Week 10 Flashcards
What are the macromolecules of translation?
- ribosomes (polypeptides, >50) and rRNA (3-4)
- amino acid activating enzymes (20)
- tRNA molecules (40-60)
- soluble proteins (translation factors) involved in polypeptide chain initiation, elongation, & termination
What are ribosomes composed of?
- proteins and several different rRNAs
- a large and a small subunit that assemble
What is the key role of a ribosome?
= protein synthesis, formation of peptide bonds b/n amino acids
Describe the prokaryotic ribosome
- 50S subunit
- 30S subunit
- complete prokaryotic ribosome is 70S
Describe the eukaryotic ribosome
- 60S subunit
- 40S subunit
- complete eukaryotic risbosome is 80S
What does the S in the subunits stand for?
Svedberg units
= a measure of how the ribosomal complex sediments in a gradient during centrifugation
- densities are not additive due to the way the complete ribosome sediments
Describe tRNAs
- adapters b/n amino acids and codons in mRNA
- the first anticodon position of tRNA base pairs with 3rd codon position of mRNA
Where do the amino acids attach to the tRNA?
- via the 3’-ACC-5’ sequence at the 3’ end
Key facts about the ribonucleotides in tRNA?
- A, G, C, and U
- often modified post-transcriptionally by cellular enzymes adding -CH3 or H
How many tRNA synthetase do cells contain per amino acid?
- at least one
What do tRNA synthetases do?
- catalyze formation of aminoacyl tRNAs
What joins an amino acid to their respective tRNA?
amino acyl tRNA synthetase, contain an active site, a pocket for the amino acid to bind and a pocket for the tRNA to bind
- help form the tRNA-amino acid bond (high energy!) with help of ATP to AMP conversion (ATP hydrolysis)
How is aa joined with tRNA?
with a covalent bond that is high energy, this results in the aminoacyl tRNA = charged tRNA
What molecule does the formation of amino-acyl tRNA synthetase require?
ATP - needs to be hydrolyzed to help from the high energy bind
Describe the reaction that results in the formation of the aminoacyl tRNA?
- first step: aa reacts with ATP
- then: aminoacyl-AMP and PPi are produced
- second step: amino acids transferred t tRNA and AMP is released
Steps of translation in both Eukaryotes and Prokaryotes?
- very similar in both
Initiation
Elongation
Termination
Describe the initiation complex that forms during initiation of translation in Prokaryotes
composed of mRNA, large and small ribosomal subunits, the initiation factors (IF1-3) and GTP (guanosine triphosphate)
How does the initiation complex form in Prokaryotes?
- IF-3 binds to small subunit to prevent large subunit from binding and allows small one to bind to mRNA
- tRNA charged with N-formylmethionine forms a complex with IF-2 and GTP
- all initiation factors dissociate from the complex and GTP is hydrolized to GDP
- large subunit joints to create 70S initiation complex
Where is the Shine Dalgarno sequence located in initiation?
- mRNA
- 16S rRNA, a component of 30S small ribosomal subunit contains the complement
Where does pairing between Shine-Dalgarno and rRNA complement position the ribosome?
- near the AUG start codon
At the end of initiation, where is the ribosome and where is the first tRNA in Prokaryotes?
- the ribosome is assembled on the mRAN
- the first tRNA is attached to the initiation codon
What is the Shine-Dalgarno sequence?
5’-AGGAGG-3’
also called the consensus sequence
What tRNA is specific to the initiation codon?
= the initiation codon is 5’-AUG-3’
therefore, Methionine, so Fmet-tRNA (IAC)
- the methionine is modified with formyl group (hence fMet)
Where do you see fMet?
only in prokaryotes!
What are the three distinct regions in a ribosome after it is completely assembled?
- Aminoacyl site (A)
- Peptidyl site (P)
- Exit site (E)
What happens at the A site?
The aminoacyl site accepts newly charged aminoacyl tRNAs specific for the codon at that position
What happens at the P site?
the peptidyl site is the position where the peptide bond forms b/n amino acid on tRNA on that site and the newest one at the A site
What happens at the E site?
