problem set 12
Which of the following amino acid changes could result from a mutation that changed a single base? For each change that could result from the alteration of a single base, determine which position of the codon (first, second, or third nucleotide) in the mRNA must be altered for the change to occur. d.) Pro-> Ala
All four codons for Pro can be mutated at the first position to produce Ala codons: CCU (Pro)—Change the first position to G to produce GCU (Ala). CCC (Pro)—Change the first position to G to produce GCC (Ala). CCA (Pro)—Change the first position to G to produce GCA (Ala). CCG (Pro)—Change the first position to G to produce GCG (Ala).
A synthetic mRNA added to a cell-free protein-synthesizing system produces a peptide with the following amino acid sequence: Met-Pro-Ile-Ser-Ala. What would be the effect on translation if the following components were omitted from the cell-free protein-synthesizing system? What, if any, type of protein would be produced? Explain your reasoning. d.) Elongation factor G
EF-G is necessary for the movement of the ribosome along the mRNA in a 5' to 3' direction. Once the formation of the peptide bond occurs between the Met and Pro, the lack of EF-G would prevent the movement of the ribosome along the mRNA, so no new codons would be read. However, the dipeptide Met-Pro would be formed because its formation would not require EF-G.
Referring to the genetic code presented in Figure 15.10, give the amino acids specified by the following bacterial mRNA sequences. ...........
Each of the mRNA sequences begins with the three nucleotides AUG. This indicates the start point for translation and allows for a reading frame to be set. In bacteria, the AUG initiation codon codes for N-formylmethionine. Also, for each of these mRNA sequences, a stop codon is present either at the end of the sequence or within the interior of the sequence. The amino terminal refers to the end of the protein with a free amino group and will be the first peptide in the chain. The carboxyl terminal refers to the end of the protein with a free carboxyl group and is the last amino acid in the chain. For the following peptide chains reading from left to right, the first amino acid is located at the amino end, while the last amino acid is located at the carboxyl end.
Define the following terms as they apply to the genetic code: Overlapping code
If an overlapping code were present, then a single nucleotide would be expected to be included in more than one codon. The result for a sequence of nucleotides within a single gene would be to encode more than one type of polypeptide. However, because the genetic code is nonoverlapping, codons within the same gene do not overlap. Where overlap occurs is in overlapping genes in some viruses, where the same segment of the genome encodes multiple—two or even three (in case of HIV Env gene)—peptides. In such cases, the codons of different peptides are translated in different frames in nonoverlapping fashion.
Define the following terms as they apply to the genetic code: Nonoverlapping code
In a nonoverlapping code, a single nucleotide is part of only one codon. This results in the production of a single type of polypeptide from one polynucleotide sequence.
Define the following terms as they apply to the genetic code: Universal code
In a universal code, each codon specifies, or codes, for the same amino acid in all organisms. The genetic code is nearly universal, but not completely. Most of the exceptions occur in mitochondrial genomes.
If a tRNA had the anticodon sequence 5' CGA 3', what would be the sequence and polarity of the corresponding codon in the mRNA? In the DNA on the non-template strand?
5' UCG 3' in the mRNA; 5' TCG 3' in the non-template strand of the DNA
What role do the initiation factors play in protein synthesis?
Initiation factors are proteins that are required for the initiation of translation. In bacteria, there are three initiation factors (IF-1, IF-2, and IF-3). Each one has a different role. IF-1 promotes the disassociation of the large and small ribosomal subunits. IF-3 binds to the small ribosomal subunit and prevents it from associating with the large ribosomal subunit. IF-2 is responsible for binding GTP and delivering the fMet-tRNA^fMet to the initiator codon on the mRNA. In eukaryotes, there are more initiation factors, but many have similar roles. Some of the eukaryotic initiation factors are necessary for recognition of the 5′ cap on the mRNA. Others possess RNA helicase activity, which is necessary to resolve secondary structures.
A synthetic mRNA added to a cell-free protein-synthesizing system produces a peptide with the following amino acid sequence: Met-Pro-Ile-Ser-Ala. What would be the effect on translation if the following components were omitted from the cell-free protein-synthesizing system? What, if any, type of protein would be produced? Explain your reasoning. b.) Initiation factor 2
No translation would occur. IF-2 is necessary for translation initiation. The lack of IF-2 would prevent fMet-tRNA^fMet from being delivered to the small ribosomal subunit, thus blocking translation.
