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.
Proteins
Large molecules are called macromolecules. There are four important macromolecules that make up living organisms. Proteins are large macromolecules that are made of long chains of individual molecules called amino acids. These are formed from different combinations of twenty amino acids, each identified by a letter. Proteins are used in building structures and regulating functions in the body. Carbohydrates are giant molecules made by linking together sugar monomers (smaller molecules that are chemically similar e.g. monosaccharides) to form polysaccharides (polymers). These provide the energy for life. Lipids (also called fat) are large structures formed from a limited set of smaller monomers, formed by nonpolar covalent bonds and therefore insoluble in water. These are used to store energy in living organisms. Finally, Nucleic acids are formed from four kinds of nucleotide monomers linked together in long chains. This is used to store genetic information.
There are a combination of atoms in many of the macromolecules of life. These are called functional groups which are certain chemical groups (set of atoms) in monomers whose properties affect how macromolecules function and interact with each other e.g. polarity of hydroxyl group (-OH) bonds helps dissolve substances in water by linking to other molecules (Sadava et al., 2009, p. 40). Proteins are made of of different amounts and sequences of amino acids. These are monomers that are the building block of proteins. It contains two functional groups – carboxyl (-COOH) and amine (-NH2) – attached to the same carbon atom. Also attached is a hydogen atom and a side chain called R group.
Here is a link to the various amino acids from MilliporeSigma, a Life Sciences company (MilliporeSigma – Amino Acids Reference Charts., n.d.). Each of the twenty Amino acids is assigned an alphabet. Polypeptide chains are an unbranched (linear) polymer of covalently linked (called peptide linkages or peptide bonds) amino acids in a precise sequence. Proteins are made of one or more of these polypeptide chains. These chains give a three-dimensional structure for the proteins. These chains have a beginning and an end. It begins with a N terminus which is the starting amino acid and ends with C terminus which is the ending amino acid. Amino acids polymerize to form proteins when the corboxyl functional group of one amino acid reacts with the amino functional group of another amino acid forming a peptide linkage or bond.
Atom > Molecule > Functional Group, R Group > Amino Acid > Polypeptide chain > Protein
Parts that make up proteins
There are different types of proteins. Enzymes are catalytic proteins that speed up biochemical reactions. Defensive proteins are antibodies that recognize and respond to non-self-organisms invading the body. Hormonal and Regulatory proteins control physiological processes such as insulin that regulate sugar. Receptor proteins receive and respond to molecular signals from inside and outside the organism. Storage proteins store chemical building blocks – amino acids – for later use. Structural proteins provide physical stability and movement like collagen. Transport proteins carry substances within the organisms like hemoglobin. Genetic regulatory proteins regulate when, how, and to what extent a gene is expressed (cell reads the instructions in gene to make proteins). Chaperone proteins are proteins that protect other newly formed proteins from their shapes being wrongly shaped due to environment. Cancer cells use chaperone proteins to protect new cancer causing proteins so new drugs called HSP (heat shock proteins) – inhibiting drugs were used to fight it (Sadava et al., 2009, p. 49).
Proteins have four levels of structures of amino acid polypeptide chains that make the shape of the protein. The shape and surface chemistry of the protein contribute to protein function. These structures are called primary, secondary, tertiary and quaternary structures. Secondary structures are formed when the polypeptide chain forms helixes or pleated sheets due to hydrogen bonds. Tertiary structure are formed from the secondary structures causing folds due to various interactions like ionic bonds, hydrogen bonds, van der Waals forces, hydrophobic side chains and disulfide bridges (a type of covalent bond). Quarternary structure occurs when the tertiary structures of multiple polypeptides join to form a larger molecule. Proteins can be denatured – lose their secondary, tertiary or quaternary structure due to increase in temperature, changes in pH, high concentration of polar substances or non polar substances. Denaturization is reversible as long as the primary structure is not affected. e.g. boiling egg denatures proteins including primary structure so it is not reversible.
One way to test for the presence of protein is by using biuret reagent, which contains copper ions. This reagent turns dark purple when the copper ions react with the nitrogen atoms in the covalent peptide bonds of the protein. The intensity of the color depends on the number of peptide bonds. Here is an interesting video of the biuret reagent being used to identify proteins in multiple test samples here.
Part 2 of this article talks about carbohydrates, lipids and nucleic acids, the other macromolecules that are important to life.
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 Research, 28: 235-242. doi:10.1093/nar/28.1.235
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