The exit site is where the tRNA that has had its amino acid removed, following peptide bond formation, exits the ribosome
Describe the amino acid on the initiator tRNA in Eukaryotes
- it is not formylated, it is just MET (not fMET)
Where does the initiation complex form in Eukaryotes for translation?
- at the 5’-terminus of the mRNA (the 7-methylguanosine cap on the 5’ end) and there is no Shine-Dalgarno sequence in eukaryotes!
- then ribosome scans inward from there
Which sequence influences the efficiency of which AUG in vicinity of 5’ 7-MG cap is used to start translation in eukaryotes?
= KOZAK sequence
- 5’-GCC (A or G) CC AUG G-3’
- the AUG start codon is imbedded within the Kozak sequence
- spacing of the nucleotides is important but some difference can occur but need A or G two nt before AUG and a G after!
What promotes translation initiation in eukaryotes?
- the poly A tail of the eukaryotic mRNA interacts with the mRNA 5’ 7MG cap structure via cap binding protein complex (CBC) to promote translation initation
During elongation, where does the anticodon of an incoming tRNA bind?
- binds with the codon of the mRNA that is exposed at the A site
- occurs with the help of EF-Tu (Elongation factor Tu) and GTP
How does bind formation occur during chain elongation?
- peptide bond is formed by peptidyl transferase
- the dipeptide is attached to the tRNA in the A site
- tRNA in the P site is now devoid of its amino acid
- therefore bond formation occurs b/n the NH2 group of the amino acid attached to the tRNA in the A site and the -COO group of aa attached to tRNA in P site via peptidyl transferase activity of the ribosome
How does the ribosome move on to the next codon after the peptidyl bond forms?
- with the help of EF-G and GTP
- at this point the tRNA that was originally in the P site is now devoid of its aa and is ejected from the ribosomal E site and newly charged aminoacyl tRNA specific to unbound codon in A site binds
What is the role of GTP in elongation?
= provides energy
When does elongation end?
= when one of the stop codons is encountered
- specifically, when a chain-termination codon (stop codon) enters the A site of the ribosome
What are the stop codons?
UAA
UAG
UGA
What happens when a stop codon is encountered?
a release factor binds to the A site
- essentially there is no tRNA molecule that can bind to the stop codons and that is why they stop elongation
What does release factor 1 recognize?
UAG and UAA stop codons
What does release factor 2 recognize?
UAA and UGA stop codons
What do RF-1 and RF-2 do?
- both release factors alter the activity of peptidyl transferase, which results in a water molecule being added to the carboxyl terminus of the nascent polypeptide releasing it and thereby ending elongation/translation
How is the ribosome dismantled?
- RF-3 and GTP help in dismantling
Which researchers won the Nobel Prize in Chemistry in 2009 for their discovery of ribosome structure?
- Ramakrishnan, Steitz, and Yonath
How does Chloromycetin inhibit bacterial protein synthesis?
- stops formation of peptide bonds
How does Erythromycin inhibit bacterial protein synthesis?
- stops translocation of mRNA along ribosome
How does Neomycin inhibit bacterial protein synthesis?
- stops interaction between tRNA and mRNA
How does Streptomycin inhibit bacterial protein synthesis?
- stops initiation of translation
How does Tetracycline inhibit bacterial protein synthesis?
- stops binding of tRNA to ribosome
How does Paromomycin inhibit bacterial protein synthesis?
- stops the validation of mRNA-tRNA match
What is a nonsense mutation
- formation of premature stop codon that prevents the synthesis of full-length protein
What are some quality control mechanisms in the cell
- mechanisms that ensure the quality of mRNA and mechanisms that ensure the quality of proteins
How is the quality of mRNA ensured?
- by degrading mRNAs with errors that can create problems in translation (like nonsense mutations or if they stall ribosomes or have unusual secondary structures or if damaged by chemicals)
What are chaperones and how do they help in quality control of proteins?
= they assist in the proper folding of newly-synthesized proteins
- chaperones are often associated with the ribosome during translation