Chpt 29: Transcription Flashcards
Types of RNA
- ribosomal RNA-rRNA
- transfer RNA-tRNA
- messenger RNA-mRNA
- small nuclear RNA-snRNA
- micro RNA-miRNA
- small interfering RNA- siRNA
Transcription of Genes
Genes may or may not be transcribed depend on the needs of particular cell type
- expressed=Turned on
- unexpressed=Turned off
Gene
- discrete functional unit of DNA
- when expressed/transcribed can produce a functional product
a) rRNA, tRNA, snRNA
b) mRNA- translated into polypeptide sequence - open reading Frame
tRNA
transfer RNA
- small single stranded ribonucleotides
- adaptor between RNA and protein
- at least one tRNA per amino acid
- folds into clover leaf or L shape due to intramolecular Hydrogen Bonding between complementary base pairs
Post transcriptional modifications
-bases modified to produce 3’ end CCA (not encoded in DNA) which is an attachment site for amino acids
Anticodon:
- 3 nucleotide sequence specifies amino acid attachment to 3’end
- will H-bond to the complementary base seq on mRNA called CODON
rRNA
ribosomal RNA
- single stranded ribonucleotide
- incorporated into ribosome
- folds due to intramolecular H-bonds of complementary base pairs to form complex structure
- Size differs between prokaryotes and eukaryotes
Eukaryotic vs Prokaryotic rRNA
Prokaryotic rRNA-
70s ribosome divides into 50S and 30S subunits
-50s large ribosome subunit contains 23S and 5s rRNA
-30s small ribosome subunit contains 16S rRNA
Eukaryotic rRNA:
80S ribosome divides into 60S and 40S subunits
-60S large ribosome subunit contains 28S, 5.8S, and 5S rRNA
-40S small ribosome subunit contains 18S rRNA
mRNA
Messenger RNA
1) single stranded ribonucleotide
- in a heterogenous population the mRNA size varies by length of gene (protein encoded)
2) NO intramoleculer H-bonds
Translated into protein sequence
- read by ribosome and broken up into codons
- anticodons of tRNA bind to codon of mRNA during translation
Prokaryotic mRNA and eukaryotic mRNA
BOTH have 5’ and 3’ UTR-untranslated regions that doesn’t encode protein
Prokaryotes
-Polycistronic- encode multiple polypeptide chains
Eukaryotes
- monocistronic-encode single polypeptide chain
- process in the nucleus and capped, polyaddenylated, and spliced
snRNA
Small Nuclear RNA-EUKARYOTES ONLY
- small ribonucleotides
- involved in splicing (spiceosome)
RNA polymerase
synthesizes RNA in the 5’ to 3’ direction complementar to DNA template
- antiparallel to DNA template
- does not synthesize primers for replication
Requires:
- DNA template
- ribonucleoside triphosphate-A, U, G ,C
- Mg 2+ (2)
- NO primer needed because synthesis begins de novo at +1 nucleotide
- NO nuclease acitivity because Error rate is 1mistake/ 10^4/5 base pairs
Prokaryotic RNA polymerases
Single RNA polymerase
-multiple subunits
Eukaryotic RNA polymerases
Three RNA polymerases with multiple subunits
RNA poly I
-synthesizes pre 45S rRNA as single transcript which contains 18S, 5.8S and 28S rRNA
-functions in nucleolus’
-insensitive to alpha amanitin
RNA poly II
- synthesizes pre-mRNA and snRNA
- functions in nucleoplasm (outside the nucleolus)
- strongly inhibited by alpha aminitin
- contains a C-terminal domain called the CDT consisting of multiple repeats of YSPTSPS consensus sequence
RNA poly III
- synthesizes tRNA and 5.0S rRNA
- functions in nucleoplasm
- sensitive to high concentrations of alpha amanitin
Three stages of Transcription
Initiation
- identificaiton of promotor
- unwinds region surrounding promotor
Elongation
-RNA polymerase synthesizes RNA
Termination
-detects termination signals
Promotor
conserve “consensus” nucleotide sequences
-identified by sigma factors
RNA polymerase Active Site
Growing RNA chain provides 3’ OH
-RNA poly provides three conserve Asp residues which bind 2 Mg2+ ions
Prokaryotic RNA polymerase structure
Holoenzyme (core enzyme + sigma factor) Core enzyme-RNA synthesis -2 alpha subunits -1 beta subunit -1 beta prime subunit -1 omega subunit
Sigma Factor-identifies promotor
-different sigma factors identify different promotors
Termination Rho factor
-some require Rho some don’t
Prokaryotic Initiation step
Holoenzyme binds to Promotor
Prokaryotic Promotors
1) -10 Sequence
- Pribnow or TATA box
- 5’ TATAAT 3’
2) -35 sequence
UP element
Upstream element
- found in only high expressed genes
- 40 to 60 nucleotides 5’ from transcriptional start site
- Binds alpha subunit of RNA polymerase
Consensus Sequence
a nominal sequence inferred from multiple imperfect example
-average
Types of Sigma Factors
FOR PROKARYOTES Sigma 70-Most genes Sigma 32- Heat shock Sigma 28- Stationary phase, stress Sigma 54-Nitrogen metabolism -adds specificity to RNA polymerase -Serves as a switch; Quickly changes gene expression in response to environmental conditions
Prokaryotic Elongation Step
HOLOenzyme synthesizes RNA complementary to DNA template
-sigma factor is released after addition of first nucleotide (usually purine)
0Topoisomerase I and II relax supercoiling ahead of unwinding of helix
-unwound regions is called transcriptional bubble
Naming the DNA strands
- template
- coding
Template=noncoding=antisense (-) strand
-strand read by RNA polymerase-complementary to mRNA seq
Coding= Sense (+) strand
-DNA strands with same sequence as mRNA except U subs for T
Prokaryotic Termination step
RHO dependent termination
-Requires Rho factor
Rho independent termination Requires 2 features 1)DNA sequences must contain a palindrome -RNA transcript forms stable hairpin 2) 3' to hairpin -RNA contains stretch of U's -lower melting temp
