Chapter 7 Flashcards
What is the general purpose of mRNA?
Codes for protein
Where and when is mRNA processed? Why can it work that way (location of modifying factors)?
In the nucleus during transcription
modifying factors are docked on the phosphorylated C-terminus tail of RNAPII
What is the relationship between the nucleolus and RNA?
It is the site of most rRNA synthesis and ribosome subunit assembly
Where and how does mRNA leave its processing site? What factors are required and what changes does it undergo?
Require 5* cap, exon junctions, and polyA tail
Passes through nuclear pore complex
Once in cytoplasm, 5* cap is exchanged for an initiation factor for protein synthesis
What is RNA capping and what is its purpose?
Helps with export from the nucleus, stability, and translation
Made up of a modified guanosine nucleotide on the 5* end of the RNA
Attached by 5→5 triphosphate bridge
What is polyadenylation and what is its purpose? How is it created?
Helps with export from the nucleus, stability, and translation
AAUAAA sequence signals for downstream cleavage by nuclease
Poly(A) polymerase adds AMP to the chain (ATP → PP + AMP)
Length of tail correlates with stability
Do prokaryotes, eukaryotes, or both have introns?
Only eukaryotes
What does an exon junction complex do?
Recognizes two exons spliced together
What are the conserved sequences for introns and exons? (general)
conserved sequences that mark the boundary and an A within the intron that serves as a branch point
Do introns have a purpose?
Yes, encode some small RNAs and are involved in cell differentation
Describe the chemical mechanism for the removal of introns (ignore enzymes for now)
Two transesterification reactions result in cleavage first at the 5* end then the 3* end of the intron, followed rapidly by ligation of the two exons
Intermediate formation of a lasso (lariat) with “A” as branch point
What does the spliceosome do? What is it made of (describe)? What do U1 and U2 do?
Catalyzes cleavage of intron and ligation of exon
Make of 5 snRNPs (Several proteins and a snRNA)
snRNA base pair with splitting sites and branch points
U1 recognizes splice site, U2 recognizes branch point
What is the purpose of alternative splicing?
Different mRNA/protein from same gene
Cell differentiation
Describe RNA world
RNA can act as template and catalyst (ribozyme) and is easier to synthesize than DNA, may have been first
What binds to the promoter in prokaryotes? Are there any conserved sequences?
Sigma factor, 2 (don’t need to know location, help sigma factor find promoter)
How many RNA polymerases do eukaryotes have?
3
What is the TATA box?
Conserved sequence upstream of the start of transcription
What is transcription factor IID?
The transcription factor that is the first to find DNA, its TBP protein recognizes the TATA box and bends the DNA
What is transcription factor IIH?
Acts as a helicase (uses ATP hydrolysis) and covalently adds phosphates to the tail of RNA polymerase II, a type of kinase
Describe eukaryotic initiation
The polymerase and its transcription factors all bind to the DNA and start transcribing when TFIIH opens the DNA helix and phosphorylates the tail of RNA Polymerase II
What are tRNAs? (general)
adaptors between mRNA and amino acid during protein synthesis
What adds amino acids to tRNA? How? What is a ‘charged’ tRNA called?
Amino acyl tRNAsynthestases add amino acids to tRNA via ATP→AMP, 20 types
Charged tRNA is called an amnoacyltRNA
Where does the energy for peptide bond formation come from?
Forming the bond between the amino acid and tRNA takes energy (ATP→AMP)
Breaking releases energy, catalyzes peptide bond formation
How do anticodons work? Give an example (ex: if the anticodon is 5* GCC 3*
Anti-codons base pair with codons and go 3→5 rather than 5→3
Ex: anticodon 5GCC3 pairs with 3CGG5 which is really 5GGC3 or Gly
What is wobble base pairing?
flexibility in 3rd base of codon, makes same amino acid
What is the eukaryotic 80S ribosome made of? What is the name and role of its non-protein components?
Made of ribosomal proteins and rRNA, has a large and small subunit
rRNA - core of ribosome (gives structure), catalyze protein synthesis
Describe the three sites of a eukaryotic 80S ribosome. Include the enzyme for peptide bond catalysis.
A Site: Where all aminoacyl tRNAs (except initiator tRNA) enter the ribosome
P Site: Peptidyl site, where the peptide bond is formed
Catalyzed by peptidyl transferase, a ribozyme (catalytic RNA)
E Site: Exit site, where tRNAs leave ribosome
Describe the process of translation relating to the ribosome sites starting from initiation (first tRNA) and ending with the final codon
Initiator tRNA carrying anticodon for AUG binds to P site, then second tRNA binds to A site and its amino acid is peptide bonded to the start codon. tRNA in P site moves to E and A moves to P. Synthesis continues until release factor binds to A site. Release factor is a protein that resembles a tRNA and hydrolyzes GTP to release amino acid.
What is a proteosome?
Proteasome is a large protein machine that degrades proteins marked by ubiquitin
Describe the chemical mechanism of initiation (binding to the mRNA)
Include all components and where the energy comes from
When the initiator tRNA and the small ribosomal subunit bind to the mRNA
Many initiation factors (eIFs) also bind to sununit and mRNA. They recognize 5* cap and subunit/tRNA moves to find AUG
Then GTP is hydrolyzed by eIF2s, the eIFs release, and large subunit joins complex
Describe initiation in prokaryotes (attaching to RNA)
Include where binding occurs
Initiation factors bind to 30S ribosomal subunit
Initiator tRNA and mRNA bind to Ribosome Binding Site (RBS)
Describe the transfer of energy for charging tRNAs, binding initiation factors, moving around amino acids,, and releasing
ATP → AMP for each charged tRNA
Hydrolyze GTP → Initiation factors
2 GTP per amino acid → guide to A site, translocation
Hydrolyze GTP → Release site
What was the first codon whose amino acid pair was discovered?
A poly U sequence
How were the matching amino acids for codons discovered?
Started with a poly U sequence, then made AAA and CCC
Then could create any RNA sequence, but could not control reading frame
Then made three nucleotide codons
Captured a complex of ribosome, mRNA codon, and aminoacyl-tRNA
