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Ch. 6 Biochemistry I. Atoms, Elements and Compounds Atoms: building blocks of matter 1. matter: anything that has mass and takes up space 2. chemistry: the study of matter’s composition and properties 3. atoms: building blocks of matter. Made of: a. protons (p+): positively charged particles located in nucleus b. neutrons (n0): particles with no charge located in nucleus c. electrons (e-): negatively charged particles that move around the outside of the nucleus in energy levels 4. overall charge of atom = p+ + e- = 0 5. nucleus = core of atom = p+ + n0 = mass of atom B. Elements: a pure substance that cannot be broken down into other substances by physical or chemical means 1. 92 naturally occurring elements exist 2. C, H, N, O are the elements most abundant in living things. What elements are important? 1. C 7. S 13. Cu 2. H 8. Ca 14. Zn 3. O 9. Fe 15. Cl 4. P 10. Mg 16. Mo 5. K 11. B 17. I 6. N 12. Mn I C HOPKNS CaFe Mg B Mn CuZn Cl Mo C, H, & O - 96% of Human weight Water (H2O) - 75 - 85% of cell weight What makes elements important? a. Metabolism - photosynthesis, respiration, & other metabolism b. Heredity and evolution c. Growth and development d. Growth regulation e. Physiological ecology 3. trace elements = required in very small amounts (ex: iodine) 4. isotopes: atoms of the same element that have different numbers of neutrons. a. Ex : carbon-12 (p + n) carbon-14 5. radioactive isotopes: unstable isotopes that give off radiation a. nucleus becomes unstable due to having extra neutrons. Nucleus decays or breaks apart, giving off radiation. b. Ex: carbon-14 is used in dating remains while others are used in radiation therapy for cancer C. Compounds: a pure substance formed when two or more different elements combine (ex: water, salt, methane). 1. compounds always form from a specific combination of elements in a fixed ratio 2. compounds can’t be broken down into simpler compounds or elements by physical means 3. compounds do not always have the properties of the elements that make them up (ex: NaCl does not have the properties of sodium or chlorine) D. Chemical Bonds 1. covalent: 2 atoms share electrons (ex: water, sugars, fats, proteins) a. molecule: a compound in which the atoms are held together by covalent bonds b. covalent bonds can be single, double or triple depending on how many pairs of electrons are shared 2. ionic bond: transfer of electrons from one atom to another (ex: NaCl—salt). When atoms lose or gain electrons they either have a positive or negative charge. a. ion = charged atom b. in living things, ions include Na+, K+, Ca2+, Cl- and carbonate ions. These ions help maintain homeostasis and cellular communication. c. Electrical attraction between ions holds atoms together 3. # of electrons each energy level can hold: 1st—2 e2nd—8 e3rd – 18 e4th – 32 ea. atoms are stable if the outermost energy level is full (8 electrons) b. some atoms donate or accept electrons more easily than other atoms. Metallic atoms tend to donate electrons Nonmetals tend to accept electrons c. ionic compounds break down into ions when dissolved in water and can carry an electric current E. van der Waals Forces: attractive forces between molecules (ex: water molecules) 1. caused by temporary areas of slightly positive and negative charges created by unequal distribution of the electron cloud around a molecule 2. strength of molecule attraction depends on size and shape of molecule and its ability to attract electrons. 3. van der waals forces are not as strong as covalent or ionic bonds 4. help hold water molecules together to form droplets and a surface F. Polar Molecule: molecule with oppositely charged ends (ex: water) 1. Oxygen end of water is bigger and pulls harder on the electrons causing the oxygen end to be slightly negative and the hydrogen ends to be slightly positive. Opposites attract so that is why water molecules stick together and you can skip a rock across a pond’s surface. II. Chemical Reactions: process by which atoms or groups of atoms in substances are reorganized into different substances 1. in living things, chemical reactions allow growth, development, reproduction and adaptation. A. Chemical Equations: chemical reactions are expressed in equations. Reactants → Products C6H12O6 + O2 → CO2 + H2O (glucose and oxygen react to form carbon dioxide and water) 1. atoms are neither created nor destroyed in a chemical equation—only rearranged (law of conservation of mass). C6H12O6 + 6O2 → 6CO2 + 6H2O B. Activation energy: the minimum amount of energy needed for reactants to form products in a chemical reaction 1. reactions may be exothermic (release energy like heat/ light) or endothermic (energy is absorbed causing cold) C. catalysts: a substance that lowers the activation energy needed to start a chemical reaction 1. enzymes: special proteins that act as biological catalysts in living organisms to speed up the rate of chemical reactions a. enzymes may be used again after a reaction b. ex: amylase found in saliva speeds the breakdown of starch 2. substrates: the reactants that bind to the enzyme 3. active site: the specific location where a substrate binds on an enzyme a. once bonded, the active site changes shape and forms the enzyme-substrate complex which helps chemical reactions occur between substrates to form the new product which is then released. III. Water and Solutions A. Water’s Polarity 1. polar molecules: molecules that have an unequal distribution of charges causing oppositely charged regions. 