Backbone chain

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IUPAC definition

Main chain
Backbone
That linear chain to which all other chains, long or short or both,
may be regarded as being pendant.

Note: Where two or more chains could equally be considered to be the
main chain, that one is selected which leads to the simplest representation
of the molecule.[1]

In polymer science, the backbone chain of a polymer is the longest series of covalently bonded atoms that together create the continuous chain of the molecule. This science is subdivided into the study of organic polymers which consist of a carbon backbone and inorganic polymers which have backbones containing only main group elements.

An example of a biological backbone (polypeptide)

In biochemistry, organic backbone chains make up the primary structure of macromolecules. Biological macromolecules have a central chain of covalently bonded atoms which forms a backbone. This backbone forms the primary sequence thus directing folding and the nature of their complex structure. The backbone is therefore directly related to biological molecules’ function. The macromolecules within the body can be divided into four main subcategories, each of which are involved in very different and important biological processes: Proteins, Carbohydrates, Lipids, and Nucleic acids.[2] Each of these molecules has a different backbone which is initially the driving factor of their different structure and function in the body.

Character of the backbone[edit]

Polymer Chemistry:

In a way the character of the backbone chain depends on the type of polymerization: in step-growth polymerization the monomer moiety becomes the backbone, and thus the backbone is typically functional, like in polythiophenes or low band gap polymers in organic semiconductors.[3] In chain-growth polymerization, typically applied for alkenes, the backbone is not functional, but is bearing the functional side chains or pendant groups.

The character of the backbone, i.e. its flexibility, determines the thermal properties of the polymer (such as the glass transition temperature), e.g. in polisiloxanes the backbone chain is very flexible, resultin in very low glass transition temperature of -123 °C.[4] The polymers with a rigid backbone are prone to crystallization (e.g. polythiophenes) in thin films and in solution. Crystallization in its turn affects the optical properties of the polymers, its optical band gap and electronic levels.[5]

Biochemistry:

The character of the backbone chain is different for each of the four different macromolecular classes.

Proteins: In proteins (or polypeptides), the backbone is formed by the polymerization between amino and carboxylic acid groups inherent at the head of each of the twenty amino acids. Each amino acid is connected to the next by a bond between the carbonyl carbon and the amine nitrogen forming an amide. The arrangement or sequence of the amino acids in the backbone forms the primary structure of the protein. This primary structure is the basis for the secondary, tertiary, and quaternary structures of proteins. The entire function of a protein is relative to its primary amino acid sequence in the backbone. Because there are twenty amino acids and many proteins are thousands of amino acids long, there are seemingly endless possible sequences of amino acids in a polypeptide backbone.[2][6]

Carbohydrates: Carbohydrate backbones are formed by glycosidic linkages between individual monosaccharides. In this linkage, an ether is formed by the removal of water in a condensation reaction causing the monosaccharides to be covalently bonded to the same oxygen atom. These linkages can be designated as Alpha or Beta depending on their relative stereochemistry to their anomeric carbons. Anywhere from 2 to 50,000 monosaccharides can be bound in this manner.[2][7]

Lipids: The primary biological lipids which are connected by a backbone are triglycerides and glycerophospholipids. These lipids have fatty acid side chains which are connected to a glycerol backbone by an ester bond. This bond is formed by the removal of water in a condensation reaction between the carboxylic acid head of the fatty acid and one of the hydroxyl groups of the glycerol. Because of the structure of glycerol, these backbones are only 3 carbons long.[2]

Nucleic Acids: Nucleic acid backbones are connected by an ester bond between the 3’ carbon of the ribose sugar of one nucleotide and the phosphate group of the next. This backbone can be called a pentose-phosphate polymer. They are formed through the removal of water in a condensation reaction similar to that in the formation of a polypeptide backbone. Also similar to a polypeptide, the base of each nucleotide sticks out from the backbone and form a secondary structure.[8][9]

Overview of common backbones[edit]

In polymer chemistry:

A condensation reaction between two amino acids forming a polypeptide backbone

In Biology:

  • Proteins (polypeptides)

Proteins are important biological molecules and play an integral role in the structure and function of viruses, bacteria, and eukaryotic cells. Their backbone is characterized by amide linkage between the carbonyl group and amino group of successive amino acids. These amino acid sequences are translated from cellular mRNAs by ribosomes in the cytoplasm of the cell.[11] The ribosomes have enzymatic activity which directs the condensation reaction forming the amide linkage between each successive amino acid. The sequence of the amino acids in the polypeptide backbone is known as the primary structure of the protein. This primary structure leads to folding of the protein into the secondary structure formed by hydrogen bonding between the carbonyl oxygens and amine hydrogens in the backbone and tertiary structure formed by interactions between residues of the individual amino acids. 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 therefore indicates its biological function.[2]

The condensation of glucose and fructose to form sucrose.
triglyceride and glycerophospholipid (showing glycerol backbone)
  • Carbohydrates

