Chemical Foundations for Cells Chapter 6 - The Chemistry of Life You are chemical, and so is every living and nonliving thing in the universe. Elements • Fundamental forms of matter • Can’t be broken apart by normal means • 92 occur naturally on Earth, 28 elements common to most life on Earth Most Common Elements in Living Organisms Carbon Hydrogen Oxygen Nitrogen Phosphorus Sulfur What Are Atoms? • Smallest particles that retain properties of an element • Made up of subatomic particles: – Protons (+) – Electrons (-) – Neutrons (no charge) Examples of Atoms electron proton neutron Hydrogen Helium Figure 2.2 Page 22 Atomic Number • Number of protons • All atoms of an element have the same atomic number • Atomic number of hydrogen = 1 • Atomic number of carbon = 6 Mass Number Number of protons + Number of neutrons Isotopes vary in mass number Isotopes • Atoms of an element with different numbers of neutrons (different mass numbers) • Carbon 12 has 6 protons, 6 neutrons • Carbon 14 has 6 protons, 8 neutrons Radioisotopes • Have an unstable nucleus that emits energy and particles • Radioactive decay transforms radioisotope into a different element • The end product of radioactive decay is the decay element • Decay occurs at a fixed rate Uses of Radioisotopes • • • • Tracers Thyroid scan PET scan Radiation therapy • Drive artificial pacemakers normal thyroid scan enlarged thyroid detector ring in PET scanner the only section of body in ring greatest activity (red) ring intercepts any emissions from labeled molecules What Determines whether Atoms Will Interact? The number and arrangement of their electrons Shell Model • First shell – Lowest energy – Holds maximum of 2 electrons • Second shell (and 3rd and 4th) – Can hold up to 8 electrons CALCIUM 20p+ , 20e- Electron Vacancies • Unfilled shells make atoms likely to react • Hydrogen, carbon, oxygen, and nitrogen all have vacancies in their outer shells CARBON 6p+ , 6e- NITROGEN 7p+ , 7e- HYDROGEN 1p+ , 1e- HYDROGEN 1p+, 1e- HELIUM 2p+, 2e- CARBON 6p+, 6e- NITROGEN 7p+, 7e- OXYGEN 8p+, 8e- SODIUM 11p+, 11e- CHLORINE 17p+, 17e- CALCIUM 20p+, 20e- Chemical Bonds, Molecules, & Compounds • Bond is union between electron structures of atoms • Atoms bond to form molecules • Molecules may contain atoms of only one element - O2 • Molecules of compounds contain more than one element - H2O Chemical Bookkeeping • Use symbols for elements when writing formulas • Formula for glucose is C6H12O6 – 6 carbons – 12 hydrogens – 6 oxygens Chemical Bookkeeping • Chemical equation shows reaction Reactants ---> Products • Equation for photosynthesis: 6CO2 + 6H2O ---> + C6H12O6 + 6H2O Important Bonds in Biological Molecules Ionic Bonds Covalent Bonds Hydrogen Bonds Ionic Bonding • One atom loses electrons, becomes positively charged ion • Another atom gains these electrons, becomes negatively charged ion • Charge difference attracts the two ions to each other electron transfer SODIUM ATOM 11 p+ 11 e- CHLORINE ATOM 17 p+ 17 e- SODIUM ION 11 p+ 10 e- CHLORINE ION 17 p+ 18 e- Cation Anion Formation of NaCl • Sodium atom (Na) – Outer shell has one electron • Chlorine atom (Cl) – Outer shell has seven electrons • Na transfers electron to Cl, forming Na+ and Cl• Ions remain together as NaCl Covalent Bonding Atoms share a pair or pairs of electrons to fill outermost shell •Single covalent bond •Double covalent bond •Triple covalent bond Molecular hydrogen Polar or Nonpolar Bonds • Nonpolar if atoms share electrons equally – Hydrogen gas (H - H) • Polar if electrons spend more time near nucleus with most protons – Water – Electrons more attracted to O nucleus than to H nuclei Hydrogen bond Water molecule Ammonia molecule Hydrogen Bonding • Atom in one polar covalent molecule is attracted to oppositely charged atom in another such molecule or in same molecule Water molecule Ammonia molecule Figure 2.11a Page 27 