Referring to the genetic code presented in Figure 15.10, give the amino acids specified by the following bacterial mRNA sequences. d. 5´-GUACUAAGGAGGUUGUAUGGGUUAGGGGACAUCAUUUUGA-3´
Solution: Amino Val—Leu-Arg- Arg-Leu-Tyr-Gly-Leu-Gly-Asp-Ile-Ile-Leu-(Ile, Met, Thr, Asn, Lys, Ser, or Arg)----Carboxyl For the last potential readable codon only 1base is shown and could potentially be part of a codon that encodes for Ile (AUU, AUG, or AUA), Met (AUG), Thr (ACU, ACC, ACA, or ACG), Asn (AAU OR AAC), Lys (AAA or AAG), Ser (AGU or AGC), or Arg (AGA or AGG).
What is the significance of the fact that many synonymous codons differ only in the third nucleotide position?
Synonymous codons code for the same amino acid, or, in other words, they have the same meaning. A nucleotide at the third position of a codon pairs with a nucleotide in the first position of the anticodon. Unlike the other nucleotide positions involved in the codon-anticodon pairing, this pairing is often weak, or "wobbles," and nonstandard pairings can occur. Because the "wobble," or nonstandard base pairing with the anticodons, affects the third nucleotide position, the redundancy of codons ensures that the correct amino acid is inserted in the protein when nonstandard pairing occurs
Arrange the following components of translation in the approximate order in which they would appear or be used in prokaryotic protein synthesis: 30S initiation complex 70S initiation complex release factor 1 elongation factor G initiation factor 3 elongation factor Tu fMet-tRNA^fMet
The components are in order according to when they are used or play a key role in translation. The potential exception is initiation factor 3. Initiation factor 3 could possibly be listed first because it is necessary to prevent the 30s ribosome from associating with the 50s ribosome. It binds to the 30s subunit prior to the formation of the 30s initiation complex. However, during translation events the release of initiation factor 3, allows the 70s initiation complex to form, a key step in translation.
A synthetic mRNA added to a cell-free protein-synthesizing system produces a peptide with the following amino acid sequence: Met-Pro-Ile-Ser-Ala. What would be the effect on translation if the following components were omitted from the cell-free protein-synthesizing system? What, if any, type of protein would be produced? Explain your reasoning. e.) Release factors RF-1, RF-2, and RF-3
The release factors RF-1 and RF-2 recognize the stop codons and bind to the ribosome at the A site. They then interact with RF-3 to promote cleavage of the peptide from the tRNA at the P site. The absence of the release factors prevents termination of translation at the stop codon, resulting in a larger peptide.
Define the following terms as they apply to the genetic code: Termination codon
The termination codon signals the termination or end of translation and the end of the protein molecule. There are three termination codons—UAA, UAG, and UGA—which can also be referred to as stop codons or nonsense codons. These codons do not code for amino acids.
How many codons would be possible in a triplet code if only three bases (A, C, and U) were used?
To calculate the number of possible codons of a triplet code if only three bases are used, the following equation can be used: 3n , where n is the number of nucleotides within the codon. So, the number of possible codons is equal to 33 , or 27 possible codons.
A nontemplate strand on bacterial DNA has the following base sequence. What amino acid sequence will be encoded by this sequence? 5´-ATGATACTAAGGCCC-3´
To determine the amino acid sequence, we need to know the mRNA sequence and the codons present. The nontemplate strand of the DNA has the same sequence as the mRNA, except that thymine-containing nucleotides are substituted for the uracilcontaining nucleotides. So the mRNA sequence would be as follows: 5'-AUGAUACUAAGGCCC-3'. Assuming that the AUG indicates a start codon, then the amino acid sequence would be starting from the amino end of the peptide and ending with the carboxyl end: fMet-Ile- Leu-Arg-Pro.
Process (Replication, Transcription, RNA processing, or Translation) most immediately affected by deletion of sequence. f.) -10 consensus sequence
Transcription. In bacteria, the -10 sequence is an important component of the promoter. Deletion of the -10 sequence will prevent transcription initiation from occurring.
