The Nature of Molecules and the Properties of Water Chapter 2 1
Nature of Atoms Matter has mass and occupies space All matter is composed of atoms Understanding the structure of atoms is critical to understanding the nature of biological molecules 2
Atomic Structure Atoms are composed of Protons Positively charged particles Located in the nucleus Neutrons Neutral particles Located in the nucleus Electrons Negatively charged particles Found in orbitals surrounding the nucleus 3
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Hydrogen 1 Proton 1 Electron Oxygen 8 Protons 8 Neutrons 8 Electrons a. b. proton (positive charge) electron (negative charge) neutron (no charge) 4
Atomic number Number of protons equals number of electrons Atoms are electrically neutral Atomic number = number of protons Every atom of a particular element has the same number of protons Element Any substance that cannot be broken down to any other substance by ordinary chemical means 5
Atomic mass Mass or weight? Mass refers to amount of substance Weight refers to force gravity exerts on substance Sum of protons and neutrons is the atom s atomic mass Each proton and neutron has a mass of approximately 1 Dalton 6
Electrons Negatively charged particles located in orbitals Neutral atoms have same number of electrons and protons Ions are charged particles unbalanced Cation more protons than electrons = net positive charge Anion fewer protons than electrons = net negative charge 7
Isotopes Atoms of a single element that possess different numbers of neutrons Radioactive isotopes are unstable and emit radiation as the nucleus breaks up Half-life time it takes for one-half of the atoms in a sample to decay 8
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Carbon-12 Carbon-13 Carbon-14 6 Protons 6 Neutrons 6 Electrons 6 Protons 7 Neutrons 6 Electrons 6 Protons 8 Neutrons 6 Electrons 9
Electron arrangement Key to the chemical behavior of an atom lies in the number and arrangement of its electrons in their orbitals Bohr model electrons in discrete orbits Modern physics defines orbital as area around a nucleus where an electron is most likely to be found No orbital can contain more than two electrons 10
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Electron Shell Diagram Corresponding Electron Orbital Energy Level K One spherical orbital (1s) Electron Shell Diagram Energy level L Corresponding Electron Orbitals x y z One spherical orbital (2s) Three dumbbell-shaped orbitals (2kk) Electron Shell Diagram Electron Orbitals y z x Neon 11
Energy levels Electrons have potential energy related to their position Electrons farther from nucleus have more energy Be careful not to confuse energy levels, which are drawn as rings to indicate an electron s energy, with orbitals, which have a variety of three-dimensional shapes and indicate an electron s most likely location 12
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Energy released Energy absorbed Nucleus N M L K K L M N Nucleus 13
Redox During some chemical reactions, electrons can be transferred from one atom to another Still retain the energy of their position in the atom Oxidation = loss of an electron Reduction = gain of an electron Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. + + + Oxidation Reduction 14
Elements Periodic table displays elements according to valence electrons Valence electrons number of electrons in outermost energy level Inert (nonreactive) elements have all eight electrons Octet rule atoms tend to establish completely full outer energy levels 15
Periodic Table of the Elements Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 1 H 3 Li 11 Na 19 K 37 Rb 55 Cs 87 Fr 4 Be 12 Mg 20 Ca 38 Sr 56 Ba 88 Ra 21 Sc 39 Y 57 La 89 Ac 22 Ti 40 Zr 72 Hf (Lanthanide series) Key 1 H 23 V 41 Nb 73 Ta 24 Cr 42 Mo 74 W 25 Mn 75 Re 76 Os 27 Co 45 Rh 77 Ir 104 105 106 107 108 109 58 Ce Pr 59 atomic number chemical symbol 43 Tc 26 Fe 44 Ru 28 Ni 46 Pd 78 Pt 110 Rf Ob Sg Bh Hs Mt Ds 29 Cu 47 Ag 79 Au 30 Zn 48 Cd 80 Hg 5 B 13 Al 31 Ga 49 In 81 Tl 6 C 14 Si 32 Ge 50 Sn 82 Pb 8 O 2 7 N 15 P 33 As 51 Sb 83 Bi 60 61 62 63 64 65 66 67 68 Nd Pm Sm Eu Gd Tb Dy Ho Er 16 S 34 Se 52 Te 84 Po 9 F 17 Cl 35 Br 53 I 85 At 111 112 113 114 115 116 117 He 10 Ne 18 Ar 36 Kr 54 Xe 86 Rn 118 Rg Cn Uut Fl Uup Lv Uus Uuo 69 70 71 Tm Yb Lu C O H N Na Cl Ca P K S Fe Carbon (C) Oxygen (O) Hydrogen (H) Nitrogen (N) Sodium (Na) Chlorine (Cl) Calcium (Ca) Phosphorus (P) Potassium (K) Sulfur (S) Iron (Fe) 90 91 92 93 94 95 (Actinide series) Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr a. b. 96 97 98 99 100 101 102 103 Mg Magnesium (Mg) 16
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 90 naturally occurring elements Only 12 elements are found in living organisms in substantial amounts Four elements make up 96.3% of human body weight Carbon, hydrogen, oxygen, nitrogen Organic molecules contain primarily CHON Some trace elements are very important C O H N Na Cl Ca P K S Fe Mg b. Carbon (C) Oxygen (O) Hydrogen (H) Nitrogen (N) Sodium (Na) Chlorine (Cl) Calcium (Ca) Phosphorus (P) Potassium (K) Sulfur (S) Iron (Fe) Magnesium (Mg) 17
Chemical Bonds Molecules are groups of atoms held together in a stable association Compounds are molecules containing more than one type of element Atoms are held together in molecules or compounds by chemical bonds 18
