A diagram of a furanose (sugar-ring) molecule with carbons labelled numerically

Directionality, in molecular biology, refers to the end-to-end chemical orientation of a single strand of nucleic acid. The chemical convention of naming carbon atoms in the nucleotide sugar-ring numerically gives rise to a 3′ end and a 5′ end. The relative positions of structures along a strand of nucleic acid, including genes, transcription factors, and polymerases are usually noted as being either upstream (towards the 5′ end) or downstream (towards the 3′ end). Labeled diagram of (deoxy)Ribose I, the creator of this image, hereby release it into the public domain. ... A furanose is a simple sugar that contains a furan ring and is a sub-terminal ketone which gives it reducing power. ... Molecular biology is the study of biology at a molecular level. ... This article or section does not cite its references or sources. ... A nucleotide is a chemical compound that consists of a heterocyclic base, a sugar, and one or more phosphate groups. ... A furanose is a simple sugar that contains a furan ring and is a sub-terminal ketone which gives it reducing power. ... For other meanings of this term, see gene (disambiguation). ... In molecular biology, a transcription factor is a protein that binds DNA at a specific promoter or enhancer region or site, where it regulates transcription. ... ITaq DNA polymerase A polymerase (EC 2. ...

The importance of having this type of naming convention is easily demonstrated by the fact that nucleic acids can only be synthesized in vivo in a 5′ to 3′ direction, as the polymerase used to construct new strands must attach a new nucleotide to the 3′ hydroxyl (-OH) group via a phosphodiester bond. Traditionally DNA and RNA sequences are written going from 5′ to 3′. ITaq DNA polymerase A polymerase (EC 2. ... // Hydroxyl group The term hydroxyl group is used to describe the functional group -OH when it is a substituent in an organic compound. ... Diagram of phosphodiester bonds between nucleotides A phosphodiester bond is a group of strong covalent bonds between the phosphorus atom in a phosphate group and two other molecules over two ester bonds. ... The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ... This article or section does not adequately cite its references or sources. ...

3′ end

Diagram of phosphodiester bonds (circled) between nucleotides

The 3′ (pronounced "three prime") end of a strand is so named due to it terminating at the hydroxyl (-OH) group of the third carbon in the sugar-ring, and is known as the tail end. The 3′-hydroxyl is necessary in the synthesis of new nucleic acid molecules as it is ligated (joined) to the 5′-phosphate of a separate nucleotide, allowing the formation of strands of linked nucleotides. Diagram of Phosphodiester bonds between Nucleotides I made this diagram using ChemDraw Std 8. ... Diagram of Phosphodiester bonds between Nucleotides I made this diagram using ChemDraw Std 8. ... Diagram of phosphodiester bonds between nucleotides A phosphodiester bond is a group of strong covalent bonds between the phosphorus atom in a phosphate group and two other molecules over two ester bonds. ... // Hydroxyl group The term hydroxyl group is used to describe the functional group -OH when it is a substituent in an organic compound. ... A furanose is a simple sugar that contains a furan ring and is a sub-terminal ketone which gives it reducing power. ... It has been suggested that sticky end/blunt end be merged into this article or section. ...

Molecular biologists can use nucleotides that lack a 3′-hydroxyl (dideoxyribonucleotides) to interrupt the replication of DNA. This technique is known as both the Dideoxy termination method and the Sanger method, and was used to work out the order of nucleotides in DNA. Molecular biology is the study of biology at a molecular level. ... A nucleotide is an organic molecule consisting of a heterocyclic nucleobase (a purine or a pyrimidine), a pentose sugar (deoxyribose in DNA or ribose in RNA), and a phosphate or polyphosphate group. ... The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ... DNA sequencing is the process of determining the nucleotide order of a given DNA fragment, called the DNA sequence. ... The chain termination or Sanger or dideoxy method is a process used to sequence (read the bases) of DNA. It is named after Frederick Sanger who developed the process in 1975. ...

The 3′ end is also the site of post-translational polyadenylation, which attaches a chain of 50 to 250 adenosine residues to messenger RNA immediately after translation. This chain helps in determining how long the messenger RNA lasts in the cell, and therefore how much protein is produced from it. Polyadenylation is the covalent linkage of a polyadenylyl moiety to a messenger RNA (mRNA) molecule. ... The chemical structure of adenosine Adenosine is a nucleoside comprised of adenine attached to a ribose (ribofuranose) moiety via a β-N9-glycosidic bond. ... The life cycle of an mRNA in a eukaryotic cell. ... Translation is the second process of protein biosynthesis (part of the overall process of gene expression). ...

5′ end

The 5′ (pronounced "five prime") end is named as the strand terminates at the chemical group attached to the fifth carbon in the sugar-ring. If a phosphate group is attached to the 5′ end, ligation of two nucleotides can occur, via a phosphodiester bond from the 5′-phosphate to the 3′-hydroxyl group of another nucleotide. If it is removed no ligation can occur. Molecular biologists can use this phenomenon to their advantage by removing the 5′-phosphate with a phosphatase to prevent any unwanted nucleic acid ligation. A furanose is a simple sugar that contains a furan ring and is a sub-terminal ketone which gives it reducing power. ... Above is a ball-and-stick model of the inorganic hydrogenphosphate anion (HPO42−). Colour coding: P (orange); O (red); H (white). ... It has been suggested that sticky end/blunt end be merged into this article or section. ... A nucleotide is a chemical compound that consists of a heterocyclic base, a sugar, and one or more phosphate groups. ... Diagram of phosphodiester bonds between nucleotides A phosphodiester bond is a group of strong covalent bonds between the phosphorus atom in a phosphate group and two other molecules over two ester bonds. ... Molecular biology is the study of biology at a molecular level. ... A phosphatase is an enzyme that hydrolyses phosphoric acid monoesters into a phosphate ion and a molecule with a free hydroxyl group. ...

The 5′ end is the site at which post-translational capping occurs, a process which is vital to producing mature messenger RNA. Capping ensures the stability of the messenger RNA while it undergoes translation, providing resistance to the degradive effects of exonucleases. It consists of a methylated nucleotide (methylguanosine) attached the messenger RNA in a rare 5′ to 5′ triphosphate linkage. The 5 cap is a specially altered dinucleotide end to the 5 end of preliminary messenger RNA as found in eukaryotes. ... The life cycle of an mRNA in a eukaryotic cell. ... Translation is the second process of protein biosynthesis (part of the overall process of gene expression). ... Exonucleases are enzymes that cleave nucleotides one at a time from an end of a polynucleotide chain. ... Methylation refers to the replacement of a hydrogen atom (H) with a methyl group (CH3), regardless of the substrate. ...

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