Process (Replication, Transcription, RNA processing, or Translation) most immediately affected by deletion of sequence. d.) terminator
Transcription. The terminator is necessary for transcription termination. Deletion of the terminator will result in the production of an abnormally long RNA transcript
What is the difference between a transition and a transversion? Which type of base substitution is usually more common?
Transition mutations are base substitutions in which one purine (A or G) is changed to the other purine, or a pyrimidine (T or C) is changed to the other pyrimidine. Transversions are base substitutions in which a purine is changed to a pyrimidine or vice versa. Although transversions would seem to be statistically favored because there are eight possible transversions and only four possible transitions, about twice as many transition mutations are actually observed in the human genome
List one major piece of evidence that DNA does not serve directly as the template for protein synthesis in eukaryotes.
Translation in eukaryotes occurs in the cytoplasm; DNA is confined to the nucleus.
Process (Replication, Transcription, RNA processing, or Translation) most immediately affected by deletion of sequence. e.) start codon
Translation. The start codon is necessary for translation initiation.
Process (Replication, Transcription, RNA processing, or Translation) most immediately affected by deletion of sequence. g.) Shine-Dalgarno
Translation. The Shine-Dalgarno sequence or ribosome-binding site is bound by the 30s subunit during the initiation of translation. If the sequence is deleted, then the ribosome will not bind to the mRNA molecule and translation will not occur.
Process (Replication, Transcription, RNA processing, or Translation) most immediately affected by deletion of sequence. c.) poly(A) tail
Translation. The poly(A) tail is involved in mRNA stability. If the tail is missing, then the mRNA will be degraded more rapidly thus affecting translation.
Assume that the nucleotide at the 5' end of the first tRNA's anticodon (the tRNA on the left) in Figure 15.11 were mutated from G to U. Give all codons with which the new, mutated anticodon could pair.
5'—UCA—3' and 5'—UCG—3'
What is the difference between a missense mutation and a nonsense mutation? Between a silent mutation and a neutral mutation?
A base substitution that changes the sequence and the meaning of a mRNA codon, resulting in a different amino acid being inserted into a protein, is called a missense mutation. Nonsense mutations occur when a mutation replaces a sense codon with a stop (or nonsense) codon. A nucleotide substitution that changes the sequence of an mRNA codon, but not the meaning is called a silent mutation. In neutral mutations, the sequence and the meaning of an mRNA codon are changed. However, the amino acid substitution has little or no effect on protein function.
Contrast the effects of frameshift, missense and nonsense mutations on a protein amino acid sequence.
A frameshift mutation changes the reading frame and causes the wrong amino acids to be inserted into the polypeptide after the change in the DNA. Missense mutations result in a single amino acid substitution in the protein (the total number of amino acids remains unchanged). Nonsense mutations replace a codon specifying an amino acid with a stop codon. The protein is shortened or truncated.
Define the following terms as they apply to the genetic code: Sense codon
A sense codon is a group of three nucleotides that code for an amino acid. In a standard genetic code there are 61 sense codons that code for the 20 amino acids commonly found in proteins.
A series of tRNAs have the following anticodons. Consider the wobble rules listed in Table 15.2 and give all possible codons with which each tRNA can pair...........
From the wobble rules outlined in Table 15.2, we can see that when A occurs at the 5' of the anticodon it can pair only with U in the 3' end of the codon. When C is present at the 5' of the anticodon, it can only pair with G at the 3' of the codon. However, both U and G, when present at the 5' end of the anticodon, can pair with two different nucleotides at the 3' end of the codon (U with A or G; and G with U or C). The rare base iosine (I) is also found at the 5' of the anticodon of tRNA on occasion. Iosine can pair with A, U, or C at the 3' end of the codon.
A synthetic mRNA added to a cell-free protein-synthesizing system produces a peptide with the following amino acid sequence: Met-Pro-Ile-Ser-Ala. What would be the effect on translation if the following components were omitted from the cell-free protein-synthesizing system? What, if any, type of protein would be produced? Explain your reasoning. g.) GTP
GTP is required for initiation, elongation, and termination of translation. If GTP is absent, no protein synthesis will occur.
