In Chapter 29 there is a description of the process of translation.
The four-letter alphabet of nucleic acids is translated into the 20-letter alphabet of proteins in a complicated process.
The chapter begins with an introduction to the major components of translation.
The structure of the adaptor molecule that recognizes the codons on the mRNAs and the enzymes that attach them are discussed first.
The specificity of these reactions is explored in terms of correct binding of tRNAs to a given synthesizer.
An example of specificity at the level of amino acid selection is ThreonyltRNA.
The isosteric valine and the isoelectronic serine are discriminated between by this enzyme.
There are a number of ways in which the correct tRNA is chosen, ranging from those which require multiple contact points to alanyl-tRNA.
The structure and composition of the ribosome is the next topic for the authors.
The ribosome is now recognized as a ribozyme, with theRNA components playing a major role in catalysis.
The experiments that showed the polarities of polypeptide formation are next.
Chapter 29 includes the tRNA, the start codon, and the 16S rRNA sequence.
The function of the sites on the ribosome that bind aminoacyl-tRNAs and peptidyltRNAs, the role of GTP, and the mechanism of the translocation of the peptidyl-tRNA were studied.
The lack of strict one-to-one interactions between the three nucleotides of the anticodons and the mRNA codons is explained by the wobble hypothesis.
Ini tiation, elongation, and release factors are critical to translation.
The role of release factors that recognize translation stop codons is described.
The chapter ends with a brief overview of translation in eukaryotes, emphasizing the major contrasting features with respect to translation in prokaryotes.
The overall complexity of the process is highlighted, as are the differences in the initiator tRNA, the selection mechanism of the codon, and the ribosomes.
The mechanisms of several potent inhibitors of translation are presented.
You should be able to complete the objectives once you have mastered this chapter.
The features common to all tRNAs are listed.
Relate the two-dimensional representation of the structure to its three-dimensional configuration.
Mention the high-energy bonds that are consumed in the reaction.
An experiment showed that the tRNA is more likely to recognize a codon than the acyl-tRNA.
List the number of macromolecular components of the ribosome.
List the evidence that supports the idea that ribosomes have roles to play.
The growth of the polypeptide chain has a correlation with the ribosome movement.
AUG codon selection mechanisms and numbers of IFs and RFs are noted.
Explain to the correct answer to question 4 how aminoacyl-tRNAs can be pro duced in the cell.
Indicate the ways in which different tRNAs may be recoged.
In an experiment, it was found that Cys-tRNACys can be converted to Ala-tRNACys and used in a system that is capable of making proteins.
The wobble hypothesis accounts for the looseness of the amino acid acceptor stem of the tRNAs that allows sufficient flexibility for peptidyl-tRNA and aminoacyl-tRNA to be brought together.
An experiment is carried out in which labeled amino acids are added to an in vitro trans lation system.
There are dashes, X, and A and B at the ends of the intact protein.
Match the functions or characteristics in the right column with the translation components in the left column.
Give the number of high-energyphosphate bonds consumed and the cofactor involved for each step of translation.
Antibiotics act by blocking the synthesis of genes.
The molecule consists of two stems, each of which is made of two segments.
The anticodon and amino acid accepting regions are 80 A from each other, and the molecule is L-shaped.
The 3' termini of functional tRNAs has a CCA sequence.
Different features for their interactions with ribosomes and elonga tion factors are what transferRNAs need.
The formation of an intermediate containing a mixed anhydride linkage toAMP is a two-step reaction.
The 2'- or 3'-hydroxyl of the tRNA is linked by an ester bond to the amino acid.
The activa tion domain is where the b sheet domains are located.
There are two classes of enzymes, class I and class II.
A, b, d, e are some of the ways in which tRNAs are recognized.
The 3' CCA sequence is common to all tRNAs and cannot be used to distinguish among them.
Through base-pairing between codon and anticodon, the tRNA would sociate with Cys codons in the mRNA.
The Cys codons are the only ones that would be included in the labeled alanine.
The experiment shows that the tRNA and the amino acid read the same thing.
If an incorrect amino acid is attached to a tRNA, it will be incorporated into the protein.
The answer is incorrect because two-thirds of the ribosome is rRNA.
It shows that the components contain all the information needed to form a structure, and that there is no template or other factors involved.
The ribosome serves as a model for self-assembly.
The study of the roles of individual components can be done through the determination of the effects of substitution.
Answer (a) is incorrect because the free group of the activated carboxyl of the growing polypeptide on a peptidyl-tRNA is added to the A site of the ribosome.
Answer (e) is incorrect because it doesn't involve tRNAs that recognize translation stop codons and instead involves peptidyl transferase donating the growing polypeptide chain to H2O.
The chains grow in the direction of the amino-tocarboxyl side of the molecule.
