SmartWork5 Chapter 6
How does the tRNA synthetase enzyme charge a tRNA with the correct amino acid?
Each different tRNA synthetase has one region that recognizes the tRNA anticodon and a second region that attaches the matching amino acid to the CCA at the 3' end of the tRNA. There are many aminoacyl-tRNA synthetases in the cell. Each one makes multiple contacts with the specific tRNA. One part of the enzyme recognizes the anticodon base triplet. A second region carries the matching amino acid that is added to the CCA at the 3' end of the tRNA.
What is the benefit of protein synthesis in polyribosomes?
More protein can be produced from a single RNA. Having more than one ribosome bound to a single mRNA allows many polypeptide chains to be synthesized simultaneously. This allows much more protein to be produced from one mRNA molecule than if each ribosome had to wait for the previous one to finish.
How many different aminoacyl-tRNA synthetases do most organisms have?
One for each amino acid. Because there are 20 common amino acids found in proteins, there are 20 different aminoacyl-tRNA synthetase enzymes, as each one must recognize the appropriate amino acid along with the appropriate tRNA molecule.
Which of the following statements is supported by the information in this image and is consistent with your knowledge regarding genomic architecture in prokaryotes and eukaryotes?
The eukaryotic cell must have a nuclear spliceosome to remove introns from RNA.
Export of RNA from the nucleus requires the RNA to have which characteristic(s)?
To be exported, RNAs must have the features of a processed mRNA. This includes being properly spliced (no introns), having a 5' cap and a poly-A tail.
What recognizes the stop codons in an mRNA?
release factor- When the ribosome encounters a stop codon, instead of a tRNA binding, a protein called release factor binds and catalyzes the addition of a water molecule to the carboxyl end of the polypeptide and releases it.
RNA polymerases join nucleotides through what kind of bond?
Phosphodiester
How do tRNAs become attached to the correct amino acid?
aminoacyl-tRNA synthetases- Enzymes called aminoacyl-tRNA synthetases recognize tRNAs with a specific anticodon as well as the amino acid for that tRNA and catalyze a reaction to join them together. This is called "charging" a tRNA.
The catalytic sites for peptide bond formation during translation is found in which part of the ribosome?
large subunit RNAs- The catalysis of the peptide bonds in the growing polypeptide chain during translation is performed by the rRNA of the large subunit. The ribosome is a ribozyme; proteins play a largely structural role.
Based on the figure, which of these statements is/are correct?
-For different genes, opposite strands of DNA can serve as a template. -RNA is always polymerized in the 5'-to-3' direction.
The sequence of the template strand of a DNA molecule is 5'-ACTGGCAATG-3'. What is the sequence of the RNA transcribed from this DNA?
5'-CAUUGCCAGU-3'- One of the major chemical differences between DNA and RNA is the presence of thymine (not uracil) in DNA and the presence of uracil (not thymine) in RNA. If the sequence of the template strand of a DNA molecule is 5'-ACTGGCAATG-3', then 5'-CAUUGCCAGU-3' must be the sequence of the RNA transcribed from this DNA. Transcription generates an antiparallel and complementary strand of nucleic acid. When a single-stranded nucleic acid sequence is written out, it is conventional to write the sequence in the 5'-to-3' direction. Therefore, 5'-CAUUGCCAGU-3' RNA is complementary to 5'-ACTGGCAATG-3' DNA.
The sequence of the coding strand of a DNA molecule (that is, the DNA strand that contains the codons specifying the protein sequence) is 5'-CGGATGCTTA-3'. What is the sequence of the RNA made from this DNA?