Which of the following amino acid changes could result from a mutation that changed a single base? For each change that could result from the alteration of a single base, determine which position of the codon (first, second, or third nucleotide) in the mRNA must be altered for the change to occur. f.)
Only two of the three Ile codons can be mutated at a single position to produce Asn codons: AUU (Ile)—Change the second position to A to produce AAU (Asn). AUC (Ile)—Change the second position to A to produce AAC (Asn).
Define the following terms as they apply to the genetic code: Reading frame
The reading frame refers to how the nucleotides in a nucleic acid molecule are grouped into codons containing three nucleotides. Each sequence of nucleotides has three possible sets of codons, or reading frames.
A synthetic mRNA added to a cell-free protein-synthesizing system produces a peptide with the following amino acid sequence: Met-Pro-Ile-Ser-Ala. What would be the effect on translation if the following components were omitted from the cell-free protein-synthesizing system? What, if any, type of protein would be produced? Explain your reasoning. f.) ATP
ATP is required for the charging of the tRNAs with amino acids by the aminoacyltRNA synthetases. Without ATP, the charging would not take place, and no amino acids will be available for protein synthesis. So no protein synthesis will occur.
Assume that the number of different types of bases in RNA is four. What would be the minimum codon size (number of nucleotides) required to specify all amino acids if the number of different types of amino acids in proteins were: ........
The number of codons possible must be equal to or greater than the number of different types of amino acids because the codons encode for the different amino acids. To calculate how many possible codons are possible for a given codon size with four different types of bases in the RNA, the following formula can be used: 4n , where n is the number of nucleotides within the codon.
Assume that the number of different types of bases in RNA is four. What would be the minimum codon size (number of nucleotides) required to specify all amino acids if the number of different types of amino acids in proteins were: a. 2 b. 8 c. 17 d. 45 e. 75
a.) 1, because 4^1 = 4 codons, which is more than enough to specify two different amino acids. b.) 2 c.) 3 d.) 3 e.) 4
Examine Figure 15.14 of a tRNA. What do you think would be the potential effect of a mutation in the part of the tRNA gene that encodes: (a) the acceptor stem; (b) the anticodon; (c) one of the red-colored nucleotides?
(a) The tRNA would not attach to the amino acid. (b) The tRNA would potentially pair with the wrong codon. (c) Potentially the tRNA would be charged with the wrong amino acid.
Explain the wobble hypothesis? In what sense might this be beneficial?
. The 5' nucleotide of the anticodon in tRNA can pair with more than one nucleotide in the mRNA. Thus, although each tRNA can be charged with only one specific amino acid, the anticodon can recognize more than one codon for that particular amino acid. This reduces the number of tRNAs needed for translation.
What is the minimum number of nucleotides in an mRNA molecule necessary to encode a protein of 141 amino acids.
426 (don't forget the termination codon)
A series of tRNAs have the following anticodons. Consider the wobble rules listed in Table 15.2 and give all possible codons with which each tRNA can pair e.) 5´-CAG-3´
Codon: 3'-GUC-5
Referring to the genetic code presented in Figure 15.10, give the amino acids specified by the following bacterial mRNA sequences. a. 5´-AUGUUUAAAUUUAAAUUUUGA-3´
Solution: Amino fMet-Phe-Lys-Phe-Lys-Phe Carboxyl
What will be the anticodon of the next tRNA added to the A site of the ribosome?
The anticodon 3' UGC 5' is complementary to the codon 5' ACG 3', which is located at the A site of the ribosome. Notice the anticodon and codon are antiparallel.
What will be the next amino acid added to the growing polypeptide chain?
The codon 5' ACG 3' encodes the amino acid threonine.
What events bring about the termination of translation?
The process of termination begins when a ribosome encounters a termination codon. Because the termination codon would be located at the A site, no corresponding tRNA will enter the ribosome. This allows for the release factors (RF-1, RF-2, and RF-3) to bind the ribosome. RF-1 recognizes and interacts with the stop codons UAA and UAG, while RF-2 can interact with UAA and UGA. A RF-3-GTP complex binds to the ribosome. Termination of protein synthesis is complete when the polypeptide chain is cleaved from the tRNA located at the P site. During this process, the GTP is hydrolyzed to GDP.