Multiple H bonds holding two molecules together Hydrogen Bonding in DNA Figure 2.11d Page 27 Water Is a Polar Covalent Molecule • Molecule has no net charge O • Oxygen end has a slight negative charge H H • Hydrogen end has a slight positive charge Figure 2.12a Page 28 Slight negative charge at this end No overall charge H H Slight positive charge at this end Stop here for Unit 2 Quiz #1 Photo Album by Administrator Properties of Water Water is an excellent solvent – polar and ionic substances dissolve well • Bonds to hydrophilic substances • Repels hydrophobic ones • Temperature moderating effects • Good evaporative coolant • Expands when it freezes – density anomaly • Cohesive and adhesive Liquid and Solid Water What can you infer? Photo Album by Administrator Evaporative cooling Liquid water Ice Arrangement of water molecules in solid ice versus water Hydrogen bond Ice Hydrogen bonds are stable Liquid water Hydrogen bonds constantly break and re-form Evaporation Vascular tissue Xylem (up) Phloem (down) Adhesion Transpiration Cohesion Surface tension of water allows a water strider to walk on water Salts • Compounds that release ions other than H+ and OH- when dissolved in water • Example: NaCl releases Na+ and Cl– • Many salts dissolve into ions that play important biological roles A crystal of salt (NaCl) dissolving in water Na+ – + Na+ Cl– – + Cl– + – – + + – + – + – – – Ion in solution Salt crystal – Hydrated Ions in Solution – – + + – – – + + – – + + Na+ – + Cl– + + + + – – + + + – + + + + – Hydrogen Ions: H+ • Unbound or naked protons • Have important biological effects • When water ionizes it forms hydrogen and hydroxide ions Acids & Bases • Acids – Donate H+ when dissolved in water – Acidic solutions have pH < 7 • Bases – Accept H+ when dissolved in water – Has an excess of OH – ions – Basic solutions have pH > 7 The pH Scale • Measures H+ concentration of fluid • Change of 1 on scale means 10X change in H+ concentration Highest H+ Lowest H+ 0---------------------7-------------------14 Acidic Neutral Basic Examples of pH • Pure water is neutral with pH of 7.0 • Acidic – Stomach acid: pH 1.0 - 3.0 – Lemon juice: pH 2.3 • Basic – Seawater: pH 7.8 - 8.3 – Baking soda: pH 9.0 Neutralization Reaction HCI + NaOH hydrochloric sodium acid hydroxide (a base) NaCl + H2O sodium chloride (a salt) Na+ Cl _ Acid Precipitation • Normal rain has a pH of 5.6 due to carbon dioxide in atmosphere • Burning of fossil fuels and industrial pollution add sulfur dioxide and nitrous oxides to atmosphere • Acid rain is 4.6 or lower • Snow melts dump lots of acid into ecosystem at worst possible time Effects of acid precipitation on a fir forest in the Czech Republic Damage to a statue in Germany between 1908 and 1968 Buffer Systems • Minimize shifts in pH • Partnership between weak acid and the base it forms when dissolved • They work together to counter shifts in pH by acting as a base or an acid to neutralize the effects of adding either H+ or 0H- Carbonic Acid-Bicarbonate Buffer System • When blood pH rises, carbonic acid dissociates to form bicarbonate and H+ H2C03 -----> HC03- + H+ • When blood pH drops, bicarbonate binds H+ to form carbonic acid HC03- + H+ -----> H2C03 Adding a base to solution: HCO3 H2CO3 carbonic acid _ + H+ bicarbonate Adding an acid to solution: HCO3 _ bicarbonate + H+ H2CO3 carbonic acid Atoms have positively charged have neutral (a) (b) number present equals number may differ in atomic number of each element have negatively charged (c) number in outer shell determines formation of (d) H Chemical Bonds electron transfer between atoms creates Na electron sharing between atoms creates H CI ions (e) unequal equal sharing sharing creates creates attraction between ions creates (f) nonpolar covalent bonds (g) (–) (–) O H (+) H H example is (+) Water can lead to has important qualities due to polarity and (h) H (+) (–) O
