These are some of my notes as I read and study about the underlying biochemical interactions associated with genetics and living organisms. The reference section has the list of books that I’ve read.
All living organisms are made of atoms. Atoms consist of a positively charged nucleus with negatively charged electrons going around it. The nucleus consists of positively charged protons and neutrons which are electrically neutral. An element consist of only kind of atom. Each element has an atom made of different number of protons, the number is the atomic weight of the element. The elements are listed in periodic table here. An isotope of an element contains a different number of neutrons but the same number of protons. Every living organism is mostly made up of the following elements – Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus and Sulphur, though other elements are also important to life – Sodium, Potassium, Calcium, Magnesium etc (Sadava et al., 2009, p. 22).
The number of electrons in an atom determines how the element will combine with other atoms to form stable associations called molecules. Electrons move around the nucleus in regions called electron shells. There are different levels of electron shells. The first shell can only contain 2 electrons. Once this shell is filled, the next shell can take up to 8 electrons. Once the second shell is filled, additional shells can also take up to 8 electrons. This is called the octet rule. Atoms with partially filled outer shells are more capable of combining with other atoms compared to atoms with fully filled outer shells which are stable. Atoms with partially filled outer shells, called valence shell, form bonds with other atoms by exchanging or sharing electrons called valence electrons to cause stability. This leads to forming molecules. An ion is an electrically charged particle as atoms in it loses or gains electron. A cation is an ion that has lesser number of electrons than protons causing a positive electrical charge whereas an anion is an ion that has more number of electron than protons causing a negative electrical charge.
Chemical bonds are attractive forces that joins two atoms in a molecule. A compound is a molecule made of linked atoms of different elements. Isomers are molecules with the same chemical compositions but their atoms are arranged differently. There are different chemical bonds – covalent bond, ionic bond, hydrogen bond and van der Vaal bond. A covalent bond forms when two atoms share one or more electrons such that both atoms attain a stable number of electrons in their outer shells. Covalent bonds are very strong. The sharing may not be equal. If the one of the atoms has a larger nucleus than the other, it will pull the shared electrons towards it. This attractive force is called electronegativity. Higher electronegativity leads to polar covalent bonds (e.g. H2O – water). Atoms in a molecule with similar electronegativity create nonpolar covalent bonds. Ionic bonds are formed when one or more electrons are transferred from one atom to another atom which has a much larger electronegativity. Both atoms become ions with the atom that loses the electron becoming a positively charged cation (e.g. Na – Sodium in NaCl) and the atom that gains the electron becoming a negatively charged anion (e.g. Cl – Chlorine in NaCl). Hydrogen bonds are formed between a negatively charged oxygen atom in one water molecule with a positively charged hydrogen atom in another water molecule. This type of bond is weaker that covalent and ionic bonds and this bond is created and broken many times between different water molecules. This bond gives water its unique properties like its cohesive strength, surface tension, the ability to store heat, the ability to dissolve many substances etc (Sadava et al., 2009, p. 31). Hydrogen bonds can also occur between non water molecules. The van der Vaals force is a weak bond created between nonpolar molecules that are in close to each other due to random variations in the electron distribution in the molecules. Though its the weakest among the 4 bonds, the sum of all interactions in a van der Vaal force tends to create a substantial attraction. This helps in making nonpolar molecules stick together in a polar environment inside organisms (Sadava et al., 2009, p. 30).
Polar water molecules can also interact with other polar molecules through hydrogen bonds. These polar molecules are hydrophilic or water loving. Nonpolar molecules tend to aggregate with other nonpolar molecules rather than polar water molecules through van der Vaal forces. These nonpolar molecules are hydrophobic or water hating. The hydrophilic molecules are responsible for certain molecules (solute) to be soluble in water (solvent) to produce a solution. Most important biological molecules are soluble in water (Sadava et al., 2009, p. 32). When some substances dissolve in water, hydrogen ions are released. These hydrogen ions attach to other molecules and change their properties. The amount of hydrogen ions in solution is measured using the pH scale. If the amount of hydrogen ions is increased above a certain limit, the solution becomes acidic. If the concentration of hydrogen ions is decreased below a certain limit, then the solution becomes alkaline or basic. Substances that fully dissolve and ionize in water are strong acids or strong bases. These reactions are not reversible. Substances that do not fully dissolve or ionize in water are weak acids or weak bases. These reactions are reversible. Water is a weak acid and a weak base because of its tendency to ionize into a hydrogen cation and hydroxide anion. All living things strive to maintain internal consistency called homeostatis (Sadava et al., 2009, p. 34). This includes maintaining the pH level with the use of buffers, which are a weak acid and a weak base. A chemical reaction happens when moving atoms collide with enough energy to combine or change the bonding pattern. The atoms or molecules that combine are called reactants and result is called the product, which could be either energy or another type of atom or molecule.
In 1897, J. J. Thomson, a British physicist discovered electrons while running experiments using cathode ray tubes (October 1897: The Discovery of the Electron, 2000). He was awarded the Nobel Prize in Physics in 1906. Here is a video of the modern version of the experiment. In 1911, one of J. J. Thomson’s students, Ernest Rutherford discovered protons while running his famous gold foil experiment (This Month in Physics History, 2006). Ernest Rutherford later won the Nobel Prize in Chemistry in 1908. A video of the recreation of the experiment is here. Through experiments by F. W. Aston with an improved mass spectrometer in 1920, he identified isotopes of different elements for which he was awarded the Nobel Prize in Chemistry in 1922 (Bauer, S. H., 2001). Here is a video of a modern mass spectrometer being used. French biologist and Chemist Louis Pasteur, more famous for the discovery of the causes and prevention of diseases, observed optical isomers of tartaic acid using polarised light (Everts, 2020). Here is a modern day re-enactment of the experiment using a polarimeter.
Sadava, D. E., Hillis, D. M., Heller, C. H., & Berenbaum, M. (2009). Small Molecules and the Chemistry of Life. In Life: The Science of Biology, 9th Edition (Ninth ed., pp. 21–35). W. H. Freeman.
Royal Society of Chemistry – Periodic Table. (n.d.). https://www.rsc.org. https://www.rsc.org/periodic-table
October 1897: The Discovery of the Electron. (2000). American Physical Society. https://www.aps.org/publications/apsnews/200010/history.cfm
This Month in Physics History. (2006). American Physical Society. https://www.aps.org/publications/apsnews/200605/history.cfm|
Bauer, S. H. (2001) Mass spectrometry in the mid-1930’s: were chemists intrigued?, Journal of the American Society for Mass Spectrometry, Volume 12, Issue 9 http://www.sciencedirect.com/science/article/pii/S1044030501002860
Everts, S. (2020, September 30). A Chiral Anniversary And Other Discoveries In Wine Science. Chemical & Engineering News. https://cen.acs.org/articles/91/i40/Chiral-Anniversary-Discoveries-Wine-Science.html