Solved: Staphylococcus nuclease is an enzyme that

Name the following compounds:

What nonapeptide is coded for by the following fragment of mRNA?

What is the sequence of bases in the template strand of DNA that codes for the mRNA in Problem 20?

What is the sequence of bases in the sense strand of DNA that codes for the mRNA in Problem 20 ?

What would be the C-terminal amino acid if the codon at the 3-end of the mRNA in Problem 20 underwent the following mutations? a. The i rst base is changed to A. c. The third base is changed to A. b. The second base is changed to A. d. The third base is changed to G.

What would be the base sequence of the segment of DNA responsible for the biosynthesis of the following hexapeptide? Gly-Ser-Arg-Val-His-Glu

Propose a mechanism for the following reaction:

A segment of DNA has 18 base pairs. It has 7 cytosines in the segment. a. How many uracils are in the segment? b. How many guanines are in the segment?

Match the codon with the anticodon: Codon Anticodon AAA ACC GCA CCU CUU UUU AGG AGG CCU UGA GGU AAG UCA GUC GAC UGC

Using the single-letter abbreviations for the amino acids in Table 22.2 , write the sequence of amino acids in a tetrapeptide represented by the i rst four different letters in your i rst name. Do not use any letter twice. (Because not all letters are assigned to amino acids, you might have to use one or two letters in your last name.) Write one of the sequences of bases in mRNA that would result in the synthesis of that tetrapeptide. Write the sequence of bases in the sense strand of DNA that would result in formation of that fragment of mRNA.

Which of the following pairs of dinucleotides are present in equal amounts in DNA? a. CC and GG c. CA and TG e. GT and CA b. CG and GT d. CG and AT f. TA and AT

Human immunodei ciency virus (HIV) is the retrovirus that causes AIDS. AZT was one of the i rst drugs designed to interfere with retroviral DNA synthesis. When cells take up AZT, they convert it to AZT-triphosphate. Explain how AZT interferes with DNA synthesis.

If an mRNA contained only U and G in random sequence, what amino acids would be present in the protein when the mRNA is translated?

Why is the codon a triplet rather than a doublet or a quartet?

RNAase, the enzyme that catalyzes the hydrolysis of RNA, has two catalytically active histidine residues at its active site. One of the histidine residues is catalytically active in its acidic form, and the other is catalytically active in its basic form. Propose a mechanism for RNAase.

The amino acid sequences of peptide fragments obtained from a normal protein were compared with those obtained from the same protein synthesized by a defective gene. They were found to differ in only one peptide fragment. Their amino acid sequences are shown here: Normal: Gln-Tyr-Gly-Thr- Arg-Tyr-Val Mutant: Gln-Ser-Glu-Pro-Gly-Thr a. What is the defect in DNA? b. It was later determined that the normal peptide fragment is an octapeptide with a C-terminal Val-Leu. What is the C-terminal amino acid of the mutant peptide

Which cytosine in the following sense strand of DNA could cause the most damage to the organism if it were deaminated? A:T:G:T:C:G:C:T:A:A:T:C

5-Bromouracil, a highly mutagenic compound (that is, a compound that causes changes in DNA), is used in cancer chemotherapy. When administered to a patient, it is converted to the triphosphate and incorporated into DNA in place of thymine, which it resembles sterically. Why does it cause mutations? (Hint: The bromo substituent increases the stability of the enol tautomer.)

Sodium nitrite, a common food preservative (page 954) , is capable of causing mutations in an acidic environment by converting cytosines to uracils. Explain how this occurs.

Why does DNA not unravel completely before replication begins?

Staphylococcus nuclease is an enzyme that catalyzes the hydrolysis of DNA. The reaction is catalyzed by Ca 2+ , Glu 43, and Arg 87. Propose a mechanism for this reaction. Recall that the nucleotides in DNA have phosphodiester linkages.

The i rst amino acid incorporated into a polypeptide chain during its biosynthesis in prokaryotes is N -formylmethionine. Explain the purpose of the formyl group. ( Hint: The ribosome has a binding site for the growing peptide chain and a binding site for the incoming amino acid.)

