Exam 7: From DNA to Protein

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The length of a particular gene in human DNA, measured from the start site for transcription to the end of the protein-coding region, is 10,000 nucleotides, whereas the length of the mRNA produced from this gene is 4000 nucleotides.What is the most likely reason for this difference?

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The gene contains one or more introns.

Which of the following statements about the proteasome is FALSE?

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C

A mutation in the tRNA for the amino acid lysine results in the anticodon sequence 5?-UAU-3? (instead of 5?-UUU-3?).Which of the following aberrations in protein synthesis might this tRNA cause?  The Genetic Code \text { The Genetic Code } U C A G UUU Phe (F) UCU Ser (S) UAU Tyr (Y) UGU Cys (C) UUC - UCC - UAC - UGC - U UUA Leu (L) UCA -- UAA Stop UGA Stop UUG - UCG - UAG Stop UGG Trp (W) CUU Leu (L) CCU Pro (P) CAU His (H) CGU Arg (R) CUC - CCC - CAC - CGC - C CUA - CCA - CAA Gin (Q) CGA - CUG - CCG - CAG - CGG - AUU Ile (I) ACU Thr (T) AAU Asn (N) AGU Ser (S) AUC - ACC - AAC - AGC - A AUA - ACA - AAA Lys (K) AGA Arg (R) AUG Met (M) ACG - AAG - AGG - GUU Val (V) GCU Ala (A) GAU Asp (D) GGU Gly (G) GUC - GCC - GAC - GGC - G GUA - GCA - GAA Glu (E) GGA - GUG - GCG - GAG - GGG - Table 7-29

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B

You have discovered an alien life-form that surprisingly uses DNA as its genetic material, makes RNA from DNA, and reads the information from RNA to make protein using ribosomes and tRNAs, which read triplet codons.Because it is your job to decipher the genetic code for this alien, you synthesize some artificial RNA molecules and examine the protein products produced from these RNA molecules in a cell-free translation system using purified alien tRNAs and ribosomes.You obtain the results shown in Table 7-48. Message Peptides produced poly UA ... Tyr-Cys-Tyr-Cys ... poly UC ... Phe-Lys-Phe-Lys .... poly UAC \ldots lle-lle-lle-lle ... + ... Ser-Ser-Ser-Ser... + ... Pro-Pro-Pro-Pro ... poly UCA ... Ala-Ala-Ala-Ala ... + ... His-His-His-His... + ... Val-Val-Val-Val... poly AUA \ldots Arg-Arg-Arg-Arg ... + ... Glu-Glu-Glu-Glu... + ... Tyr-Tyr-Tyr-Tyr ... Table 7-48 From this information, which of the following peptides can be produced from poly UAUC?

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Genes in eukaryotic cells often have intronic sequences coded for within the DNA.These sequences are ultimately not translated into proteins.Why?

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A strain of yeast translates mRNA into protein inaccurately.Individual molecules of a particular protein isolated from this yeast have variations in the first 11 amino acids compared with the sequence of the same protein isolated from normal yeast cells, as listed in Figure 7-33.What is the most likely cause of this variation in protein sequence? normal sequence variants Met Met Met Met Met Met Met Thr Thr Thr Thr Thr Thr Thr Ala Ala Ala Ala Ala Ala Ala Ile Ala Gly val Ile Ile Ile Val Val Val Val Val Val Va Ser Ser Ser Ser Ser Ser Ser Asn Asn Asn Asn Asn Asn Asn Thr Thr Thr Thr Thr Thr Thr Gln Gln Gln Gln Gln Gln Gln Ile Ile Ile Ile Ala Gly Val Lys Lys Lys Lys Lys Lys Lys Figure 7-33  The Genetic Code \text { The Genetic Code } U C A G UUU Phe (F) UCU Ser (S) UAU Tyr (Y) UGU Cys (C) UUC - UCC - UAC - UGC - U UUA Leu (L) UCA -- UAA Stop UGA Stop UUG - UCG - UAG Stop UGG Trp (W) CUU Leu (L) CCU Pro (P) CAU His (H) CGU Arg (R) CUC - CCC - CAC - CGC - C CUA - CCA - CAA Gin (Q) CGA - CUG - CCG - CAG - CGG - AUU Ile (I) ACU Thr (T) AAU Asn (N) AGU Ser (S) AUC - ACC - AAC - AGC - A AUA - ACA - AAA Lys (K) AGA Arg (R) AUG Met (M) ACG - AAG - AGG - GUU Val (V) GCU Ala (A) GAU Asp (D) GGU Gly (G) GUC - GCC - GAC - GGC - G GUA - GCA - GAA Glu (E) GGA - GUG - GCG - GAG - GGG - Table 7-29

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Which of the following statements is FALSE?

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You have a bacterial strain with a mutation that removes the transcription termination signal from the Abd operon.Which of the following statements describes the most likely effect of this mutation on Abd transcription?

