Chapter Two: The Chemistry of Biology

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Chapter outline

1. Elements and atoms
   1. Matter
      1. Matter refers to the "stuff" that everything, living or nonliving, is made of.
      2. The special type of matter which cannot be broken down is called an element.
   2. Elements
      1. Elements cannot be broken down by chemical reactions.
      2. Carbon, hydrogen, and oxygen are examples of elements.
      3. Each element has a one or two letter symbol which is used to identify it.
      4. Over one hundred elements have currently been discovered.
      5. Any amount of an element will exhibit that element's chemical properties.
   3. Atoms
      1. The nucleus
         1. At the center of every atom is a ball consisting of two particles, protons and neutrons.
         2. Protons have a positive charge.
         3. Neutrons have a neutral charge.
      2. Electrons are tiny negatively charged particles which orbit the nucleus.
      3. The positive charge of a proton is equal to the negative charge of an electron.
      4. Atoms normally have the same number of protons as electrons, so the overall charge is neutral.
   4. Atomic mass and atomic number
      1. An element's atomic number is the number of protons in an atom of that element.
      2. An element's atomic mass is the number of protons plus the number of neutrons in an atom of that element.
   5. Isotopes
      1. All isotopes of an element have the same number of protons and electrons, but they have a different number of neutrons.
      2. Different isotopes of the same element may have different chemical properties.
2. Molecules and their formation
   1. Molecules
      1. Molecules are collections of atoms formed through chemical reactions.
      2. The atoms in a molecule are held together by a bond.
   2. Ionic bonds
      1. An ionic bond occurs when one atom donates one or more electrons to another atom.
      2. As a result, one atom becomes becomes positively charged, and the other becomes negatively charged, so they attract to one another and stay together.
   3. Covalent bonds
      1. A covalent bond occurs when two atoms share one or more electrons to become more stable.
      2. Since atoms always tend to become more stable, the bond is not broken easily.
   4. Nonpolar molecules and polar molecules
      1. In molecules where all of the electrons are shared equally, the charge is neutral everywhere in the molecule. These molecules are nonpolar.
      2. Polar molecules are those in which the electrons are not shared equally, to some areas have a slight positive charge, and some have a slight negative charge.
3. Molecular and structural formulas
   1. Molecular and structural formulas are used to describe the composition and structure of a molecule.
   2. Molecular formulas
      1. Molecular formulas are simply a list of the symbol of each element in the molecule followed by the number of atoms of that element in the molecule.
      2. For example, the molecular formula for glucose is C₆H₁₂O₆.
      3. When writing chemical reactions, scientists indicate that more than one of a molecule was present by adding a number before the molecular formula. Eight molecules of glucose would be written as 8C₆H₁₂O₆.
   3. Structural formulas
      1. Structural formulas are actual sketches of the bonds between the atoms in a molecule.
      2. In a structural formula, the atoms are represented by their symbols, and the bonds are indicated by lines between the symbols.
      3. If two molecules have an identical molecular formula, only their structural formula can be used to tell the difference.
4. Chemical reactions
   1. A chemical reaction is the breaking of bonds and/or the formation of new bonds between atoms.
   2. The substances which existed before a chemical reaction are called the reactants, and the substances produced by the reaction are called the products.
   3. The number of atoms of an element which existed before a chemical reaction always equals the number of atoms of that element which existed after the chemical reaction was completed.
   4. Cells use various chemical reactions to break down food, store it, and use it to drive other processes.
5. Acids, bases, and buffers
   1. Acids and bases are a way of classifying compounds based upon what happens to them when they are placed in water.
   2. Acids
      1. When placed in water, acids release H+ ions.
      2. On the pH scale, acids have a pH less than 7.
   3. Bases
      1. Bases release OH- ions when placed in water.
      2. Bases have a pH greater than 7 on the pH scale.
   4. Buffers
      1. Buffers can neutralize the pH of a solution by combining with either H+ ions or OH- ions.
      2. They are helpful in unicellular organisms, since many reactions can occur only at pH's which are not too acidic or basic.
6. Organic compounds and the importance of carbon
   1. Organic molecules are those which contain carbon, oxygen, and hydrogen.
   2. Carbon is the "backbone" of these molecules because it can form four bonds with other atoms.
   3. Functional groups
      1. Organic molecules have functional groups where bonding with other molecules generally occurs.
      2. Molecules with the same functional groups usually have similar chemical properties.
      3. Organic molecules are often classified based on their functional groups.
7. Different types of organic compounds
   1. Carbohydrates
      1. Carbohydrates are formed by joining sugar molecules. Sugars are characterized by having the same number of carbon atoms as oxygen atoms and having twice as many hydrogen atoms.
      2. Disaccharides are carbohydrates with two sugars, and polysaccharides are carbohydrates with more than two sugars.
      3. Cells use carbohydrates to store energy and as components of many cellular structures.
   2. Lipids
      1. Lipids are composed of molecules called fatty acids.
      2. Lipids do not dissolve in water, so they are said to be hydrophobic.
      3. Phospholipids
         1. Phospholipids consist of two nonpolar fatty acid molecules, a polar phosphate ion, and a glycerol molecule.
         2. Phospholipids are a very important part of the cell membrane because the phosphate ion is polar and the fatty acids are nonpolar.
   3. Proteins
      1. Proteins are long chains of amino acids.
      2. All amino acids have an amino group (NH₂) and a carboxyl group (COOH).
      3. The variable group differs between amino acids, giving them certain properties.
      4. Amino acids bond together to form proteins through what is called a peptide bond.
8. Enzymes and coenzymes
   1. Enzymes
      1. Enzymes are catalysts: molecules which increase the rate of a chemical reaction.
      2. All enzymes are complex protein molecules folded upon themselves to form a three-dimensional shape.
      3. The area of the enzyme at which the substrate joins is called the active site.
   2. Substrates
      1. A subtrate is the molecule to which an enzyme attaches.
      2. Enzymes attach only to specific substrates which fit into the enzyme's active site.
      3. The induced-fit hypothesis states that an enzymes active site can change slightly so that a substrate which does not match perfectly can still fit.
   3. Coenzymes
      1. Coenzymes are organic molecules which aid in enzyme-catalyzed reaction, but they are not proteins.
      2. Often, coenzymes bond with electrons which are released from the reaction catalyzed by the enzyme.
9. Factors which affect the efficiency of an enzyme
   1. Inhibitors
      1. Competitive inhibitors
         1. Competitive inhibitors have a structure to the enzyme's substrate.
         2. The enzyme may bond with the competitive inhibitor instead of the substrate, so the reaction catalyzed by the enzyme will occur at a much slower rate.
      2. Noncompetitive inhibitors
         1. Noncompetitive do not bond to the active site of an enzyme and block the subtrate.
         2. They react with portions of the active site, thus changing its shape so that the substrate cannot fit.
   2. Allosteric factors
      1. Many enzymes have an area called its regulatory site. Molecules which attach to the regulatory site are called allosteric factors.
      2. By joining to the regulatory site, allosteric factors can change the shape of the active site, which may either help or harm the enzyme.
   3. pH
      1. Acids and bases release H+ and OH- ions when dissolved in water.
      2. These ions are charged, so they can stretch and pull the enzyme's three-dimensional structure.
      3. Solutions with very high or very low pH's have many ions, enough to pull the enzyme's active site completely out of shape so that it can no longer function.
      4. Certain enzymes can function best at somewhat acidic or basic pHs.
   4. Temperature
      1. At higher temperatures, molecules move around faster, so it becomes more likely that an enzyme will come in contact with its substrate.
      2. When the temperature is too high, the enzyme may be ripped apart (denatured) so that it loses all function.
      3. At very low temperatures, the enzymes and substrates move around very slowly, so they do not come in contact very often and the reaction proceeds slowly.
10. Diffusion
    1. Diffusion
       1. Diffusion is the movement of molecules from an area of high concentration to an area of low concentration.
       2. A concentration gradient is a difference in concentration between two areas. Molecules move "down" a concentration gradient; that is, toward the area with a lower concentration.
    2. Osmosis
       1. Osmosis is the diffusion of water.
       2. Water potential is synonymous with water concentration; areas with a high concentration of water have a high water potential.
       3. Osmotic potential is the likelihood for osmosis to occur toward a particular area. Areas with a low concentration of water have a high osmotic potential.