5'-CGGAUGCUUA-3' One of the major chemical differences between DNA and RNA is the presence of thymine (not uracil) in DNA and the presence of uracil (not thymine) in RNA. If the sequence of the coding strand of a DNA molecule (that is, the DNA strand that contains the codons specifying the protein sequence) is 5'-CGGATGCTTA-3', then the sequence of the RNA made from this DNA would be 5'-CGGAUGCUUA-3'. Transcription generates an antiparallel and complementary strand of nucleic acid. When a single-stranded nucleic acid sequence is written out, it is convention to write the sequence in the 5'-to-3' direction. Therefore, 5'-CGGAUGCUUA-3' RNA is complementary to 5'-CGGATGCTTA-3' DNA. Review the figure below to help you keep track of coding versus template strands of DNA and how RNA is related to each.
An RNA chain elongates in what direction?
5'-to-3' only- Like the DNA polymerase that carries out DNA replication, RNA polymerases catalyze the formation of the phosphodiester bonds that link the nucleotides together and form the sugar-phosphate backbone of the RNA chain. Therefore, the RNA strand elongates in the 5' to 3' direction only. This is because to add a nucleotide, there must be an available 3' hydroxyl group for the incoming nucleotide triphosphate to react with. Once this reaction takes place, a phosphodiester bond is established between the neighboring nucleotides, and the nucleic acid chain has grown by one nucleotide in length.
The Translation II animation shows the arginine aminoacyl-tRNA entering the A site and arginine being added to the growing polypeptide. What would be the consequence of an alteration in the arginine tRNA anticodon sequence from UCC to ACC? Note the following mRNA codons: Arginine: AGA, AGG, CGU, CGC, CGA, CGG Threonine: ACU, ACC, ACA, ACG Tryptophan: UGG
Arginine will occasionally be added to the growing peptide in place of tryptophan. Changing the tRNA anticodon does not alter the amino acid that is added to that tRNA, so the mutated tRNA in this question will still be bound to arginine. The altered anticodon will no longer bind to the AGG codon for arginine in the mRNA. Instead, this altered tRNA will bind to the UGG codon in mRNA and add an arginine instead of the normal tryptophan. This will occasionally lead to arginine being added in place of tryptophan in the growing polypeptide. The actual tryptophan-charged tRNA is still in the cell, so sometimes the correct tryptophan will also be added to the growing polypeptide.
What determines the nucleotide sequence of a newly transcribed RNA molecule?
Complementary base-pairing with a DNA during transcription Complementary base-pairing with DNA during transcription is what determines the nucleotide sequence of a newly transcribed RNA molecule. RNA polymerase uses the information—that is, the nucleotide sequence of the template strand of DNA—to synthesize a complementary RNA molecule.
Determine whether the following statement is true or false: Because introns are largely genetic junk, they do not need to be removed with any degree of precision during RNA splicing.
False- Introns must be removed precisely; removing even one nucleotide too many—or leaving an intronic nucleotide in the spliced mRNA—would shift the reading frame. Leaving larger pieces of intron in the mature mRNA would code for the insertion of extra amino acids. In either case, the consequences of imprecise splicing would be the production of an aberrant protein.
In eukaryotes, which parts of a gene are transcribed into RNA?
Introns and exons- In eukaryotes, the introns and the exons of a gene are transcribed into RNA. This initial product is spliced into mature mRNA before the molecule is exported from the nucleus. Introns are spliced out by the activity of the spliceosome, leaving only exons in the mature mRNA.
Using the genetic code here, determine the amino acids that a polynucleotide of UC would code for.
Leu, Ser- A poly-UC molecule would be UCUCUCUCUCUC, and thus would have nonoverlapping triplets of UCU and CUC. Based on the genetic code, these triplets code for Ser (UCU) and Leu (CUC).
Which part of a protein is synthesized by a ribosome first?
N-terminus Remember that the covalent peptide bond that links amino acids into polymers involves the amino group of one amino acid and the carboxyl group of the other. Therefore, in any polypeptide, there will always be a free amino group at one end of the molecule and a free carboxyl group at the other. The nature of the peptidyl transferase activity of the ribosome is such that the amino group of the new amino acid being added reacts with the carboxyl group of the growing polypeptide. Therefore, the first amino acid in the polypeptide (that is, the one specified for by the first codon) will have its amino group remain free. This is referred to as the N-terminus. Additionally, because translation proceeds 5' to 3' along the mRNA molecule, the amino acids coded for at the 5' end of the transcript will be located at the N-terminus of the polypeptide.
