3.2 Nucleic Acid Structure

3.2 Nucleic Acid Structure

Nucleic acids store and transmit biological information, and one of them, ATP, also carries usable energy between reactions. CLEP chemical-composition questions ask what a nucleotide contains, how DNA differs from RNA, and how nucleotides are linked. This section stays on structure. Copying a chromosome at a replication fork is a later topic. Here the goal is the parts, the backbone, the base-pairing rules, and the shape of the two kinds of nucleic acid.

A Nucleotide Has Three Parts

A nucleotide has three pieces: a pentose sugar of five carbons, a nitrogenous base, and at least one phosphate group. The base is attached to the sugar, and the phosphate is attached to the sugar as well. A sugar plus a base, with no phosphate, is a nucleoside. Adding phosphate makes the nucleotide. In a polymer, each repeating unit still contributes one sugar, one base, and one phosphate to the chain.

The sugar identifies the nucleic acid. Deoxyribose is the sugar in DNA. Ribose is the sugar in RNA. The chemical difference is small and exam-famous: deoxyribose lacks an oxygen atom on the 2-prime carbon that ribose still has. That missing oxygen makes the DNA backbone chemically more stable than an RNA backbone.

Two families of bases

The bases fall into two ring families. Purines have two fused rings. The purines in nucleic acids are adenine and guanine. Pyrimidines have a single ring. Cytosine, thymine, and uracil are the pyrimidines. Adenine and guanine are the larger, two-ring bases. Cytosine, thymine, and uracil are the smaller, one-ring bases.

DNA and RNA do not use the same set. DNA uses adenine, thymine, guanine, and cytosine. RNA uses adenine, uracil, guanine, and cytosine. Uracil replaces thymine in RNA. Uracil is not a base in DNA, and thymine is not the usual base in RNA. Both polymers use adenine, guanine, and cytosine. The swap to remember is thymine versus uracil, together with deoxyribose versus ribose.

The Backbone, the Ends, and the Two Polymers

Nucleotides join by phosphodiester bonds. Each bond links the phosphate of one nucleotide to the sugar of the next. The repeating pattern is sugar, phosphate, sugar, phosphate. That pattern is the sugar-phosphate backbone. The bases hang off the sugars. They are not bonded to one another along the strand. A common mistake is to picture the backbone as base bonded to base. The covalent backbone is sugar and phosphate. Bases become important when two strands pair, and even then the pairing is hydrogen bonding, not the covalent backbone.

Each strand has direction because the sugar is asymmetric. One end exposes a phosphate on the 5-prime carbon of the sugar. The other end exposes a hydroxyl on the 3-prime carbon. Those are the 5-prime end and the 3-prime end. Sequences are written from the 5-prime end toward the 3-prime end. The two ends are chemically different, so a strand is not the same if you flip it end for end.

DNA is usually double-stranded. The two strands run in opposite directions, a relationship called antiparallel. One strand runs 5-prime to 3-prime while its partner runs 3-prime to 5-prime. RNA is usually single-stranded. RNA can fold into local double regions, but the usual exam contrast is double-stranded DNA versus single-stranded RNA. The two DNA strands are held together by hydrogen bonds between bases. Phosphodiester bonds run along each strand, not across the pair.

Watson-Crick pairs

Complementary base pairing follows the Watson-Crick rules. Adenine pairs with thymine in DNA, and adenine pairs with uracil in RNA. Guanine pairs with cytosine in both. A two-ring purine pairs with a one-ring pyrimidine, which keeps the width of a DNA pair even. Adenine does not pair with guanine, and thymine does not pair with cytosine, in the standard pair.

An adenine-thymine pair uses two hydrogen bonds. A guanine-cytosine pair uses three. A region rich in guanine and cytosine therefore has more hydrogen bonds per pair than a region rich in adenine and thymine. That comparison is about pair stability. It is not a lesson on opening a replication fork.

Worked example: a four-base pair

Write one DNA strand in the 5-prime to 3-prime direction as ATGC. The antiparallel partner, written beside it from its 3-prime end toward its 5-prime end, reads TACG. If you instead write the partner in the conventional 5-prime to 3-prime direction, you reverse it and get GCAT. Check the pairs either way: adenine with thymine, thymine with adenine, guanine with cytosine, and cytosine with guanine.

Count the hydrogen bonds across those four pairs. The two adenine-thymine pairs contribute two bonds each, for four. The two guanine-cytosine pairs contribute three bonds each, for six. The duplex has ten hydrogen bonds between bases. Separately, count the covalent backbone. A strand of four nucleotides contains three phosphodiester bonds, because each bond joins two neighbors. Two strands contain six phosphodiester bonds. None of those covalent bonds runs from a base to a base. The ten hydrogen bonds are the cross-links between bases. The six phosphodiester bonds are the backbone.

This counting item hides two traps. Uracil never appears in the DNA pair, so the partner of adenine here is thymine, not uracil. The backbone count is a phosphodiester count, not a count of bases glued end to end.

ATP Is a Nucleotide Energy Carrier

ATP, adenosine triphosphate, is a nucleotide, not a separate kind of molecule with an unrelated design. Its base is adenine, its sugar is ribose, and it carries three phosphate groups linked to the 5-prime carbon of that sugar. Those linked phosphates are why ATP can serve as an energy carrier: transferring or releasing a phosphate group leaves ADP, adenosine diphosphate. That is a structure point. Glycolysis and the rest of cellular respiration are later topics. What belongs here is that a cell-wide energy carrier is chemically a ribonucleotide with a chain of three phosphates.