Nucleic acid

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

A nucleic acid is a complex, high-molecular-weight biochemical macromolecule composed of nucleotide chains that conveys genetic information. 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 are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). functions/diffs

significance

The chemical structure of nucleic acids

Components

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, they consist of long chains of nucleotide monomers connected by covalent chemical bonds. RNA molecules may contain as few as 75 nucleotides to more than 5000 nucleotides, while a DNA molecule may be composed of more than 1,000,000 nucleotide units.

A nucleotide is a chemical compound with three components: a nitrogen-containing base, a pentose (five-carbon) sugar (a relatively simple carbohydrate), and one or more phosphate groups. The nitrogen-containing base of a nucleotide (also called the nucleobase) is typically a derivative of either purine or pyrimidine. The most common bases in nucleotides 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 the two classes of nucleic acids, 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).

Organization

phosphodiester groups The sugars and phosphates in nucleic acids are connected to each other in an alternating chain, linked by shared oxygens, forming a phosphodiester functional group

Nucleic acids may be single-stranded or double-stranded. A double-stranded nucleic acid consists of two single-stranded nucleic acids linked by hydrogen bonds. RNA is usually single-stranded, but any given strand is likely to fold back upon itself to form double-helical regions. DNA is usually double-stranded, though some viruses have single-stranded DNA as their genome.

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

DNA consists of two helical deoxyribonucleotide chains coiled around a common axis. The chains run in opposite directions, and are held together by hydrogen bonds between pairs of bases from each chain. Adenine is always paired with thymine, and guanine with cytosine (i.e., a purine pairs with a pyrimidine).

Because pairing causes the nucleotide bases to face inward toward the helical axis, the sugar and phosphate groups of the nucleotides run along the outside; the two chains they form are sometimes called the backbones of the helix. In fact, it is chemical bonds between the phosphates and the sugars that link one nucleotide to the next in the DNA strand. Thus, the sugar-phosphate backbones play a primarily structural role.

stability due to h-bonding between base pairs dna of many chromosomes and dna-containing viruses is in the form of long, unbranched, double-helical threads, whereas dna of many viruses and in mitochondria are circular and in some cases twisted into a supercoiled form.

Function

Nucleic acids are primarily biology's means of storing and transmitting genetic information, though RNA is also capable of acting as an enzyme.

In contrast, the nucleobases (which are the variable part of the nucleotide) carry genetic information. Within a gene, the sequence of nucleotides along a DNA strand 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.

DNA

DNA contains the genetic information that allows living things to function, grow and reproduce. This information is held in the sequence of pieces of DNA called genes. Genetic information in genes is transmitted through complementary base pairing. For example, when a cell uses the information in a gene, the DNA sequence is copied into a complementary RNA sequence in a process called transcription. Usually, this RNA copy is then used to make a matching protein sequence in a process called translation. Alternatively, a cell may simply copy its genetic information in a process called DNA replication. The details of these functions are covered in other articles, here we focus on the interactions that happen in these processes between DNA and other molecules.

Transcription and translation

File:RNA pol.jpg

T7 RNA polymerase producing a mRNA (green) from a DNA template (red and blue). The protein is shown as a purple ribbon. Image derived from PDB 1MSW.

Further information: Genetic code, Transcription (genetics), Protein biosynthesis

A gene is s sequence of DNA that contains genetic information and can influence the phenotype of an organism. Within a gene, the sequence of bases along a DNA strand defines a messenger RNA sequence which then defines a protein sequence. The relationship between the nucleotide sequences of genes and the amino-acid sequences of proteins is determined by the rules of translation, known collectively as the genetic code. The genetic code consists of three-letter 'words' (called codons) formed from a sequence of three nucleotides (e.g. ACT, CAG, TTT). In transcription, the codons of a gene are copied into messenger RNA by RNA polymerase. This RNA copy is then decoded by a ribosome that reads the RNA sequence by base-pairing the messenger RNA to transfer RNA, which carries amino acids. There are 64 possible codons (4 bases in 3 places $4^{3}$) that encode 20 amino acids. Most amino acids, therefore, have more than one possible codon. There are also three 'stop' or 'nonsense' codons signifying the end of the coding region, these are the UAA, UGA and UAG codons.

File:Dna-split.png

DNA replication

Replication

Cell division is essential for an organism to grow, but when a cell divides it must replicate the DNA in its genome so that the two daughter cells have the same genetic information as their parent. The double-stranded structure of DNA provides a simple mechanism for DNA replication. Here, the two strands are separated and then each strand's complementary DNA sequence is recreated by an enzyme called DNA polymerase. This enzyme makes the complementary strand by finding the correct base through complementary base pairing, and bonding it onto the original strand. All such DNA polymerases extend a DNA strand in a 5 prime to 3 prime direction. In this way, the base on the old strand dictates which base appears on the new strand, and the cell ends up with an perfect copy of its DNA.

RNA

Messenger RNA (mRNA)

Messenger RNA is RNA that carries information from DNA to the ribosome sites of protein synthesis in the cell. Once mRNA has been transcribed from DNA, it is exported from the nucleus into the cytoplasm (in eukaryotes mRNA is "processed" before being exported), where it is bound to ribosomes and translated into protein. After a certain amount of time the message degrades into its component nucleotides, usually with the assistance of RNA polymerases.

Transfer RNA (tRNA)

Transfer RNA is a small RNA chain of about 74-93 nucleotides that transfers a specific amino acid to a growing polypeptide chain at the ribosomal site of protein synthesis during translation. It has sites for amino-acid attachment and an anticodon region for codon recognition that binds to a specific sequence on the messenger RNA chain through hydrogen bonding. It is a type of non-coding RNA.

Ribosomal RNA (rRNA)

Ribosomal RNA is a component of the ribosomes, the protein synthetic factories in the cell. Eukaryotic ribosomes contain four different rRNA molecules: 18S, 5.8S, 28S, and 5S rRNA. Three of the rRNA molecules are synthesized in the nucleolus, and one is synthesized elsewhere. rRNA molecules are extremely abundant and make up at least 80% of the RNA molecules found in a typical eukaryotic cell.

In the cytoplasm, ribsomal RNA and protein combine to form a nucleoprotein called a ribosome. The ribosome binds mRNA and carries out protein synthesis. Several ribosomes may be attached to a single mRNA at any time.

Catalytic role

A ribozyme (from ribonucleic acid enzyme, also called RNA enzyme or catalytic RNA) is an RNA molecule that catalyzes a chemical reaction. 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. Although RNA contains only four bases, in comparison to the twenty amino acids commonly found in proteins, some RNAs are still able to catalyse chemical reactions. These include cutting and ligating other RNA molecules and also the catalysis of peptide bond formation in the ribosome

References

ISBN links support NWE through referral fees

• Stryer, Lubert. 1995. Biochemistry, 4th edition. New York, N.Y.: W.H. Freeman.

External links

• An Ambigraphic Nucleic Acid Notation

Template:ChemicalSources

Nucleic acids
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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