WHAT IS DNA? — Biology Notes
Deoxyribonucleic acid (DNA) is a molecule that carries most of the genetic instructions used in the development, functioning, and reproduction of all known living organisms and many viruses. DNA is a nucleic acid; alongside proteins and carbohydrates, nucleic acids compose the three major macromolecules essential for all known forms of life. DNA stores instructions for making other large molecules, called proteins. These instructions are stored inside each of your cells, distributed among 46 long structures called chromosomes. These chromosomes are made up of thousands of shorter segments of DNA, called genes. Each gene stores the directions for making protein fragments, whole proteins, or multiple specific proteins. DNA is well-suited to perform this biological function because of its molecular structure, and because of the development of a series of high-performance enzymes that are fine-tuned to interact with this molecular structure in specific ways. The match between DNA structure and the activities of these enzymes is so effective and well-refined that DNA has become, over evolutionary time, the universal information-storage molecule for all forms of life. Nature has yet to find a better solution than DNA for storing, expressing, and passing along instructions for making proteins. DNA Structure DNA molecules are the polymer. Polymers are large molecules that are built up by repeatedly linking together smaller molecules, called monomers. Think of how a freight train is built by linking lots of individual boxcars together, or how this sentence is built by sticking together a specific sequence of individual letters (plus spaces and punctuation). In all three cases, the large structure—a train, a sentence, a DNA molecule—is composed of smaller structures that are linked together in non random sequences— boxcars, letters, and, in the biological case, DNA monomers. DNA monomers are called nucleotides. A molecule of DNA is a bunch of nucleotide monomers, joined one after another into a very long chain. There are four nucleotide monomers. They have short and easy to remember names: A, C, T, G. Each nucleotide monomer is built from three simple molecular parts: a sugar, a phosphate group, and a nucleobase. (Don’t confuse this use of “base” with the other one, which refers to a molecule that raises the pH of a solution; they’re two different things.) The sugar and acid in all four monomers are the same. All four nucleotides (A, T, G and C) are made by sticking a phosphate group and a nucleobase to a sugar. The sugar in all four nucleotides is called deoxyribose. It’s a cyclical molecule—most of its atoms are arranged in a ring structure. The ring contains one oxygen and four carbons. A fifth carbon atom is attached to the fourth carbon of the ring. Deoxyribose also contains a hydroxyl group (-OH) attached to the third carbon in the ring. The phosphate group is a phosphorous atom with four oxygen atoms bonded to it. The phosphorous atom in phosphate has a marked tendency to bond to other oxygen atoms (for instance, the oxygen atom sticking off the deoxyribose sugar of another nucleotide). The four nucleotide monomers are distinguished by their bases. Each type of nucleotide has a different nucleobase stuck to its deoxyribose sugar. A nucleotide contains adenine T nucleotide contains thymine G nucleotide contains guanine C nucleotide contains cytosine All four of these nucleobases are relatively complex molecules, with the unifying feature that they all tend to have multiple nitrogen atoms in their structures. For this reason, nucleobases are often also called nitrogenous bases. Phosphodiester bonds in DNA polymers connect the 5’ carbon of one nucleotide to the 3’ carbon of another nucleotide. The nucleotide monomers in a DNA polymer are connected by strong electromagnetic attractions called phosphodiester bonds. Phosphodiester bonds are part of a larger class of electromagnetic attractions between atoms that chemists refer to as covalent bonds. In order to keep things organized, biochemists have developed a numbering system for talking about the molecular structure of nucleotides. These numbers are applied to the carbon atoms in the sugar, starting at the carbon immediately to the right of the oxygen in the deoxyribose ring, and continuing in a clockwise fashion: the numbers range from 1’ (“one prime”), identifying the carbon immediately to the right of the oxygen) all the way to 5’ (“five prime”), identifying the carbon that sticks off the fourth and final carbon in the deoxyribose ring. The phosphodiester bonds that join one DNA nucleotide to another always link the 5’ carbon of the first nucleotide to the 3’ carbon of the second nucleotide. This forms a covalent bond between the oxygen sticking off the 3’ carbon of the second nucleotide and the phosphorous atom in the phosphate group that sticks off the 5’ carbon of the first nucleotide. These bonds are called 5’-3’ phosphodiester bonds. Each time nucleotides are bound together, a water molecule is removed (or “lost”) through a process called dehydration synthesis. Many molecules rely on dehydration synthesis to assist with forming or breaking down polymers. Chromosomes are made of two DNA polymers that stick together via non-covalent hydrogen bond. Chromosomal DNA consists of two DNA polymers that make up a 3-dimensional (3D) structure called a double helix. In a double helix structure, the strands of DNA run antiparallel, meaning the 5’ end of one DNA strand is parallel with the 3’ end of the other DNA strand. The nucleotides forming each DNA strand are connected by noncovalent bonds, called hydrogen bonds. Considered individually, hydrogen bonds are much weaker than a single covalent bond, such as a phosphodiester bond. But, there are so many of them that the two DNA polymers are very strongly connected to each other. The hydrogen bonds that join DNA polymers happen between certain hydrogen atoms on one base (called hydrogen bond donors) and certain oxygen or nitrogen atoms on the base across from it (called hydrogen bond acceptors). Adenine (“A”) and Thymine (“T”) each have one donor and one acceptor, whereas Cytosine (“C”) has one donor and two acceptors, and Guanine (“G”) has one acceptor and two donors. The A nucleotides are always hydrogen bonded to T nucleotides, and C nucleotides are always hydrogen bonded to G nucleotides. This selective binding is called complementary base pairing and creates consistency in the nucleotide sequences of the two DNA polymers that join together to make a chromosome. This was first observed by Erwin Chargaff, who developed methods for counting nucleotides in DNA samples, and found that the percent of A nucleotides always equalled the percent of T nucleotides, and the percent of G nucleotides always equalled the percent of C nucleotides (within a margin of error). Now, we know that complementary base pairing can be explained by reference to hydrogen bonding between the donors and acceptors on the bases of each nucleotide: A-nucleotides and T nucleotides have a match (one donor and one acceptor each), and C nucleotides and G nucleotides have a match (the former has one donor and two acceptors, while the latter has one acceptor and two donors).
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