A synthetic mRNA added to a cell-free protein-synthesizing system produces a peptide with the following amino acid sequence: Met-Pro-Ile-Ser-Ala. What would be the effect on translation if the following components were omitted from the cell-free protein-synthesizing system? What, if any, type of protein would be produced? Explain your reasoning. c.) Elongation factor Tu
Although translation initiation or delivery of the Met to the ribosome-mRNA complex would occur, no further amino acids would be delivered to the ribosome. EF-Tu is necessary for elongation because it binds GTP and the charged tRNA, forming a three-part complex that enters the A site of the ribosome. If EF-Tu is not present, then the charged tRNA will not enter the A site, thus stopping translation.
Define the following terms as they apply to the genetic code: Initiation codon
An initiation codon establishes the appropriate reading frame and specifies the first amino acid of the protein chain. Typically, the initiation codon is AUG; however, GUG and UUG can also serve as initiation codons although rarely. An initiation codon establishes the appropriate reading frame and specifies the first amino acid of the protein chain. Typically, the initiation codon is AUG; however, GUG and UUG can also serve as initiation codons although rarely.
Compare and contrast the process of protein synthesis in bacterial and eukaryotic cells, giving similarities and differences in the process of translation in these two types of cells.
Bacterial and eukaryotic cells share several similarities as well as have several differences in protein synthesis. Initially, bacteria and eukaryotes share the universal genetic code. However, the initiation codon, AUG, in eukaryotic cells codes for methionine, whereas in bacteria the AUG codon codes for N-formylmethionine. In eukaryotes, transcription takes place within the nucleus, whereas most translation takes place in the cytoplasm (although some translation does take place within the nucleus). Therefore, transcription and translation in eukaryotes are kept temporally and spatially separate. However, in bacterial cells transcription and translation are coupled and occur nearly simultaneously. Stability of mRNA in eukaryotic cells and bacterial cells is also different. Bacterial mRNA is typically short-lived, lasting only a few minutes. Eukaryotic mRNA may last hours or even days. Charging of the tRNAs with amino acids is essentially the same in both bacteria and eukaryotes. The ribosomes of bacteria and eukaryotes are different as well. Bacteria and eukaryotes have large and small ribosomal subunits, but they differ in size and composition. The bacterial large ribosomal consists of two ribosomal RNAs, while the eukaryotic large ribosomal subunit consists of three. During translation initiation, the bacterial small ribosomal subunit recognizes the Shine-Dalgarno consensus sequence in the 5' UTR of the mRNA and to regions of the 16S rRNA. In most eukaryotic mRNAs, the small subunit binds the 5' cap of the mRNA and scans downstream until it encounters the first AUG codon. Finally, elongation and termination in bacterial and eukaryotic cells are functionally similar, although different elongation and termination factors are used.
How does the process of initiation differ in bacterial and eukaryotic cells?
Bacterial initiation of translation requires that sequences in the 16S rRNA of the small ribosomal subunit bind to the mRNA at the ribosome binding site or the Shine- Dalgarno sequence. The Shine-Dalgarno sequence is essential in placing the ribosome over the start codon (typically AUG). In eukaryotes, there is no Shine-Dalgarno sequence. The small ribosomal subunit recognizes the 5' cap of the eukaryotic mRNA with the assistance of initiation factors. Next, the ribosomal small subunit migrates along the mRNA scanning for the AUG start codon. In eukaryotes, the start codon is located with a consensus sequence called the Kozak sequence (5'-ACCAUGG-3'). Transcription in eukaryotes also requires more initiation factors.
Which of the following amino acid changes could result from a mutation that changed a single base? For each change that could result from the alteration of a single base, determine which position of the codon (first, second, or third nucleotide) in the mRNA must be altered for the change to occur. c.) Phe -> Ile
Both Phe codons (UUU and UUC) could be mutated at the first position to produce Ile codons: UUU (Phe)—Change the first position to A to produce AUU (Ile). UUC (Phe)—Change the first position to A to produce AUC (Ile)
Which of the following amino acid changes could result from a mutation that changed a single base? For each change that could result from the alteration of a single base, determine which position of the codon (first, second, or third nucleotide) in the mRNA must be altered for the change to occur. b.) Phe -> Ser
Both Phe codons (UUU and UUC) could be mutated at the second position to produce Ser codons: UUU (Phe)—Change the second position to C to produce UCU (Ser). UUC (Phe)—Change the second postion to C to produce UCC (Ser).
