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directionality molecular biology wikipedia jump to content main menu main menu move to sidebar hide navigation main page contents current events random article about wikipedia contact us contribute help learn to edit community portal recent changes upload file special pages search search appearance donate create account log in personal tools donate create account log in contents move to sidebar hide top 1 5 end 2 3 end 3 see also 4 further reading 5 external links toggle the table of contents directionality molecular biology 25 languages العربية bosanski català čeština ελληνικά español فارسی français galego עברית italiano 日本語 한국어 македонски nederlands polski português русский srpskohrvatski српскохрватски српски srpski ไทย türkçe اردو 粵語 中文 edit links article talk english read edit view history tools tools move to sidebar hide actions read edit view history general what links here related changes upload file permanent link page information cite this page get shortened url switch to legacy parser print export download as pdf printable version in other projects wikidata item appearance move to sidebar hide from wikipedia the free encyclopedia end to end chemical orientation of a single strand of nucleic acid this article needs more citations please help improve this article by adding citations to reliable sources unsourced material may be challenged and removed find sources directionality molecular biology news newspapers books scholar jstor may 2023 learn how and when to remove this message a furanose sugar ring molecule with carbon atoms labeled using standard notation the 5 is upstream the 3 is downstream dna and rna are synthesized in the 5 to 3 direction directionality in molecular biology and biochemistry is the end to end chemical orientation of a single strand of nucleic acid in a single strand of dna or rna the chemical convention of naming carbon atoms in the nucleotide pentose sugar ring means that there will be a 5 end usually pronounced five prime end which frequently contains a phosphate group attached to the 5 carbon of the ribose ring and a 3 end usually pronounced three prime end which typically is unmodified from the ribose oh substituent in a dna double helix the strands run in opposite directions to permit base pairing between them which is essential for replication or transcription of the encoded information nucleic acids can only be synthesized in vivo in the 5 to 3 direction as the polymerases that assemble various types of new strands generally rely on the energy produced by breaking nucleoside triphosphate bonds to attach new nucleoside monophosphates to the 3 hydroxyl oh group via a phosphodiester bond the relative positions of structures along strands of nucleic acid including genes and various protein binding sites are usually noted as being either upstream towards the 5 end or downstream towards the 3 end see also upstream and downstream directionality is related to but different from sense transcription of single stranded rna from a double stranded dna template requires the selection of one strand of the dna template as the template strand that directly interacts with the nascent rna due to complementary sequence the other strand is not copied directly but necessarily its sequence will be similar to that of the rna transcription initiation sites generally occur on both strands of an organism s dna and specify the location direction and circumstances under which transcription will occur if the transcript encodes one or rarely more proteins translation of each protein by the ribosome will proceed in a 5 to 3 direction and will extend the protein from its n terminus toward its c terminus for example in a typical gene a start codon 5 atg 3 is a dna sequence within the sense strand transcription begins at an upstream site relative to the sense strand and as it proceeds through the region it copies the 3 tac 5 from the template strand to produce 5 aug 3 within a messenger rna mrna the mrna is scanned by the ribosome from the 5 end where the start codon directs the incorporation of a methionine bacteria mitochondria and plastids use n formylmethionine instead at the n terminus of the protein by convention single strands of dna and rna sequences are written in a 5 to 3 direction except as needed to illustrate the pattern of base pairing 5 end edit in the dna segment shown the 5 to 3 directions are down the left strand and up the right strand the 5 end pronounced five prime end designates the end of the dna or rna strand that has the fifth carbon in the sugar ring of the deoxyribose or ribose at its terminus a phosphate group attached to the 5 end permits ligation of two nucleotides i e the covalent binding of a 5 phosphate to the 3 hydroxyl group of another nucleotide to form a phosphodiester bond removal of the 5 phosphate prevents ligation to prevent unwanted nucleic acid ligation e g self ligation of a plasmid vector in dna cloning molecular biologists commonly remove the 5 phosphate with a phosphatase the 5 end of nascent messenger rna is the site at which post transcriptional capping occurs a process which is vital to producing mature messenger rna capping increases the stability of the messenger rna while it undergoes translation providing resistance to the degradative effects of exonucleases 1 it consists of a methylated nucleotide methylguanosine attached to the messenger rna in a rare 5 to 5 triphosphate linkage the 5 flanking region of a gene often denotes a region of dna which is not transcribed into rna the 5 flanking region contains the gene promoter and may also contain enhancers or other protein binding sites the 5 untranslated region 5 utr is a region of a gene which is transcribed into mrna and is located at the 5 end of the mrna this region of an mrna may or may not be translated but is usually involved in the regulation of translation the 5 untranslated region is the portion of the dna starting from the cap site and extending to the base just before the aug translation initiation codon of the main coding sequence this region may have sequences such as the ribosome binding site and kozak sequence which determine the translation efficiency of the mrna or which may affect the stability of the mrna 3 end edit phosphodiester bonds circled between nucleotides the 3 end three prime end of a strand is so named due to it terminating at the hydroxyl 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 molecular biologists can use nucleotides that lack a 3 hydroxyl dideoxyribonucleotides to interrupt the replication of dna this technique is known as the dideoxy chain termination method or the sanger method and is used to determine the order of nucleotides in dna the 3 end of nascent messenger rna is the site of post transcriptional polyadenylation which attaches a chain of 50 to 250 adenosine residues to produce mature messenger rna this chain helps in determining how long the messenger rna lasts in the cell influencing how much protein is produced from it the 3 flanking region is a region of dna that is not copied into the mature mrna but which is present adjacent to 3 end of the gene it was originally thought that the 3 flanking dna was not transcribed at all but it was discovered to be transcribed into rna and quickly removed during processing of the primary transcript to form the mature mrna the 3 flanking region often contains sequences that affect the formation of the 3 end of the message it may also contain enhancers or other sites to which proteins may bind the 3 untranslated region 3 utr is a region of the dna which is transcribed into mrna and becomes the 3 end of the message but which does not contain protein coding sequence everything between the stop codon and the polya tail is considered to be 3 untranslated the 3 untranslated region may affect the translation efficiency of the mrna or the stability of the mrna it also has sequences which are required for the addition of the poly a tail to the message including the hexanucleotide aauaaa see also edit sense molecular biology further reading edit harvey lodish arnold berk paul matsudaira chris a kaiser 2004 molecular cell biology 5th ed new york city w h freeman and company isbn 978 0 7167 4366 8 gao m fritz dt ford lp wilusz j march 2000 interaction between a poly a specific ribonuclease and the 5 cap influences mrna deadenylation rates in vitro molecular cell 5 3 479 488 doi 10 1016 s1097 2765 00 80442 6 pmc 2811581 pmid 10882133 external links edit a molecular biology glossary retrieved from https en wikipedia org w index php title directionality_ molecular_biology oldid 1226252572 categories dna molecular genetics rna hidden categories articles with short description short description matches wikidata articles needing additional references from may 2023 all articles needing additional references this page was last edited on 29 may 2024 at 13 38 utc page was rendered with parsoid text is available under the creative commons attribution sharealike 4 0 license additional terms may apply by using this site you agree to the terms of use and privacy policy wikipedia is a registered trademark of the wikimedia foundation inc a non profit organization privacy policy about wikipedia disclaimers contact wikipedia legal safety contacts code of conduct developers statistics cookie statement mobile view search search toggle the table of contents directionality molecular biology 25 languages add topic