AP BIOLOGY CHEMISTRY/BIOCHEMISTRY

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1 AP BIOLOGY CHEMISTRY/BIOCHEMISTRY I. Chemical Elements A. Matter 1. space and has mass. 2. All matter (living and nonliving) is composed of basic. a. Elements cannot be broken down to substances with different or. b. Six elements ( ) are commonly found in living things. B. Atomic Structure 1. Chemical and physical properties of atoms (e.g., mass) depend on the subatomic particles. a. Different atoms contain specific numbers of,, and. b. Protons and neutrons are in the nucleus of atoms; electrons move around the nucleus. c. are positively charged particles; neutrons have no charge; both have about 1 atomic mass unit of weight. d. are negatively charged particles. 2. Isotopes have different mass. a. are atoms with the same number of protons but differ in the number of neutrons; e.g., a carbon atoms has six protons but may have more or less than usual six neutrons. b. Isotopes have many uses: 1) Determine diet of ancient peoples by determining proportions of isotopes in mummified or fossilized human tissues. 2) Used as tracers of biochemical pathways. 3) Determine age of fossils using radioactive isotopes. 4) Radiation used in medical treatment. 5) Source of radiation used in medical diagnostic procedures including PET scan. C. Energy Levels 1. Protons are positively charged; electrons are negatively charged. Oppositely charged protons and electrons are attracted to each other. 2. An atom's proton number determines its number of electrons and its chemical properties. 3. Arrangement of an atom's electrons is determined by total number of electrons and electron shell they occupy. a. is the ability to do work. b. Electrons with least amount of potential energy are located in K shell closest to nucleus; electrons having more potential energy are located in shells farther from the nucleus. c. Atomic Configurations 1) Bohr model helps determine number of electrons in outer shell. 2) Inner shell contains up electrons; additional shells contain electrons. 3) Elements are arranged in rows in periodic table according to number of electrons in outer shell. d. How atoms react with one another depends upon the number of electrons in outer shell. 1) Atoms with filled outer shells do not with other atoms. 2) In atom with one shell, outer shell is filled when it contains two electrons. 3) For atoms with more than one shell, the octet rule applies; outer shell is stable when it contains eight electrons. 4) Atoms with unfilled outer shells react with other atoms so each has stable outer shell. 5) Atoms give up, accept, or share electrons in order to have a stable outer shell. e. Electron Orbitals 1) is a volume of space where rapidly moving electrons are predicted to be found. 2) An orbital has a characteristic energy state and a characteristic shape. 3) At first energy level ( ), there is only one spherically shaped orbital where at most two electrons are found about the nucleus. 4) At second energy level ( ), there is one spherically shaped orbital and three dumbbell shaped orbitals; the second energy level contains at most eight electrons. 5) Higher energy levels may contain more orbitals; however, outer shells have a maximum of four orbitals and eight electrons.

2 4.Chemical Formulas and Equations a. A indicates the number of atoms in each substance; H2O has Hydrogen (H) Atoms and Oxygen (O) Atom. b. The formula also indicates the number of molecules; 6H2O is six molecules of water. c. A is always balanced; the same number of each type of atom is on both sides. II. Compounds and Molecules A. Molecules 1. are atoms held together by chemical bonds. 2. Molecules form when two or more atoms react with one another (e.g., O2). 3. Two or more different elements react or bond together to form a (e.g., H2O). 4. Electrons possess energy; bonds that exist between atoms in molecules contain energy. B. Ionic Bonding 1. form when electrons are transferred from one atom to another. 2. Losing or gaining electrons, atoms participating in ionic reactions fill outer shells, and are more stable. 3. Example: sodium with one less electron has positive charge; chlorine has extra electron that has negative charge. Such charged particles are called 4. Attraction of oppositely charged ions holds the two atoms together in an C. Covalent Bonding 1. results when two atoms share electrons so each atom has octet of electrons in outer shell. 2. Hydrogen can give up electron to become hydrogen ion (H+) or share with another atom to complete its outer shell of two electrons. 3. represent shared atoms as a line between two atoms; e.g., single covalent bond (H-H), double covalent bond (O=O), and triple covalent bond (N three lines N). 4. Three dimensional shape of molecules is not represented by structural formulas but is critical in understanding the biological action of molecules: action of insulin, HIV receptors, etc. D. Nonpolar and Polar Covalent Bonds 1. In, sharing of electrons is 2. With, the sharing of electrons is a. In water molecule (H2O), sharing of electrons by oxygen and hydrogen is not equal; the oxygen atom with more protons dominates the H2O association. b. Attraction of an atom for electrons in a covalent bond is called ; an oxygen atom is more electronegative than hydrogen atom. c. Oxygen in water molecule, more attracted to electron pair, assumes small negative charge. 3. Hydrogen Bonding a. is weak attractive force between slightly positive hydrogen atom of one molecule and slightly negative atom in another or the same molecule. b. Many hydrogen bonds taken together are relatively strong. c. Hydrogen bonds between complex molecules of cells help maintain structure and function.

