Characteristics of Nucleic Acids

Characteristics of Nucleic Acids
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Important nucleic acids in nature include deoxyribonucleic acid, or DNA, and ribonucleic acid, or RNA. They are called acids because they are proton (i.e., hydrogen atom) donors, and therefore they carry a negative charge.

Chemically, DNA and RNA are polymers, meaning that they consist of repeating units, often a very large number of them. These units are called nucleotides. All nucleotides in turn include three distinct chemical portions: a pentose sugar, a phosphate group and a nitrogenous base.

DNA differs from RNA in three primary ways. One is that it the sugar that makes up the structural "backbone" of the nucleic acid molecule is deoxyribose, whereas in RNA it is ribose. If you're at all familiar with chemical nomenclature, you will recognize that this is a small difference in the overall structural scheme; ribose has four hydroxyl (-OH) groups, while deoxyribose has three.

The second difference is that while one of the four nitrogenous bases found in DNA is thymine, the corresponding base in RNA is uracil. The nitrogenous bases of nucleic acids are what dictate the ultimate characteristics of these molecules, because the phosphate and sugar portions do not vary within or between molecules of the same type.

Finally, DNA is double-stranded, meaning that it consists of two long chains of nucleotides chemically bound by two nitrogenous bases. The DNA is wound into a "double helix" shape, like a flexible ladder twisted in opposite directions at both ends.

General Characteristics of DNA

Deoxyribose consists of a five-atom ring, four carbons and an oxygen, shaped like a pentagon or perhaps home plate in baseball. Because carbon forms four bonds and oxygen two, this leaves eight binding sites free on the four carbon atoms, two per carbon, one above and one below the ring. Three of these spots are occupied by hydroxyl (-OH) groups, and five are claimed by hydrogen atoms.

This sugar molecule may bond to one of four nitrogenous bases: adenine, cytosine, guanine and thymine. Adenine (A) and guanine (G) are purines, while cytosine (C) and thymine (T) are pyrimidines. Purines are larger molecules than pyrimidines; because the two strands of any complete DNA molecule are bound in the middle by their nitrogenous bases, these bonds must form between one purine and one pyrimidine to keep the total size of the two bases across the molecule roughly constant. (It helps to refer to any diagram of nucleic acids when reading, such as those in the References.) As it happens, A bonds exclusively to T in DNA, while C bonds exclusively to G.

Deoxyribose bound to a nitrogenous base is called a nucleoside. When a phosphate group is added to deoxyribose at the carbon two spots away from where the base is attached, a complete nucleotide is formed. The peculiarities of the respective electrochemical charges on the various atoms in nucleotides are responsible for double-stranded DNA naturally forming a helical shape, and the two DNA strands in the molecule are called complementary strands.

General Characteristics of RNA

The pentose sugar in RNA is ribose rather than deoxyribose. Ribose is identical to deoxyribose except that the ring structure is bound to four hydroxyl (-OH) groups and four hydrogen atoms instead of three and five respectively. The ribose portion of a nucleotide is bound to a phosphate group and a nitrogenous base, as with DNA, with alternating phosphates and sugars forming the RNA "backbone." The bases, as noted above, include A, C and G, but the second pyrimidine in RNA is uracil (U) rather than T.

Whereas DNA is concerned only with information storage only (a gene is simply a strand of DNA that codes for a single protein), different types of RNA assume different functions. Messenger RNA, or mRNA, is made from DNA when the ordinarily double-stranded DNA splits into two single strands for the purpose of transcription. The resulting mRNA ultimately makes its way toward the parts of cells where protein manufacture occurs, carrying the instructions for this process delivered by DNA. A second type of RNA, transfer RNA (tRNA), takes part in the manufacture of proteins. This occurs on cell organelles called ribosomes, and ribosomes themselves consist chiefly of a third type of RNA called, aptly, ribosomal RNA (rRNA).

The Nitrogenous Bases

The five nitrogenous bases – adenine (A), cytosine (C), guanine (G) and thymine (T) in DNA and the first three plus uracil (U) in RNA – are the portions of nucleic acids that are ultimately responsible for the diversity of gene products across living things. The sugar and phosphate portions are essential in that they provide structure and scaffolding, but the bases are where the codes are generated. If you think of your laptop computer as a nucleic acid or at least a string of nucelotides, the hardware (e.g., disk drives, monitor screen, microprocessor) is analogous to the sugars and phosphates, whereas whatever software and apps you are running are like nitrogenous bases, because the unique assortment of programs you have loaded on to your system effectively makes your computer a one-of-a-kind "organism."

As described earlier, nitrogenous bases are classified as either purines (A and G) or pyrimidines (C, T and U). A always pairs in a DNA strand with T, and C always pairs with G. Importantly, when a DNA strand is used as a template for RNA synthesis (transcription), at each point along the growing RNA molecule, the RNA nucleotide that is created from the "parent" DNA nucleotide includes the base that is the one the "parent" base always bonds to. This is explored in a further section.

