Macromolecules of Life (Part 2)

Continuing with my notes as I read and study about the underlying biochemical interactions associated with genetics and living organisms. This post focuses on large molecules that are important to life. The reference section has the list of books that I’ve read. Part two contains notes on carbohydrates, lipids and nucleic acids.

Carbohydrates

Carbohydrates have a series of carbon atoms bonded with hydrogen atoms, either an aldehyde (CHO) or ketone (COC) functional group and hydroxyl (OH) functional groups.  They are a source of stored energy, are used to transport the stored energy and serve as carbon skeletons (a pattern in which carbon atoms are bonded together in a molecule) that be re-arranged into new molecules.  there are four main categories of carbohydrates – monosaccharides or simple sugars (e.g. glucose), disaccharides – consists of two monosaccharides linked by covalent bonds (sucrose is made from a glucose and fructose monosaccharides), oligosaccharides – made of three to twenty monosaccharides (they are covalently bonded to proteins and lipids on the outer cell surfaces as recognition signals e.g. blood groups) and polysaccharides – made of many monosaccharides (e.g. starch, cellulose).  The covalent bonding are formed through condensation reactions and are called glycosidic linkages.  Glucose (blood sugar) is used to transport energy which is used by cells as an energy source by releasing stored energy and producing water and carbon dioxide (Sadava et al., 2009, p. 50).  Glucose can be straight form or in ring form but the ring form is more common since its stable.  Pentoses are 5 carbon sugars (e.g. ribose and deoxyribose forms the backbones of RNA and DNA molecules). 

Atom > Molecule > Functional Group > Monosaccharide > Disaccharide, Oligosaccharide, Polysaccharide

Parts that make up carbohydrates

Carbohydrates can be chemically modified by adding functional groups which are important intermediates in cellular energy reactions.  (e.g. sugar phosphates made by modifying glucose with a phosphate group).  When amino acids are used to modify carbohydrates, amino sugars are formed like glucosamine.  These are important in extracellular matrix where they form parts of glycoproteins which help keeping tissues together. 

Simple sugars i.e. monosaccharides and disaccharides, can be detected using Benedict’s reagent. The color of the solution changes to orange red as the electrons in the sugars bind with the copper ions in the reagent, causing the reddish color. The intensity of the color will depend on the amount of sugar in the solution. Here is an interesting set of videos (before boiling and after boiling) that show this reaction. Some polysaccharides like starch can be detected using Lugol’s solution as they don’t react well with Benedict’s reagent. Lugol’s solution contains iodine which reacts with the starch molecules changing its color from brown to purple. You can watch a video of the experiment here.

Lipids

Lipids are also called fats or triglycerides.  These are insoluble in water due to their nonpolar covalent bonds.  when these nonpolar hydrocarbons are close enough, weak but additive van der Waals forces hold them together.  When triglycerides are solid, they are called fats, when they are liquid, they are called oils. 

Some example of the types of lipids are as follows:

  • Fats and oil store energy.
  • Phospolipids have structural roles in cell membranes .
  • Carotenoids and chlorophylls help in capturing light energy. A type of carotenoids in humans is used to make a pigment called cis-retinal, which is needed for vision.
  • Steroids have regulatory roles as hormones and vitamins.  Hormones are chemical signals carrying messages from one part of the body to another.  Vitamins are not synthesized by the body and has to be acquired by diet.
  • Waxes – sheen on human hair repels water and keeps the hair pliable. 

Triglycerides are composed of two types of molecules – one molecule of Glycerol, a molecule with 3 hydoxyl (-OH) groups and 3 molecules of fatty acids, a long nonpolar hydrocarbon chain with a polar carboxl group (-COOH) whose structure is formed through ester linkages.  Saturated fatty acids, e.g. animals fats have many long chain saturated fatty acids packed tightly together like a straight chain due to single bonds between carbon (C) atoms.  They are solids at room temperature and have high melting point.  Plant fats are unsaturated fatty acids as there are kinks in the chains due to double bonds between some of the C atoms.  These fats are usually liquid at room temperature and has a low melting point. 

Lipids are amphipathic where one end of the molecule is hydophilic while the other end is hydrophobic.  This prevents oil from mixing with water by aggregating.  Phospolipids are lipids where phospate containing compounds replace one of the fatty acids.  The phospate end is hydophilic while the two fatty acids are hydrophobic.  This forms a bilayer which prevents water from the center and is used as biological membranes. 

Nucleic acids

Nucleic acids are macromolecules that are used in the storage and transport of genetic information.  DNA or Deoxyribonucleic acid is a type of nucleic acid that contains genetic information and is passed from generation to generation. RNA or Ribonucleic acid is a nucleic acid that acts as an intermediary to create proteins from the genetic info stored in DNA.

References

Sadava, D. E., Hillis, D. M., Heller, C. H., & Berenbaum, M. (2009). Proteins, Carbohydrates and Lipids. In Life: The Science of Biology, 9th Edition (Ninth ed., pp. 39–57). W. H. Freeman.

Sadava, D. E., Hillis, D. M., Heller, C. H., & Berenbaum, M. (2009). Nucleic Acids and the Origin of Life. In Life: The Science of Biology, 9th Edition (Ninth ed., pp. 61–73). W. H. Freeman.

MilliporeSigma – Amino Acids Reference Charts. (n.d.). https://www.sigmaaldrich.com. https://www.sigmaaldrich.com/life-science/metabolomics/learning-center/amino-acid-reference-chart.html

ChemAxon (2020). MarvinSketch v 20.21 [Computer Software]. https://chemaxon.com/products/marvin

Pettersen, E. F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., Ferrin, T.E. UCSF Chimera–a visualization system for exploratory research and analysis. J Comput Chem. 2004 Oct; 25(13):1605-12.

The Protein Data Bank H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne (2000) Nucleic Acids Research28: 235-242. doi:10.1093/nar/28.1.235

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