Chapter 2 Lecture and Animation Outline To run the animations you must be in Slideshow View. Use the buttons on the animation to play, pause, and turn audio/text on or off. Please Note: Once you have used any of the animation functions (such as Play or Pause), you must first click on the slide’s background before you can advance to the next slide. See separate PowerPoint slides for all figures and tables pre-inserted into PowerPoint without notes and animations. 1 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

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 Scanning Tunneling Microscopy Oxygen atoms on rhodium crystal 2

Atomic Structure Atoms are composed of Protons Neutrons Electrons Positively charged particles Located in the nucleus Neutrons Neutral particles Electrons Negatively charged particles Found in orbitals surrounding the nucleus Bohr Atomic Model http://d1jqu7g1y74ds1.cloudfront.net/wp-content/uploads/2010/02/c-atom_e1.gif 3

Atomic number Number of protons equals number of electrons Number of protons determines atom’s identity 5

Atomic mass Mass or weight? Mass – refers to amount of substance Weight – refers to force gravity exerts on substance An object has the same mass despite if it’s on Earth or the Moon which would change the weight Sum of protons and neutrons is the atom’s atomic mass Each proton and neutron has a mass of approximately 1 Dalton or atomic mass unit (a.m.u.) 6

Mass (in Daltons or a.m.u.) Properties of Subatomic Particles Subatomic Particle Summary subatomic particle Mass (in Daltons or a.m.u.) charge proton 1 + neutron neutral electron almost 0 -

Elements Element Any substance that cannot be broken down to any other substance by ordinary chemical means A given element is made up one type of atom Iron is an element because it is made up of only iron atoms 8 http://www.periodictable.com/Samples/026.32/s9s.JPG

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 12

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 Quantum model – orbital as area around a nucleus where an electron is most likely to be found 13

Electron Shell Diagram Electron Shell Diagram Electron Orbitals Electron Shell Diagram Corresponding Electron Orbital Energy Level K One spherical orbital (1s) Electron Shell Diagram Electron Orbitals y z x 14 Neon Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Reactivity of Elements Valence electrons (e-) – electrons in outermost energy level Inert (nonreactive) elements have all eight electrons Octet rule – atoms with 8 e- (2 e- for small atoms) in outer energy level are stable First energy level can hold 2 All others can hold 8 Atoms want to have full energy levels Ne Li 15 1 valence e- 8 valence e-

Reactivity of Elements Octet rule – Chemical bonds between atoms are based on unfilled outer energy levels Atom will want to gain, lose, or share electrons 16

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 O2, a diatomic molecule H2O, a compound 17 http://en.wikipedia.org/wiki/File:Oxygen_molecule.png https://commons.wikimedia.org/wiki/File:Water_molecule_3D.svg

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 19

covalent bond Single covalent bond Hydrogen gas H H H H H2 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. covalent bond Single covalent bond Hydrogen gas H H H H H2 Double covalent bond oxygen gas O O O O O2 Triple covalent bond Nitrogen gas N N N N N2 20

Covalent Bonds Polar covalent bonds Nonpolar covalent bonds Electrons not shared equally Example is water Nonpolar covalent bonds Electrons shared equally

Structural vs. Molecular Formulas Shows number and types of elements Structural formulas Shows arrangement of atoms and types of bonds present 22 http://www.cliffsnotes.com/assets/276058.png

Carbon and Organic Molecules Carbon can form up to 4 single covalent bonds Carbon atoms can form linear chains or rings These carbon “backbones” form basis of organic molecules Glucose (C6H12O6) 23 http://www.nutritionalhq.com/wp-content/uploads/2011/08/Glucose-molecule-model.jpg

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 24 http://www.chem.ubc.ca/courseware/pH/section10/eshift1.jpg http://www.chem.ubc.ca/courseware/pH/section10/eshift1.jpg

Water – Polar Covalent Bond

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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 6H2O + 6CO2 → C6H12O6 + 6O2 reactants products 27

Chemical reactions Extent of chemical reaction influenced by Temperature Concentration of reactants and products Catalysts Many reactions are reversible 28

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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. 30 a. Solid b. Liquid c. Gas 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 Partial electrical charges develop Oxygen is partially negative δ+ Hydrogen is partially positive δ– δ δ+ δ+ δ+ 31 http://academic.brooklyn.cuny.edu/biology/bio4fv/page/image15.gif

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 32

Hydrogen atom Water molecule + – Hydrogen bond a. Oxygen atom Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Hydrogen atom Water molecule + – Hydrogen bond a. Oxygen atom Hydrogen atom Hydrogen bond + – An organic molecule 33 b . Oxygen atom

Adhesion – water molecules stick to other polar molecules by hydrogen bonding Cohesion – water molecules stick to other water molecules by hydrogen bonding 34

Properties of water Water has a high specific heat A large amount of energy is required to change the temperature of water Water has a high heat of vaporization The evaporation of water from a surface causes cooling of that surface 35 http://www.baltimoresun.com/media/photo/2012-05/70086876.jpg

Properties of water Solid water is less dense than liquid water - Bodies of water freeze from the top down 36 http://www.hdwallpapersplus.com/wp-content/uploads/2012/10/iceberg_2.jpg

37 http://sailboatdiaries.com/wp-content/uploads/iceHbonds.gif

4. Water is a good solvent Water dissolves polar molecules and ions 38 Hydration shells Water molecules Salt crystal Cl– Na+ +  – 38 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Both solvent and solute make up a solution 4. Water is a good solvent When H2O dissolves a polar or ionic compounds like NaCl water is the solvent NaCl is the solute Both solvent and solute make up a solution 39 http://bio1151.nicerweb.com/Locked/media/ch03/03_07DissolvingSalt-L.jpg

5. Water organizes nonpolar molecules Hydrophilic “water-loving” Hydrophobic “water-fearing” Water causes hydrophobic molecules to aggregate or assume specific shapes Hydrophobic molecule 40 http://www.uic.edu/classes/bios/bios100/lecturesf04am/hydrophobic.jpg

Acids and bases Pure water [H+] of 10–7 mol/L Considered to be neutral Neither acidic nor basic [H+] = [OH-] pH is the negative logarithm of hydrogen ion concentration of solution pH = -log[H+] pH= –log 10-7 = -(-7)=7 42

Acids and Bases - pH Acid (pH < 7) Base (pH > 7) 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 (pH > 7) Substance that combines with H+ dissolved in water, and thus lowers the [H+] 43

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 45

Buffers Minimize pH Changes Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. 9 8 7 6 Buffering range 5 pH 4 3 2 1 1X 2X 3X 4X 5X Amount of base added 46

Buffers 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 (H2O) Carbon dioxide (CO2) Carbonic acid (H2CO3) Bicarbonate ion (HCO3–) Hydrogen ion (H+) + + 47