Self Study- RNA & Transcription Flashcards
What are the differences between RNA and DNA?
- Ribose instead of deoxyribose. 2’ OH group makes bonds more susceptible to chemical hydrolysis so is less stable than DNA
- Contains uracil instead of thymidine
- Has a number of modified bases (including methylated, all done post-transcriptionally)
- Primary single-stranded, which is not as stable (often form intramolecular base pairing called hairpins or RNA-protein complexes to increase stability)
mRNA
What is it?
polycistronic vs monocistronic mRNA?
mRNA Half-life (Exceptions)
- mRNA is direct carrier of genetic info from DNA to protein, 1% of RNA, determines cell’s phenotype and biochemical activity
- Polycistronic (prokaryotes)- mRNA encodes multiple proteins
- Monocistronic (Eukaryotes)- mRNA encodes 1 polypeptide chain
mRNA halflife is only minutes to hours, very short (Especially for histones). Exceptions include:
- Unfertilized egg (mRNA exists in inactive state until fertilization)
- mRNA for Hb in reticulocytes doesn’t turnover
Modifications to mRNA to extend half-life (5’ to 3’ direction)
- Inverted methylated bases- 5’ Cap- guards against nuclease attack, forms 5’phos-5’phos linkage w/ first nuelcotide of mRNA
- Leader sequence- After cap, 5’-nontranslated sequence
- Start codon- first 3 nuceotide sequence for amino acid translation
- Stop codon- last 3 nucleotide sequence, followed by 3’ non-translated tail
- poly A tail- 20-200 adenine nucleotides, length determines stability (not in histones)
tRNA
Functions (2)
Active sites (how many and function)
How much of cellular RNA
Functions:
- Activate amino acids for protein synthesis on ribosome
- Recognize codons in mRNA to ensure correct AA incorporated into peptide
Active Sites (2):
- Acceptor stem- 3’ OH terminal CCA which binds AA’s
- Anticodon loop- anticodon triplet which recognizes codons on mRNA
rRNA
function
percentage of cellular RNA
What are Svedberg units (S)
Are large and small particles in prokaryotes/eukaryotes?
Where are they synthesized?
- components of ribosomes where protein synthesis occurs
- 80% of RNA (most abundant)
- sedimentation coefficient during centrifugation, used for naming RNA/protein particles in ribosomes
- In both prokaryotes and eukaryotes but different sizes
- in nucleolus
Other RNAs
snRNA (Small nuclear RNAs)
scRNA (Small cytoplasmic RNAs)
mtRNA (mitochondrial RNAs)
RNP (ribonucleoprotein particles)
Ribozymes
RNAi (RNA interference)
- recognize introns on mRNA participating in splicing
- Select proteins for export where it serves as a signal recognition particle
- tRNA/rRNA/mRNA transcribed from mtDNA, only 1 tRNA per AA (4% of cellular RNA)
- function in RNA processing, splicing, transport, translation control, protein recognition particles that target proteins for export
- Enzymatic RNAs, part of RNP
- Control cell’s phenotype by shutting down development genes or altering their levels of expression, control cell differentiation
Transcription
Where does it take place?
Direction of transcription? How is DNA read?
Transcription bubble? Where does it form?
What is a Pribnow box?
Are promter sequences symmetrical?
Are promoter sequences of equal strength?
- In nucleus or mitochondria
- 5’ to 3’, DNA read 3’ to 5’
- Point at which DNA is initially opened, forms at promoter which is recongized by RNA polymerase
- TATAAT sequence at -10 region where promoter is often found
- No, this ensurs it proceeds in only 1 direction
- No, can be weaker or stronger depending on enhancers or repressors (sequences that serve as protein binding sites that aid or hurt transcription)
RNA polymerases
Direction
Requirements
Proofreading activity?
- 5’ to 3’
- DNA template (but don’t need primer)
- No, mroe error-prone
Prokaryotic RNA polymerase
Subunits
holoenzyme?
Core enzyme?
Antibiotic sensitive to…
- 2 alpha, beta, beta’, omega, sigma
- All subunits together
- All but sigma subunit, which is released from RNA polymerase as it begins to synthesize RNA
- rifampicin
Eukaryotic RNA polymerases
4 types (function, inhibitor sensitivity, % of activity)
Nucleolar organizer
4 types:
- RNA Polymerase I- for rRNA, makes a single transcript w/ all subunits (not inhibited, 50% of activity)
- RNA Polymerase II- for mRNA, codes for proteins made from structural genes (very sensitive to alpha-amanitin [mushroom poison], 40% of activity)
- RNA Polymerase III- for tRNA & 5S rRNA (inhibited by alpha-amanitin, 10%)
- mitchondrial RNA polymerase- all types in mt, sensitive to rifampicin
- Nucleolar organizer is area in nucleolus with several hundred copies of each rRNA gene (which has a copy of each subunit)
Post-transcriptional RNA processing
What does modification of primary transcript typically include?
rRNA
tRNA
mRNA
- Modification includes:
1. removal of external/internal nucleotides by ribonucleases
2. base modification
3. addition of nucleotides - rRNA: each terminal sequence and spacer sequences removed by ribonucleases
- tRNA:
1. 5’ end removed by ribonuclease P (ribozyme)
2. 3’ end removed and terminal CCA synthesized
3. Nucleotide bases modified (more than all nucleic acids) - mRNA:
1. Add 3’ terminal polyA tail, methylated internal nucleotides, methylated inverted 5’ cap
2. Remove intron via splicing
Splicing
What are snRNPs (snurps)
How does splicing occur?
How do intron sequences start and end?
What is alternative splicing?
- Bind mRNA primary transcript to remove introns by splicing
- Break RNA at 5’ end of intron and join exons together
- Start w/ GU (donor site) and end w/ AG (acceptor site). But not all GU and AG sequences are splice sites, U1RNA and U2RNA are snurps that can discriminate this
- When some exons are also removed to form slightly different mature mRNAs which code for slightly different proteins (i.e. tropomyosin in different cell types)
RNA Turnover
How are RNA molecules fixed?
Is there RNA repair?
tRNA and mRNA half-life
What degrades RNA?
- They get degraded and replaced by new ones
- No
- tRNA: ~5 days, mRNA: 30 min-30 hrs
- Ribonucleases (exo or endo nucleases)
