• AP BIOLOGY – CHEMISTRY/BIOCHEMISTRY

• I. Chemical Elements

•     A. Matter

•         1. Matter takes up space and has mass.         2. All matter (living and nonliving) is composed of basic elements.             a. Elements cannot be broken down to substances with different chemical or physical properties.

            b. Six elements (C, H, N, O, P, and S) 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 protons, neutrons, and electrons.             b. Protons and neutrons are in the nucleus of atoms; electrons move around the nucleus.             c. Protons are positively charged particles; neutrons have no charge; both have about 1                 atomic mass unit of weight.             d. Electrons are negatively charged particles.         2. Isotopes have different mass.             a. Isotopes 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. Energy 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 to two electrons; additional shells contain eight 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 react 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) Orbital 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 (K shell), there is only one spherically shaped orbital where at most two electrons                     are found about the nucleus.                 4) At second energy level (L shell), 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.

•      4.Chemical Formulas and Equations             a. A chemical formula indicates the number of atoms in each substance; H2O has TWO Hydrogen                 (H) Atoms and ONE Oxygen (O) Atom.             b. The formula also indicates the number of molecules; 6H2O is six molecules of water.             c. A chemical equation is always balanced; the same number of each type of atom is on both sides.

• II. Compounds and Molecules

•     A. Molecules

•         1. Molecules 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 compound (e.g., H2O).

        4. Electrons possess energy; bonds that exist between atoms in molecules contain energy.

•     B. Ionic Bonding

•  

•         1. Ionic bonds 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 ions.         4. Attraction of oppositely charged ions holds the two atoms together in an ionic bond.

• C. Covalent Bonding

•         1. Covalent bond 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. Structural formulas 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 nonpolar covalent bonds, sharing of electrons is equal.         2. With polar covalent bonds, the sharing of electrons is unequal.             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 electronegativity; 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. Hydrogen bond 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.

•   B. Properties of Water •         1. The temperature of liquid water rises and falls more slowly than that of most other liquids.

            a. Calorie 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 heat of vaporization.             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 hydrophilic.             c. Nonionized and nonpolar molecules that cannot attract water are hydrophobic.         4. Water molecules are cohesive and adhesive.             a. Cohesion allows water to flow freely without molecules separating, due to hydrogen bonding.             b. Adhesion 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, hydrogen bonding 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.

• . Acids and Bases

•         1. Covalently bonded water molecules ionize; the atoms dissociate into ions.         2. When water ionizes or dissociates, it releases a small but equal number of H+ and OH- ions;             thus its pH is neutral.         3. Water dissociates into hydrogen and hydroxide ions: H - O - H  H+  +  OH-.         4. Acid molecules dissociate in water, releasing hydrogen ions (H+) ions: HCl  H+  +   Cl-.         5. Bases are molecules that take up hydrogen ions or release hyroxide ions. NaOH  Na+ + OH-.         6. The pH scale 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. PH values 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) Acid is a substance with pH less than 7; base 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;                     as move up pH scale, each unit has 10 times the basicity of previous unit.         7. Buffers keep pH steady and within normal limits in living organisms.             a. Buffers stabilize pH of a solution by taking up excess hydrogen or hydroxide ions.             b. Carbonic acid helps keep blood pH within normal limits: H2CO3  H+  +  HCO3-.

• IV. Organic Molecules

•     A. Definitions

•         1. Most common elements in living things are carbon, hydrogen, nitrogen, and oxygen.         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. Organic molecules have carbon bonded to other atoms and determine structure and function of living things.         5. Inorganic molecules 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. Functional groups are clusters of atoms with characteristic structure and functions.             a. Polar molecules (with +/- charges) are attracted to water molecules and are hydrophilic.             b. Nonpolar molecules are repelled by water and do not dissolve in water; these are hydrophobic.             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. Isomers are molecules with identical molecular formulas but differ in arrangement of their atoms                 (e.g., glyceraldehyde and dihydroxyacetone).

• C. Building Polymers

•         1. Four classes of polymers (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 monomers, the subunits of polymers.

