Biology 30 The Chemistry of Living Things Hierarchy of organization: Chemistry: MATTER: Periodic Table: ELEMENT: Ex. oxygen, gold, copper, carbon COMPOUND: Ex. salt (NaCl), H 2 O 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 Number: Atomic weight (or mass number): Ex. 6 12C = At. wt => 12 = 6p + 6n atomic # 6 C mass # 12. 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 13 C => How many neutrons? Proton? Electrons? Radioactive isotope (p. 21, Fig 2.5 A&B) 14 6 C = => 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 H 2 O => compound How are electrons attracted to another? Electronegativity: Non-Polar covalent bond: Ex. Oxygen (O 2 ), Methane (CH 4 ) Polar covalent bond: Occurs when: Ex. Water (H 2 O) Biology 30 The Chemistry of Living Things Page 2 of 10
IONIC BOND ION: CATION: ANION: Electrolyte: Ex. table salt (NaCl) Na + + Cl - <---> NaCl cation anion 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. Water: Polar molecule Hydrogen bonding BETWEEN each water molecule H-bond 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 H 2 O (refers to the separation of H 2 O) H 2 O <--> H + + OH - or H 2 O + H 2 O <--> H 3 O + + 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 + ] 0.00001M = - log [10-5 ] = - (-5) = 5 When: ph = 7 ph < 7 ph > 7 Inverse relationship: Increase [H + ] Decrease [H + ] Most biological systems: Exception: (a) (b) <-------- ----------> 1. ph values of acidic solutions 2. ph values of basic (alkaline) solutions (c) (d) 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 0 7 14 (e) (f) (g) ACIDS: BASES: BUFFERS: Biology 30 The Chemistry of Living Things Page 4 of 10
Ex. Carbonic acid - bicarbonate buffer system (2 nd most important body buffering system) If ph rises... H 2 CO 3 -------> HCO - 3 + H +. releases H +. (acid) (base) H + donor H+ acceptor If ph drops... H 2 CO 3 <------- HCO 3 - + 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 valence (outer shell) electrons - Forms covalent bonds with: 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 + P i 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 Monomers Usage Maltose Lactose Sucrose 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