
describe the siRNA formation process and function
DICER chops double-stranded RNA into siRNA and mRNA where siRNA is bound to RISC and separated, then mRNA is bound to RISC and degrades it
Why is it important for RISC to degrade mRNA?
in the event that some mRNA could be harmful if translated or if its not meant to be expressed as a protein
how is miRNA formed?
using the enzyme DICER for processing
describe the miRNA formation process and function
DICER processes the RNA and removes the hairpin loop, then is transferred into RISC and separated, in which miRNA uses it in identifying mRNA targets to repress translation or degrade mRNA
what is the key difference between miRNA and siRNA?
siRNA is rapid degradation of mRNA before it approaches translation, miRNA is controlled and more flexible
what genes utilize miRNA over siRNA?
endogenous genes; genes that are naturally present in an organism
RNA decay
The process by which RNA is destroyed over time
