Lecture 8/31/18 Flashcards
What is a fundamental part of tRNAs 3D structure?
Number of modified biochemical mods
A. Psi = Psuedouriodine
B. D = dihydrouridine
Remember AA is attached to CCA-3’ (acceptor stem)
What happens at the 3rd position of the anticodon?
Wobble position (3rd nucleotide in an ANTICODON)
A messy (sloppy) binding site that goes along with the redundancy or degeneracy of the RNA
Generates variation
Some tRNA genes contain intron. Why are these introns are spliced out by a specialized set of proteins but not the spliceosome?
Dependent on there 3D structures . They fold and introns are placed on the outside. The splice-some only works with linear structures and cant work with tRNA. They require specialized proteins to remove introns
True or false: tRNA modifications are important for structure
True
How are tRNAs charged w/ AA
Aminoacyl-tRNA synthase hydrolyzes ATP to fuel coupling of AA to tRNA
- Aa linked to Carboxyl group (AMP)
- Carboxyl transferee to 3’ end of RNA
What are two things that ensure correct AA bonding in peptides
AA synthase (AA specific and tRNA specific) 1. Built in proof reading mechanism tRNA is an adapter that couples the right AA
What’s the proofreading mechanism in tRNA synthetases
Each amino acrylic t-Synthetases are AA specific
PrimaryBS - specific AA
SecondaryBS - allow similarly AA
Signals inactivation and AA gets kicked out
(Anticodon are recognized by tsynthetases too)
How are AAs added to polypeptide chain
N-terminus to C-terminus
Formation of peptide bond is energetically favorable
What cells types might need more ribosomes?
Rapidly replicating Cells
What are characteristics of ribosomes?
A= amino acrylic tRNA bind, P=Peptidyl-tRNA site , E = GTFO
2 sites are always occupied
2/3s of it RNA;
It’s a riboenzyme; RNA itself that change conformations to enduce protein syn and proteins are there for structure support
Prokaryotes and Eukaryotic ribosomes share similar structure and function
What are the steps of protein synthesis ? (4)
- New tRNA binds to A site
- C-term end of released from tRNA in P site (peptide bond formed)
- Large subunit held by small unit moves across mRNA shifting to P and E sites on small subunits
- Small subunits moves 3 nucleotides along the mRNA and ejects tRNA in the E site
What are elongation factors?
EF-TU & EF-G in Prok
EF1 & EF2 in EUK
EF-TU AND EF1 increased accuracy
How is protein synthesis initiated?
binding of specific proteins (elF4g) to poly A tail and (elF4E) to 5’ cap
What is the consensus sequence around a start codon?
AUG - EUK
ATG in PROK
Must be flanked acc and g if not then ribosome will skip to the next AUG
What binding to an A site terminates protein?
release factor binds to A site and a stop codon ex: UAG is read
What did fungal biology lead to?
Fungi prevented bacterial attack using small molecules by targeting ribosomal function in bacteria
Lead to creation of ANTIBIOTICS
What is nonsense mediated decay?
Prevents premature stop codons by eliminating the mRNA that contains it .
- As mRNA leaves nucleopore it is tested by ribosome
- Since EJC are bond at exon junctions it runs through a stop codon while EJC is present its premature
- .mRNA is then rapidly removed
When do proteins fold?
Immediality after synthesis
ENERGETICALLY FAVORABLE
What are heatshock proteins?
Recognize proteins damaged by heat
Recognize wrongly placed hydrophobic regions on outside of proteins
Bind to them with hsp60
What is hsp60
Barrel shaped protein that encloses a protein that misfolded proteins.
By unraveling them and then encourages correct protein formation
What forms when incorrectly proteins are not eliminated?
Protein aggregates form and lead to proteopathies
Prison disease, Alzheimer’s, and Parkinson’s
What is the last ditch effort to eliminate misfolded proteins
proteasome chop them up
When it is not fixed.
Mark them for death via ubiquitin
How do proteasomes work?
Marked proteins enter proteosome
Special E3 proteins recognize misfolded proteins and add ubiquitin peptides linked lysine 4 (key identifier of proteodamage)
Use atp hydrolysis to unfold protein and degrade it
What are chaperones?
Cells use additional chaperones to ensure that peptides fold onto the correct function or refold them if they got damaged