At what site does the charged initiator tRNA first bind on the ribosome?
P site- In addition to a binding site for an mRNA molecule, each ribosome contains three binding sites for tRNA molecules, called the A site, the P site, and the E site. The charged initiator tRNA first binds on the ribosome at the P site. In eukaryotes, the initiator tRNA is charged with methionine and is loaded into the P site of the small ribosomal subunit, along with additional proteins called translation initiation factors. This small ribosomal subunit, with the initiator tRNA loaded into the P site, binds to the 5ʹ end of an mRNA molecule by recognizing the 5ʹ cap that is present on all eukaryotic mRNAs. To add an amino acid to a growing peptide chain, a charged tRNA enters the A site by base-pairing with the complementary codon on the mRNA molecule. Its amino acid is then linked to the growing peptide chain, which is held in place by the tRNA in the neighboring P site. Next, the large ribosomal subunit shifts forward, moving the spent tRNA to the E site before ejecting it. This cycle of reactions is repeated each time an amino acid is added to the polypeptide chain.
Investigators treat cells with a chemical that introduces random mutations into the DNA, including single-nucleotide changes that turn one base into another. They then isolate two mutants: one produces a protein that carries an alanine at a site that normally contains a valine; the other produces a protein that carries a methionine instead of the valine. When these mutant cells are subjected to the same mutagenic treatment, they both produce proteins that contain a threonine at the site of the original valine. Assuming that the mutations causing these alterations are single-nucleotide changes, what were the codons that specified each of the amino acids discussed?
Val, GUG; Ala, GCG; Met, AUG; Thr, ACG Methionine is specified by a single codon, AUG, because it also always functions as the start translation codon. This provides a starting point to solve the rest of the question. Working backward from the methionine AUG, the codon specifying valine must have been GUG (the mutation having changed the initial G to an A). If that is the case, the codon specifying alanine must be GCG (the mutation having changed the U in GUG to a C in GCG). Finally, the codon specifying threonine must be ACG (one mutation changing AUG to ACG, the other changing GCG to ACG). Each of these was one nucleotide positon off from the other.
The genetic code was originally deciphered, in part, by experiments in which synthetic polynucleotides with repeating sequences were used as mRNAs to direct protein synthesis in cell-free extracts. Under these conditions, ribosomes could be made to start translation anywhere within the RNA molecules, with no start codon necessary. What peptide would be made by translation from a synthetic mRNA made of the repeating dinucleotide CGCG...?
a peptide containing alternating arginines and alanines The sequence of nucleotides in an mRNA molecule is read consecutively in groups of three, termed codons. In this question, and depending on where translation begins along the repetitive polynucleotide CGCG..., two different codons are possible: CGC and GCG. These two codons specify arginine and alanine, respectively. The peptide produced would therefore contain alternating residues of these two amino acids. An mRNA sequence can be translated in any one of three different reading frames, depending on where the decoding process begins. However, in the cell, and unlike the synthetic example of this question, only one of the three possible reading frames in mRNA specifies the correct protein. A special signal at the beginning of each mRNA molecule sets the correct reading frame—the AUG start translation codon.
The genetic code was originally deciphered, in part, by experiments in which synthetic polynucleotides with repeating sequences were used as mRNAs to direct protein synthesis in cell-free extracts. Under these conditions, ribosomes could be made to start translation anywhere within the RNA molecules, with no start codon necessary. What peptide would be made by translation from a synthetic mRNA made entirely of adenine (poly-A)?
a polymer of lysine: Lys-Lys-Lys... The genetic code was originally deciphered, in part, by experiments in which synthetic polynucleotides with repeating sequences were used as mRNAs to direct protein synthesis in cell-free extracts. Under these conditions, ribosomes could be made to start translation anywhere within the RNA molecules, meaning that no start codon was necessary. A polymer of lysine (Lys-Lys-Lys...) would be made by translation from a synthetic mRNA made entirely of adenine (poly-A). Because no start codon was necessary, the ribosome could recognize any of the three reading frames of this synthetic polynucleotide (...AAAAAAAAAAAAAAA...) and begin translation. Because the synthetic polynucleotide is just repeating adenines, all reading frames are "AAA," which codes for lysine. Similarly, a synthetic poly-U mRNA as shown below would yield a polymer composed entirely of phenylalanine.
