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Honors Biology Ch. 6 Chemistry in Biology I. Atoms, Elements, and Bonding - Living and nonliving things are made of atoms. A.Element - pure substance of only 1 type of atom - 98 natural elements - CHNOPS The Size of Cells and Their Components B. Atoms - smallest unit of matter Atomic Models Electron Shell Nucleus Hydrogen (H) Helium (He) B. Atoms - smallest unit of matter 1. Nucleus contains: - Protons - Neutrons Charge positive neutral Mass 1 1 2. Electrons negative 0 C. Isotopes - forms of an element with varying number of neutrons - 12C vs. 14C D. Compounds and Bonding - 2 or more elements chemically bonded 1.Covalent Bonds: - attraction due to shared electrons - ex. water Water Is Covalent Electron pair forms covalent bond Each spends some time w/one, then the other atom Oxygen Molecule (O2) Oxygen Atom Oxygen Atom 2. Ionic Bonds: - attraction due to electrons transferred from one atom to another creating + and - ions - ex. table salt (NaCl) Ionic Bonding in NaCl Sodium has 1 electron in outer shell; chlorine has 7. Sodium can lose 1 electron; Chlorine can gain 1 electron. Sodium becomes a positive ion; Chlorine a negative ion. Ionic Bonding in NaCl Opposites attract. Sodiums nestle between chlorines. Perfectly cubical crystals. Cl- Cl- Cl- ClNa+ Na+ Cl- Cl- Na+ Na+ Cl- Cl- Na+ Na+ - Na+ - Na+ Cl Cl - Cl ClCl- Cl- Cl Na+ Cl Na+ Na+ Na+ Na+ +Na Cl +Na Cl +Na Cl Cl- Na-+ Cl Na-+ Na+ Na+ Cl- Cl- Cl + - Na+ - Na+ Na+ Na Cl Cl Cl ClNa+ Na+ Na+ Na+ Cl- Cl- Cl- ClNa+ Na+ Na+ Na+ Some Elements Are Molecular. Hydrogen gas One electron from each hydrogen atom is shared, forming a single covalent bond Oxygen gas Two oxygen atoms share four electrons, forming a double bond E. Acids, Bases, and pH 1.Acids: + - form H ions in solution 2.Bases: - form OH- (hydroxide) ions in solution 3.pH: - measure of how acidic or basic a solution is - logarithmic scale The pH Scale Oven Bleach Sea Cleaner Water Urine Stomach Orange Baking Acid Juice Soda Lemon Blood Ammonia Coffee Juice Hand Soap Lime Juice Vinegar Water 0 1 2 3 4 5 6 7 8 9 10 11 12 13 Neutral pH+ = pOH– Increasingly Acidic Increasingly Basic 14 Universal pH Indicator II.Water A.Water Is Polar - water molecules have positive and negative ends Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled closer to oxygen. – This results in a partial negative charge on the oxygen and a partial positive charge on the hydrogens. Polar Covalent Bonds in a Water Molecule O + H H H 2O + II.Water A.Water Is Polar - hydrogen bonds form between water molecules Hydrogen Bonds between Water Molecules – + H + – – + Hydrogen bonds H + – A.Water Is Polar - polarity gives special properties How Polarity Makes Water Behave Strangely (3:52) + – H H + – O H + + O H + Hydrogen Bonds - solvent of life Negative oxygen regions of polar water molecules are attracted to sodium ions (Na+). – Na + + – Positive hydrogen regions of polar water molecules cling to chloride ions (Cl–). – + Na + Cl– + Cl – – + + + – + – + – – – – A Crystal of Table Salt Dissolving in Water - strong cohesion and adhesion Water surface tension Water conducting cells 100 µm Water is transported great heights up the stem. Cohesion among Water Molecules - strong cohesion and adhesion Meniscus Capillarity Adhesion among Water Molecules - high specific heat - good evaporative coolant - less dense when frozen Hydrogen bond Ice Hydrogen bonds are stable Liquid water Hydrogen bonds constantly break and re-form Ice: Crystalline Structure and Floating Barrier III. Organic Compounds - Living organisms are made up of organic compounds. A.Major Differences Between: Living vs. Nonliving Systems Systems complex compounds high energy simple compounds low energy - All organic compounds contain carbon. - Exceptions: CO2, CO, CaCO3 - Carbon can form 4 covalent bonds. - Carbon based molecules form chains, branched chains, rings, etc. Chlorophyll A Chlorophyll B Buckminsterfullerene B. 4 Classes of Organic Compounds: 1. Carbohydrates 2. Lipids 3. Proteins 4. Nucleic Acids IV. Carbohydrates - contain C, H, O (1:2:1) - include sugars, starches, cellulose - used for energy storage and to build cell walls - names usually end in "-ose" A. Monosaccharides: - single (simple) sugar A. Monosaccharides: - single (simple) sugar - C6H12O6, C5H10O5 - ex. glucose (source of energy in cells), fructose (fruit sugar), galactose B. Disaccharides: - double sugar B. Disaccharides: - double sugar - C12H22O11 - ex. sucrose (table sugar), lactose (milk sugar) C. Polysaccharides : C. Polysaccharides - many sugars 1. Starch - Made of many 10 - 1000 glucose molecules - in plants (potatoes, grains) - Glycogen: animal starch Storage polysaccharides of plants and animals Chloroplast Starch Mitochondria Glycogen granules 0.5 m 1 m Amylose Amylopectin Starch: a plant polysaccharide Glycogen Glycogen: an animal polysaccharide 2. Cellulose: - long starch chains bonded side by side - very strong - found in the plant cell walls The Arrangement of Cellulose in Plant Cell Walls Cell walls Cellulose microfibrils in a plant cell wall Microfibril About 80 cellulose molecules associate to form a microfibril, the main architectural unit of the plant cell wall. 0.5 m Plant cells Parallel cellulose molecules are held together by hydrogen bonds between hydroxyl groups attached to carbon atoms 3 and 6. OH CH2OH OH CH2OH O O O O OH OH OH OH O O O O O O CH OH CH2OH OH 2 H CH2OH OH CH2OH OH O O O O OH OH OH O OH O O O O O CH OH CH OH 2 2OH H CH2OH OH OH CH2OH O O O O OH OH OH O O OH O O O O CH OH OH CH2OH 2 H Glucose monomer Cellulose molecules A cellulose molecule is an unbranched glucose polymer. Starch and Cellulose Structures H O C CH2OH H 4 H OH O H HO H OH OH glucose OH C H H CH2OH HO C H H C OH H C OH H C OH H H OH 4 HO H O OH H 1 H OH glucose and glucose ring structures CH2OH CH2OH O HO O 1 OH 4 O O 4 1 OH OH OH O O 1 OH CH2OH CH2OH O 4 1 OH O OH OH Starch: 1– 4 linkage of glucose monomers OH CH2OH O HO OH 1 O 4 OH O OH CH2OH OH CH2OH O O O OH OH O OH CH2OH Cellulose: 1– 4 linkage of glucose monomers OH V. Lipids - fats, oils, waxes, steroids - not soluble in water - more energy (calories) in lipids than in carbohydrates - energy storage, insulation, cell membrane, coatings, and many hormones Glycerol Triglycerides 3 Fatty Acids . Lipid Structure Saturated vs. Unsaturated Fatty Acids Animal fat Vegetable oil What Are Trans Fatty Acids? Carcinogenic ‘Natural’ Cell Membrane Phospholipid Bilayer Steroids Cholesterol Testosterone Estradiol Cortisol Progesterone Aldosterone VI. Proteins: - the most abundant and varied of organic compounds - contain C, H, N, O (S) A. Types of Protein 1.Structural: - keratin (hair, fingernails) - collagen 2.Contractile: - actin and myosin (muscle) 3.Pigments: - melanin (in skin, hair, iris) 4.Hormones: - regulate body functions (insulin) 5.Antibodies: - fight disease 6.Enzymes: - amylase (in saliva), lactase B. Structure of Proteins - very complex 1. Amino Acids - building blocks of proteins - 20 different amino acids - proteins contain between 50 - 2000 amino acids 2. Peptide Bond - joins 2 amino acids - polypeptide: many amino acids Peptide Bond 3. Levels of Protein Structure Primary Structure Secondary Structure Tertiary Structure Quaternary Structure 3. Levels of Protein Structure a) Primary Structure: - sequence of amino acids b) Secondary Structure: - helix or pleated sheet c) Tertiary Structure: - amino acids interact to form the polypeptide into a 3 dimension shape d) Quaternary Structure: - 2 or more tertiary polypeptides C. Enzymes - protein catalysts - speed up chemical reactions - each enzyme catalyzes only one specific substrate - most function at a specific temperature and pH C. Enzymes C. Enzymes VII. Nucleic Acids - 2 major types: A.DNA - contains hereditary information (genes) - double helix VII. Nucleic Acids - 2 major types: A.DNA - contains hereditary information (genes) - double helix B. RNA - controls protein synthesis - single helix DNA RNA Protein Information Flow: The End NaCl Dissolved by Water NaCl is ionicly bonded Water is polar and charged O sticks to Na+ H sticks to Cl- ƒ2-6 Chapter 2 65 Universal pH Indicator pH 5.0 pH 4.0 pH 7.0 pH 8.0 pH 6.0 pH 9.0 pH 10.0 Information Flow: DNA RNA Protein