Ionic bonds Formed by the attraction of oppositely charged ions Gain or loss of electrons forms ions Na atom loses an electron to become Na + Cl atom gains an electron to become Cl Opposite charges attract so that Na + and Cl remain associated as an ionic compound Electrical attraction of water molecules can disrupt forces holding ions together 19
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Na Na + Sodium atom Sodium ion (+) Cl Cl Chlorine atom Chloride ion ( ) a. Cl Na + Cl Na + Cl Na + Cl Na + Cl b. NaCl crystal 20
Covalent bonds Form when atoms share 2 or more valence electrons Results in no net charge, satisfies octet rule, no unpaired electrons Strength of covalent bond depends on the number of shared electrons Many biological compounds are composed of more than 2 atoms may share electrons with 2 or more atoms 21
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Single covalent bond Hydrogen gas H H H 2 covalent bond H H Double covalent bond oxygen gas O O O 2 O O Triple covalent bond Nitrogen gas N N N 2 N N 22
Electronegativity Atom s affinity for electrons Differences in electronegativity dictate how electrons are distributed in covalent bonds Nonpolar covalent bonds = equal sharing of electrons Polar covalent bonds = unequal sharing of electrons 23
Chemical reactions Chemical reactions involve the formation or breaking of chemical bonds Atoms shift from one molecule to another without any change in number or identity of atoms Reactants = original molecules Products = molecules resulting from reaction 6H 2 O + 6CO 2 C 6 H 12 O 6 + 6O 2 reactants products 24
Extent of chemical reaction influenced by 1. Temperature 2. Concentration of reactants and products 3. Catalysts Many reactions are reversible 25
Water Life is inextricably tied to water Single most outstanding chemical property of water is its ability to form hydrogen bonds Weak chemical associations that form between the partially negative O atoms and the partially positive H atoms of two water molecules Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. a. Solid b. Liquid c. Gas 27 a: Glen Allison/Getty Images RF; b: PhotoLink/Getty Images RF; c: Jeff Vanuga/Corbis
Polarity of water Within a water molecule, the bonds between oxygen and hydrogen are highly polar Oxygen is much more electronegative than Hydrogen Partial electrical charges develop Oxygen is partially negative δ + Hydrogen is partially positive δ 28
c. Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Bohr Model Ball-and-Stick Model + + + 8p 8n + 104.5 + + a. b. Space-Filling Model + +
Hydrogen bonds Cohesion polarity of water allows water molecules to be attracted to one another Attraction produces hydrogen bonds Each individual bond is weak and transitory Cumulative effects are enormous Responsible for many of water s important physical properties 30
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Water molecule + Hydrogen atom Hydrogen bond a. Oxygen atom Hydrogen atom + Hydrogen bond b. An organic molecule Oxygen atom 31
Cohesion water molecules stick to other water molecules by hydrogen bonding Adhesion water molecules stick to other polar molecules by hydrogen bonding 32
Properties of water 1. Water has a high specific heat A large amount of energy is required to change the temperature of water 2. Water has a high heat of vaporization The evaporation of water from a surface causes cooling of that surface 3. Solid water is less dense than liquid water Bodies of water freeze from the top down 33
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Water molecules Na+ Hydration shells Na + Cl + + Cl + + + Salt crystal 34
4. Water is a good solvent Water dissolves polar molecules and ions 5. Water organizes nonpolar molecules Hydrophilic water-loving Hydrophobic water-fearing Water causes hydrophobic molecules to aggregate or assume specific shapes 6. Water can form ions H 2 O OH + H + hydroxide ion hydrogen ion 35
Acids and bases Pure water [H + ] of 10 7 mol/l Considered to be neutral Neither acidic nor basic ph is the negative logarithm of hydrogen ion concentration of solution 36
Acids and Bases - ph Acid Any substance that dissociates in water to increase the [H + ] (and lower the ph) The stronger an acid is, the more hydrogen ions it produces and the lower its ph Base Substance that combines with H + dissolved in water, and thus lowers the [H + ] 37
Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Hydrogen Ion Concentration [H + ] ph Value Examples of Solutions 10 0 0 Acidic 10 1 1 Hydrochloric acid 10 2 2 Stomach acid, lemon juice 10 3 3 Vinegar, cola, beer 10 4 4 Tomatoes 10 5 5 Black coffee 10 6 6 Urine 10 7 Pure water 10 8 8 Seawater 10 9 9 Baking soda 10 10 10 Great Salt Lake 10 11 11 Household ammonia 10 12 12 Household bleach 13 10 13 10 14 14 Basic Sodium hydroxide 38
Buffers Substance that resists changes in ph Act by Releasing hydrogen ions when a base is added Absorbing hydrogen ions when acid is added Overall effect of keeping [H+] relatively constant 39
ph Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 9 8 7 6 5 4 3 2 1 0 Buffering range 0 1X 2X 3X 4X 5X Amount of base added 40
Most biological buffers consist of a pair of molecules, one an acid and one a base Copyright The McGraw-Hill Companies, Inc. Permission required for reproduction or display. + + + Water (H 2 O) + Carbon dioxide (CO 2 ) Carbonic acid (H 2 CO 3 ) Bicarbonate ion (HCO 3 ) + Hydrogen ion (H + ) 41