The carboxyl ends of the growing chains that are already present in all stages of completion are added to when the labeled amino acid is introduced into the system.
After a short time, the completed chains will be labeled with polypeptides only near their carboxyl end.
As time goes on, more and more polypeptides will become complete chains.
10-formyltetrahydrofolate acts as a carrier of formyl groups and is a substrate for a transformylase reaction that converts Met-tRNAf to fMet-tRNAf.
After the free tRNA leaves, the extended polypeptide on its new tRNA is moved to the P site.
The large amounts of EF-Tu in the cell bind all of the aminoacyl-tRNAs and protect them from hydrolysis.
The formation of a peptide bond per se does not require a cofactor.
The activated aminoacyl-tRNA provides the energy for the exergonic reaction.
Differences between their ribosomes can result in the inhibition of the prokaryotic translation.
Some antibiotics interact with theRNA components that are unique tobacterial ribosomes and can prevent growth without affecting the human cells.
The first AUG codon is usually served to initiate the synthesis by the Eukaryotic ribosomes.
The answer is correct because the ribosome is involved in the association of the mRNA and the cap.
Puromycin is an analogue of aminoacyl-tRNA.
The binding of peptidyl-tRNA to the A site of the ribosome causes it to stop the growth of the polypeptide chain in the P site.
Increasing their concentration would decrease the extent of inhibition because they compete with the A site.
One toxin molecule can inactivate many translocase molecules by modifying them covalently, which is incorrect because the toxin acts catalytically and is thus extremely deadly.
Give the sequence for the first four acids.
Give the sequence that would result.
Give the sequence.
There is a 10% error rate in the formation of aminoacyl-adenylates and a 99% success rate in the hydrolysis of incorrect aminoacyl-adenylates.
The 30S and 50S ribosomal subunits form a 70S particle instead of an 80S particle, which is distressing to students of biochemistry.
There are possible codons for valine.
If threonyl-tRNA is the only way to discriminate between serine and threonine, it will couples Ser to threonyl-tRNA at a rate several-fold.
It was found that some strains ofbacteria can protect themselves by having genes that can recognize a chain-terminating codon and insert an amino acid instead.
Even though it may contain an altered amino acid, the result would be a normal length, functionalProtein of normal length that may be functional.
The change of a C-G to a G-U base pair causes alanyl-tRNA to be recognized.
The methionine codon AUG works to initiate a polypeptide chain and direct methionine into internal positions.
Adding a radioactively labeled amino acid and either natural or synthetic mRNAs to a system containing the other components is usually what is done in a lab.
The advantage is taken of the fact that the solution of trichloroacetic acid can cause the formation of aprotein.
It is possible to observe the extent to which radioactivity has been incorporated into acid-precipitable material as a function of time.
Poly(U) is used in an experiment as a synthetic messenger in a system derived from wheat germ.
Explain the results of each procedure.
In a complete system 3000 cpm are found at the end of 30 minutes and the values below 150 cpm are not significant above the background level.
The name implies that the template is the template for the synthesis of a mRNA molecule.
The codons of a molecule are read in a certain direction.
The location of the initiation codon can be established because there is only one AUG in the mRNA sequence.
The expected sequence is Met-Leu-Met-Phe.
The AUG that is closest to the 5' end of the mRNA molecule is usually the first triplet.
There are two AUGs, so there will be two Met residues in the polypeptide that is produced.
His-Ala-Lys is the sequence.
The sequence must contain at least one of the chain-termination codons.
The reading frame can be inferred from the fact that UAA and UAG occur in the same sequence.
0.11% of the tRNAs will be faulty.
100 are faulty and 900 are correct for every 1000 produced.
The intermediates are bound to the active site of the aminoacyl-tRNA synthesis.
99 of the 100 incorrect tRNAacyladenylates will not form acylcyls.
Only one will become an incorrect tRNA.
The fraction of incorrect tRNAs is 0.11%.
The Svedberg unit is a measure of the veloc ity with which a particle moves.
It is a property of a particle that depends on size and shape.
The total coefficients of the particles should be less than the total coefficients of the contact surfaces of the particles.
Three codons could pair with the anticodon beginning with I; two codons could pair with the anticodon beginning with U or G; and only one codon could pair with the anticodon beginning with A or C.
There are three codons that will pair with IGG.
A minimum of three tRNAs is required.
The anticodon UAA could decode both UUA and UUG.
There are two different combinations of two tRNAs that could decode the other four codons.
The first combination would be two tRNAs that have anticodons with A in the second position and G in the third, one with I in the first position to decode CUU, CUC, and CUA, and the other with U or C in the first position to decode Two tRNAs with anticodons with A in the second position and G in the third, one with G in the first position to decode CUU and CUC, and the other with U in the first position to decode CUA and CUG, would be part of the second
Threonyl-tRNA synthesise has a mechanism.
