Biomolecules: Nucleic Acids

Show the structures of the products you would obtain hydroboration-oxidation of the following alkenes:

a)

b) 

Propose structures for compounds that fit the following mass-spectral data:

(a) A hydrocarbon with \({{\bf{M}}^ + }{\rm{ =  }}{\bf{132}}\)  

(b) A hydrocarbon with \({{\bf{M}}^ + }{\rm{ =  }}{\bf{1}}66\)

(c) A hydrocarbon with \({{\bf{M}}^ + }{\rm{ =  84}}\)         

Write molecular formulas for compounds that show the following molecular ions in their high-resolution mass spectra, assuming that C, H, N, and O might be present. The exact atomic masses are: 1.00783 \(\left( {{}^1{\bf{H}}} \right)\), 12.00000 \(\left( {{}^{12}C} \right)\), 14.00307 \(\left( {{}^{14}N} \right)\), 15.99491 \(\left( {{}^{16}O} \right)\).

(a) \({{\bf{M}}^ + }{\rm{ =  98}}{\rm{.0844}}\)  

(b \({{\bf{M}}^ + }{\rm{ =  123}}{\rm{.0320}}\)

Give IUPAC names for the following compounds:

Propose a structure consistent with the following spectral data for a ${\mathbf{C}}_{\mathbf{8}}{\mathbf{H}}_{\mathbf{18}}{\mathbf{O}}_{\mathbf{2}}$ compound   :

IR: $\mathbf{3350}{\mathbf{cm}}^{\mathbf{-}\mathbf{1}}$ ${}^{\mathbf{1}}\mathbf{H}$ NMR: $\mathbf{1}\mathbf{.}\mathbf{24}\mathbf{\delta }$  (12 H, singlet);  $\mathbf{1}\mathbf{.}\mathbf{56}\mathbf{\delta }$(4 H, singlet); $\mathbf{1}\mathbf{.}\mathbf{95}\mathbf{\delta }$ (2 H, singlet)

Propose structures for alcohols that have the following NMR spectra:

$\mathbf{\left(}\mathbf{a}\mathbf{\right)}\mathbf{ }{\mathbf{C}}_{\mathbf{9}}{\mathbf{H}}_{\mathbf{12}}\mathbf{O}$

$\mathbf{\left(}\mathbf{b}\mathbf{\right)}\mathbf{ }{\mathbf{C}}_{\mathbf{8}}{\mathbf{H}}_{\mathbf{10}}{\mathbf{O}}_{\mathbf{2}}$

Melamine, used as a fire retardant and a component of the writing surface of white boards, can be prepared from s-trichlorotriazine through a series of SNAr reactions with ammonia. The first substitution takes place rapidly at room temperature. The second substitution takes place near 100 °C, and the third substitution requires even higher temperature and pressure. Provide an explanation for this reactivity.

The proton and carbon NMR spectra for each of three isomeric ketones with the formula \({{\bf{C}}_{\bf{7}}}{{\bf{H}}_{{\bf{14}}}}{\bf{O}}\) are shown below. Assign a structure to each pair of spectra.

Draw the full structure of the DNA dinucleotide AG.

Draw the full structure of the RNA dinucleotide UA.

What sequence of bases on one strand of DNA is complementary to the following sequence on another strand?

(5’) GGCTAATCCGT (3’)

Show how uracil can form strong hydrogen bonds to adenine.

What RNA base sequence is complementary to the following DNA base sequence?

(5’) GGCTAATCCGT (3’)

From what DNA base sequence was the following RNA sequence transcribed?

(5’) UUCGCAGAGU (3’)

List codon sequences for the following amino acids:

(b) Phe 

(c) Leu 

(d) Tyr

What amino acid sequence is coded by the following mRNA base sequence?

CUU-AUG-GCU-UGG-CCC-UAA

What is the base sequence in the original DNA strand on which the mRNA sequence in problem 28-9 was made?

CUU-AUG-GCU-UGG-CCC-UAA

 List anticodon sequences on the tRNAs carrying the amino acid shown as below:

(b) Phe 

(c) Leu 

(d) Tyr

p-Dimethoxytrityl (DMT) ethers are easily cleaved by mild acid treatment. Show the mechanism of the cleavage reaction.

Propose a mechanism to account for the cleavage of the β-cyanoethyl protecting group from the phosphate groups on treatment with aqueous ammonia. (Acrylonitrile, H₂C=CHCN, is a by-product.) What kind of reaction is occurring?