Which biochemical reaction is catalyzed by a ribozyme?
Peptide bond formation in protein synthesis- Peptide bond formation in protein synthesis is catalyzed by a ribozyme. When the tRNA molecules associate with the mRNA, the rRNA of the ribosomal subunits orients the newly incoming amino acid with the growing peptide chain in a way that encourages the addition reaction between the two. Even though the ribosome is composed of both RNA and protein, the peptidyl transferase reaction is accomplished by the RNA, not protein, component of the ribosome.
Introns are removed by which of the following?
RNA splicing in the nucleus- Introns are removed by RNA splicing in the nucleus. In fact, the factors responsible for splicing sit on the tail of RNA polymerase II, the enzyme responsible for carrying out transcription of protein-coding genes. Therefore, as soon as the transcript begins elongating, it quickly receives a 5' cap and then begins splicing to remove introns, even while transcription continues. After splicing, the 3' end of the transcript is also modified and then the mature mRNA is exported to the cytosol for translation.
Which macromolecule(s) is/are critical in the active site of the ribosome for catalysis of peptide bond formation?
Ribosomal RNA- The ribosomal RNA is the critical component in the active site as this site is made of only ribosomal RNA. The protein helps support the RNA but does not participate in the catalysis of peptide bond formation. The ribosomal RNA base-pairs with the tRNA holding the growing polypeptide, helping to position it in the correct orientation. Other RNA nucleotides base-pair with the incoming tRNA to position the amino acids. Further hydrogen-bonding positions the amino acids, facilitating new peptide bond formation.
An RNA message is decoded by which of the following?
Ribosomes. Protein synthesis, which is also called translation, is the "decoding" process that is carried out by the peptidyl transferase activity of the ribosome. Ribosomes bind to mRNA and allow for a charged tRNA with the complementary anticodon to recognize a particular mRNA codon and then transfer the amino acid to the growing polypeptide chain.
At which site on the DNA of a gene does RNA polymerase release its newly made RNA?
Terminator- Signals in the nucleotide sequence of a gene tell RNA polymerase where to start and stop transcription. Transcription is initiated by the promoter region, which is not transcribed. Transcription is stopped at the terminator, which, unlike the promoter, is actually transcribed. The terminator sequence functions to stop transcription by causing RNA polymerase to release both the newly formed transcript and the DNA template.
Some antibiotics function by inhibiting translation. One class blocks the interaction between EF-Tu and the aminoacyl-tRNA. What specific effect would this have on the ribosome and translation?
The aminoacyl-tRNA will not enter the A site on the ribosome. EF-Tu binds to free aminoacyl-tRNAs and helps deliver them to the A site of the ribosome. If the anticodon is compatible with the codon of the mRNA, the tRNA binds in the A site and EF-Tu hydrolyzes GTP to dissociate. Free aminoacyl-tRNAs do not enter the A site alone. One class of antibiotics binds to EF-Tu and blocks the binding to aminoacyl-tRNAs. This has the effect of blocking translation since aminoacyl-tRNAs do not enter the A site on their own, thus halting translation.
To which part of an mRNA molecule do ribosomal subunits first bind?
The initial binding site for a ribosome is the 5' end of an mRNA molecule, upstream of the important AUG that serves as the start translation signal. Initiation of translation is outlined in the steps shown in the figure below. Pay special attention to how the small ribosomal subunit, pre-loaded with an initiator tRNA and other translation initiation factors, binds to the 5' untranslated region and then slides along the mRNA until it reaches the start AUG codon. Once this happens, the rest of the ribosome complex can assemble so that translation can begin in earnest.
