Exam #3

Question 1

degenerate code

Answer 1

multiple triplet determine same AA

Question 2

Anticodon is complementary to _______

Answer 2

mRNA codon

Question 3

standard Stop Codon = Nonsense Codon:

Answer 3

UAG, UAA, UGA

Question 4

standard Start Codon

Answer 4

Also encodes Met, Val

Question 5

1960’s used polynucleotide phosphorylse: ______

Answer 5

link together nucleotides without using template:

(RNA)n + NDP = (RNA)n+1 + Pi

Question 6

Mitochondrion have nonstandard _____

Answer 6

nonstandard genetic code

Question 7

Niremberg experiment found:_____

Answer 7

UUU made Phe, AAA made Lys, etc.

Question 8

Reading frame

Answer 8

A Way of dividing the sequence of nucleotides into a set of consecutive, non-overlapping triplets

Question 9

Could a single nucleotide deletion restore the FUNCTION of a protein-coding gene interrupted by the insertion of a 4-nt sequence?

Answer 9

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.

Question 10

In the genetic code used by mitochondria in many species, UGA codes for tryptophan rather than a Stop signal. How does mitochondrial translation terminate?

Answer 10

Degeneracy.There are still two more stop codons: UAA and UAG.
Additionally, Mammalian mitochondria have AGA and AGG as Stop rather than ARg.

Question 11

DNA stop codons:

Answer 11

TAA, TAG, TGA

Question 12

DNA start codon:

Answer 12

ATG

Question 13

A peptide with X residues will be formed from translation of _____ nucleotides

Answer 13

3X + 3.

Need +3 at the end for Stop Codon

Question 14

Translation always occurs in direction of:

Answer 14

5’ to 3’ end

Question 15

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?

Answer 15

Things that all tRNAs have in common: Acceptor Stem, TpsiC Loop

Question 16

How to distinguish pre-tRNA from mature tRNAs?

Answer 16

Mature tRNAs have processed 5’ end with single phosphate group and 3’ end with CCA sequence.

Question 17

Sense DNA vs RNA

Answer 17

Sense DNA has same sequence (except T instead of U) as RNA

Question 18

Antisense DNA vs RNA

Answer 18

Antisense DNA is what actually gets translated to RNA. It has opposite sequence as RNA.

Question 19

Wobble position tends to be ________

Answer 19

Wobble position tends to be modified nucleotides.

Question 20

Which pairs of amino acids might have aaRSs that use a double-sieve proof reading mechanism?

Answer 20

Asn and Gln, Asp and Glu, Gly and Ala, Ser and Thr, Val and Leu

Question 21

Explain the significance of the observation that fMet-Leu-Phe activate the phagocytic functions of mammalian leukocytes

Answer 21

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

Question 22

Why can’t eukaryotic ribosomes translate circular mRNA molecule even in the presence of required cofactors?

Answer 22

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.

Question 23

Some mutations that do not alter the identity of encoded amino acid lead to diminished production of protein. How?

Answer 23

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.

Question 24

Why can translation of mRNA be inhibited by a segment of its complementary sequence, a so called anti-sense RNA?

Answer 24

Ribosomes cannot translate double-stranded RNA.

Question 25

Eukaryotic initiation factor eIF2B is a guanine nucleotide exchange factor. Explain why eIF2B enhances the activity of eIF2.

Answer 25

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.

Question 26

The tRNA-EF-Tu recognition system prevents the incorporation of the wrong amino acid during translation by:

Answer 26

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.

Question 27

The rate of peptidyl transferase reaction increases as the pH increases. Why?

Answer 27

Peptidyl transferase reaction = A-site tRNA nucleophilically attacks P-site tRNA. Thus, raising the pH increases the nucleophic power of A-site tRNA.

Question 28

All cells contain an enzyme called peptidyl-tRNA hydrolase, and cells that are deficient in the enzyme grow very slowly. Why?

Answer 28

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.

Question 29

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.

Answer 29

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.

Question 30

Explain the antibiotic effect of paromomycin, a type of aminoglycosides

Answer 30

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.

Question 31

Explain the antibiotic effect of paromomycin, a type of aminoglycosides

Answer 31

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.

Question 32

Class 1 tRNA synthetases are for what types of AAs?

Answer 32

Hydrophobic AAs.

Mostly result in single subunit 2’ oxygen acylation.

Question 33

Class 2 tRNA synthetases are for what types of AAs?

Answer 33

Hydrophilic AAs.

Mostly result multi-subunit 3’ oxygen acylation.

Question 34

What is the reaction mechanism of how tRNAs are charged with Amino Acids?

Answer 34

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.

Question 35

tRNA(Ala) recognition by tRNA synthetase is special because:

Answer 35

anticodon is not recognized. Instead, tRNA(Ala) is the only tRNA with G3-U70 pair on the acceptor stem

Question 36

tRNA (Ser, Leu, Tyr) are special because:

Answer 36

Unusually long variable arm

Question 37

Create a mRNA with necessary prokaryotic control sites that codes for ProAlaLys

Answer 37

5’-AGGAGCUX (Shine Dalgarno Sequence) + AUG(Start codon) + Pro Ala Lys codons + UAA/UAG/UGA (Stop codon)-3’