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After treating cells with a mutagen, you isolate two mutants.One carries alanine and the other carries methionine at a site in the protein that normally contains valine.After treating these two mutants again with mutagen, you isolate mutants from each that now carry threonine at the site of the original valine (see Figure 7-67).Assuming that all mutations caused by the mutagen are due to single nucleotide changes, deduce the codons that are used for valine, alanine, methionine, and threonine at the affected site.  After treating cells with a mutagen, you isolate two mutants.One carries alanine and the other carries methionine at a site in the protein that normally contains valine.After treating these two mutants again with mutagen, you isolate mutants from each that now carry threonine at the site of the original valine (see Figure 7-67).Assuming that all mutations caused by the mutagen are due to single nucleotide changes, deduce the codons that are used for valine, alanine, methionine, and threonine at the affected site.    Figure 7-67  \text { The Genetic Code }   \begin{array}{|l|l|l|l|l|} \hline & \text { U } & \text { C } & \text { A } & \text { G } \\ \hline &\text { UUU Phe (F) } & \text { UCU Ser (S) } & \text { UAU Tyr (Y) } & \text { UGU Cys (C) } \\ &\text { UUC - } & \text { UCC - } & \text { UAC - } & \text { UGC - } \\  \text { U } &\text { UUA Leu (L) } & \text { UCA -- } & \text { UAA Stop } & \text { UGA Stop } \\ &\text { UUG - } & \text { UCG - } & \text { UAG Stop } & \text { UGG Trp (W) } \\ \hline &\text { CUU Leu (L) } & \text { CCU Pro (P) } & \text { CAU His (H) } & \text { CGU Arg (R) } \\ &\text { CUC - } & \text { CCC - } & \text { CAC - } & \text { CGC - } \\  \text { C}&\text { CUA - } & \text { CCA - } & \text { CAA Gin (Q) } & \text { CGA - } \\ &\text { CUG }- & \text { CCG }- & \text { CAG }- & \text { CGG }- \\ \hline &\text { AUU Ile (I) } & \text { ACU Thr (T) } & \text { AAU Asn (N) } & \text { AGU Ser (S) } \\ &\text { AUC - } & \text { ACC - } & \text { AAC - } & \text { AGC - } \\  \text { A}&\text { AUA - } & \text { ACA - } & \text { AAA Lys (K) } & \text { AGA Arg (R) } \\ &\text { AUG Met (M) } & \text { ACG - } & \text { AAG - } & \text { AGG - } \\ \hline &\text { GUU Val (V) } & \text { GCU Ala (A) } & \text { GAU Asp (D) } & \text { GGU Gly (G) } \\ &\text { GUC - } & \text { GCC - } & \text { GAC - } & \text { GGC - } \\  \text { G}&\text { GUA - } & \text { GCA - } & \text { GAA Glu (E) } & \text { GGA - } \\ &\text { GUG - } & \text { GCG - } & \text { GAG - } & \text { GGG - } \\ \hline \end{array}   Table 7-29 Figure 7-67  The Genetic Code \text { The Genetic Code } U C A G UUU Phe (F) UCU Ser (S) UAU Tyr (Y) UGU Cys (C) UUC - UCC - UAC - UGC - U UUA Leu (L) UCA -- UAA Stop UGA Stop UUG - UCG - UAG Stop UGG Trp (W) CUU Leu (L) CCU Pro (P) CAU His (H) CGU Arg (R) CUC - CCC - CAC - CGC - C CUA - CCA - CAA Gin (Q) CGA - CUG - CCG - CAG - CGG - AUU Ile (I) ACU Thr (T) AAU Asn (N) AGU Ser (S) AUC - ACC - AAC - AGC - A AUA - ACA - AAA Lys (K) AGA Arg (R) AUG Met (M) ACG - AAG - AGG - GUU Val (V) GCU Ala (A) GAU Asp (D) GGU Gly (G) GUC - GCC - GAC - GGC - G GUA - GCA - GAA Glu (E) GGA - GUG - GCG - GAG - GGG - Table 7-29

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One strand of a section of DNA isolated from the bacterium E.coli reads: 5′-GTAGCCTACCCATAGG-3′  The Genetic Code \text { The Genetic Code } U C A G UUU Phe (F) UCU Ser (S) UAU Tyr (Y) UGU Cys (C) UUC - UCC - UAC - UGC - U UUA Leu (L) UCA -- UAA Stop UGA Stop UUG - UCG - UAG Stop UGG Trp (W) CUU Leu (L) CCU Pro (P) CAU His (H) CGU Arg (R) CUC - CCC - CAC - CGC - C CUA - CCA - CAA Gin (Q) CGA - CUG - CCG - CAG - CGG - AUU Ile (I) ACU Thr (T) AAU Asn (N) AGU Ser (S) AUC - ACC - AAC - AGC - A AUA - ACA - AAA Lys (K) AGA Arg (R) AUG Met (M) ACG - AAG - AGG - GUU Val (V) GCU Ala (A) GAU Asp (D) GGU Gly (G) GUC - GCC - GAC - GGC - G GUA - GCA - GAA Glu (E) GGA - GUG - GCG - GAG - GGG - Table 7-29 A.Suppose that an mRNA is transcribed from this DNA using the complementary strand as a template.What will be the sequence of the mRNA in this region (make sure you label the 5′ and 3′ ends of the mRNA)? B.How many different peptides could potentially be made from this sequence of RNA, assuming that translation initiates upstream of this sequence? C.What are these peptides? (Give your answer using the one-letter amino acid code.)