Which would be more deleterious: the loss of a single nucleotide from the protein-coding region of a gene or the loss of three nucleotides in that same region?
The loss of a single nucleotide would be more deleterious than the loss of three nucleotides in that same region because removing a single nucleotide from the protein-coding region of a gene would alter the reading frame in the mRNA. Such mutations cause every codon in the mRNA to be misread and produce a protein with a garbled and nonfunctional sequence of amino acids. In some cases, the resulting protein is even shortened, as the change in reading frame can introduce premature stop codons. Removing three nucleotides—or one codon—from the mRNA produces a protein that is missing a single amino acid. Unless that amino acid is critical for the activity or folding of the protein, the mutation will have little effect on protein function.
In an experiment conducted in 1962, investigators took tRNAs bearing cysteine and chemically converted the charged amino acid to an alanine. They then introduced these "hybrid" alanine-bearing tRNAs into a cell-free translation system from which they removed all of the normal, cysteine-bearing tRNAs. How did this chemical manipulation affect the proteins produced by this altered system?
The proteins contained alanines where cysteines were supposed to be. This experiment demonstrated that ribosomes do not "check" the identity of the amino acids attached to tRNAs. Unlike DNA polymerase, ribosomes do not have a proofreading mechanism that ensures proper sequence of the product. Once an amino acid has been coupled to a tRNA, the ribosome will "blindly" incorporate that amino acid into the position dictated by the codon-anticodon match. It also reinforces the crucial role that the aminoacyl-tRNA synthetases play in the accuracy of translation. Thus, the tRNA is involved in two equally important recognition events: (1) the proper charging of the tRNA by an aminoacyl-tRNA synthetase, and (2) the proper anticodon recognition when a message is within the ribosome.
To crack the genetic code, researchers introduced synthetic messenger RNAs into in vitro translation systems and determined which proteins were produced from these synthetic mRNAs. mRNAs consisting of poly-UUC led to production of three different proteins: poly-Phe, poly-Ser, and poly-Leu. What best explains this result?
The synthetic mRNA was read in all three reading frames. The genetic code does not change in vitro as compared to in vivo. However, unlike when in vivo, in which translation begins at an initiating methionine start codon, when in vitro, the ribosome can be forced to translate any message in all three reading frames. Thus the UUCUUCUUCUUC message was read three different ways. Starting at the first U, UUC codes for Phe, as shown in the figure. If the ribosome started at the second U, the message was read as repeating UCU codons, so poly-Ser was produced. In the third reading frame, the ribosome read the message as repeating CUU codons, resulting in poly-Leu.
What is true of eukaryotic mRNAs?
They are translated after they are exported from the nucleus. Unlike prokaryotes, where transcription and translation can occur simultaneously, these two events are separated in time and space in eukaryotes. In eukaryotes, transcription takes place in the nucleus and the transcript must also undergo processing here to become a mature mRNA. After this occurs, the mRNAs are exported to the cytosol where they interact with ribosomes to carry out translation.
How many nucleotides are necessary to specify a single amino acid?
Three- Three nucleotides are necessary to specify a single amino acid, and these groupings of three nucleotides are referred to as codons. With four different bases to choose from (A, U, C, G), the combination of three nucleotides is the smallest grouping to provide enough diversity to code for all 20 different amino acids: 4 × 4 × 4 = 64 different possible codon sequences. 64 codons is larger than the number of different amino acids (20), which means that many of the amino acids have more than one codon that will specify their placement into a polypeptide.
In principle, how many reading frames in an RNA molecule can potentially be translated into protein?