2. hydrogen bond: the attraction of the positive hydrogen end of a water molecule to the negative end of another water molecule in water a. a strong type of van der Waals force B. Mixtures with water 1. mixture: a combination of two or more substances in which each substance retains its individual characteristics and properties 2. types of mixtures: a. homogenous mixture (solution): uniform composition throughout (substances evenly distributed). Ex: salt water, air, tea, saliva, gasoline solute = substance being dissolved solvent = dissolving medium water = universal solvent b. heterogenous mixture: components remain distinct (you can identify the individual components) 1.suspension = particles settle out to bottom (ex: sand/ water) 2. colloid = particles do not settle out (ex: blood, fog, smoke, milk) C. Acids and Bases 1. acids: substances that release hydrogen ions (H+) when dissolved in water; ex: HCl (hydrochloric acid) 2. bases: substances that release hydroxide ions (OH-); ex: NaOH (sodium hydroxide) 3. pH: the measure of concentration of H+ in a solution. 0←--------------------------7--------------------------→14 increasingly acidic neutral increasingly basic < 7 = acidic > 7 = basic (alkaline) 7 = neutral = pure water Acid = forms hydrogen ions (H+) in water Ex: HCl (stomach acid) Base = forms hydroxide ions (OH-) in water Ex: NaOH (sodium hydroxide) 4. buffers: mixtures that can react with acids or bases to keep pH within a particular range a. in living cells, buffers keep the pH within 6.5 to 7.5. Neutralization Reaction: Acid + Base Water’s Unique Properties: We can only survive a few days w/o water (makes up 70% of cells) Because it is polar, water attracts other polar molecules (water, sugar) and ions (salt). (Universal solvent) Polarity allows for cohesion (water molecules stick together) which creates surface tension (leaves, insects float on surface). Explains why you can skip a flat rock across a pond. Water is adhesive (forms H bonds w/ molecules on other surfaces). This allows water to creep up tubes (capillary action in plants – water travels from roots to leaves defying gravity). Water resists changes in temp. Water requires more heat to increase in temp. than most other substances. Likewise, water loses a lot of heat when it cools – acts as an insulator. One of few substances to expand when it freezes. Ice is less dense than water and floats. Water expands as it freezes inside cracks in rocks – breaks apart, forming soil over time. IV. The Building Blocks of Life Organic Chemistry: the study of compounds containing carbon which is found in almost all biological molecules. 1. life on earth is considered “carbon-based” and carbon compounds lead to diversity of life on Earth. 2. carbon has 4 electrons in its outer energy level so it can form 4 covalent bonds with other atoms. 3. these compounds can be straight chains, branched chains, or rings. B. Macromolecules/ Polymers: large molecules that are formed by joining smaller organic molecules together. 1. polymers are made from repeating units of identical or nearly identical compounds called monomers that are linked by covalent bonds 2. 4 major categories of macromolecules: carbohydrates, lipids, proteins and nucleic acids. a. carbohydrates: main source of energy for plants/animals; structural support in plant cell walls (cellulose) and exoskeletons of insects and crustaceans (chitin); stored in liver and skeletal muscle (glycogen); plants store glucose as starch (CH2O)n general formula for carbohydrates n is the number of CH2O units in a chain 3-7 n units = simple sugars (monosaccharides) ex: glucose 2 monosaccharides = disaccharide (ex: sucrose, lactose) polysaccharides = complex (3+) sugars; ex: starch, glycogen, cellulose, chitin (makes tough outer shell of shrimp, lobsters and certain insects) b. Lipids = secondary energy source (stored energy) Lipo = fat C, H, O (C:H ratio higher than in carbs) Fats, oils, waxes Make up cell membrane (phospholipids) Insoluble in water (nonpolar) Stored under skin and around organs Energy storage, insulation, and protective coatings Triglycerides: a fat if solid at room temperature, an oil if liquid at room temperature—stored in fat cells in human body Waxes: protective coating on leaves to prevent water loss Saturated Fats: carbons in the chain are bonded to the max number of H atoms Stack easily—solids at room temp. Ex: animal fat—lard, butter Unsaturated Fats: double bonds b/w carbon atoms and have less than the max number of H atoms Bent shape—less likely to form solids Liquids at room temp. Ex: vegetable oils (corn, canola), fish oils (cod liver oils) Steroids: cholesterol and hormones Estrogen and testosterone = sex hormones Anabolic steroids = synthetic version of testosterone (male sex hormone)—muscle, bone mass during puberty, maintaining masculine characteristics C. Proteins: build and repair body tissues Composes muscle, skin and hair C, H, O, N and sometimes S Carry out cell metabolism Amino acids= building blocks of protein 20 amino acids make up all proteins peptide bonds link amino acids together 1. proteins may have up to four levels of structure: a. primary: number of amino acids and their order b. secondary: 3-d folded shape (helix or pleat) c. tertiary: globular d. 4th: combine with other proteins D. Nucleic acids: Store and transmit genetic information DNA (deoxyribonucleic acid): 5 carbon sugar (deoxyribose), phosphate group, and a N base make up a repeating unit in DNA called a nucleotide RNA (ribonucleic acid): involved in protein synthesis—helps DNA make protein ATP (adenosine triphosphate) = energy molecule used by cells