Editing Polymer backbone (section)

==Biopolymers==
Major families of biopolymers are [[polysaccharide]]s (carbohydrates), [[peptide]]s, and [[polynucleotide]]s.  Many variants of each are known.<ref name=Voet16>{{cite book |first1=Donald |last1=Voet |first2=Judith G. |last2=Voet |first3=Charlotte W. |last3=Pratt |title=Fundamentals of Biochemistry: Life at the Molecular Level |url=https://books.google.com/books?id=9T7hCgAAQBAJ |date=2016 |publisher=Wiley |edition=5th |isbn=978-1-118-91840-1}}V</ref>

===Proteins and peptides===
Proteins are characterized by [[Peptide bond|amide linkages]] (-N(H)-C(O)-) formed by the condensation of [[amino acid]]s. The sequence of the amino acids in the polypeptide backbone is known as the [[Protein primary structure|primary structure]] of the protein. Like almost all polymers, protein fold and twist, forming into the [[Protein secondary structure|secondary structure]], which is rigidified by [[hydrogen bonding]] between the [[Carbonyl group|carbonyl]] oxygens and amide hydrogens in the backbone, i.e. C=O---HN. Further interactions between residues of the individual amino acids form the protein's [[Protein tertiary structure|tertiary structure]]. For this reason, the primary structure of the amino acids in the polypeptide backbone is the map of the final structure of a protein, and it therefore indicates its biological function.<ref>{{cite book |vauthors=Berg JM, Tymoczko JL, Stryer L |chapter=3.2 Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains |chapter-url=https://www.ncbi.nlm.nih.gov/books/NBK22364/ |id=NBK22364 |title=Biochemistry |publisher=W.H. Freeman |edition=5th |year=2002 |isbn=0-7167-3051-0 |url=https://www.ncbi.nlm.nih.gov/books/NBK21154/}}</ref><ref name=Voet16 /> Spatial positions of backbone atoms can be reconstructed from the positions of alpha carbons using computational tools for the backbone reconstruction.<ref>{{Cite journal|last=Badaczewska-Dawid|first=Aleksandra E.|last2=Kolinski|first2=Andrzej|last3=Kmiecik|first3=Sebastian|title=Computational reconstruction of atomistic protein structures from coarse-grained models|journal=Computational and Structural Biotechnology Journal|volume=18|pages=162–176|doi=10.1016/j.csbj.2019.12.007|pmid=31969975|pmc=6961067|issn=2001-0370|year=2020}}</ref>
[[File:Sucrose condensation.svg|thumb|A simplified example of condensation showing the ''alpha'' and ''beta'' classification. [[Glucose]] and [[fructose]] form [[sucrose]]. The synthesis of glycogen in the body is driven by the enzyme [[glycogen synthase]] which uses a [[uridine diphosphate]] (UDP) leaving group.]]

=== Carbohydrates ===
Carbohydrates arise by condensation of [[monosaccharide]]s such as [[glucose]]. The polymers can be classified into [[oligosaccharide]]s (up to 10 residues) and [[polysaccharide]]s (up to about 50,000 residues). The backbone chain is characterized by an ether bond between individual monosaccharides.  This bond is called the [[Glycosidic bond|glycosidic linkage]].<ref>{{Cite journal|last=Buschiazzo|first=Alejandro|year=2004|title=Crystal structure of glycogen synthase: homologous enzymes catalyze glycogen synthesis and degradation|journal=The EMBO Journal |volume=23|issue=16|pages=3196–3205|doi=10.1038/sj.emboj.7600324|pmc=514502|pmid=15272305}}</ref> These backbone chains can be unbranched (containing one linear chain) or branched (containing multiple chains). The glycosidic linkages are designated as [[Anomer|''alpha'' or ''beta'']] depending on the relative [[stereochemistry]] of the [[anomer]]ic (or most [[oxidized]]) carbon. In a [[Fischer projection|Fischer Projection]], if the glycosidic linkage is on the same side or face as carbon 6 of a common biological saccharide, the carbohydrate is designated as ''beta'' and if the linkage is on the opposite side it is designated as ''alpha''. In a traditional "[[Cyclohexane conformation|chair structure]]" projection, if the linkage is on the same plane (equatorial or axial) as carbon 6 it is designated as ''beta'' and on the opposite plane it is designated as ''alpha''. This is exemplified in [[sucrose]] (table sugar) which contains a linkage that is ''alpha'' to glucose and ''beta'' to [[fructose]]. Generally, carbohydrates which our bodies break down are ''alpha''-linked [[Glycogen|(example: glycogen)]] and those which have structural function are ''beta''-linked (example: [[cellulose]]).<ref name=Voet16 /><ref>{{cite book |vauthors=Bertozzi CR, Rabuka D |chapter=Structural Basis of Glycan Diversity |chapter-url=https://www.ncbi.nlm.nih.gov/books/NBK1955/ |veditors=Varki A, Cummings RD, Esko JD, et al |title=Essentials of Glycobiology |publisher=Cold Spring Harbor Laboratory Press |year=2009 |isbn=9780879697709 |edition=2nd |url=https://www.ncbi.nlm.nih.gov/books/NBK1908/ |pmid=20301274}}</ref>

=== Nucleic acids ===
[[File:DNA condensation.svg|thumb|Condensation of [[adenine]] and [[guanine]] forming a [[phosphodiester bond]], the [[Nucleoside triphosphate|triphosphorylated ribose]] of the incoming nucleotide is attacked by the 3' [[Hydroxy group|hydroxyl]] of the polymer, releasing [[pyrophosphate]].]]
[[Deoxyribonucleic acid]] (DNA) and [[RiboNucleic Acid|ribonucleic acid]] (RNA) are the main examples of [[polynucleotide]]s. They arise by condensation of nucleotides. Their backbones form by the condensation of a hydroxy group on a [[ribose]] with the [[phosphate]] group on another ribose. This linkage is called a [[phosphodiester bond]]. The condensation is catalyzed by [[enzyme]]s called [[polymerase]]s. DNA and RNA can be millions of nucleotides long thus allowing for the [[genetic diversity]] of life. The bases project from the pentose-phosphate polymer backbone and are [[hydrogen bond]]ed in pairs to their [[Complementary nucleotide|complementary]] partners (A with T and G with C). This creates a [[Nucleic acid double helix|double helix]] with pentose phosphate backbones on either side, thus forming a [[Protein secondary structure|secondary structure]].<ref>{{cite book |vauthors=Alberts B, Johnson A, Lewis J, et al |chapter=DNA Replication Mechanisms |chapter-url=https://www.ncbi.nlm.nih.gov/books/NBK26850/ |id=NBK26850 |title=Molecular Biology of the Cell |publisher=Garland Science |edition=4th |year=2002 |isbn=0-8153-3218-1 |url=https://www.ncbi.nlm.nih.gov/books/NBK21054/}}</ref><ref name=Voet16 /><ref>{{cite book |vauthors=Lodish H, Berk A, Zipursky SL, et al |chapter=4.1, Structure of Nucleic Acids |chapter-url=https://www.ncbi.nlm.nih.gov/books/NBK21514/ |title=Molecular Cell Biology |publisher=W.H. Freeman |edition=4th |year=2000 |isbn=0-7167-3136-3 |url=https://www.ncbi.nlm.nih.gov/books/NBK21475/ |id=NBK21514}}</ref>