Three- Translation functions in a manner analogous to reading an mRNA sentence that is made up of several three-letter words (codons). If translation starts on the second or third letter of the first word and then starts "reading" words in three-letter groupings, a completely different "sentence" (protein) results. If translation begins on the fourth nucleotide in this mRNA "sentence," the words that it "reads" are back to placing the same amino acids as the first line, because the genetic code works based off of triplet codons. These three potential starting points, each potentially resulting in its own unique amino acid sequence, are what is called reading frames. In reality, only one of the three reading frames will result in the translation of the proper protein.
At which step of gene expression can cells amplify the number of copies of a protein made from a single gene?
Transcription and translation- Proteins can be made in large quantities by transcribing many mRNAs from the gene, and then each mRNA can be translated into many copies of the protein. In contrast, if just a few mRNAs are made, only a few copies of the protein are made.
Determine whether the following statement is true or false: Some genes do not encode proteins but instead encode functional RNA.
True- Some genes do not encode proteins but instead encode functional RNA. Unlike mRNA, these functional RNAs are transcribed but are not used as a template for translation. These non-protein-coding RNAs include tRNA, rRNA, and miRNA and, like proteins, have various roles serving as regulatory, structural, and catalytic components of cells.
Determine whether the following statement is true or false: Once translation is complete, all of the proteins shown being synthesized in this image are expected to be identical.
True- The polyribosome is a series of ribosomes that can simultaneously translate the same mRNA molecule. All of the individual ribosomes are using the same mRNA, and therefore are all reading the same information, which will lead to the synthesis of identical proteins. The formation of polyribosomes greatly increases the efficiency of protein production from a single mRNA molecule.
The genetic code was originally deciphered, in part, by experiments in which synthetic polynucleotides with repeating sequences were used as mRNAs to direct protein synthesis in cell-free extracts. Under these conditions, ribosomes could be made to start translation anywhere within the RNA molecules, with no start codon necessary. What peptide would be made by translation from a synthetic mRNA made of the repeating trinucleotide UCGUCG...?
a polymer of serine (Ser-Ser-Ser...), a polymer of arginine (Arg-Arg-Arg...), and a polymer of valine (Val-Val-Val...) Write out the sequence UCGUCGUCGUCGUCGUCG. This represents six iterations of the same repeated triplet. Now, identify the three different reading frames and determine if they are similar or different. In principle, an mRNA sequence can be translated in any one of three different reading frames, depending on where the decoding process begins. For the peptides produced by translation from a synthetic mRNA made of the repeating trinucleotide UCGUCG..., a polymer of serine (Ser-Ser-Ser...), a polymer of arginine (Arg-Arg-Arg...), and a polymer of valine (Val-Val-Val...) are expected. This is because each of the three reading frames will be read but each will generate a distinct polypeptide. In one reading frame, the sequence UCGUCGUCG... codes for a polymer of serine; in another, the sequence CGUCGUCGU... codes for a polymer of arginine; and in the final one, the sequence GUCGUCGUC... codes for a polymer of valine. Thus, a mixture of the three different peptides will be produced.
Amino acids are attached to their tRNA molecules by which of the following?
aminoacyl-tRNA synthetases- For translation to accurately transmit the protein-coding information contained within a gene, there needs to be a direct, linear relationship between the mRNA codon, a tRNA anticodon, and the amino acid attached to the tRNA. The recognition of a codon by the anticodon is accomplished through complementary base-pairing. However, the attachment of the proper amino acid to a tRNA harboring the correct anticodon specificity is accomplished by a group of enzymes known as aminoacyl-tRNA synthetases. Cells have enough different versions of this enzyme so that there is a separate enzyme for recognizing each anticodon and then covalently attaching the appropriate amino acid. Once the amino acid has been linked to the tRNA, the tRNA is said to be "charged" and is ready to bind its specific codon on the ribosome-bound mRNA, resulting in the addition of the proper amino acid to the growing polypeptide chain.
Within the ribosome, the formation of peptide bonds is catalyzed by what component?
an RNA molecule in the large ribosomal subunit- The eukaryotic ribosome is a large complex of four rRNAs and more than 80 small proteins, arranged into two subunits: the large and the small ribosomal subunits. The small ribosomal subunit matches the tRNAs to the codons of the mRNA, while the large subunit catalyzes the formation of the peptide bonds that covalently link the amino acids together into a polypeptide chain. The peptidyl transferase activity of the ribosome is responsible for formation of the peptide bonds in the growing polypeptide.