3 III. Chemistry of Water A. First Cells Evolved in Water 1. All living things are 70-90% water. 2. Because water is a polar molecule, water molecules are hydrogen bonded to each other. 3. With hydrogen bonding, water is liquid between 0 degrees C and 100 degrees C which is critical for life. B. Properties of Water 1. The temperature of liquid water rises and falls more slowly than that of most other liquids. a. is amount of heat energy required to raise temperature of one gram of water 1 degree C. b. Because water holds heat, its temperature falls more slowly than other liquids; this protects organisms from rapid temperature changes and helps them maintain normal temperatures. 2. Water has a high a. Hydrogen bonds between water molecules require a large amount of heat to break. b. This property moderates earth's surface temperature; permits living systems to exist here. c. When animals sweat, evaporation of the sweat takes away body heat, thus cooling the animal. 3. Water is universal solvent, facilitates chemical reactions both outside of and within living systems. a. Water is a universal solvent because it dissolves a great number of solutes. b. Ionized or polar molecules attracted to water are c. Nonionized and nonpolar molecules that cannot attract water are 4. Water molecules are cohesive and adhesive. a. allows water to flow freely without molecules separating, due to hydrogen bonding. b. is ability to adhere to polar surfaces; water molecules have positive, negative poles. c. Water rises up tree from roots to leaves through small tubes. 1) Adhesion of water to walls of vessels prevents water column from breaking apart. 2) Cohesion allows evaporation from leaves to pull water column from roots. 5. Water has a high surface tension measured by how difficult it is to break the surface of a liquid. a. As with cohesion, causes water to have high surface tension. b. Permits a rock to be skipped across pond surface; supports insect walking on water surface. 6. Unlike most substances, frozen water is less dense than liquid water. a. Below 4 degrees C, hydrogen boding becomes more rigid but more open, causing expansion. b. Because ice is less dense, it floats; therefore bodies of water freeze from the top down. c. If ice was heavier than water, ice would sink and ponds would freeze solid. C. Acids and Bases 1. Covalently bonded water molecules ionize; the atoms into ions. 2. When water ionizes or dissociates, it releases a small but equal number of H+ and OH- ions; thus its. 3. Water dissociates into hydrogen and hydroxide ions: H - O - H H+ + OH-. 4. molecules dissociate in water, releasing hydrogen ions (H+) ions: HCl H+ + Cl-. 5. are molecules that take up hydrogen ions or release hyroxide ions. NaOH Na+ + OH-. 6. The indicates acidity and basicity (alkilinity) of a solution. a. Measure of free hydrogen ions as a negative logarithm of the H+ concentration (-log [H+]). b. range from 0; most acidic to 14; most basic. 1) One mole of water has 10 to the 7 moles/liter of hydrogen ions; therefore, has neutral ph of 7. 2) is a substance with ph less than 7; is a substance with ph greater than 7. 3) As logarithmic scale, each lower unit has 10 times the amount of hydrogen ions as next higher ph unit;

