lecture 15 Flashcards
(25 cards)
what is the difference between DNA and RNA?
-has uracil pyramidine instead of thymine
-has ribose sugar which has an -OH on the 2’ carbon, where as deoxyribose has -H on 2’ carbon
RNA HAS catalytic activity
what is the function of mRNA, rRNA, and tRNA?
-mRNA: conveys genetic message of DNA , are protein producing genes , ONLY form of RNA that undergoes translation
-rRNA: combines with many proteins to make the ribosome, responsible for translation
tRNA: carries amino acids to the ribsome for construction of proteins
what genes does RNA pol 1,2,3 transcribe?
1: rRNA–> metabolic activity
2: mRNA
3: tRNA
what are the other 4 RNA in eukaryotes and their function?
telomerase RNA—– template for synthesis of repeating DNA sequence
SNOrna—- rna processing
snRNA—in nucleus where it participates in mRNA processing and intron removal
miRNA + siRNA —recognize regulatory RNA,
postranscriptional gene expression,
controlling stability or translatability of mRNA
the coding strand (nontemplate) is _____ to the template strand
complementary & identical to the RNA
what activates the RNA pol in bacteria ?
what does it mean that is is a holoenzyme?
what are the 5 subunits of bacterial RNA pol?
-binding to sigma subunit–> induces conformational change in the core enzyme, allowing it to bind to the promoter
-when incontact with its subunits, it has full enzymatic activity
a’ and a: for structure
b: for catalytic activity
b’: for DNA binding
omega–> for complex assembly
in prokaryotes, what is the promoter like?
upstream of the + 1 nucleotide
-10 region is the Pribnow box: 6 AT rich region, closer to promoter
-35 region: TTGACA, more upstream
-35 and -10 regions are not conserved. and have variation
how does transcription intiation in prokaryotes work?
—holoenzyme binds to ds promoter–> forms closed promoter complex
—around -10 holoenzyme unwinds DNA around -10–> forms open promoter complex
how does transcription elongation in prokaryotes?
-holoenzyme beings RNA synthesis by using template strand and stays intact until 8-10 RNA nt have been joined
-are the 8-10 RNA nt–> sigma factor disassociates from the core enzyme
-RNA pol continues as DNA unwinds
-end product is RNA that is complementary to the template strand & identical to the nontemplate except the U
how does transcription intrinsic termination work in prokaryotes?
what makes the RNA pol slow down + release the transcript?
dependent on repeat DNA sequences that are inverted, which produces mRNA with complementary segments that are able to pair with itself + formation of stem loop (hairpin) of the string of uracils complementary to the adenines
hairpin +poly UUU at the 3’ end causes RNA pol to slow down –> A/U is weak, so its makes RNA pol release the transcript
how does Rho dependent termination work in prokaryotes?
-mRNA gene rho utilization site is transcribed–> producing the rut site
rho protein will attach to the rut site & moves towards the RNA pol
-when RNA pol reaches the termination sequences with inverted sequences, causing the hairpin in the mRNA, RNA will pause & rho protein will catch it
rho makes mRNA drop off the RNA pol
what is the eukaryotic promoter like?
TATA box at -25, which has 6 bp TATAAA because its easier to separate
how does RNA pol 2 bind to the promoter in eukaryotes?
what are TF functions?
which proteins form TF11D and what forms the intiation & pre initiation complex?
help from transcription factors (TF)
-bind to promoter regulatory sequences& influence initiation directly or indirectly —> those that are directly interacting w RNA pol 2 are TFII (TF2)
-TFIID ( TATA binding protein + TBP associated factor) binds TATA
–Initation complex forms when: A,B, RNA pol 2, F join TFIID at TATA
–Preintiation complex forms when: when E and H join
-once assembled, directs RNA pol to +1 region
what are enhancer + silence sequences?
bind proteins that bind with the proteins at the promoter and drive transcription –> usually upstream of the genes they regulate
bind proteins that bind DNA and fold them, so RNA pol 2 can’t start
what is euchromatin and heterochromatin?
euchromatin: uncondensed & can undergo transcription
hereterocrhomatin: condenses and show low levels on gene transcription
promoters recognize by pol 1 have what 2 elements ?
pol 3 promoters have?
– core element + upstream control element
- internal control region ( ICR)
how does eukaryotic elongation and termination work?
elongation—> RNA pol 2 is reales from the GTF in the preinitiaton complex
termination: there is a polyadenylation signal on the mRNA, downstream of the stop codon, which ribonuclease will cleave RNA
-after cleavage–>poly A polymerase adds 100-200 AA’s at the end of the 3’ end, which stabilizes the mRNA
RNase: attacks and digests the residual RNA transcript attached to RNA pol 2 after cleavage
how does capping of the pre-mRNA work by RNA pol 2 in eukaryotes?
what is the purpose?
-guanylyl transferase adds G to the 5’ end of pre mRNA
the G without 2 phosphates is joined to the mRNA to form a 5 to 5 linkage
- methyl transferase adds methyl to the nitrogen of the new guanine with 2 phosphates
- protecting from degradation + allows for transport + allows intron splicing
which eukaryotic mRNA transcripts do not undergo poly adenylation?
histone proteins
what are introns and exons ?
how are introns removed
introns do not have complementary regions in mRNA, so they must be getting rid of via snRNA
-exons are joined together and have their complementary regions in mRNA
how does splicing work?
what is the splice some?
5’ splice site is at the 5’ intron end—> GU
3’ splice sit have pyrimidine rich region AG at the end
snRNA + proteins, which base pair with/ RNA to find the right site
the splice some cleaves the 5’ splice site
forms lariat intron structure, that binds 5’ intron end
3’ splice site is cleaved
splices exons + released the lariat
what is the significance of the CTD of RNA pol 2?
associated with capping, splicing, and polyadenylation
-phosphorylation of the CTD allows the binding of 5’ capping enzymes to carry out their functions
-has RNAse that gets rid of the additional RNA pol on the 3’ end after cleavage
what is alternative pre mRNA splicing?
can be spliced in alternative patterns in different types of cells, which can produce different mature mRNA is different cells
ex: rat a tropomyosin
some rRNA have ___ activity and are able to ____ splice introns without the aid of proteins
catalytic actiivty
self splice
