Nucleic acid

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A space-filling model of a section of a DNA molecule.

A nucleic acid is a polymer comprising numerous nucleotides (each composed of a phosphate unit, a sugar unit, and a "base" unit) linked recursively through the sugar and phosphate units to form a long chain with base units protruding from it. As found in biological systems, nucleic acids carry the coded genetic information of life according to the order of the base units extending along the length of the molecule. The connectedness of living organisms can be seen in the fact that such nucleic acids are found in all living cells and in viruses, and the flow of genetic information is essentially the same in all organisms.

The most common nucleic acids, deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), form a team that together oversees and carries out the construction of the tens of thousands of protein molecules needed by living organisms according to the ever-changing context of each cell. DNA is often compared to a blueprint, since it contains instructions for constructing other components of the cell, such as proteins and RNA molecules. Genes are those limited DNA segments carrying genetic information, and segments adjoining genes are often regulatory sequences whose function is to turn the adjoining gene's expression on or off according to stimulation received by a regulatory protein. Other sections of the DNA may be involved in the complex choreography by which long, narrow double strands of DNA become coiled and bundled multiple times whenever a cell replicates itself and then becomes unfolded in order to code for the production of proteins. For other sections of DNA, no function has yet been identified.

RNA may be thought of as the intermediate between the DNA blueprint and the actual workings of the cell, serving as the template for the synthesis of proteins from the genetic information stored in DNA. Some RNA molecules (called ribozymes, from RNA enzymes) are also involved in the catalysis of biochemical reactions. RNA serves directly as the genetic blueprint for certain viruses.

The nucleic acids DNA and RNA are found in the nuclei of eukaryotic cells and the cytoplasms of prokaryotes (which lack a nucleus). In eukaryotes, DNA is also present in other cellular compartments (called organelles), such as mitochondria in both animals and plants and chloroplasts in plants only.

Contents

The chemical structure of nucleic acids

Nucleic acids are composed of repeating nucleotide units

A schematic diagram of a double-stranded nucleic acid. Covalent bonds (solid lines) connect pentose sugars (green-hatched circles) to phosphates (dotted circles) to form the sugar-phosphate backbone, which provides structural support. The interior of the molecule contains nitrogenous bases (red-slashed circles) joined together via hydrogen bonds (dotted lines).

Nucleic acids are polymers of repeating units (called monomers). Specifically, nucleic acids are long chains of nucleotide monomers connected by covalent chemical bonds. RNA molecules may comprise as few as 75 or more than 5,000 nucleotides, while a DNA molecule may comprise more than 1,000,000 nucleotide units.

A nucleotide is a chemical compound comprising the union of three molecular components: a nitrogen-containing base, a pentose (five-carbon) sugar, and one or more phosphate groups. One phosphate group per nucleotide is standard for the nucleotides that make up DNA and RNA. Both the base and the pentose in a nucleotide are a cyclic and hence stable molecule whose core is at least one closed ring of atoms, with bases having one or two nitrogen atoms in a ring of carbon atoms and sugars having one oxygen in a ring of carbon atoms. The nitrogen-containing base of a nucleotide (also called the nucleobase) is typically derived from either purine or pyrimidine. The most common nucleotide bases are the purines adenine and guanine and the pyrimidines cytosine and thymine (or uracil in RNA).

The sugar component is either deoxyribose or ribose. (“Deoxy” simply indicates that the sugar lacks an oxygen atom present in ribose, the parent compound.)

There are two major compositional differences between RNA and DNA:

  1. The sugar units in RNA molecules are riboses, while DNA is built of nucleotides with a deoxyribose sugar.
  2. One of the four major nucleobases in RNA is uracil (U) instead of thymine (T).

Nucleic acids form single or double-stranded structures

A comparison of the DNA double-helix and a single-stranded RNA, showing the chemical structures of the bases.

Nucleic acids are constructed from chains of nucleotides attached by phosphodiester bonds. These bonds are formed between the phosphate residue of one nucleotide and one of two possible carbon atoms on the sugar molecule of an adjacent nucleotide. These sugar-phosphate interactions play a primarily structural role, forming what is sometimes referred to as the "backbone" of the nucleic acid.

Nucleic acids organize into single-stranded or double-stranded molecules. The DNA of many chromosomes and DNA-containing viruses forms long, unbranched, double-helical threads, in which two strands of DNA spiral around a common axis. The strands run in opposite directions, held together by hydrogen bonds that exist between pairs of bases from each strand. The base adenine is always paired with thymine, and guanine with cytosine (and a purine pairs with a pyrimidine). The stability created by the hydrogen-bonding between these complementary base pairs makes DNA a sturdy form of genetic storage.

The DNA of many viruses and the DNA found in mitochondria are circular; in some cases, they also twist into a supercoiled form. RNA is usually single-stranded, but it may contain double-helical regions where a given strand has folded back on itself.

Nucleic acids store and transmit genetic information

DNA encodes instructions for the synthesis of proteins

DNA contains the genetic information that allows living things to function, grow and reproduce. This information is encoded in the biochemical composition of the molecule itself; specifically, in its particular sequence of nucleobases (which are the variable part of the DNA molecule). A particular sequence of nucleotides along a segment of the DNA strand (i.e., a gene) defines a messenger RNA sequence, which in turn defines a protein.

