Study Guide: Biochemistry
A. Hydrophilic vs Hydrophobic. Since biological chemistry occurs largely in an aqueous environment, the interaction of a biological molecule with water is very important. That interaction is influenced by two primary causes: size and polarity (charge). The smaller a molecule is, the more likely it is to be willing to associate with water (dissolve). Also, the more polar and/or charged a molecule is, the more likely it is to be willing to associate with water. Since biological molecules are often very large, it is common for the different parts of the molecule to interact differently in water. For instance, a protein, which is composed of many different ...view middle of the document...
The many, many different organic molecules are formed by attaching a variety of functional groups to hydrocarbon skeletons. Each functional group has its own characteristic behavior, and the combinations of the behaviors of a molecule’s functional groups and the effects of the hydrocarbon skeleton create the overall nature of the molecule. Classes of organic molecules are largely characterized by their functional groups.
C. Important Functional Groups
1. Hydroxyl Group (found in alcohols and carbohydrates). This is a polar functional group due to the polar covalent bond between oxygen and hydrogen. Molecules whose most influential functional group is a hydroxyl group are called alcohols, and their systematic names end in –ol. Example: ethanol.
2. Carboxyl Group (found in organic acids). The carboxyl is sometimes written –COOH. The H on the OH dissociates easily in appropriate circumstances, thus liberating H+ (a hydrogen ion) and creating –COO-. This makes this functional group a proton donor, and thus acidic. It also makes the carboxyl group a strong hydrophilic force. Molecules whose most influential functional group is a carboxyl group are considered to be organic acids; their systematic names end in –ate. Example: acetate.
3. Amino Group. The amino is sometimes written –NH2. The amino group is polar, due to the polarity of the N-H bond. It also tends to pick up an extra hydrogen ion (due to the negative character or the N, and the pair of uninvolved valence electrons), thus becoming NH3+. This makes it a hydrogen acceptor, and thus alkaline in character. It also makes it a strong hydrophilic influence. Molecules whose most influential functional group is an amino group are organic bases, and their names end in –amine. Example: diphyenylamine.
4. Phosphate Group: This functional group is always charged, either -1 or -2. This makes it strongly hydrophilic in nature and influence. Phosphates may be attached to organic molecules (organic phosphate) or unattached (free or inorganic phosphate). When diagramming the structures of phosphate-containing organic molecules, the organic phosphate is often abbreviated as a P inside a circle. Free phosphate is often abbreviated Pi (i for “inorganic).
D. Structures of Important Classes of Biological Molecules
1. Hydrocarbon: [hydro=hydrogen; carbon=carbon] These are molecules consisting of only hydrogen and carbon They come in many sizes and arrangements. They may be saturated (contain only single covalent bonds) or unsaturated (containing at least one double covalent bond). They are very non-olar, since the C-C bond and the C-H bond are both completely non-polar. Most carbohydrates are quite hydrophobic.
Examples: ethane benzene
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