Which of the following amino acid changes could result from a mutation that changed a single base? For each change that could result from the alteration of a single base, determine which position of the codon (first, second, or third nucleotide) in the mRNA must be altered for the change to occur. e.) Asn -> Lys
Both codons for Asn can be mutated at a single position to produce Lys codons: AAU (Asn)—Change the third position to A to produce AAA (Lys). AAU (Asn)—Change the third position to G to produce AAG (Lys). AAC (Asn)—Change the third postion to A to produce AAA (Lys). AAC (Asn)—Change the third position to G to produce AAG (Lys).
A codon that specifies the amino acid Gly undergoes a single-base substitution to become a nonsense mutation. In accord with the genetic code given in Figure 15.10, is this mutation a transition or a transversion? At which position of the codon does the mutation occur?
By examining the four codons that encode for Gly, GGU, GGC, GGA, and GGG, and the three nonsense codons, UGA, UAA, and UAG, we can determine that only one of the Gly codons, GGA, could be mutated to a nonsense codon by the single substitution of a U for a G at the first position: GGA -> UGA Because uracil is a pyrimidine and guanine is a purine, the mutation is a transversion.
A series of tRNAs have the following anticodons. Consider the wobble rules listed in Table 15.2 and give all possible codons with which each tRNA can pair b.) 5´-AAG-3
Codon: 3'-UUC-5'
A series of tRNAs have the following anticodons. Consider the wobble rules listed in Table 15.2 and give all possible codons with which each tRNA can pair d.) 5´-UGG-3´
Codons: 3'-ACC-5' or 3'-GCC-5'
A series of tRNAs have the following anticodons. Consider the wobble rules listed in Table 15.2 and give all possible codons with which each tRNA can pair c.) 5´-IAA-3´
Codons: 3'-AUU-5' or 3'-UUU-5' or 3'-CUU-5'
A series of tRNAs have the following anticodons. Consider the wobble rules listed in Table 15.2 and give all possible codons with which each tRNA can pair. a.) 5´-GGC-3´
Codons: 3'-CCG-5' or 3'-UCG-5'
How many different mRNA sequences can encode a polypeptide chain with the amino acid sequence Met-Leu-Arg? (Be sure to include the stop codon.)
From Figure 15.10, we can determine that leucine and arginine each have six different potential codons. There are also three potential stop codons. As for methionine, only one codon, AUG, is typically found as the initiation codon. (However, UUG and GUG have been shown to serve as start codons on occasion. For this problem, we will ignore these rare cases.) Therefore, the number of potential sequences is the product of the number of different potential codons for this tripeptide, which gives us a total of (1 × 6 × 6 × 3) = 108 different mRNA sequences that can code for the tripeptide Met-Leu- Arg.
Referring to the genetic code presented in Figure 15.10, give the amino acids specified by the following bacterial mRNA sequences. b. 5´-AGGGAAAUCAGAUGUAUAUAUAUAUAUGA-3´
Solution: Amino Arg-Glu-Ile-Arg-Cys-Ile-Tyr-Ile-Tyr-(Asp or Glu)----carboxyl For the last potential readable codon only 2 bases are shown and could potentially code for either Asp (GAU or GAC) or Glu (GAA or GAG)
Give the amino acid sequence of the protein encoded by the mRNA in Figure 15.21
Met-Pro-Thr-Thr-Ala-Ser-Val-Pro-Leu-Arg
Referring to the genetic code presented in Figure 15.10, give the amino acids specified by the following bacterial mRNA sequences. c. 5´-UUUGGAUUGAGUGAAACGAUGGAUGAAAGAUUUCUCGCUUGA-3
Solution: Amino Phe-Gly-Leu-Ser-Glu-Thr-Met-Asp-Glu-Arg-Phe-Leu-Ala Carboxyl
A synthetic mRNA added to a cell-free protein-synthesizing system produces a peptide with the following amino acid sequence: Met-Pro-Ile-Ser-Ala. What would be the effect on translation if the following components were omitted from the cell-free protein-synthesizing system? What, if any, type of protein would be produced? Explain your reasoning a. Initiation factor 3
No translation would occur. IF-3 is required to prevent the associate of the 30s and 50s ribosomes prior to translation initiation. The lack of IF-3 would result the 30s ribosome associating with the 50s ribosome prior to the formation of the 30s initiation complex thus preventing the initiation complex from forming. Since translation initiation requires a free small subunit, initiation would occur at a slower rate or not all because more of the small ribosomal subunits would remain bound to the large ribosomal subunits.