The relationship between the nucleotide sequence and the amino-acid sequence of the protein is determined by simple cellular rules of translation, known collectively as the genetic code. The genetic code is the relation between the sequence of bases in DNA (or its RNA transcript) and the sequence of amino acids in proteins. Amino acids are coded by groups of three bases (called codons) starting from a fixed point (e.g. ACT, CAG, TTT). These codons can then be translated with messenger RNA and then transfer RNA from the chemical language of nucleic acids to that of amino acids, with each codon corresponding to a particular amino acid.

The double-helical structure of DNA facilitates its own replication

The double-helical structure of DNA is also crucial for understanding the simple mechanism of DNA replication. Cell division is essential for an organism's growth and development, but when a cell divides, it must replicate its DNA so that it may transmit the characteristics of the parent to the two daughter cells. During DNA replication, the two strands are first separated, and then each strand's complementary DNA sequence is recreated by an enzyme called DNA polymerase. This enzyme synthesizes the complementary strand by finding the correct base through complementary base pairing and bonding it to the original strand. In this way, the base on the original strand dictates which base appears on the new strand, and the cell ends up with a perfect copy of its DNA.

Three types of RNA are involved in protein synthesis

RNA has a greater variety of possible structures and chemical properties than DNA due to the diversity of roles it performs in the cell. Three principal types of RNA are involved in protein synthesis:

  • Messenger RNA (mRNA) serves as the template for the synthesis of a protein. It carries information from DNA to the ribosome, a specialized structure where the message is then translated into a protein.
  • Transfer RNA (tRNA) is a small chain of about 70-90 nucleotides that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of synthesis. It pairs the amino acid to the appropriate codon on the mRNA molecule.
  • Ribosomal RNA (rRNA) molecules are extremely abundant and make up at least 80 percent of the RNA molecules found in a typical eukaryotic cell. In the cytoplasm, rRNA molecules combine with proteins to perform a structural role, as components of the ribosome.

RNA serves as a genetic blueprint in some viruses

Some viruses contain either single-stranded or double-stranded RNA as their source of genetic information. Retroviruses, for example, store their genetic information as RNA, though they replicate in their hosts via a DNA intermediate. Once in the host's cell, the RNA strands undergo reverse transcription to DNA in the cytosol and are integrated into the host's genome, the complete DNA sequence of one set of chromosomes. Human immunodeficiency virus (or HIV) is a retrovirus that is considered to cause acquired immune deficiency syndrome (AIDS), a condition in which the human immune system begins to fail, leading to life-threatening opportunistic infections.

Some RNA molecules function as enzymes

In the 1980s, scientists discovered that certain RNA molecules (called ribozymes) may function as enzymes, whereas previously only proteins were believed to have catalytic ability. Many natural ribozymes catalyze either their own cleavage or the cleavage of other RNAs, but they have also been found to catalyze the aminotransferase activity of the ribosome.

The discovery of ribozymes provides a possible explanation for how early RNA molecules might have first catalyzed their own replication and developed a range of enzymatic activities. Known as the RNA world hypothesis, this explanation posits that RNA evolved before either DNA or proteins from free-floating nucleotides in the early "primordial soup." In their function as enzymes, RNA molecules might have begun to catalyze the synthesis of proteins, which are more versatile than RNA, from amino acid molecules. Next, DNA might have been formed by reverse transcription of RNA, with DNA eventually replacing RNA as the storage form of genetic material. There are remaining difficulties with the RNA world hypothesis; however, the multi functional nature of nucleic acids suggests the interconnectedness of life and its common origins.

References

  • Goodenbour, J. M, and T. Pan. 2006. Diversity of tRNA Genes in Eukaryotes. Nucleic Acids Research 34: 6137-6146.
  • Joseph, N., V. Duppatla, and D. N. Rao. 2006. Prokaryotic DNA Mismatch Repair. Progress in Nucleic Acid Research and Molecular Biology 81: 1-49.
  • Stryer, L. 1995. Biochemistry, 4th edition. New York, NY: W.H. Freeman. ISBN 0716720094.


Nucleic acids edit
Nucleobases: Adenine - Thymine - Uracil - Guanine - Cytosine - Purine - Pyrimidine
Nucleosides: Adenosine - Uridine - Guanosine - Cytidine - Deoxyadenosine - Thymidine - Deoxyguanosine - Deoxycytidine
Nucleotides: AMP - UMP - GMP - CMP - ADP - UDP - GDP - CDP - ATP - UTP - GTP - CTP - cAMP - cGMP
Deoxynucleotides: dAMP - dTMP - dUMP - dGMP - dCMP - dADP - dTDP - dUDP - dGDP - dCDP - dATP - dTTP - dUTP - dGTP - dCTP
Nucleic acids: DNA - RNA - LNA - PNA - mRNA - ncRNA - miRNA - rRNA - siRNA - tRNA - mtDNA - Oligonucleotide

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