4 as move up ph scale, each unit has 10 times the basicity of previous unit. 7. keep ph steady and within normal limits in living organisms. a. stabilize ph of a solution by taking up excess hydrogen or hydroxide ions. b. helps keep blood ph within normal limits: H2CO3 H+ + HCO3-. IV. Organic Molecules A. Definitions 1. Most common elements in living things are 2. These four elements constitute about 95% of your body weight. 3. Chemistry of carbon allows the formation of an enormous variety of organic molecules. 4. have carbon bonded to other atoms and determine structure and function of living things. 5. do not contain carbon and hydrogen together; inorganic molecules (e.g., NaCl) can play important roles in living things. B. Carbon Skeletons and Functional Groups 1. Carbon has four electrons in outer shell; bonds with up to four other atoms (usually H, O, N, or another C). 2. Ability of carbon to bond to itself makes possible carbon chains and rings; these structures serve as the backbones of organic molecules. 3. are clusters of atoms with characteristic structure and functions. a. Polar molecules (with +/- charges) are attracted to water molecules and are. b. Nonpolar molecules are repelled by water and do not dissolve in water; these are c. Hydrocarbon is hydrophobic except when it has an attached ionized functional group such as carboxyl (acid) (--COOH); then molecule is hydrophilic. d. Cells are 70-90% water; the degree organic molecules interact with water affects their function. 4. are molecules with identical molecular formulas but differ in arrangement of their atoms (e.g., glyceraldehyde and dihydroxyacetone).

5 C. Building Polymers 1. Four classes of (polysaccharides, triglycerides, polypeptides, and nucleic acids) provide great diversity. 2. Small organic molecules (e.g., monosaccharides, glycerol and fatty acid, amino acids, and nucleotides) serve as the subunits of polymers. D. Condensation and Hydrolysis 1. are the large macromolecules composed of three to millions of monomer subunits. 2. Polymers build by different bonding of different monomers; mechanism of joining and breaking these bonds is and 3. Cellular carry out condensation and hydrolysis of polymers. 4. During, a water is removed (condensation) and a bond is made (synthesis). a. When two monomers join, a hydroxyl (--OH) group is removed from one monomer and a hydrogen is removed from the other. b. This produces the water given off during a condensation reaction. 5. break down polymers in reverse of condensation; a hydroxyl (--OH) group from water attaches to one monomer and hydrogen (--H) attaches to the other. V. Carbohydrates A. Monosaccharides and Disaccharides 1. are simple sugars with a carbon backbone of three to seven carbon atoms. a. Best known sugars have six carbons (hexoses). 1) Glucose and fructose isomers have same formula (C6H12O6) but differ in structure. 2) is commonly found in blood of animals; is immediate energy source to cells. 3) is commonly found in fruit. 4) Shape of molecules is very important in determining how they interact with one another. 2. and are five-carbon sugars (pentoses); contribute to the backbones of RNA and DNA respectively. 3. contain two monosaccharides joined by condensation. a. is composed of galactose and glucose and is found in milk. b. is two glucose molecules; forms in digestive tract of humans during starch digestion. c. is composed of glucose and fructose and is transported within plants. B. Polysaccharides are chains of glucose molecules or modified glucose molecules (chitin). 1. is straight chain of glucose molecules with few side branches. 2. is highly branched polymer of glucose with many side branches; called "animal starch," it is storage carbohydrate of animals. 3. is glucose bonded to form microfibrils; primary constituent of plant cell walls. a. Cotton is nearly pure cellulose. b. Cellulose is not easily digested due to the strong linkage between glucose molecules. c. Grazing animals can digest cellulose due to special stomachs and bacteria. 4. is polymer of glucose with amino acid attached to each; it is primary constituent of crabs and related animals like lobsters and insects. VI. Lipids A. Lipids are varied in structure. 1. Many are insoluble in water because they lack polar groups. 2. Fat provides insulation and energy storage. 3. from plasma membranes and steroids are important cell messengers. B. Fats and Oils 1. A is a long hydrocarbon chain with a carboxyl (acid) group at one end. a. Because the carboxyl group is a polar group, fatty acids are soluble in water. b. Most fatty acids in cells contain 16 to 18 carbon atoms per molecule. c. have no double bonds between their carbon atoms.