Terms to know

• acid - A substance which, when dissolved in water, release H+ ions.
• allosteric factor - A molecule which attaches to the regulatory site of an enzyme, causing a change in the enzymes structure.
• atom - The smallest amount of an element which still exhibits the properties of that element. An atom consists of a nucleus composed of protons and neutrons with electrons orbiting around it.
• atomic mass - The number of protons plus the number of neutrons in an atom of a particular element.
• atomic number - The number of protons in an atom of a particular element.
• base - A substance which, when dissolved in water, release OH- (hydroxide) ions.
• buffer - Compound which tends to neutralize the pH of a solution by combining with either H+ or OH- ions.
• carbohydrate - An organic molecule which is formed through the joining of sugar molecules. All carbohydrates have an equal number of carbon atoms and oxygen atoms, and they have twice as many hydrogen atoms.
• chemical reaction - When substances (the reactants) come together and react by rearranging their bonds to form new substances (the products).
• coenzyme - Organic molecules which are not proteins but still aide in reactions catalyzed by enzymes.
• covalent bond - A bond between two atoms in which the electrons are shared.
• diffusion - The movement of molecules from an area of high concentration to an area of low concentration.
• element - Matter which cannot be further broken down by chemical reactions.
• enzyme - Protein molecules which catalyze chemical reactions by joining to specific reactants in the reaction called substrates.
• ionic bond - A bond formed as a result of the jumping of electrons from one atom to another. Since the atoms either gained or lost electrons, they became ions, and the force of attraction between oppositely charged ions holds the bond together.
• isotope - A form of an element with a different number of neutrons in the nucleus than normal.
• lipid - An organic molecules which consists of fatty acids. Lipids do not dissolve in water.
• matter - The "stuff" that everything is made of.
• molecular formula - A way of describing a molecule by writing the symbol for each element in the molecule followed by a subscript indicating the number of atoms of that element in the molecule.
• molecule - A combination of atoms through chemical bonds.
• organic molecule - Any molecule which contains atoms of carbon, hydrogen, and oxygen. Its carbon backbone allows for a complex structure, and its functional groups allows it to form bonds to other molecules.
• osmosis - A special name for the diffusion of water.
• product - Any molecule formed as a result of a chemical reaction.
• protein - A type of organic molecule which consists of a long chain of amino acid molecules. They are synthesized by ribosomes based on the cell's genetic code.
• reactant - A substance which existed before a chemical reaction.
• structural formula - A method of writing a molecule by actually sketching its physical structure. Atoms are represented by their abbreviation, and bonds between atoms are indicated by lines.
• substrate - The substance to which an enzyme binds in catalyzing a chemical reaction.