[AP Biology 1.6] Nucleic Acids

The last section of “Unit 1: The Chemistry of Life” focuses on Nucleic Acids. This section discusses the importance of DNA and RNA within cells, and it examines the structure of each of these molecules to determine why they have different functions. We will look at how DNA and RNA are formed, and examine the many roles they serve within cells.

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Heritable information provides for continuity of life.

Describe the structural similarities and differences between DNA and RNA

DNA and RNA molecules have structural similarities and differences related to their function –

  1. Both DNA and RNA have three components – sugar, a phosphate group, and a nitrogenous base – that form nucleotide units that are connected by covalent bonds to form a linear molecule with 5’ and 3’ ends, with the nitrogenous bases perpendicular to the sugar-phosphate backbone.
  2. The basic structural differences between DNA and RNA include the following:
    1. DNA contains deoxyribose and RNA contains ribose.
    2. RNA contains uracil and DNA contains thymine
    3. DNA is usually double-stranded; RNA is usually single-stranded
    4. The two DNA strands in double-stranded DNA are antiparallel in directionality

1.5 Nucleic Acids Overview

The big picture in this section of the AP Biology curriculum is that heritable information provides for continuity of life. “Heritable” means that it can be passed from one generation to the next, while the “continuity of life” describes the ongoing process of organisms growing, replicating their DNA, and creating a new generation of organisms that share that DNA. This section focuses more specifically on DNA and RNA. We will be looking at how they are similar, how they are different, and the various roles they serve in cells.

The structure of DNA was first worked out in 1953, by researchers Watson and Crick. The team used x-ray crystallography images produced by Rosalind Franklin, who unfortunately died of cancer before she was awarded the Nobel Prize like the rest of the team. Her method of using X-rays to view the structure of DNA ultimately led to the model we still use today.

DNA actually stands for “deoxyribonucleic acid” – a name that references the sugar ribose and the nucleotide bases that are at the heart of every DNA molecule. “Deoxy” references the fact that unlike normal ribose, deoxyribose has lost an oxygen atom. At the molecular level, DNA gets its structure through two main features – the sugar-phosphate backbone and the hydrogen bonds formed between complementary nucleotide bases.

Each nucleotide in the sequence is bonded to the next through a phosphodiester bond, which is created through a dehydration reaction facilitated by the enzyme DNA polymerase. In this bond, the hydroxyl group on the pentose sugar molecule connects to the phosphate group on the new nucleotide. Thus, the new strand is constructed from the 5’ end (with a phosphate group) to the 3’ end (with a hydroxyl). The DNA polymerase molecule moves along the template strand in the opposite direction, from 3’ to 5’, since the two strands run antiparallel.

Within the structure of a DNA molecule, the nitrogenous bases stick out perpendicularly from the sugar-phosphate backbone. The sugar-phosphate backbone creates a helix structure, due to the angle of the bonds it is made out of. With the addition of nitrogenous bases that form hydrogen bonds with the antiparallel strand, this molecule takes on a double-helix structure – also called a duplex.

This duplex has two grooves that wind their way up the molecule. The first groove, the major groove, is formed by the structure of the sugar-phosphate backbone. As the second strand is synthesized, another groove is created. The minor groove is formed by the gap between the two strands, which is filled with nitrogenous bases. Enzymes that interact with DNA use these grooves to recognize DNA molecules, attach to them, and complete their function.

RNA molecules are slightly different than DNA molecules. “RNA” stands for ribonucleic acid. Unlike DNA, the sugar molecule used in RNA is ribose – complete with that extra oxygen atom that deoxyribose is missing.

While this is just one tiny atomic change in the structure of a much larger molecule, the oxygen atom actually causes many changes in the function of RNA. For one, RNA is a less stable molecule. The oxygen atom is much more reactive than a single hydrogen and often engages in hydrolysis reactions that disrupt the structure of RNA. Second, RNA is most commonly a single-stranded molecule in part due to the physical presence of the oxygen atom. The oxygen atom bonded with the hydrogen creates a large hydroxyl group that sits just above the nitrogenous base from the nucleotide below. This hinders the ability of the nitrogenous bases to form hydrogen bonds with each other.

The other difference that makes RNA different from DNA is that it uses Uracil instead of thymine. While all of the other nitrogenous bases are the same, RNA may use uracil for a few different reasons. Uracil is easier to create, though it is very similar to cytosine and can degrade quickly. Since RNA is short-lived, this is not an issue. DNA requires a more stable base to help store information correctly for long periods of time.

While DNA is pretty much only found as a duplex in nature, RNA can take on many different forms. In addition to the single-stranded, single-helix structure most commonly seen as messenger RNA (mRNA), other common secondary structures include transfer RNA (tRNA) and ribosomal RNA (rRNA).

Transfer RNA, or tRNA for short, is used to add new amino acids to a growing peptide chain. tRNA is created when a single-stranded RNA molecule folds back on itself to create small structures known as ‘hairpins.’ On one side of a tRNA molecule, 3 nitrogenous bases are left exposed. These bases will hydrogen bond with a codon on an mRNA molecule, allowing a ribosome to know it has selected the right amino acid. The other end of the tRNA carries a specific amino acid, and can only bind to one amino acid and no others. The other parts of a tRNA molecule ensure the molecule can be processed by a ribosome.

While ribosomes themselves are mostly made of protein, they have an RNA component that intertwines with the protein structure – known as rRNA – that aids in the process of translation. rRNA helps the ribosome hold mRNA and tRNA in place as the translation process unfolds. It also helps catalyze the dehydration reaction needed to form new peptide bonds between amino acids!

In addition to these forms of RNA, scientists are constantly discovering new uses for RNA within cells. For instance, there is also microRNA that has functions in regulating genes within the nucleus, RNAs that function as enzymes for certain reactions, and many other special-function RNAs that are still being discovered!

Besides a few viruses that use RNA as their main information molecule, organisms on Earth overwhelmingly use DNA to store information and RNA to translate that information into proteins. Let’s consider the structure of each molecule to see why they serve these roles well.

The duplex structure of DNA is very stable. Not only are the two strands held together by hydrogen bonds between complementary bases, but the sugar used (deoxyribose) is also much less likely to react with other molecules because it does not have the reactive oxygen atom present in RNA. This structure makes DNA strong and ensures it will last a long time without damage. Further, DNA is strong enough to be stored in a complex manner.

If we were to stretch out all of the DNA contained in 1 cell of your body, it would be around 5 feet long. But, DNA can be wrapped around storage proteins called histones to create nucleosomes. Nucleosomes can be packed tightly together into a fiber called chromatin, which can then be packed even further into a chromosome. This allows 6 billion nucleotides to be stored within the nucleus of a cell – that’s only about 1/500th of an inch!

By contrast, RNA is not a very stable molecule. But, it serves its many roles in the cell that DNA could not complete. RNA polymerase – an enzyme that makes RNA from the DNA template – can quickly create an RNA transcript that can carry the information out of the nucleus. RNA can interact with ribosomes to create new proteins, and these molecules can fold into protein-like shapes that serve as enzymes and gene regulators within cells. Because RNA uses uracil and has an extra oxygen atom in the ribose sugar, RNAs break down quickly. That is okay, since each RNA molecule is only needed for a short time and more can easily be made through transcription of the DNA code!