Transcription/Translation Flashcards
Transcription is the first step in ___
gene regulation
what is responsible for RNA synthesis
RNA polymerase
What is the difference between RNA pol and DNA pol
RNA pol doesn’t require a primer sequence to initiate RNA synthesis
RNA polymerase I (its products and location)
Products - 5.8S, 18S and 28S (ribosomal RNAs) structural component- excluding 5S rRNA
Location - nucleolus
RNA polymerase II (its products and location)
Products - Nuclear pre - mRNA
Location - nucleus
RNA polymerase III (its products + function and location)
Products - transfer RNA (tRNA)
The function of the product - serve as adaptor molecules that align amino acids during mRNA template
Location - Nucleus
Genome size increases therefore, there is a ____ protein-coding sequence and ______ non - coding sequences
a decrease in protein-coding sequences
Increase non - coding sequences
What are transcription factors
proteins required for RNA polymerase II to initiate transcription
There are 2 categories of transcription factors:
- General transcription factors - involves in transcription from all polymerase II promoters
- Gene-specific transcription factors - bind to the promoter and an enhancer element
What is the function of the general transcription factors
Recruits RNA polymerase II
Formation of the preinitiation complex
What if the function of gene-specific transcription factors
bind to promoter + enhancer element
Steps of Transcription: (9 steps)
- TATA box (regulatory seuqunece) transcribed by RNA pol. II
- TBP binds to the TATA box
- TAFs are proteins associated with TBP in the genral transcription factor, TFIID
- TFIIB binds with TFFID at core pormoter
- RNA pol. II + TFIIIF are recruited using TFIIB to get to TFIID + promoter
- C- terminal domain of RNA pol. II requires phosphorylation prior to initiation of transcription
- TFIIE + TFIIH complete the formation of the initiation complex
- TFIIH has both a kinase activity that phosphorylates CTD and a helicase that unwinds the DNA
- RNA pol. II starts synthesis and leaves the promoter and TFIID behind
Steps in Elongation:
Translation
- tRNA/ribosome complex is startingat AUG start site of mRNA (P site of the ribosome)
- The next charge tRNA comes to the A site
- Peptide bond formation occurs between the amino acids
- Ribosome moves downstream - now the A site is ready for the next charged tRNA
- Repeat steps 1-4
What is different about a mature mRNA versus a regular mRNA
A mature mRNA consists of a 3’poly AA tail, PABP and 5’m7G cap eIFs
Steps in Initiation - Translation
- met tRNA + small ribosomal subunit + initiation factors
* Charged tRNA binds to 40S subunit before 40S binds to the mRNA - the 40S/tRNA/initiation factor complex meets up with a mature mRNA + binds to the 5’m7Gcap
- The entire complex sites on 5’end of the mRNA + slides along the mRNA with it finds AUG start codon.
- This requires energy
- There is not a 60S ribosomal unit yet in step 3! - Most of the complex (except for 40S subunit + tRNA) dissociate form start site 60S subunit attaches to 40S + tRNA
- GTP hydrolysis is required to release the initiation factors.
What is PABP
PABP is a Poly A binding protein
- It helps recruit enzymes for polyadenylation and remain bond to the poly-a-tail until translation
- Protects poly-A tail fro degradation
- Binds mRNA to translation initiation factors to facilitate binding to the small ribosomal subunit
Splicing - what is it and when/where does it occur?
Splicing - introns are removed and exons are joined together to form a mature mRNA
- Occurs in the nucleus before the RNA migrates to the cytoplasm to be translated into proteins
- Only the pre mRNA transcript contains both introns and exons. Mature mRNA only contain uninterrupted coding information
Name for coding and non - coding sequences
Intorns = non - coding sequences
Exons = coding sequences
Do Prokaryotes and Eukaryotes have introns?