Carbohydrates have many roles in the body including functioning as, structural units, enzyme cofactors and cell surface recognition sites but, their most prevalent role is as energy storage and delivery in cellular metabolic pathways. The most simple carbohydrates are single sugar residues like glucose, our body’s energy delivery molecule, called monosaccharides. Oligosaccharides (up to 10 residues) and polysaccharides (up to about 50,000 residues) consist of saccharide residues bonded in a backbone chain which is characterized by an ether bond known as a glycosidic linkage. These backbone chains can be unbranched (containing one linear chain) or branched (containing multiple chains). The glycosidic linkages are designated as Alpha or Beta depending on their stereochemistry relative to their anomeric (or most oxidized) carbon. If the linkage is on the same side as the saccharide anomeric carbon it is designated as Beta and if it is on the opposite side 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 (example: glycogen) and those which have structural function are beta-linked (example: cellulose).[2][7]

  • Lipids

Energy in the body that is not used or converted to glycogen is converted to fat in the form of triglycerides and stored in adipose tissue. Triglycerides have a lot of oxidizable carbon to carbon bonds making them excellent energy storage devices. They consist of three fatty acids connected by an ester bond to a glycerol backbone. Glycerophospholipids are amphipathic molecules that make up cell membranes. They consist of two fatty acids and a phosphate group bonded to a glycerol backbone. Because the fatty acid “tails” are hydrophobic and the phosphate “heads” are hydrophilic, glycerophospholipids create a phospholipid bilayer which separates the cell’s internal environment from its external environment.[2][12]

  • Nucleic Acids
Condensation of Adenine and Guanine forming a phosphodiester bond, the basis of the nucleic acid backbone.

Nucleic acids DNA and RNA are of great importance because they code for the production of all cellular proteins. They are made up of monomers called nucleotides which consist of an organic base: A, G, C and T or U, a pentose sugar, and a phosphate group. They have a backbone in which the 3’ carbon of the ribose sugar is connected to the phosphate group via a phosphodiester bond. This bond is formed through the elimination of water in a condensation reaction with the help of a class of cellular enzymes called polymerases. The sequence of bases in the backbone is also known as the primary structure. Nucleic acids can be hundreds of millions of nucleotides long thus leading to the genetic diversity of life. The bases stick out from the pentose-phosphate polymer backbone in DNA and are hydrogen bonded in pairs to their complementary partner (A with T and G with C) creating a double helix with pentose phosphate backbones on either side thus forming a secondary structure.[2][9]

References[edit]

  1. ^ "Glossary of basic terms in polymer science (IUPAC Recommendations 1996)" (PDF). Pure and Applied Chemistry. 68 (12): 2287–2311. 1996. doi:10.1351/pac199668122287. 
  2. ^ a b c d e f g h Voet, Donald, Judith G. Voet, and Charlotte W. Pratt. Fundamentals of Biochemistry: Life at the Molecular Level. 5th ed. Hoboken, NJ: Wiley, 2008. Print
  3. ^ Budgaard, Eva; Krebs, Frederik (2006). "Low band gap polymers for organic photovoltaics". Solar Energy Materials and Solar Cells. 91 (11): 954–985. 
  4. ^ Polymers
  5. ^ Brabec, C.J.; Winder, C.; Scharber, M.C; Sarıçiftçi, S.N.; Hummelen, J.C.; Svensson, M.; Andersson, M.R. (2001). "Influence of disorder on the photoinduced excitations in phenyl substituted polythiophenes". J. Chem. Phys. 115: 7235. doi:10.1063/1.1404984. 
  6. ^ "Biochemistry. 5th edition.Section 3.2 Primary Structure: Amino Acids Are Linked by Peptide Bonds to Form Polypeptide Chains". NCBI Bookshelf. Retrieved 10 September 2015. 
  7. ^ a b Bertozzi CR, Rabuka D. Structural Basis of Glycan Diversity. In: Varki A, Cummings RD, Esko JD, et al., editors. Essentials of Glycobiology. 2nd edition. Cold Spring Harbor (NY): Cold Spring Harbor Laboratory Press; 2009. Chapter 2. Available from: https://www.ncbi.nlm.nih.gov/books/NBK1955/
  8. ^ "Definition: Phosphate Backbone." Nature.com. Macmillan Publishers, 2014. Web. http://www.nature.com/scitable/definition/phosphate-backbone-273
  9. ^ a b Lodish H, Berk A, Zipursky SL, et al. Molecular Cell Biology. 4th edition. New York: W. H. Freeman; 2000. Section 4.1, Structure of Nucleic Acids. Available from: https://www.ncbi.nlm.nih.gov/books/NBK21514/
  10. ^ Hirsch, Andreas (1993). "Fullerene polymers". Advanced Materials. 5 (11): 859–861. doi:10.1002/adma.19930051116. 
  11. ^ Noller HF. 2017 The parable of the caveman and the Ferrari: protein synthesis and the RNA world. Phil. Trans. R. Soc. B 372: 20160187. http://dx.doi.org/10.1098/rstb.2016.0187
  12. ^ Cox RA, García-Palmieri MR. Cholesterol, Triglycerides, and Associated Lipoproteins. In: Walker HK, Hall WD, Hurst JW, editors. Clinical Methods: The History, Physical, and Laboratory Examinations. 3rd edition. Boston: Butterworths; 1990. Chapter 31. Available from: https://www.ncbi.nlm.nih.gov/books/NBK351/

See also[edit]