Where or when does RNA capping at the 5' end of the transcript take place?
as an RNA is being transcribed- RNA capping, a part of RNA processing, takes place as an RNA is being transcribed. Eukaryotic genes contain both introns and exons, and both are transcribed. Soon after transcription begins, within the first 25 nucleotides added to the growing RNA strand, a modified guanine nucleotide is added to the 5' end of the RNA. Once the cap is added and as transcription is continuing along the gene, splicing to remove introns can begin. After transcription is complete, further modification of the RNA transcript must occur, including the addition of the 3' poly-A tail, before the mature mRNA can exit the nucleus to be translated by ribosomes in the cytosol.
Where does the splicing of pre-mRNAs take place?
in the nucleus as the RNA is still being transcribed- The splicing of pre-mRNAs takes place as the RNA is still being transcribed in the nucleus. RNA capping occurs early in transcription, after RNA polymerase has produced about 25 nucleotides of RNA. Splicing begins after capping takes place, and it removes the introns from the RNA transcript. After processing, which also includes the modification of the 3' end of the transcript with a poly-A tail, the now mature mRNA transcript can leave the nucleus and enter the cytosol for translation.
The reading frame to use for translating an mRNA into functional protein is determined by the
location of an AUG. The translation of an mRNA in eukaryotes begins when the initiator tRNA encounters the first AUG in an mRNA. The complex containing the initiator tRNA starts scanning the mRNA from the 5' end to find the AUG.
Which type of RNA is converted into protein for performing its cellular function?
mRNA- There are many different types of RNA that perform functions as RNA in the cell and are never translated into protein. These include tRNA, rRNA, and miRNA. The only RNAs that code for proteins are mRNAs.
What is the source of energy that drives transcription elongation forward?
the hydrolysis of high-energy bonds of ribonucleoside triphosphates The source of energy that drives transcription elongation forward is the hydrolysis of high-energy phosphate bonds of ribonucleoside triphosphates that are being incorporated into the growing RNA molecule. The nucleoside triphosphate is hydrolyzed to yield a nucleoside monophosphate, which forms a phosphodiester bond with the free 3' hydroxyl end of the RNA polymer, and a pyrophosphate molecule, which is subsequently hydrolyzed into two molecules of inorganic phosphate. The breakdown of pyrophosphate into inorganic phosphate renders the polymerization reaction essentially irreversible. Because the energy to drive polymerization is delivered by the nucleoside triphosphates themselves, no additional energy is needed for the catalytic activity of RNA polymerase.
The information in an mRNA molecule is converted into protein sequence using
three consecutive bases, with no overlap between triplets- The genetic code consists of three consecutive bases and is read in a nonoverlapping fashion. That is, the nucleotides for one triplet are not the part of the next triplet.
Translation proceeds in a series of steps in the active site of the ribosome. Which of the following are important steps in polypeptide formation?
-The RNA in the P site makes hydrogen bonds with the 3' end of the aminoacyl-tRNA. -The hydrogen bonds formed between ribosomal RNA and tRNAs position the aminoacyl-tRNAs to catalyze peptide bond formation. The P site ribosomal RNA base-pairs with the 3' end of the tRNA holding the growing polypeptide, helping to position it in the correct orientation. The incoming aminoacyl-tRNA also forms hydrogen bonds, not covalent bonds, with the ribosomal RNA in the A site. The hydrogen bonds formed between ribosomal RNA and the tRNAs in the A and P sites help position the amino acids to catalyze peptide bonds formation. After peptide bond formation, the ribosome changes conformation and the empty tRNA in the P site is released. The tRNA holding the growing polypeptide is transferred from the A site to the P site and a new tRNA enters the A site of the ribosome.