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Figure 7-3 shows a ribose sugar.RNA bases are added to the part of the ribose sugar pointed to by arrow Figure 7-3 shows a ribose sugar.RNA bases are added to the part of the ribose sugar pointed to by arrow   Figure 7-3 Figure 7-3

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snRNAs

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Which of the following statements is FALSE?

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The ribosome is important for catalyzing the formation of peptide bonds.Which of the following statements is TRUE?

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Which of the following pairs of codons might you expect to be read by the same tRNA as a result of wobble?  The Genetic Code \text { The Genetic Code } U C A G UUU Phe (F) UCU Ser (S) UAU Tyr (Y) UGU Cys (C) UUC - UCC - UAC - UGC - U UUA Leu (L) UCA -- UAA Stop UGA Stop UUG - UCG - UAG Stop UGG Trp (W) CUU Leu (L) CCU Pro (P) CAU His (H) CGU Arg (R) CUC - CCC - CAC - CGC - C CUA - CCA - CAA Gin (Q) CGA - CUG - CCG - CAG - CGG - AUU Ile (I) ACU Thr (T) AAU Asn (N) AGU Ser (S) AUC - ACC - AAC - AGC - A AUA - ACA - AAA Lys (K) AGA Arg (R) AUG Met (M) ACG - AAG - AGG - GUU Val (V) GCU Ala (A) GAU Asp (D) GGU Gly (G) GUC - GCC - GAC - GGC - G GUA - GCA - GAA Glu (E) GGA - GUG - GCG - GAG - GGG - Table 7-29

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What do you predict would happen if you created a tRNA with an anticodon of 5?-CAA-3? that is charged with methionine, and added this modified tRNA to a cell-free translation system that has all the normal components required for translating RNAs?  The Genetic Code \text { The Genetic Code } U C A G UUU Phe (F) UCU Ser (S) UAU Tyr (Y) UGU Cys (C) UUC - UCC - UAC - UGC - U UUA Leu (L) UCA -- UAA Stop UGA Stop UUG - UCG - UAG Stop UGG Trp (W) CUU Leu (L) CCU Pro (P) CAU His (H) CGU Arg (R) CUC - CCC - CAC - CGC - C CUA - CCA - CAA Gin (Q) CGA - CUG - CCG - CAG - CGG - AUU Ile (I) ACU Thr (T) AAU Asn (N) AGU Ser (S) AUC - ACC - AAC - AGC - A AUA - ACA - AAA Lys (K) AGA Arg (R) AUG Met (M) ACG - AAG - AGG - GUU Val (V) GCU Ala (A) GAU Asp (D) GGU Gly (G) GUC - GCC - GAC - GGC - G GUA - GCA - GAA Glu (E) GGA - GUG - GCG - GAG - GGG - Table 7-29

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You have discovered a protein that inhibits translation.When you add this inhibitor to a mixture capable of translating human mRNA and centrifuge the mixture to separate polyribosomes and single ribosomes, you obtain the results shown in Figure 7-39.Which of the following interpretations is consistent with these observations? You have discovered a protein that inhibits translation.When you add this inhibitor to a mixture capable of translating human mRNA and centrifuge the mixture to separate polyribosomes and single ribosomes, you obtain the results shown in Figure 7-39.Which of the following interpretations is consistent with these observations?   Figure 7-39 Figure 7-39

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Why is the old dogma "one gene-one protein" not always true for eukaryotic genes?

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Below is a segment of RNA from the middle of an mRNA. 5′- ...UAGUCUAGGCACUGA ...-3′  The Genetic Code \text { The Genetic Code } U C A G UUU Phe (F) UCU Ser (S) UAU Tyr (Y) UGU Cys (C) UUC - UCC - UAC - UGC - U UUA Leu (L) UCA -- UAA Stop UGA Stop UUG - UCG - UAG Stop UGG Trp (W) CUU Leu (L) CCU Pro (P) CAU His (H) CGU Arg (R) CUC - CCC - CAC - CGC - C CUA - CCA - CAA Gin (Q) CGA - CUG - CCG - CAG - CGG - AUU Ile (I) ACU Thr (T) AAU Asn (N) AGU Ser (S) AUC - ACC - AAC - AGC - A AUA - ACA - AAA Lys (K) AGA Arg (R) AUG Met (M) ACG - AAG - AGG - GUU Val (V) GCU Ala (A) GAU Asp (D) GGU Gly (G) GUC - GCC - GAC - GGC - G GUA - GCA - GAA Glu (E) GGA - GUG - GCG - GAG - GGG - Table 7-29 If you were told that this segment of RNA was part of the coding region of an mRNA for a large protein, give the amino acid sequence for the protein that is encoded by this segment of mRNA.Write your answer using the one-letter amino acid code.

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Which of the following molecules of RNA would you predict to be the most likely to fold into a specific structure as a result of intramolecular base-pairing?

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