Principles of Biological Chemistry This document reviews some principles of chemistry that you will be using in Cell Biology. References at the end indicate which edition the figures are from so be aware that they may not be from your current textbook. Aqueous environment: Many of the chemical reactions associated with living organisms occur in an aqueous (water as the solvent) environment. For this reason the characteristics of water play a fundamental role in the structure and function of biological molecules. (Review corresponding sections from your Basic Biology textbook) Some important properties of carbon: Carbon normally forms 4 covalent bonds. This allows for the formation of a wide variety of structures in biological molecules: chains, rings, and branched structures. See Cooper for examples as you look at the structures of the four groups of biological macromolecules and their building blocks. Chemical formulas and structures: Before we can even consider chemical structures, it is important that you understand what the numbers associated with atoms in a structure or a chemical reaction mean. A subscript indicates the number of that type of atom that is part of the molecule. For instance, the formula CO2 means that one carbon atom and two oxygen atoms are connected in a single molecule known as carbon dioxide. When you see 6 CO2 in the equation below, what does the 6 in front of the C indicate? 6 CO 2 + 6 2 O C 6 12 O 6 + 6 O 2 There are 6 molecules (or moles) that react with 6 molecules of water to yield one molecule (notice the 1 is inferred) of glucose and 6 molecules of oxygen. Thus, a subscript refers to atoms connected in a molecule and the coefficient (number preceding a molecule) indicates the proportion of molecules/moles that will react with the other molecules in a chemical reaction. Chemical formulas indicate the number of atoms in a molecule or compound, but not necessarily how they are attached. For instance, the molecular formula for glycerol is: C38O3, but a better way to represent how the atoms are attached is: OC2C(O)C2O (see Lab #3). Actually, there are a large number of ways to depict the structure of molecules. Each has a different advantage. A number of examples are shown in the table on the next page. Note: depending on the purpose, a mixture of these depictions may be used.
Table. Examples of Different ways to draw chemical structures Type of Drawing Methane Sucrose Molecular formula C4 C1224O12 Lewis dot/electron formula Lewis structure/structural formula: Note: sometimes the relationship of the atoms in 3D space are indicated by the type of line drawn to indicate the bond: a thick line indicates the bond is projecting forward out of the page, dashed line projecting behind the page, regular line in the same plane as the page. C C Bond line notation / Line drawing Sometimes biochemists simply want to show how the atoms are connected in space and will simply show the bonds omitting the identity of the atoms. This is shown in the skeletal structure of ATP shown below (C). Ball and stick structures (B) and spacefilling models (A), show progressively more information about the specific atoms and the area occupied by them. Depictions emphasize different features of the structure. The following diagrams are from NCBI Books: http://www.ncbi.nlm.nih.gov/books/nbk22407/figure/a177/?report=objectonly Appendix: Depicting Molecular Structures Figure 1.16 Molecular Representations Comparison of (A) space-filling, (B) ball-and-stick, and (C) skeletal models of ATP.
Figure 1.17 Space Filling Models Structural formulas and space-filling representations of selected molecules are shown. In our textbook, you will primarily see molecular formulas, structural formulas, line drawings, and space-filling models. Ask if you are unsure how to interpret what you see. Chemicals and their structures can be represented by a variety of methods. You will see several types of representations in our book. Compare the following. 1. Structural formula: All atoms are shown in a flat (2D) representation (part of Fig 2.2 showing the straight chain form of carbohydrates and 2.5 showing fatty acids, 6 th ed). 2. Mixed line drawing/structural formula: Some atoms are shown, but not all of the carbon and hydrogen atoms. The lines indicate covalent bonds and a carbon is located at the ends of each line (usually the C3 is not shown at the end, but is assumed). For any of the 4 bonds to carbon that are not shown, there is a bond to hydrogen (structure of triglycerols, part of Fig 2.6, 6 th ed). 3. Space filling model: Each atom is depicted by a different color based on the cpk coloring convention: black for carbon, red for oxygen and white for hydrogen (fatty acids and trigylcerols, part of Fig 2.5 & 2.6, 6 th ed) 4. Three dimensional animations and various programs that allow you to manipulate structures allow you to interact with the structure of a variety of proteins. We will do some of that this semester. 5. Abbreviations: Since many biological molecules are polymers, the building blocks (monomers) can be represented by an abbreviation. For nucleotides, a one-letter code is used (see 2.10, 6 th ed). For amino acids, a three-letter and one-letter code exist. (see Fig 2.10 & 14, 3.5, 3.11)
Polarity: Polarity in a molecule is due to an uneven distribution of charge. The uneven charge is caused by the electrons (shared in a covalent bond) spending more time near one atom than the other. This type of bond is called a polar covalent bond. Each of the atoms of this bond will have a partial charge: a partial negative charge on one and a partial positive charge on the other. A rule of thumb to identify a polar molecule and polar covalent bonds in most organic molecules is to look for a C or atom attached to an O or N atom. Refer also to Lab #3 Relative bond strength: Before you can understand what is discussed below, be sure you know the difference between covalent, ionic and hydrogen bonds. In an aqueous environment, covalent bonds are very strong, ionic and hydrogen bonds weak, and hydrophobic interactions (i.e. between nonpolar molecules) are the weakest. Even though hydrophobic interactions are very weak, they are still extremely important. These interactions can only occur over a short distance, so they depend on a close fit between two surfaces. This is one of the reasons that shape is so critical in many molecular interactions. Atoms Look for what atoms are in the molecule. Functional groups Try to identify functional groups and evaluate their polarity (see table below). Rings Do any of the carbon chains form rings that can help you identify the class of molecules? Basic unit of polymer If the molecule is a macromolecule, can you recognize the basic structural unit (monomer) to get a better idea to what group the molecule belongs? Functional groups: See next page
FUNCTIONAL GROUPS (See also Audesirk, p 38) Structure Group name Properties Found in* ydrogen Polar or nopolar Most organic molecules (depends on what the is bound to) ydroxyl Polar (C2O)n, NA, alcohols, steroids Carboxyl Polar, acidic AA, FA Carbonyl (aldehyde or ketone) Polar (C2O)n Amine Polar, basic AA, NA Phosphate Polar, acidic NA, P-lipids * Abbreviations: (C 2O) n, = carbohydrates NA = nucleic acids AA = amino acids FA = fatty acids P-lipids = phospholipids ydrocarbon (chain length can vary; one carbon is a methyl group) Nonpolar Many organic molecules, especially lipids References: Audesirk, T, Sudesirk G, and Byers, BE (2002) Biology: Life on Earth, 6 th edition, Prentice all, New Jersey, USA Cooper, GM, ausman, RE (2004) The Cell: A Molecular Approach, 6 th edition, ASM Press & Sinauer Assoc., Washington, DC, USA Berg, JM, Tymoczko JL, Stryer, L (2002) Biochemistry, 5 th edition, Freeman, USA