Problem 1P In acidic solutions, nucleosides are hydrolyzed to a sugar and a heterocyclic base. Propose a mechanism for this reaction.

Draw the structure for each of the following: a. dCDP b. dTTP c. dUMP d. UDP e. guanosine triphosphate f. adenosine monophosphate

Problem 3P What products would be obtained from the hydrolysis of cyclic AMP?

Problem 4P Indicate whether each functional group of the five heterocyclic bases in nucleic acids can function as a hydrogen bond acceptor (A), a hydrogen bond donor (D), or both (D/A).

Using the D, A, and D/A designations in Problem 4, indicate how base pairing would be affected if the bases existed in the enol form.

Problem 6P If one of the strands of DNA has the following sequence of bases running in the 5? ? 3? direction: 5?—G—G—A—C —A—A—T—C—T—G—C —3? a. What is the sequence of bases in the complementary strand? ________________ b. What base is closest to the 5'-end in the complementary strand?

Problem 8P Using a dark line for the original parental DNA and a wavy line for DNA synthesized from parental DNA, show what the population of DNA molecules would look like in the fourth generation of replicated molecules.

The \(2^{\prime}, 3^{\prime}\)-cyclic phosphodiester that is formed (Figure \(26.7\)) when RNA is cleaved reacts with water, forming a mixture of nucleotide \(2^{\prime}\)’- and \(2^{\prime}-phosphates . Propose a mechanism for this reaction. Equation Transcription: Text Transcription: 2’,3’ 26.7 2’ 3’

Problem 9P Why do both thymine and uracil specify the incorporation of adenine?

Problem 10P If methionine is the first amino acid incorporated into an oligopeptide, what oligopeptide is encoded for by the following stretch of mRNA? 5?—G—C—A—U—G—G—A—C—C—C—C—G—U—U—A—U—U—A—A—A—C—A—C—3?

Problem 11P Four C’s occur in a row in the segment of mRNA in Problem. What oligopeptide would be formed from the mRNA if one of the four C’s were cut out of the strand? Problem If methionine is the first amino acid incorporated into an oligopeptide, what oligopeptide is encoded for by the following stretch of mRNA? 5?—G—C—A—U—G—G—A—C—C—C—C—G—U—U—A—U—U—A—A—A—C—A—C—3?

UAA is a stop codon. Why does the UAA sequence in mRNA in Problem 10 not cause protein synthesis to stop?

Problem 13P A change in which base of a codon would be least likely to cause a mutation?

Problem 14P Write the sequences of bases in the sense strand of DNA that resulted in the mRNA in Problem. Problem If methionine is the first amino acid incorporated into an oligopeptide, what oligopeptide is encoded for by the following stretch of mRNA? 5?—G—C—A—U—G—G—A—C—C—C—C—G—U—U—A—U—U—A—A—A—C—A—C—3?

Problem 15P List the possible codons on mRNA that specify each amino acid in the oligopeptide in Problem and the anticodon on the tRNA that carries that amino acid.

Problem 16P Adenine can be deaminated to hypoxanthine, and guanine can be deaminated to xanthine. Draw structures for hypoxanthine and xanthine.

Problem 17P Explain why thymine cannot be deaminated.

Problem 18P Which of the following base sequences would most likely be recognized by a restriction endonuclease? a. ACGCGT b. ACGGGT c. ACGGCA d. ACACGT e. ACATCGT f. CCAACC

Name the following compounds:

Problem 20P What nonapeptide is coded for by the following piece of mRNA? 5?—A A A—GUU—GGC—U AC—CCC—GGA—AUG—GUG—GUC—3?

Problem 21P What is the sequence of bases in the template strand of DNA that codes for the mRNA in Problem? Problem What nonapeptide is coded for by the following piece of mRNA? 5?—A A A—GUU—GGC—U AC—CCC—GGA—AUG—GUG—GUC—3?

Problem 22P What is the sequence of bases in the sense strand of DNA that codes for the mRNA in Problem? Problem What nonapeptide is coded for by the following piece of mRNA? 5?—A A A—GUU—GGC—U AC—CCC—GGA—AUG—GUG—GUC—3?

