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Biology 30 The Chemistry of Living Things Hierarchy of organization: Chemistry: MATTER: Periodic Table: ELEMENT: Ex. oxygen, gold, copper, carbon COMPOUND: Ex. salt (NaCl), H2O ELEMENTS ESSENTIAL TO LIFE: 25 of all elements are essential to life: 4 of these make up 96% of all living matter: 1. 2. 3. 4. The remaining 4% include: 1. Phosphorus (P) 2. Sulfur (S) 3. Calcium (Ca) 4. Potassium (K) The human body: O, C, H, N, Ca, P, K, S, Na, Cl, Mg Trace elements: Ex. Iron (Fe), iodine (I) Fortified Foods: ATOMS: Atoms consists of subatomic particles: Particle Found ~ Weight (Daltons) Charge atomic # 6 C mass # 12. Atomic Number: Atomic weight (or mass number): Ex. 612C = At. wt => 12 = 6p + 6n Biology 30 The Chemistry of Living Things Page 1 of 10 Electrons are found in orbitals around the nucleus SHELLS: 1st = -. 2nd and subsequent shells = OCTET Rule: exception H/He Noble Gases: Isotope: Ex. Carbon: 12, 13 & 14 6 13C => How many neutrons? Proton? Electrons? Radioactive isotope (p. 21, Fig 2.5 A&B) 14 6C = => 14 = 6p + 8n => Radioactive isotope Usefulness in science? How do the elements stay together? Chemical bonds: Three types of chemical bonds: 1. Covalent Bond (between elements) 2. Ionic Bond (between elements) 3. Hydrogen Bond (between molecules) COVALENT BOND: Types of covalents bonds: H-H => single covalent bond O=O => double covalent bond N = N => triple covalent bond H2O => compound How are electrons attracted to another? Electronegativity: Non-Polar covalent bond: Ex. Oxygen (O2), Methane (CH4) Polar covalent bond: Occurs when: Ex. Water (H2O) Biology 30 The Chemistry of Living Things Page 2 of 10 IONIC BOND ION: CATION: ANION: Electrolyte: Ex. table salt (NaCl) Na+ cation + Clanion <---> NaCl HYDROGEN BOND Living cells: electronegative atom => O or N Are weak bonds, therefore easy to break IMPORTANCE: WATER AND ITS UNUSUAL PROPETIES: Note: Understand these 5 properties & their significance to life. H-bond Water: Polar molecule Hydrogen bonding BETWEEN each water molecule a) Cohesiveness cohesion: adhesion: surface tension b) High specific heat c) High heat of vaporization Evaporative cooling: d) Density of water e) Versatile solvent Biology 30 The Chemistry of Living Things Page 3 of 10 pH, acids, bases & buffers Terms: Solution: Solvent: Solute: aqueous solution: Dissociation of H2O (refers to the separation of H2O) H2O <--> H+ + OH- or H2O + H2O <--> H3O+ + OH-. Chemical equilibrium = the amount of H+ is equal to the amount of OH. pH scale: (p. 27; Fig. 2.15) range: log based scale pH = -log[H+] = - log [10-5] = - (-5) =5 0.00001M Inverse relationship: • Increase [H+] When: pH = 7 pH < 7 pH > 7 • Decrease [H+] Most biological systems: Exception: (a) <-------- (b) ----------> (c) --------> (d) <-------- 0 (e) 7 (f) 1. pH values of acidic solutions 2. pH values of basic (alkaline) solutions 3. point at which H+ equal OH-. 4. progressing from a weak to strong acid 5. progressing from a weak to a strong base 6. results of adding more hydrogen to a solution 14 (g) ACIDS: BASES: BUFFERS: Biology 30 The Chemistry of Living Things Page 4 of 10 Ex. Carbonic acid - bicarbonate buffer system (2nd most important body buffering system) If pH rises ... H2CO3 -------> HCO3- + H+. (acid) (base) + H donor H+ acceptor If pH drops ... H2CO3 <------- HCO3- + H+. releases H+. absorbs H+. helps to maintain your blood pH at ~ 7.35 - 7.45 If blood pH: falls below 7.35 => acidosis => needs to absorb H+. rises above 7.45 => alkalosis => needs to release H+. Is this system involved in positive or negative feedback? Organic chemistry: CARBON: - Atomic # = , therefore has - Forms covalent bonds with: valence (outer shell) electrons Hydrocarbons Ex. 6 FUNCTIONAL GROUPS: 1. HYDROXYL GROUP 2. CARBONYL GROUP ALDEHYDES (C dbl bond O at the end) KETONES (C dbl bond O in middle) 3. CARBOXYL GROUP carboxylic acids. 