The Ser-tRNAThr that is mis formed is hydrolyzed by an editing site.
The decision to hydrolyze the tRNA appears to be dependent on the size of the substituent.
The hydrolytic site is cleaved if it is smaller than the correct amino acid.
If it's the same size as the correct one, it won't fit and won't be destroyed.
At the aminoacylation step, there is discrimination between larger than the correct ones and not isoelectronic ones.
If two legitimate stop codons are present in tandem, it would be very likely that the same tRNAs would bind to each of them and prevent proper chain termination.
There would be many positions of many polypeptides that would be affected by a tRNA recognition mutation.
The Shine-Dalgarno sequence is three to nine nucleotides long and is centered around 10 nucleotides upstream of the start codon.
The association of fMet-tRNAf with the AUG in the P site of the ribosome sets the reading frame.
Adding labeled pheny lalanine to the reaction mixture is necessary.
CHAPTER 29 (c) RNase A will destroy the plate tem for polyphenylalanine synthesis because it will digest poly(U) almost completely to 3'-UMP.
The ribosomes will be damaged.
No synthesis will take place.
The synthesis is increased in the experiment.
The Ile-AMP intermediate is needed for the exchange of 32PPi.
Since isoleucine is a requirement, labeled ATP will only be formed in (c).
70S ribosomes are reformed from the heavy and light subunits.
The high-energyphosphate bonds are consumed to form 199 pepitide bonds.
A fourth base in anticodon can be suppressed by an extra base.
UUUC is read as the codon for phenylalanine by a tRNA that has 3'-AAAG-5' as its anticodon.
One way to synthesise a tRNA is with a reactive amino acid analog.
See H. Oen, M. Pellegrini, D. Eilat, and C. R. Cantor.
There is a sequence of five bases at the 3' end of 16S rRNA and several bases on the 5' side of an AUG codon.
This region is the beginning of a synthesis.
The 16S rRNA's effectiveness as an initiation signal would be weakened by the replacement of G by A.
A tenfold decrease in the rate of synthesis is caused by thismutation.
For more information on this informative Mutant, see J. J. Dunn, E. Buzash-Pollert, and F.W.
In the solid-phase method, the ribosomes are used as a starting point for the synthesis of the proteins.
In the solid-phase method, the adduct of the amino acid and dicyclohexylcarbodiimide is the activated intermediate in ribosomal synthesis.
The order in which the error rates of synthesis are is 10-10, 10-5, and 10-4 per nucleotide.
The fidelity of all three processes depends on the accuracy of base-pairing.
There is no error in the synthesis of RNA.
There was a 5' activity of nuclease activity.
The mischarging of some tRNAs is corrected by the hydrolytic action of the aminoacyltRNA synthesizer.
The final stage of editing takes place when the A site on the ribosome is occupied by aminoacyl-tRNA.
GTP is not hydrolyzed until the A site of the ribosome is delivered.
Antisense RNA can be used to block the translation of an mRNA molecule.
The duplex is degraded by nucleases.
Many cells take up antisense when it is added to the medium.
Microinjection can deliver a precise quantity.
The antisenseRNA can be introduced into the cells.
H. M. Weintraub has an interesting discussion about antisense RNA and DNA as research tools and drug candidates.
The last segment will be heavily labeled.
The carboxyl terminal is where A1 (c) synthesis begins.
The three-base RNA anticodon is the only part of the genetic code that is actually match with a particular amino acid.
The other interactions of genetic code components involve "Watson-Crick" pairs.
The rate of synthesis would be slower because of the slower cycling of EF-Tu between GTP-bound and GDP-bound forms.
A nu cleophilic attack on the peptidyl-tRNA's ester bond is made by the nitrogen atom of the deprotonated a-amino group.
The growing peptide chain is transferred to the new tRNA.
The ornithinyl-tRNA is unstable because the nitrogen of the side chain will serve as a nu cleophile.
The transition state involves a six-membered ring.
A less favorable transition state with a sevenmembered ring is what makes lysyl-tRNA more stable.
GTP is exchanged for GDP bound to EF-Tu.
The GTP-GDP exchange occurs in a G protein when an activated seven-helix receptor is activated.
The GTP-GDP exchange can be triggered by photoexcited rhodopsin.
There are many G proteins that are sensitive to ADP ribosylation.
The result may suggest a binding of the helpers to the initiation factor.
The slope is smaller when eIF4H is present.
The graph shows that the helpers increase the rate.
If the helpers slowed the dissociation of eIF4 from the helix, there would be two effects.
It would be consistent with the energetics shown in Graph C if a mechanism was used to increase the processivity.