No, only eukaryotes
Two mechanisms of splicing
- Self - splicing (enzymatic activity - ribozyme) no energy required
- RNA/protein complex-mediated splicing - spliceosome
which snRNAs are required for splicesome - dependent splicing
U1, U2, U4, U5, and U6
How does the spliceosome function?
snRNA in the SNRPs bind the transcript through nucleotide interactions with the conserved splicing sites to bring the exons in close proximity for the reactions to occur
Order of events in each exon/intron/exon (splieosome)
- U1 binds 5’ site, U2 binds branch site
- U4/U5/U6 bind to U1/U2
- Axon - axon boundaries brought closer
- U4/U6/U1 leave the complex
- Transesterification reactions take place
- Intron sequences are removed with the formation of a loop (lariat)
Poly A polymerization
The 3’ poly-A tail - the poly-A polymerases recognize processed transcripts as templates to add the poly-A tail
What is the purpose of the poly(A) tail
the enhance mRNA stabilization in the cytoplasm
True or False:
The complexity of the transcriptome mirrors an increase in the genome
False
Transcription in Prokaryotes
- RNA chain Initiation
- RNA polymerase (holoenzyme) binds directly to a promoter in DNA
- Unwinds the two strand of DNA by RNA polymerase to provide a single-stranded template
- phosphodiester bonds between ribonucleotides occur
- RNA polymerase binding is guided by the recognition of cis-elements in the promoter of genes
- +1 site is where transcription states (between promoter regions and ATG)
- RNA chain elongation
Transcription in Prokaryotes - RNA chain Termination
- RNA chain grows from 5’ to 3’
- RNA poly (helicase) unwinds DNA
- DNA rewinding happens by reforming hydrogen bonds between the two DNA strands
- RNA poly detached from DNA template + RNA strand is released
What is the difference in RNA pol in prokaryotes and Eukaryotes
Prokaryotes - 1 RNA pol
Eukaryotes - 5 RNA pol - all RNA pol in eukaryotes requires the activity of trasncription facotrs to intiiate polymerization
True or False - Both prokaryotes and Eukaryotes experience post-transcriptional modifications
False - only Eukaryotes experience post-transcriptional modifications like intron splicing/5’ capping and 3’ polyadenylation
where does transcription and translation occur in both eukaryotes and prokaryotes?
Eukaryotes - transcription occurs in the nucleus and translation occurs in the cytoplasm
Prokaryotes - both occur simultaneously in the cytoplasm
RNA pol IV (its products and location)
Products - Small interfering RNAs
Location - Nucleus (plant)
RNA pol V (its products and location)
Products - some siRNAs plus noncoding (antisense) transcripts of siRNA target genes
Location - Nucleus (plant)
Which RNA pol is found in a different location than the others
RNA pol I - it is found in the nucleolus whereas the others are found in the nucleus
What assists RNA pol II and why
Transcription factors - to help recognize and initiate transcription at the promoter
Translation invovles which RNA polymerases
RNA pol I - all rRNAS but 5S rRNA
RNA pol II - mRNA
RNA pol II - tRNA, 5S rRNA
Describe the components of the Prokaryotic 70S ribosome
Large 50S subunit (28S and 5S rRNAs)+ 30S subunit (16S rRNA)
Describe the components of the Eukaryotic 80S ribosome
Large 60S subunit (28S, 5.8S and 5S rRNAs) + 40S subunit (18S)
tRNA
small adapters between amino acids and the codons in mRNA molecules
tRNA contains modified nucleotides to avoid mispairing with the codon
Aminoacyl
tRNA synthetase attaches an amino acid to its specific tRNA
What would cocur if the information and anticodon did not match a tRNA?
- The tRNA would not be able to catalyze the addition of the incorrect amino acid in the peptide chain
- would be blind to the incompatibility and would normally catalyze the incorrect amino acid.
The genetic code is composed of ____ and is non - _____ and is comma _____
nucleotide sequence and is non - reversible and is comma free
Start and Stop codons
Start- AUG
Stop - UAA, UAG, and UGA
What is Hachioji DNA
8 nucleotides instead of 4 (A-t, G-C, Z-P, S-B)
can be replicated and transcribed
What is the Wobble Rules
Wobble Rules identify base-pair interactions between mRNA (3’ end of codon) and tRNA (5’ end of anticodon) (do not follow Watson and Crick Rules
The wobble excpetion is when…
there is a degeneracy of the third nucleotide of the codon only happens AFTER the first tow nucleotides form stable interactions with the corresponding anticodon
Amber (UAG) mutations (what occurs + the result)
mutations that introduce a premature stop codon in the transcript will cause a short version of the protein
Result - leads to a lack of function and a mutant phenotype
What is the effect of a nonsense mutation
a stop codon therefore, it prevents the amber mutant from terminating their polypeotide prematurely