A primary transcript (immature, non-processed) single-stranded RNA molecule has the following nucleotide composition: 30% A, 20% G, 24% C, and 26% U. What is the nucleotide composition of the double-stranded DNA molecule from which it was transcribed?
28% A, 22% G, 22% C, and 28% T DNA contains the bases adenine (A), thymine (T), guanine (G), and cytosine (C). On the other hand, RNA contains A, G, C, and uracil (U). Because the DNA molecule is double-stranded, the nucleotide composition of both strands must be taken into account when compared to the single-stranded nature of RNA. The template DNA strand that encodes this RNA molecule would contain: 30% T, 20% C, 24% G, and 26% A. The nontemplate strand, sometimes called the "sense strand" of the DNA, which is complementary to the template strand, would contain: 30% A, 20% G, 24% C, and 26% T. The double helix would thus contain an average of these values: 28% A, 22% G, 22% C, and 28% T.
At what site do all charged tRNAs (with the exception of the initiator tRNA) first bind on the ribosome?
A site- In addition to a binding site for an mRNA molecule, each ribosome contains three binding sites for tRNA molecules, called the A site, the P site, and the E site. All charged tRNAs (with the exception of the initiator tRNA) first bind on the ribosome at the A site. To add an amino acid to a growing peptide chain, a charged tRNA enters the A site by base-pairing with the complementary codon on the mRNA molecule. Its amino acid is then linked to the growing peptide chain, which is held in place by the tRNA in the neighboring P site. Next, the large ribosomal subunit shifts forward, moving the spent tRNA to the E site before ejecting it. This cycle of reactions is repeated each time an amino acid is added to the polypeptide chain.
Translation takes place in a series of four steps. Which of these best describes this four-step cycle during elongation?
An aminoacyl-tRNA binds to the vacant A site on the ribosome; a peptide bond forms; the large subunit of the ribosome translocates, moving the bound tRNAs to the E and P sites; the small subunit of the ribosome translocates, ejecting the tRNA from the E site.
Determine whether the following statement is true or false: During translation, the growing peptide chain is always held together by the tRNA in the P site of the ribosome.
False- During translation, the growing peptide chain is not always held together by the tRNA in the P site of the ribosome. Rather, the growing peptide chain is held by either the tRNA in the P site or the tRNA in the A site.
Many antibiotics work by inhibiting bacterial protein synthesis. Investigators have isolated a promising new compound and wish to determine its mechanism of action. Using a cell-free translation system similar to the ones originally used to deduce the genetic code, the researchers incubate their drug with the synthetic polynucleotide 5'-AUGUUUUUUUUU. In the absence of the drug, this polynucleotide directs the synthesis of the peptide Met-Phe-Phe-Phe. When the drug is added, only the peptide Met-Phe is produced. Based on this observation, which is most likely the mechanism of action of this potential new antibiotic?
It blocks translocation of the large ribosomal subunit, preventing the movement of peptidyl-tRNA from the A site to the P site of the ribosome. This antibiotic likely blocks translocation of the large ribosomal subunit (step 3 in the figure below), preventing the movement of peptidyl-tRNA from the A site to the P site of the ribosome. The two-amino-acid peptide can form because the initiator tRNA that carries methionine will bind to the P site, and the A site can accomodate the tRNA that recognizes UUU (which codes for phenylalanine). Because the ribosome can't translocate, no additional amino acids can be added. Translocation inhibitors are a known mechanism of action for antibiotics. An example of an antibiotic that uses this mode of action is cycloheximide.
Shown here is a gene with the direction of transcription noted. How does the RNA polymerase know which strand to use as a template for the RNA, and which strand would it choose in this case?
It would use the bottom strand because the promoter sets the direction and the polymerase moves from 3' to 5' along the template strand. RNA polymerase binds to promoter sequences in a specific orientation. The RNA polymerase will then move away from the promoter using the promoter-dictated directionality and uses the 3' to 5' strand as a template to make a new RNA in the 5' to 3' direction.