•     D. Condensation and Hydrolysis

•         1. Polymers 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 condensation and hydrolysis.         3. Cellular enzymes carry out condensation and hydrolysis of polymers.         4. During condensation synthesis, 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. Hydrolysis reactions 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. Monosaccharides 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) Glucose is commonly found in blood of animals; is immediate energy source to cells.                 3) Fructose is commonly found in fruit.                 4) Shape of molecules is very important in determining how they interact with one another.         2. Ribose and deoxyribose are five-carbon sugars (pentoses); contribute to the backbones of RNA             and DNA respectively.         3. Disaccharides contain two monosaccharides joined by condensation.             a. Lactose is composed of galactose and glucose and is found in milk.             b. Maltose is two glucose molecules; forms in digestive tract of humans during starch digestion.             c. Sucrose is composed of glucose and fructose and is transported within plants.

•     B. Polysaccharides are chains of glucose molecules or modified glucose molecules (chitin).

•         1. Starch is straight chain of glucose molecules with few side branches.         2. Glycogen is highly branched polymer of glucose with many side branches; called "animal starch,"             it is storage carbohydrate of animals.         3. Cellulose 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. Chitin is polymer of glucose with amino acid attached to each; it is primary constituent of crabs and

            related animals like lobsters and insects.

1. Construct linear glucose

Good morning!Go to lab tables, construct one linear glucose and one linear fructose per lab table.

What is an isomer?

Convert to ring glucose bya. Disaasembling the double bond to oxygen on 1C

b. Take the hydroxide (-OH) group off 5Cc. Bond the O that was double bonded to 5C

d. Attach the OH group to 1C

Construct ring fructose:a. Detach the double bond from the O of 2C

b. Detach the –OH from 5Cc. Bond the O to 5C

d. Attach –OH group to opening in 2C

5. Make sucrose – Condensation Reactiona. Orient molecules as seen below

b. Remove –OH group from 1C on a-glucosec. Remove H from hydroxide group of 5C on fructose

d. Bond O to 1C of glucose, H2O is released

• 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. Phospholipids from plasma membranes and steroids are important cell messengers

•     B. Fats and Oils

•         1. A fatty acid 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. Saturated fatty acids have no double bonds between their carbon atoms.             d. Unsaturated fatty acids 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. Glycerol is a water-soluble compound with three hydroxyl groups.         3. Triglycerides are glycerol joined to three fatty acids by condensation.         4. Fats are triglycerides containing saturated fatty acids (e.g., butter is solid at room temperature).         5. Oils 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. Waxes 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. Phospholipids 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. Steroids 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. Cholesterol is a part of an animal cell’s membrane and a precursor of other steroids, including             aldosterone and sex hormones.

        4. Testosterone is the male sex hormone.

At each lab table, construct three fatty acids and one glycerol

molecule

2. Combine to form a triglyceride

• VII. Proteins

•     A. Protein Functions

•         1. Support proteins include keratin, which makes up hair and nails, and collagenfibers, which support many organs.         2. Enzymes are proteins that act as organic catalysts to speed chemical reactions within cells.         3. Transport functions include channel and carrier proteins in the plasma membrane and hemoglobin             that carries oxygen in red blood cells.         4. Defense functions include antibodies that prevent infection.

•         5. Hormones include insulin that regulates glucose content of blood.         6. Motion is provided by myosin and actin proteins 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. Peptide bond 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 peptide is two or more amino acids joined together.         5. Polypeptides 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.

• D. Levels of Protein Structure •         1. Shape of a protein determines function of the protein in the organism.

        2. Primary structure is sequence of amino acids joined by peptide bonds.             a. Frederick Sanger determined first protein sequence, with hormone insulin, in 1953.             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. Secondary structure results when a polypeptide takes a particular shape.             a. The alpha helix 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 beta sheet 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. Tertiary structure results when proteins of secondary structure are folded, due to various interactions             between the R groups of their constituent amino acids.         5. Quaternary structure results when two or more polypeptides combine.             a. Hemoglobin is globular protein with a quaternary structure of four polypeptides.             b. Most enzymes have a quaternary structure.

• E. Denaturation of Proteins

•         1. Both temperature and pH 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.

Construct an amino acid

• VIII. Nucleic Acids

•     A. Nucleic Acid Functions

•         1. Nucleic acids are huge polymers of nucleotides with very specific functions in cells.         2. DNA (deoxyribonucleic acid) 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. RNA (ribonucleic acid) 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. Coenzymes are molecules which facilitate enzymatic reactions.             b. ATP (adenosine triphosphate) is a nucleotide used to supply energy.             c. Nucleotides also serve as nucleic acid monomers.

                                                                                                                                                

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