Exam #3 Flashcards
degenerate code
multiple triplet determine same AA
Anticodon is complementary to _______
mRNA codon
standard Stop Codon = Nonsense Codon:
UAG, UAA, UGA
standard Start Codon
Also encodes Met, Val
1960’s used polynucleotide phosphorylse: ______
link together nucleotides without using template:
(RNA)n + NDP = (RNA)n+1 + Pi
Mitochondrion have nonstandard _____
nonstandard genetic code
Niremberg experiment found:_____
UUU made Phe, AAA made Lys, etc.
Reading frame
A Way of dividing the sequence of nucleotides into a set of consecutive, non-overlapping triplets
Could a single nucleotide deletion restore the FUNCTION of a protein-coding gene interrupted by the insertion of a 4-nt sequence?
Single nucleotide deletion can restore proper reading frame if 4-nt sequence was added after a codon and 1-nt deletion made 4-nt into 3-nt. Function would not be restored if 4nt-insertion interrupted the codon for functionally critical amino acid. Not restored if 4-nt insertion introduced a stop codon. Not restored if 1-nt deletion occurred far from 4-nt insertion.
In the genetic code used by mitochondria in many species, UGA codes for tryptophan rather than a Stop signal. How does mitochondrial translation terminate?
Degeneracy.There are still two more stop codons: UAA and UAG.
Additionally, Mammalian mitochondria have AGA and AGG as Stop rather than ARg.
DNA stop codons:
TAA, TAG, TGA
DNA start codon:
ATG
A peptide with X residues will be formed from translation of _____ nucleotides
3X + 3.
Need +3 at the end for Stop Codon
Translation always occurs in direction of:
5’ to 3’ end
Protein Xpot transports tRNAs out of nucleus so that they can be aminoacylated in the cytosol. What tRNA structural features is Xpot likely to recognize?
Things that all tRNAs have in common: Acceptor Stem, TpsiC Loop
How to distinguish pre-tRNA from mature tRNAs?
Mature tRNAs have processed 5’ end with single phosphate group and 3’ end with CCA sequence.
Sense DNA vs RNA
Sense DNA has same sequence (except T instead of U) as RNA
Antisense DNA vs RNA
Antisense DNA is what actually gets translated to RNA. It has opposite sequence as RNA.
Wobble position tends to be ________
Wobble position tends to be modified nucleotides.
Which pairs of amino acids might have aaRSs that use a double-sieve proof reading mechanism?
Asn and Gln, Asp and Glu, Gly and Ala, Ser and Thr, Val and Leu
Explain the significance of the observation that fMet-Leu-Phe activate the phagocytic functions of mammalian leukocytes
Only newly synthesized bacterial polypeptides have fMet at the N terminus. Thus, presence of fMet in mammalian body implies invasion by bacteria. Leukocytes that recognize fMet can fight bacteria with phagocytosis
Why can’t eukaryotic ribosomes translate circular mRNA molecule even in the presence of required cofactors?
In eukaryotic translation, recognition of initiation site begins by binding of eIF4E to the mRNA’s m7G cap. Obviously, circular mRNA molecule will not have G-caps.
Some mutations that do not alter the identity of encoded amino acid lead to diminished production of protein. How?
In prokaryotes, mutation in Shine-Dalgarno sequence will reduce translational efficiency.
In eukaryotes, mutations in the purine 3-nt before the AUG and mutations in the G immediately following it each reduce translational efficiency by 10-fold.
Why can translation of mRNA be inhibited by a segment of its complementary sequence, a so called anti-sense RNA?
Ribosomes cannot translate double-stranded RNA.
Eukaryotic initiation factor eIF2B is a guanine nucleotide exchange factor. Explain why eIF2B enhances the activity of eIF2.
Guanine nucleotide exchange factors (GEFs) stimulate the release of GDP to allow binding of GTP. In our case, eIF2B stimulates release of GDP from eIF2-GDP and allows binding of GTP on eIF2 to make eIF2-GTP. eIF2 then mediates met-tRNA binding to ribosome using GTP.
The tRNA-EF-Tu recognition system prevents the incorporation of the wrong amino acid during translation by:
Mischarged aminoacyl-tRNAs bind too loosely or too tightly to EF-Tu, making it difficult for EF-Tu to deliver and give them to the ribosome.
The rate of peptidyl transferase reaction increases as the pH increases. Why?
Peptidyl transferase reaction = A-site tRNA nucleophilically attacks P-site tRNA. Thus, raising the pH increases the nucleophic power of A-site tRNA.
All cells contain an enzyme called peptidyl-tRNA hydrolase, and cells that are deficient in the enzyme grow very slowly. Why?
Peptidyl-tRNA hydrolase probably hydrolizes garbage peptide-tRNA complex that accidentally got cut off before completion of translation. If these mistakes aren’t hydrolyzed, the cell can’t recycle nucleotides and tRNAs.
Genetically engineered mRNAs that code for a stretch of basic residues such as poly(Lys) induce termination of translation and destruction of nascent polypeptide. Explain how this response would protect cells from the effect of faulty transcription that produces mRNAs with mutated Stop codons.
Note that AAA codes for Lysine.
Then, the poly-A tail at the 3’ end of mature mRNA will code for poly(Lys).
Then, any mRNA with mutated Stop codons, will continue to get translated until its poly-A tail. Then, translation of the poly-A tail will induce the destruction of nascent polypeptide, safely removing the useless product.
Explain the antibiotic effect of paromomycin, a type of aminoglycosides
Paromomycin binds to a ribosome and induces a conformational change in the A-site of the 16S rRNA. The conformational change interferes with bacterial protein synthesis by causing misreading of mRNA and inhibiting translocation.
Explain the antibiotic effect of paromomycin, a type of aminoglycosides
Paromomycin binds to a ribosome and induces a conformational change in the A-site of the 16S rRNA. By inducing the same conformational changes that occur during correct tRNA–mRNA pairing, paromomycin can mask the presence of
an incorrect codon–anticodon match. Without proofreading at the aminoacyl–tRNA binding step, the ribosome synthesizes a polypeptide
with the wrong amino acids, which is likely to be nonfunctional or toxic to the cell.
Class 1 tRNA synthetases are for what types of AAs?
Hydrophobic AAs.
Mostly result in single subunit 2’ oxygen acylation.
Class 2 tRNA synthetases are for what types of AAs?
Hydrophilic AAs.
Mostly result multi-subunit 3’ oxygen acylation.
What is the reaction mechanism of how tRNAs are charged with Amino Acids?
Carboxylate anion of amino acid attack alpha phosphate of ATP to make Aminoacyl AMP. Then, tRNA’s 3’ OH (or 2’ OH) oxygen attack carboxyl carbon of Aminoacyl AMP to form Aminoacyl tRNA.
Reaction is catalyzed by tRNA synthetases.
tRNA(Ala) recognition by tRNA synthetase is special because:
anticodon is not recognized. Instead, tRNA(Ala) is the only tRNA with G3-U70 pair on the acceptor stem
tRNA (Ser, Leu, Tyr) are special because:
Unusually long variable arm
Create a mRNA with necessary prokaryotic control sites that codes for ProAlaLys
5’-AGGAGCUX (Shine Dalgarno Sequence) + AUG(Start codon) + Pro Ala Lys codons + UAA/UAG/UGA (Stop codon)-3’
