Elements and Molecular Interactions: Relevance to Biology
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Matter is made up of atoms. Atoms are composed of a nucleus (i.e. made of protons and neutrons) and one or more electrons. The nucleus is "postively" charged, while electrons are "negatively" charged. A neutron is made of an electron and a proton. A proton is made up of at least three quarks. Electrons are extremely small particles -- their mass is on the order of 10^-27 grams (note: the symbol ^ is used to represent an exponent, thus 10^-27 means 10 to the exponent -27). Protons are larger than electrons and their mass is 10^-23 grams. Neutrons are about the same mass as protons, since they are made of a proton and electron (the contribution by the electron to the overall mass is relatively insignificant). The elements that life is primarily made up of are: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), and Phosphorus (P). Many other elements can be found in trace amounts in most organisms (e.g. metals), but the five mentioned above are the ones we will focus on here. Atoms form molecules by various interactions and bonding: covalent bonds, ionic bonds, Hydrogen bonds, hydrophobic interactions and van der Waals forces. The strength of these bonds is measured in kCal/mol: Strong Bonds: Covalent bonds are strong bonds (50 to 110 kCal/mol) between two atoms, in which one pair of electrons are shared. A double covalent bond is one where two pairs of electrons are shared. Covalent bonds are the bonds that keep atoms together in organic molecules. Carbon can form up to four covalent bonds; Nitrogen, three; Oxygen, two; and Hydrogen only one. Some examples: C-C, C=C, C-H, C-O, C=O, O-H. Weak Bonds: Ionic bonds are much weaker bonds (5 kCal/mol) than covalent bonds, and are formed when one atom gives up an electron to the other. An ion is atom that has either lost or gained at least one electron. Table Salt (or sodium chloride) when dissolved in water forms ions -- i.e. sodium ions (Na+) and chloride ions (Cl-). Hydrogen bonds are also weak bonds (4 to 5 kCal/mol). A hydrogen bond forms when a molecule that has a hydrogen atom is attracted to another atom (e.g. an oxygen atom is typical) on an adjacent molecule. The two atoms have to be very close for weak bonds to take effect. There are also Hydrophobic Interactions (3 kCal/mol), which occur when non-polar molecules (such as lipids or fat) are excluded by polar molecules such as H2O (water). "Polar" means that the molecule (as a whole) has some uneven distribution of electrons -- the molecule then, is said to have a "dipole" (i.e. "two-poles"). As a result, the molecule is more negatively charged on one side and in effect, the molecule is "polar". An analogy would be the Earth -- it has a North and South pole. Water molecules form Hydrogen bonds with other water molecules (since water molecules are polar and they are made up of Hydrogen and Oxygen), which overcomes and therefore excludes non-polar molecules from the polar molecules. Fats and oils are non-polar molecules that form little globs called "micelles" in water. You may have seen this in chicken soup, where you have little globs of fats on the liquid surface. This is a result of Hydrophobic Interactions. And finally, there are van der Waals forces (less than 1 kCal/mol) of which there are two types: dipole-dipole interactions, and London Dispersion. Remember that polar molecules have an uneven electron distribution, therefore uncharged polar molecules can form dipole-dipole interactions. Nonpolar molecules are molecules that have a relatively even electron distribution. For example, if the molecule is symmetrical, it has the same types of atoms on either side, and so there is no dipole (e.g. any polarity between atoms of the molecule are cancelled out). Nonpolar molecules can, however, become temporarily "polar" due to electron movements within the covalent bonds -- a dipole is induced (this is called the London Dispersion). This asymmetrical electron distribution allows nonpolar molecules to line-up with one another. To clarify "polar" and "nonpolar" molecules, think about just two atoms joined by a covalent bond. Both atoms could be identical (e.g. both could be Hydrogen atoms), in which case the covalent bond would be nonpolar. The two atoms could be different, say one Hydrogen atom and one Carbon atom. In this case, this is still a nonpolar covalent bond. Now, imagine that you have one Hydrogen atom covalently bonded to an oxygen atom. This is a polar covalent bond. So, polarity has to do with several properties the molecule, which include at least the presence of a polar covalent bond and asymmetry. Different atoms can form different numbers of covalent bonds. Hydrogen can form only one covalent bond, oxygen forms two, nitrogen forms three, and carbon forms four. So for example, a carbon can form four covalent bonds with four hydrogens. A carbon can also form a double or even a triple bond with another carbon or nitrogen. Nitrogen gas (N2) is a triple bond between two nitrogens. Molecules are three dimensional objects -- i.e. they are not flat. Bonds arrange themselves on an atom to maximize the distance apart, in order to minimize the repulsion. This has to do with the VSEPR (i.e. Valence Shell Electron Pair Repulsion) theory. What is the biological relevance of all of this? Cells are composed of atoms and molecules, which undergo these various interactions. For example, cell membranes are composed of molecules (lipids) that are "amphipathic" (i.e. molecules with a charged, hydrophilic "head" region and an uncharged, hydrophobic "tail" region). Hydrophobic interactions (i.e. exclusion from water) is an important force in maintaining the membrane's structure/shape. Other forces, such as ionic bonds and van der Waals forces, are employed by enzymes (biological catalysts). Covalent bonds are particularly important, since they are responsible for molecular geometry and shapes of biologically relevant molecules, such as nucleic acids, lipids, sugars, and proteins. Sometimes, cells alter molecules by covalent modification for specific purposes, such as cellular signaling. For example, glycosylation is the covalent attachment of a sugar group to some other molecule, such as a protein (and this is done in the Golgi apparatus of eukaryotic cells). And, phosphorylation, which is the addition of a phosphate group to some molecule (this is used for various cellular functions, such as metabolic pathways, cell signalling or transport of molecules into the cell).
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