RNA Metabolism Flashcards
What has greater structural diversity: DNA or RNA?
RNA
What process makes RNA?
transcription of DNA
What are the 3 major types of RNA?
mRNA
rRNA
tRNA
mRNA
messenger RNA
carries info from DNA
rRNA
ribosomal RNA
makes ribosome that makes protein
tRNA
transfer RNA
translates mRNA into amino acids
siRNA
small interfering RNA
block gene expression by increasing mRNA breakdown and decrease in protein
made synthetically
miRNA
microRNA
regulate mRNA
suppress translation
come from other RNA
snRNA
small nuclear RNA
helps process mRNA
snoRNA
small nucleolar RNA
helps process rRNA
How is RNA synthesis similar to DNA synthesis?
same fundamental mechanism
same direction
uses a template
How is RNA synthesis different from DNA synthesis?
no primer required
only copies small sections at a time
only 1 strand is a template strand
RNA Polymerase
makes RNA and binds to promoter region in DNA
RNA synthesis makes more errors than DNA synthesis. Why is this not as detrimental?
more copies of RNA and higher turnover
What do the magnesium ions in RNA synthesis do?
one stabilizes the deprotonated 3’ OH
one coordinates incoming nucleotide
DNA bubble
about 17 base pairs of DNA where active replication is ongoing
What do promoters signal?
start point
level of expression
template strand
sigma factor
determines the promotor to bind to
sigma subunits
bind to different promoters
used under different conditions
In DNA dependent synthesis, RNA polymerase and sigma factor bind together and then to what?
The promotor
What opens the complex to start transcription in DNA dependent synthesis?
DNA bubble
In the elongation phase of DNA dependent synthesis, sigma factor dissociates. What binds in its place?
NusA
Can RNA polymerase be resused?
yes
cAMP receptor protein
activator; turns on genes that metabolize non-glucose sugars
Lac Repressor
shuts off genes that metabolize lactose
Protein regulation starts with?
RNA regulation
Rho independent termination
palindrome causes a hairpin to form
multi-A sequence causes RNA polymerase to pause
RNA breaks H bonds and leaves the polymerase
Rho dependent termination
rho helicase binds to rho utilization sequence and moves along the RNA strand
separates RNA from DNA to allow RNA to leave
requires ATP
RNA Polymerase 1 (eukaryotes)
makes pre-rRNA
RNA Polymerase 2 (eukaryotes)
makes pre-mRNA and some specialized
uses proteins, enzymes, and transcription factors
major promotor: TATA box
conserved and have well-defined function
RNA Polymerase 3 (eukaryotes)
makes pre-tRNA and some specialized
TF2F
gives specificity
TF2B
recruits TATA binding protein and TF2F
TF2E
helicase that opens the bubble
TF2H
kinase that phosphorylates the C terminal domain
Actinomycin D
targets RNA polymerase as a drug
antibiotic/anticancer
Rifampicin
targets RNA polymerase as a drug
antibiotic used in TB treatment
Amanitin
mushroom toxin selective for eukaryotes
primary transcript
newly made RNA
What does RNA Splicing remove?
introns
During RNA processing, mRNA is given what two things?
a 5’ cap and a 3’ poly A tail
What kind of bond is the 5’ cap ?
5’-5’ phosphodiester bond
What is the purpose of the 5’ cap?
to protect mRNA from degradation and help it bind to the ribosome
When does capping occur?
When RNA is being made
S-adenosyl-methionine (SAM)
methylates the terminal G and first few ribonucleotides in mRNA capping
How many adenosines does the poly A tail have?
80-250
In eukaryotes why is the poly A tail good?
serves as a binding site for proteins; prevents degradation
differential RNA processing allows a single gene to?
make multiple products
Multiple processing sites allows the cell type and environmental factors to?
determine the product
What does rRNA start as?
pre-rRNA
Which contains the 16s rRNA? The 18s?
16- bacteria
18- eukaryotes
Rnase D
removes from the 3’ end
Rnase P
removes from the 5’ end
All tRNA’s have 3’ terminal with the sequence?
CCA
Where do snoRNAs come from?
introns of other RNAs
Where do snRNAs come from?
larger pre-snRNAs
pri-miRNA is cleaved to?
pre-miRNA
pre-miRNA is cleaved to miRNA by what?
dicer and helicase
4 classes of introns
- self-splicing, G nucleophile
- self-splicing, A nucleophile
- Spliceosome Catalyzed
- Endonuclease Catalyzed
Self-splicing, G nucleophile
splicing occurs via 2 transesterifications
3’ OH of an external G acts as a nucleophile and breaks the strand
3’ OH of the new end attacks the 3’ end of the intron and removes it
Self-Splicing, A nucleophile
splicing occurs via 2 transesterifications
2’ OH of an internal A acts as a nucleophile and attacks the 5’ end of the intron
3’ OH of the new terminus attacks the 3’ end of the intron cutting it out
Spliceosome
has snRNPs
2’ OH attacks 5’ end
3’ OH attacks 3’ end
In Group 3 RNA Processing what do the introns contain?
GU at 5’ end
AG at 3’ end
Endonuclease
used mostly in tRNA
needs ATP
cleaves the backbone at both ends of the intron
What is the main indicator of gene expression?
[mRNA]
What is the degradation rate for vertebrates? Bacteria?
Vertebrates- 3hrs
bacteria- 1.5 min
What is mRNA degraded by?
ribonucleases
Reverse transcriptase makes DNA from?
RNA
Retroviruses
incorporate their genome into the host
have a high error rate and high mutation rate
gag
viral structural proteins
pol
encodes reverse transcriptase, integrase, and protease
env
envelope proteins
What 3 reactions does reverse transcriptase catalyze?
- DNA synthesis from viral RNA
- Degradation of viral RNA
- Complimentary strand synthesis
How does the double stranded DNA get inserted into the host?
with an integrase
HIV
lentivirus
its reverse transcriptase has a high error rate and fast mutations
leads to drug resistances
Why can’t we make a vaccine to HIV?
the envelope changes
Dolutegravir
integrase inhibitor
Zidovudine
nucleotide reverse transcriptase inhibitors
Efavirenz
NNRTI
Telomeres
made of TG repeats
protects ends of chromosomes
require a special enzyme to maintain their length
Telomerase
acts as reverse transcriptase; carries its own template;
T loop
TG strand inserts itself back into the double helix
Telomerase activity can enhance?
the ability of cells to continue to divide
Telomere length in fibroblast cells is inversely proportional to?
the age of the person they came from
Do somatic cells have telomerase activity?
no
Transcription
DNA -> RNA
Translation
RNA->Protein
Reverse Transcription
RNA -> DNA