Purines consist of a six-member nitrogen-and-carbon ring and a five-member nitrogen-and-carbon ring, like a hexagon and a pentagon that share a side. Purine synthesis involves chemical tweaking of a ribose sugar, followed by the addition of amino (-NH2) groups. Pyrimidines also have a six-member nitrogen-and-carbon ring, like purines, but lack the five-member nitrogen-and-carbon ring of purines. Purines therefore have a higher molecular mass than do pyrimidines.

The synthesis of nucleotides containing pyrimidines and the synthesis of nucleotides containing purines occur in the opposite order in one crucial step. In pyrimidines, the base portion is assembled first, and the rest of the molecule is modified into a nucleotide later. In purines, the part that ultimately becomes adenine or guanine is modified toward the end of nucleotide formation.

Transcription and Translation

Transcription is the creation of a strand of mRNA from a DNA template, carrying the same instructions (i.e., genetic code) for making a particular protein as the template does. The process occurs in the cell nucleus, where DNA is located. When a double-stranded DNA molecule separates into single strands and transcription proceeds, the mRNA that is generated from one strand of the "unzipped" DNA pair is identical to the DNA of the other strand of unzipped DNA, except that mRNA contains U instead of T. (Again, referring to a diagram is useful; see the References.) The mRNA, once complete, leaves the nucleus through pores in the nuclear membrane. After the mRNA leaves the nucleus, it attaches to a ribosome.

Enzymes then attach to the ribosomal complex and assist in the process of translation. Translation is the conversion of the mRNA's instruction into proteins. This occurs when amino acids, the sub-units of proteins, are generated from three-nucleotide "codons" on the mRNA strand. The process also involves rRNA (since translation takes place on ribsomes) and tRNA (which helps assemble amino acids).

From DNA Strands to Chromosomes

DNA strands assemble into a double helix owing to a confluence of related factors. One of these is the hydrogen bonds that naturally fall into place across different parts of the molecule. As the helix forms, the bonding pairs of nitrogenous bases are perpendicular to the axis of the double helix as a whole. Each full turn includes a total of about 10 base-base bonded pairs. What might have been called the "sides" of the DNA when laid out as a "ladder" are now called the "chains" of the double helix. These consist almost entirely of the ribose and phosphate portions of nucleotides, with the bases being on inside. The helix is said to have both major and minor grooves that determine its ultimately stable shape.

While chromosomes may be described as very long strands of DNA, this is a gross simplification. It is true that a given chromosome could, in theory, be unwound to reveal a single unbroken DNA molecule, but this fails to indicate the intricate coiling, spooling and clustering that DNA does en route to forming a chromosome. One chromosome features millions of DNA base pairs, and if all the DNA were stretched out without breaking the helix, its length would extend from a few millimeters to over a centimeter. In reality, DNA is far more condensed. Proteins called histones form from four pairs of subunit proteins (eight subunits in all). This octamer serves as a spool of sorts for the DNA double helix to wrap itself around twice, like thread. This structure, the octamer plus the DNA wrapped around it, is called a nucleosome. When a chromosome is partially unwound into a strand called a chromatid, these nucleosomes appear on microscopy to be beads on a string. But above the level of nucleosomes, further compression of the genetic material occurs, though the precise mechanism remains elusive.

Nucleic Acids and the Emergence of Life

DNA, RNA and proteins are considered biopolymers because they are repeated sequences of information and amino acids that are associated with living things ("bio"means "life"). Molecular biologists today recognize that DNA and RNA in some form predate the emergence of life on Earth, but as of 2018, no one had figured out the pathway from early biopolymers to simple living things. Some have theorized that RNA in some form was the original source of all of these things, including DNA. This is the "RNA world hypothesis." However, this presents a sort of chicken-and-egg scenario for biologists, because sufficiently large RNA molecules seemingly could not have emerged by any means other than transcription. In any event, scientists are, with increasing eagerness, presently investigating RNA as a target for the first self-replicating molecule.

Medical Therapies

Chemicals that mimic the constituents of nucleic acids are being used as drugs today, with further developments in this area underway. For example, a slightly modified form of uracil, 5-fluorouracil (5-FU), has been used for decades to treat carcinoma of the colon. It does this by imitating a true nitrogenous base closely enough so that it becomes inserted into newly manufactured DNA. This ultimately leads to a breakdown in protein synthesis.

Imitators of nucleosides (which, you may recall, are a ribose sugar plus a nitrogenous base) have been used in antibacterial and antiviral therapies. Sometimes, it is the base portion of the nucleoside that undergoes modification, and at other times the drug targets the sugar portion.

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