6 d. have double bonds in the carbon chain where there are less than two hydrogens per carbon atom. e. Saturated animal fats are associated with circulatory disorders; plant oils can be substituted for animal fats in the diet. 2. is a water-soluble compound with three hydroxyl groups. 3. are glycerol joined to three fatty acids by condensation. 4. are triglycerides containing saturated fatty acids (e.g., butter is solid at room temperature). 5. are triglycerides with unsaturated fatty acids (e.g., corn oil is liquid at room temperature). 6. Animals use fat rather than glycogen for long-term energy storage; fat stores more energy. C. Waxes 1. are a long-chain fatty acid bonded to a long-chain alcohol. 2. Solid at room temperature, waxes have a high melting point and are waterproof and resist degradation. 3. Waxes form a protective covering that retards water loss in plants, and maintains animal skin and fur. D. Phospholipids 1. are like neutral fats except one fatty acid is replaced by phosphate group or a group with both phosphate and nitrogen. 2. Phosphate group is the polar head; hydrocarbon chains become nonpolar tails. 3. Phospholipids arrange themselves in a double layer in water, so the polar heads face outward toward water molecules and nonpolar tails face toward each other away from water molecules. 4. This property enables them to form an interface or separation between two solution (e.g., the interior and exterior of a cell); the plasma membrane is a phospholipid bilayer. E. Steroids 1. differ from neutral fats; steroids have a backbone of four fused carbon rings; vary according to attached functional groups. 2. Functions vary due primarily to different attached functional groups. 3. is a part of an animal cell s membrane and a precursor of other steroids, including aldosterone and sex hormones. 4. is the male sex hormone. VII. Proteins A. Protein Functions 1. include, which makes up hair and nails, and, which support many organs. 2. are proteins that act as organic catalysts to speed chemical reactions within cells. 3. include channel and carrier proteins in the plasma membrane and that carries oxygen in red blood cells. 4. include that prevent infection.

7 5. include that regulates glucose content of blood. 6. is provided and that make up the bulk of muscle. B. Amino Acids 1. All amino acids contain an acidic group (---COOH) and an amino group (--NH2). 2. Amino acids differ in nature of R group, ranging from single hydrogen to complicated ring compounds. 3. R group of amino acid cysteine ends with a sulfhydryl (--SH) that serves to connect one chain of amino acids to another by a disulfide bond (--S S). 4. There are 20 different amino acids commonly found in cells. C. Peptides 1. is a covalent bond between amino acids in a peptide. 2. Atoms of a peptide bond share electrons unevenly (oxygen is more electronegative than nitrogen). 3. Polarity of the peptide bond permits hydrogen bonding between parts of a polypeptide. 4. A is two or more amino acids joined together. 5 are chains of many amino acids joined by peptide bonds. a. Protein may contain more than one polypeptide chain; it can have large numbers of amino acids.

8 D. Levels of Protein Structure 1. Shape of a protein determines function of the protein in the organism. 2. is sequence of amino acids joined by peptide bonds. a. Frederick Sanger determined first protein sequence, with hormone in b. First broke insulin into fragments and determined amino acid sequence of fragments. c. Then determined sequence of the fragments themselves. d. Required ten years research; modern automated sequencers analyze sequences in hours. e. Since amino acids differ by R group, proteins differ by a particular sequence of the R groups. 3. results when a polypeptide takes a particular shape. a. The was the first pattern discovered by Linus Pauling and Robert Corey. 1) In peptide bonds oxygen is partially negative, hydrogen is partially positive. 2) This allows hydrogen bonding between the C=O of one amino acid and the N H of another. 3) Hydrogen bonding between every fourth amino acid holds spiral shape of an alpha helix. 4) Alpha helices covalently bonded by disulfide (--S S--) linkages between two cysteine amino acids. b. The was the second pattern discovered. 1) Pleated beta sheet polypeptides turn back upon themselves; hydrogen bonding occurs between extended lengths. 2) Beta-keratin includes keratin of feathers, hooves, claws, beaks, scales, and horns; silk also is protein with beta sheet secondary structure. 4. results when proteins of secondary structure are folded, due to various interactions between the R groups of their constituent amino acids. 5. results when two or more polypeptides combine. a. Hemoglobin is globular protein with a quaternary structure of four polypeptides. b. Most have a quaternary structure. E. Denaturation of Proteins 1. Both can change polypeptide shape. a. Examples: heating egg white causes albumin to congeal; adding acid to milk causes curdling. b. When such proteins lose their normal configuration, the protein is denatured. c. Once a protein loses its normal shape, it cannot perform its usual function. 2. The sequence of amino acids therefore causes the protein s final shape. VIII. Nucleic Acids A. Nucleic Acid Functions 1. are huge polymers of nucleotides with very specific functions in cells. 2. is the nucleic acid whose nucleotide sequence stores the genetic code for its own replication and for the sequence of amino acids in proteins. 3. is a single-stranded nucleic acid that translates the genetic code of DNA into the amino acid sequence of proteins 4. Nucleotides have metabolic functions in cells. a. are molecules which facilitate enzymatic reactions. b. is a nucleotide used to supply energy. c. Nucleotides also serve as nucleic acid monomers.