Nucleic Acids
Nucleic Acid Basics
The monomer of a nucleic acid is known as a nucleotide. There are three components to a nucleotide: a nitrogenous base, a five-carbon sugar known as a "pentose," and a phosphate group. It is possible for there to be multiple phosphate groups in a nucleotide; if the phosphate group is missing, it is known as a nucleoside.
There are two broad categories of nitrogenous bases, pyrimidines (cytosine, thymine, and uracil) and purines (adenine, guanine). Purines have two carbon rings, while pyrimidines have one.
Fun fact!
Guanine earned its name because it was first isolated from guano!
Base Pairing
The nitrogenous bases in nucleotides are polar molecules, which makes them capable of hydrogen bonding. This hydrogen bonding is extremely important as it is essential to the proper transfer of the genetic information that is carried by nucleic acids. Something known as base pairing occurs due to these hydrogen bonds.
A purine will bind with a pyrimidine. Adenine binds to thymine (in DNA) or uracil (RNA). Guanine binds to cytosine. If you look at the image to the left, guanine and cytosine form three hydrogen bonds, while adenine only forms two (whether it be with thymine or uracil). Due to the additional hydrogen bond, a G-C pair is more stable than an A-T pair in DNA, which makes it less likely to denature.
Polymerization
As stated previously, there is a pentose in nucleotides. Each of these five carbons is named based on their order when moving in a clockwise direction, starting from the oxygen in the ring. The carbon closest to the phosphate group is known as the "five-prime" or 5' carbon, while the carbon most below it on the same side of the sugar is known as the "three-prime" or 3' carbon. These two carbons are very important as the phosphodiester linkage (the result of a covalent bond between two nucleotides) will always be in the same orientation, resulting in distinct 5' and 3' ends of the nucleic acids.
When polymerization occurs, nucleotides are bound together to form the growing nucleic acid. The order of nitrogenous bases that are present in the strand will be similar to the order of letters in a word - the order of specific bases is what determines what specific information is coded for by the nucleic acid.
Phosphodiester bonds link successive nucleotides and form a linear "backbone" for the nucleic acid. This backbone consists of the sugars and phosphates. As the bonds form in the same orientation, the backbone will have an alternating pattern of phosphate - sugar - phosphate - sugar, etc.
When writing out the order of bases in a nucleic acid, the 5' end and 3' end are often labeled so as to orient the depiction. As we will see when discussing topics such as DNA replication, transcription, and translation, several biochemical processes function based on the orientation of the nucleic acid.
Deoxyribonucleic Acid (DNA)
DNA, the "recipe of life," is a nucleic acid which has the major function of storing genetic information. It has genes - segments of DNA that code for a functional biological product (either protein or RNA). Along with the DNA coding for what to make, it also codes for when and where to make it. It is for this reason that "recipe of life" is a great definition for it: recipes not only tell you what to cook, but when to add certain ingredients, where to put them, etc.
Of the five nucleotides mentioned above, four of them are present in DNA: adenine, thymine, guanine, and cytosine. They are bound to a pentose known as deoxyribose, which is where the name DNA comes from.
DNA consists of two strands that are antiparallel and complimentary to each other. What this means is that the strands run in opposite directions of each other (see the image of two arrows) and that their base sequences are not identical, but rather if an adenine is in one strand, a thymine is in the other strand.
The hydrophilic bases between the two strands are hydrogen bonded to each other, with the hydrophobic backbone on either end of the bases. As there is an offset pairing of the two strands, the strands form a double helix (it looks like a twisted ladder) with a major groove (where the backbones are farther apart) and a minor groove (where the backbones are closer together).
There are multiple 3D forms of DNA that exist, known as B-form DNA, A-form DNA, and Z-form DNA.
Ribonucleic Acid (RNA)
RNA is a single-stranded nucleic acid. Of the five nucleotides mentioned previously, four of them are present in RNA: adenine, uracil, guanine, and cytosine. They are bound to a pentose known as ribose, which is where the name RNA comes from. The "deoxy" means that an oxygen is missing, so ribose has an oxygen on the 2' carbon, which is missing in deoxyribose.
RNA has a wide range of potential functions.
RNA can store and replicate genetic information. There are RNA viruses which have the entirety of their genetic information stored in the form of RNA. mRNA (messenger RNA) is synthesized based on the genetic code present in DNA in order to bring a copy of the "recipe" for a protein to the ribosome (or "kitchen" to stick with the recipe analogy) where the protein will be synthesized. rRNA (ribosomal RNA) is the primary component of the ribosome - the organelle responsible for making proteins that is found in every cell. At the ribosome, tRNA (transfer RNA) will bring an amino acid that matches the codon found on the mRNA and add it to the growing polypeptide chain that will make up the protein. More details about this process will be discussed as we learn about transcription and translation.
Like proteins, RNA can catalyze chemical reactions (ribozymes are a catalytic RNA molecule, kind of like an "RNA enzyme"), based on a structure that it folds into.
In addition, RNA can play a role in regulating gene expression. One example of this is miRNA, or micro RNA. These can negatively regulate gene expression by binding to complementary mRNA, destroying them, and silencing genes and preventing them from being translated.
Other Functions
Nucleic acids have a role in a wide variety of cellular processes, not just those involved in information storage.
One example of this is that they can serve as carriers for chemical energy within the cell. ATP (adenosine triphosphate) is a modified nucleotide that consists of adenine, ribose, and three phosphates. It can be used as energy in the cell; hydrolysis of ATP removes one of the phosphate groups. It is the transferring of this phosphate to another molecule that powers cellular processes. A depiction of ATP is seen below.
A variety of enyme cofactors (a non-protein molecule that is required for enzyme function) have adenosine as part of their structure, such as Acetyl-CoA, which is used in the citric acid cycle of cellular respiration to deliver the acetyl group in order to produce energy.
Nucleotides can also be used as regulatory molecules. cyclic AMP (cAMP) is a second messenger which is involved in amplyfing a message during signal transduction. cAMP is a modified adenosine monophosphate, which is created from ATP through an enzyme known as adenylyl cyclase.