Question: One of the steps in the biosynthesis of uridine monophosphate is the reaction of aspartate with carbamoyl aspartate, followed by cyclization to form dihydroorotate. Propose mechanisms for both steps.

Question: Human brain natriuretic peptide (BNP) is a small peptide of 32 amino acids used in the treatment of congestive heart failure. How many nitrogen bases are present in the DNA that codes for BNP?

Question: Human and horse insulin both have two polypeptide chains, with one chain containing 21 amino acids and the other containing 30 amino acids. They differ in primary structure in two places. At position 9 in one chain, human insulin has Ser, and horse insulin has Gly; at position 30 in the other chain, human insulin has Thr, and horse insulin has Ala. How must the DNA for the two insulins differ?

Question: The DNA of sea urchins contains about 32% A. What percentages of the other three bases would you expect in sea urchin DNA? Explain.

Question: The codon UAA stops protein synthesis. Why does the sequence UAA in the following stretch of mRNA not cause any problems?

-GCA-UUC-GAG-GUA-ACG-CCC-

Question: Which of the following base sequences would most likely be recognized by a restriction endonuclease? Explain

1. GAATTC
2. GATTACA
3. CTCGAG

Question: For what amino acids do the following ribonucleotide triplets code?

1. AAU
2. GAG
3. UCC
4. CAU

Question: From what DNA sequences were each of the mRNA codons in problem 28-26 transcribed?

1. AAU
2. GAG
3. UCC
4. CAU

If the DNA coding sequence -CAA-CCG-GAT- were miscopied during replication and became -CGA-CCG-GAT-, what effect would there be on the sequence of the protein produced?

Show the steps involved in a laboratory synthesis of the DNA fragment with the sequence CTAG.’

Draw the structure of cyclic adenosine monophosphate (CAMP), a messenger involved in the regulation of glucose production in the body. Cyclic AMP has a phosphate ring connecting the 3'- and 5'-hydroxyl groups in adenosine.

28-38 Valganciclovir, marketed as Valcyte, is an antiviral agent used for the treatment of cytomegalovirus. Called a prodrug, valganciclovir is inactive by itself but is rapidly converted in the intestine by hydrolysis of its ester bond to produce an active drug, called ganciclovir, along with an amino acid.

1. What amino acid is produced by hydrolysis of the ester bond in valganciclovir?
2.  What is the structure of ganciclovir?
3.  What atoms present in the nucleotide deoxyguanine are missing from ganciclovir?
4.  What role do the atoms missing from deoxyguanine play in DNA replication?
5.   How might valganciclovir interfere with DNA synthesis?

Identify the following bases, and tell whether each is found in DNA, RNA, or both.

Identify the following nucleotide, and tell how it is used.

Question: Amine bases in nucleic acids can react with alkylating agents in typical S_N2 reactions. Look at the following electrostatic potential maps, and tell which is the better nucleophile, guanine or adenine. The reactive positions in each are indicated.

The final step in DNA synthesis is deprotection by treatment with aqueous ammonia. Show the mechanisms by which deprotection occurs at the points indicated in the following structure:

The final step in the metabolic degradation of uracil is the oxidation of malonic semialdehyde to give malonyl coA. Propose a mechanism.

One of the steps in the biosynthesis of a nucleotide called inosine monophosphate is the formation of aminoimidazole ribonucleotide from formyglycinamidine ribonucleotide. Propose a mechanism.

One of the steps in the metabolic degradation of guanine in hydrolysis to give xanthine. Propose a mechanism.

Question: What anticodon sequences of tRNAs are coded for by the codons are :

1. AAU
2. GAG
3. UCC
4. CAU

Question: Draw the complete structure of the ribonucleotide codon UAC. For what amino acid does this sequence code?

Question: Draw the complete structure of the deoxyribonucleotide sequence from which the mRNA codon in problem 28-29 was transcribed.

Question: Give an mRNA sequence that will code for the synthesis of mentenkephalin.

Tyr-Gly-Gly-Phe-Met

Question: Give an mRNA sequence that will code for the synthesis of angiotensin II

Asp-Arg-Val-Tyr-Ile-His-Pro-Phe

Question: What amino acid sequence is coded for by the following DNA coding strand (sense strand)? (5') CTT-CGA-CCA-GAC-AGC-TTT (3’)

Question: What amino acid sequence is coded for by the following mRNA base sequence?
(5') CUA-GAC-CGU-UCC-AAG-UGA (3')