Editing Ribonucleotide (section)

==Structure==

===General structure===

[[File:AMP structure.svg|200px|thumbnail|class=skin-invert|Structure of adenosine 5'-monophosphate (AMP)]]
[[File:GMP chemical structure.png|200px|thumbnail|class=skin-invert|Structure of guanosine 5'-monophosphate (GMP)]]
[[File:Uridinmonophosphat protoniert.svg|200px|thumbnail|class=skin-invert|Structure of uridine 5'-monophosphate (UMP)]]
[[File:CMP chemical structure.png|200px|thumbnail|class=skin-invert|Structure of cytidine 5'-monophosphate (CMP)]]

The general structure of a ribonucleotide consists of a phosphate group, a ribose sugar group, and a nucleobase, in which the nucleobase can either be adenine, guanine, cytosine, or uracil. Without the phosphate group, the composition of the nucleobase and sugar is known as a nucleoside. The interchangeable nitrogenous nucleobases are derived from two parent compounds, purine and pyrimidine. Nucleotides are [[heterocyclic compounds]], that is, they contain at least two different chemical elements as members of its rings.{{citation needed|date=July 2024}}

Both RNA and DNA contain two major purine bases, adenine (A) and guanine (G), and two major pyrimidines. In both DNA and RNA, one of the pyrimidines is cytosine (C). However, DNA and RNA differ in the second major pyrimidine. DNA contains thymine (T) while RNA contains uracil (U). There are some rare cases where thymine does occur in RNA and uracil in DNA.<ref name=Nelson08 />

Here are the 4 major ribonucleotides (ribonucleoside 5'-monophosphate) which are the structural units of RNAs.
{| class="wikitable"
|-
! Nucleotide !! Symbols !! Nucleoside
|-
| Adenylate (adenosine 5'-monophosphate)  || A, AMP || Adenosine
|-
| Guanylate (guanosine 5'-monophosphate) || G, GMP || Guanosine
|-
| Uridylate (uridine 5'-monophosphate)  || U, UMP || Uridine
|-
| Cytidylate (cytidine 5'-monophosphate) || C, CMP || Cytidine
|}

===DNA deoxyribonucleotides versus RNA ribonucleotides===

In ribonucleotides, the sugar component is ribose while in deoxyribonucleotides, the sugar component is deoxyribose. Instead of a hydroxyl group at the second carbon in the ribose ring, it is replaced by a hydrogen atom.<ref>{{cite book |last1=Newsholme |first1=Eric A. |last2=Leech |first2=Anthony R. |last3=Board |first3=Mary |title=Functional biochemistry in health & disease: metabolic regulation in health and disease |year=2008 |publisher=Wiley |location=Hoboken, N.J. |isbn=978-0-471-98820-5 |edition=2nd}}</ref>

Both types of pentoses in DNA and RNA are in their β-furanose (closed five-membered ring) form and they define the identity of a nucleic acid. DNA is defined by containing 2'-deoxy-ribose nucleic acid while RNA is defined by containing ribose nucleic acid.<ref name=Nelson08 />

In some occasions, DNA and RNA may contain some minor bases. Methylated forms of the major bases are most common in DNA. In viral DNA, some bases may be hydroxymethylated or glucosylated. In RNA, minor or modified bases occur more frequently. Some examples include hypoxanthine, dihydrouracil, methylated forms of uracil, cytosine, and guanine, as well as modified nucleoside pseudouridine.<ref>{{cite book|last=Das|first=Debajyoti|title=Biochemistry|year=2010|publisher=Bimal Kumar Dhur of Academic Publishers}}</ref> Nucleotides with phosphate groups in positions other than on the 5' carbon have also been observed. Examples include ribonucleoside 2',3'-cyclic monophosphates which are isolatable intermediates, and ribonucleoside 3'-monophosphates which are end products of the hydrolysis of RNA by certain ribonucleases. Other variations include adenosine 3',5'-cyclic monophosphate (cAMP) and guanosine 3',5'-cyclic monophosphate (cGMP).<ref>{{cite book |last1=Cox |first1=Michael M. |last2=Nelson |first2=David L. |title=Principles of Biochemistry |year=2008 |publisher=W H Freeman |isbn=978-1-4292-2263-1 |oclc=216940502}}</ref>

===Linking successive nucleotides===

Ribonucleotides are linked together to form RNA strands via [[phosphodiester bonds]]. The 5'-phosphate group of one nucleotide is linked to the 3'-hydroxyl group of the next nucleotide, creating a backbone of alternating phosphate and pentose residues. There is no phosphodiester bond at each end of the polynucleotide.<ref>{{cite book |last=Raymond |first=Kenneth W. |title=General, organic, and biological chemistry: an integrated approach |year=2010 |publisher=Wiley |isbn=978-0-470-55124-0 |edition=3rd |oclc=699600111}}</ref> Phosphodiester bonds are formed between ribonucleotides by the enzyme [[RNA polymerase]]. The RNA chain is synthesized from the 5' end to the 3' end as the 3'-hydroxyl group of the last ribonucleotide in the chain acts as a nucleophile and launches a hydrophilic attack on the 5'-triphosphate of the incoming ribonucleotide, releasing pyrophosphate as a by-<ref>{{cite book |editor1-first=Moselio |editor1-last=Schaechter |editor2-first=Joshua |editor2-last=Lederberg |title=The Desk Encyclopedia of Microbiology |year=2004 |publisher=Elsevier |location=Amsterdam |isbn=0-12-621361-5 |edition=1st |oclc=1055874153}}</ref> product. Due to the physical properties of the nucleotides, the backbone of RNA is very hydrophilic and polar. At neutral pH, nucleic acids are highly charged as each phosphate group carries a negative charge.<ref>{{cite book |last1=Turner |first1=Phil |last2=McLennan |first2=Alexander |last3=Bates |first3=Andy |last4=White |first4=Mike |display-authors=1 |title=Molecular Biology |series=Instant Notes |year=2005 |publisher=CRC, Taylor & Francis |isbn=0-415-35167-7 |edition=3rd |oclc=61745541}}</ref>

Both DNA and RNA are built from nucleoside phosphates, also known as mononucleotide monomers, which are thermodynamically less likely to combine than amino acids. Phosphodiester bonds, when hydrolyzed, release a considerable amount of free energy. Therefore, nucleic acids tend to spontaneously hydrolyze into mononucleotides. The precursors for RNA are GTP, CTP, UTP and ATP, which is a major source of energy in group-transfer reactions.<ref>{{cite book|last=Nelson|first=David|title=Lehninger Principles of Biochemistry|year=2008|publisher=W H Freeman and Co|pages=274–275}}</ref>