Chapter 10

Draw the principal ionic species of \(5^{\prime}\) -GMP occurring at pH 2.

Adhering to the convention of writing nucleotide sequences in the \(5^{\prime} \rightarrow 3^{\prime}\) direction, what is the nucleotide sequence of the DNA strand that is complementary to d-ATCGCAACTGTCACTA?

The DNA strand that is complementary to the template strand copied by RNA polymerase during transcription has a nucleotide sequence identical to that of the RNA being synthesized (except T residues are found in the DNA strand at sites where U residues occur in the RNA). An RNA transcribed from this nontemplate DNA strand would be complementary to the mRNA synthesized by RNA polymerase. Such an RNA is called antisense RNA because its base sequence is complementary to the "sense" mRNA. One strategy to thwart the deleterious effects of genes activated in disease states (such as cancer) is to generate antisense RNAs in affected cells. These antisense RNAs would form double- stranded hybrids with mRNAs transcribed from the activated genes and prevent their translation into protein. Suppose transcription of a cancer-activated gene yielded an mRNA whose sequence included the segment \(5^{\prime}-\) UACGGUCUAAGCUGA. What is the corresponding nucleotide sequence \(\left(5^{\prime} \rightarrow 3^{\prime}\right)\) of the template strand in a DNA duplex that might be introduced into these cells so that an antisense RNA could be transcribed from it?

A 10 -kb DNA fragment digested with restriction endonuclease \(E c o \mathrm{RI}\) yielded fragments \(4 \mathrm{kb}\) and \(6 \mathrm{kb}\) in size. When digested with \(\mathrm{BamHI}\) fragments \(1,3.5,\) and \(5.5 \mathrm{kb}\) were generated. Concomitant digestion with both \(E c o R I\) and \(B a m H I\) yielded fragments \(0.5,1,3,\) and \(5.5 \mathrm{kb}\) in size. Give a possible restriction map for the original fragment.

Gene expression is controlled through the interaction of proteins with specific nucleotide sequences in double-stranded DNA. a. List the kinds of noncovalent interactions that might take place between a protein and DNA. b. How do you suppose a particular protein might specifically interact with a particular nucleotide sequence in DNA? That is, how might proteins recognize specific base sequences within the double helix?

Restriction endonucleases also recognize specific base sequences and then act to cleave the double-stranded DNA at a defined site. Speculate on the mechanisms by which this sequence recognition and cleavage reaction might occur by listing a set of requirements for the process to take place.

A carbohydrate group is an integral part of a nucleoside. a. What advantage does the carbohydrate provide? Polynucleotides are formed through formation of a sugarphosphate backbone. b. Why might ribose be preferable for this backbone instead of glucose? c. Why might 2-deoxyribose be preferable to ribose in some situations?

Phosphate groups are also integral parts of nucleotides, with the second and third phosphates of a nucleotide linked through phosphoric anhydride bonds, an important distinction in terms of the metabolic role of nucleotides. a. What property does a phosphate group have that a nucleoside lacks? b. How are phosphoric anhydride bonds useful in metabolism? c. How are phosphate anhydride bonds an advantage to the energetics of polynucleotide synthesis?

The bases of nucleotides and polynucleotides are "information symbols." Their central role in providing information content to DNA and RNA is clear. What advantages might bases as "information symbols" bring to the roles of nucleotides in metabolism?

Structural complementarity is the key to molecular recognition, a lesson learned in Chapter 1. The principle of structural complementarity is relevant to answering problems \(5,6,7,11,12,\) and 19 The quintessential example of structural complementarity in all of biology is the DNA double helix. What features of the DNA double helix exemplify structural complementarity?