Define the following terms as they apply to the genetic code: Nonsense codon
Nonsense codons or termination codons signal the end of translation. These codons do not code for amino acids.
Process (Replication, Transcription, RNA processing, or Translation) most immediately affected by deletion of sequence. b.) 3' splice site
RNA processing. The 3' splice site is necessary for proper excision of the intron. Therefore, RNA processing events will be affected.
Process (Replication, Transcription, RNA processing, or Translation) most immediately affected by deletion of sequence. a.) ori site
Replication. The ori site or origin of replication is necessary for the initiation of replication
Which of the following amino acid changes could result from a mutation that changed a single base? For each change that could result from the alteration of a single base, determine which position of the codon (first, second, or third nucleotide) in the mRNA must be altered for the change to occur. a. Leu -> Gln
Solution: Of the six codons that encode for Leu, only two could be mutated by the alteration of a single base to produce the codons for Gln: CUA (Leu)—Change the second position to A to produce CAA (Gln). CUG (Leu)—Change the second position to A to produce CAG (Gln).
How is the reading frame of a nucleotide sequence set?
The initiation codon on the mRNA sets the reading frame.
The following amino acid sequence is found in a tripeptide: Met-Trp-His. Give all possible nucleotide sequences on the mRNA, on the template strand of DNA, and on the nontemplate strand of DNA that could encode this tripeptide.
The potential mRNA nucleotide sequences encoding for the tripeptide Met-Trp-His can be determined by using the codon table found in Figure 15.10. From the table, we can see that the amino acid His has two potential codons, while the amino acids Met and Trp each have only one potential codon. Therefore, there are two different mRNA nucleotide sequences that could encode for the tripeptide. Once the potential mRNA nucleotide sequences have been determined, the template and nontemplate DNA strands can be derived from these potential mRNA sequences. (1) 5'-AUGUGGCAU-3' DNA template: 3'-TACACCGTA-5' DNA nontemplate: 5'-ATGTGGCAT-3 (2) 5'-AUGUGGCAC-3' DNA template: 3'-TACACCGTG-5' DNA nontemplate: 5'-ATGTGGCAC-3'
Hemoglobin is a complex protein that contains four polypeptide chains. The normal hemoglobin found in adults—called adult hemoglobin—consists of two alpha and two beta polypeptide chains, which are encoded by different loci. Sickle-cell hemoglobin, which causes sickle-cell anemia, arises from a mutation in the beta chain of adult hemoglobin. Adult hemoglobin and sickle-cell hemoglobin differ in a single amino acid: the sixth amino acid from one end in adult hemoglobin is glutamic acid, whereas sickle-cell hemoglobin has valine at this position. After consulting the genetic code provided in Figure 15.10, indicate the type and location of the mutation that gave rise to sickle-cell anemia.
There are two possible codons for glutamic acid, GAA and GAG. Single-base substitutions at the second position in both codons can produce codons that encode valine: GAA--------> GUA (Val) GAG--------> GUG (Val) Both substitutions are transversions. However, in the gene encoding the β chain of hemoglobin, the GAG codon is the wild-type codon and the mutated GUG codon results in the sickle-cell phenotype.
Give the elongation factors used in bacterial translation and explain the role played by each factor in translation.
Three elongation factors have been identified in bacteria: EF-TU, EF-TS, and EF-G. EF-TU joins with GTP and then to a tRNA charged with an amino acid. The charged tRNA is delivered to the ribosome at the A site. During the process of delivery, the GTP joined to EF-TU is cleaved to form an EF-TU-GDP complex. EF-TS is necessary to regenerate EF-TU-GTP. The elongation factor EF-G binds GTP and is necessary for the translocation or movement of the ribosome along the mRNA during translation.