What would be the C-terminal amino acid if the codon at the \( 3^ \prime\)-end of the mRNA in Problem 20 underwent the following mutations? a. The first base is changed to A. b. The second base is changed to A. c. The third base is changed to A. d. The third base is changed to G.

Problem 24P What would be the base sequence of the segment of DNA that is responsible for the biosynthesis of the following hexapeptide? Gly-Ser-Arg-V al-His-Glu

Propose a mechanism for the following reaction:

Problem 26P A segment of DNA has 18 base pairs. It has 7 cytosines in the segment. a. How many thymines are in the segment? b. How many guanines are in the segment?

Match the codon with the anticodon:

Problem 28P Using the single-letter abbreviations for the amino acids in Table, write the sequence of amino acids in a tetrapeptide represented by the first four different letters in your first name. Do not use any letter twice. (Because not all letters are assigned to amino acids, you might have to use one or two letters in your last name.) Write the sequence of bases in mRNA that would result in the synthesis of that tetrapeptide. Write the sequence of bases in the sense strand of DNA that would result in formation of that fragment of mRNA. Table Codon Anticodon AAA ACC GCA CCU CUU UUU AGG AGG CCU UGA GGU AAG UCA GUC GAC UGC

Problem 29P Which of the following pairs of dinucleotides are present in equal amounts in DNA? a. CC and GG b. CG and GT c. CA and TG d. CG and AT e. GT and CA f. TA and AT

Human immunodeficiency virus (HIV) is the retrovirus that causes AIDS. AZT was one of the i rst drugs designed to interfere with retroviral DNA synthesis. When cells take up AZT, they convert it to AZT-triphosphate. Explain how AZT interferes with DNA synthesis.

Problem 31P If an mRNA contained only U and G in random sequence, what amino acids would be present in the protein when the Mrna is translated?

Problem 32P Why is the codon a triplet rather than a doublet or a quartet?

Problem 34P The amino acid sequences of peptide fragments obtained from a normal protein and from the same protein synthesized by a defective gene were compared. They were found to differ in only one peptide fragment; their amino acid sequences are shown here: Normal: GIn-Tyr-Gly-Thr-Arg-Tyr-Val Mutant: Gln-Ser-Glu-Pro-Gly-Thr a. What is the defect in DNA? ________________ b. It was later determined that the normal peptide fragment is an octapeptide with a C-terminal Val-Leu. What is the C-terminal amino acid of the mutant peptide?

Which cytosine in the following sense strand of DNA could cause the most damage to the organism if it were deaminated? \(A-T-G-T-C-G-C-T-A-A-T-C\) Equation Transcription: Text Transcription: A - T - G -T - C - G - C - T - A - A - T - C

\(5\)-Bromouracil, a highly mutagenic compound (that is, a compound that causes changes in DNA), is used in cancer chemotherapy. When administered to a patient, it is converted to the triphosphate and incorporated into DNA in place of thymine, which it resembles sterically. Why does it cause mutations? (Hint: The bromo substituent increases the stability of the enol tautomer.) Equation Transcription: Text Transcription: 5

Sodium nitrite, a common food preservative (page \(954\)) , is capable of causing mutations in an acidic environment by converting cytosines to uracils. Explain how this occurs. Equation Transcription: Text Transcription: 954

Problem 39P Staphylococcus nuclease is an enzyme that catalyzes the hydrolysis of DNA. The reaction is catalyzed by Ca2+ , Glu 43, and Arg 87. Propose a mechanism for this reaction. Recall that the nucleotides in DNA have phosphodiester linkages.

Problem 38P Why doesn’t DNA unravel completely before replication begins?

The first amino acid incorporated into a polypeptide chain during its biosynthesis in prokaryotes is N -formylmethionine. Explain the purpose of the formyl group. (Hint: The ribosome has a binding site for the growing peptide chain and a binding site for the incoming amino acid.)

RNAase, the enzyme that catalyzes the hydrolysis of RNA, has two catalytically active histidine residues at its active site. One of the histidine residues is catalytically active in its acidic form, and the other is catalytically active in its basic form. Propose a mechanism for RNAase.