4. AMINo GROUP amines 5. PHOSPHATE GROUP Ex. ATP ---> ADP + Pi 6. METHYL GROUP Biology 30 The Chemistry of Living Things Page 5 of 10 Biological Molecules: 4 classes of large biological molecules in living organisms: 1. Carbohydrates 2. Proteins 3. Nucleic acids 4. Lipids (not a true macromolecule) Classifying organic compounds: Monomers: Polymers: Formation of polymers: Fig 2.13 Dehydration reactions (synthesis): Ex. glucose + glucose = maltose Breaking of polymers: Hydrolysis (water;loosening or splitting) Ex. digestive enzymes Types of Macromolecules: CARBOHYDRATES: Classified by: 1. Monosaccharides = (mono = single; sacchar = sugar) Simple sugar composed of: 2. Disaccharides =(Di = two; saccharide = sugar) Fig. 2.13b Results from the removal of: Disaccharide Maltose Lactose Sucrose Monomers Usage 3. Polysaccharide fig.2.15 -2 important biological functions: 1. Energy storage (starch & glycogen) a) Starch: b) Glycogen: Biology 30 The Chemistry of Living Things Page 6 of 10 2. Structural support (cellulose & chitin) a) Cellulose: b) Chitin: LIPIDS: (Fig. 2.16) 1. Fats: macromolecules constructed from: a) glycerol = 3C -OH b) Fatty acid (carboxylic acid) carboxyl: hydrocarbon tail: Formation of fats Triglycerides: SATURATED UNSATURATED Ex. Ex. 2. Phospholipids Fig. 2.17 Composed of: Hydrophilic heads & Hydrophobic tails Micelles: Surfactant (surface active agent): 3. Steroids (Fig 2.18) Functions of lipids: 1. 2. 3. 4. 5. 6. PROTEINS: (Fig 2.20) Peptide bond Biology 30 The Chemistry of Living Things Page 7 of 10 -N-C-C-N-C-C- = backbone Polypeptide chain = There are 20 amino acids which make up proteins (Fig 2.19) Amino acids contain both carboxyl and amino functional groups. Levels of protein structure (Fig 2.21): a) Primary structure (1˚): b) Secondary structure (2˚): 2 types of secondary structure: α helix ß pleated sheet c) Tertiary structure (3˚): d) Quaternary structure (4˚): Ex. Hemogoblin = 4 subunits Denaturation: Causes of denaturation: 1. 2. 3. 4. 8 Functions of proteins: 1. structural support 2. storage 3. transport 4. hormonal 5. receptor 6. contractile 7. defense 8. enzymatic Enzymes: Fig. 2.22 • • Catalysts: • How enzymes work? • Specificity: • Recycled (reusable) Biology 30 The Chemistry of Living Things Page 8 of 10 Catalytic cycle: E + S --> ES complex --> E + P Substrate: Active site: Induced fit model: Factors that affect enzyme activity: 1. Environmental conditions (optimum conditions) a) b) c) 2. Cofactors and coenzymes: • cofactors = inorganic (zinc, iron) • coenzymes = organic (vitamins) 3. Enzyme inhibitors (p.85, Fig. 5.16) • competitive inhibitors: non-competitive inhibitors: NUCLEIC ACIDS: Nucleotide = building block of a nucleic acid; composed of: a) Pentose (5-C sugar) b) Nitrogeneous bases: c) Phosphate Group: 3 Examples of Nucleotide based molecules: 1. DNA = deoxyribonucleic acid (Fig 2.24) DNA: the double helix = 3-D shape = Watson & Crick => 1953 Contains: Biology 30 The Chemistry of Living Things Page 9 of 10 2. RNA = ribonucleic acid (Fig 2.24) Contains: 3. ATP = adenosine triphosphate (Fig 2.26) Functions of Nucleotide based molecules a) b) c) d) Biology 30 The Chemistry of Living Things Page 10 of 10