Chapter 2 Lecture and Animation Outline To run

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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 2 rhodium crystal

Atomic Structure • Atoms are composed of – Protons Bohr Atomic Model • Positively charged particles • Located in the nucleus – Neutrons • Neutral particles • Located in the nucleus – Electrons http: //d 1 jqu 7 g 1 y 74 ds 1. cloudfront. net/wpcontent/uploads/2010/02/c-atom_e 1. gif • Negatively charged particles • Found in orbitals surrounding the nucleus 3

Atomic number • Number of protons equals number of electrons • Atomic number = number of protons • 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

Properties of Subatomic Particles Subatomic Particle Summary subatomic particle Mass (in Daltons or a. m. u. ) charge proton 1 + neutron 1 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/s 9 s. 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 Orbitals Electron Shell Diagram Corresponding Electron Orbital Energy Level K One spherical orbital (1 s) Electron Shell Diagram Electron Orbitals y z x 14 Neon Copyright © The Mc. Graw-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 Li 1 valence e- Ne 8 valence e- 15

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 O 2, a diatomic molecule http: //en. wikipedia. org/wiki/File: Oxygen_molecule. png H 2 O, a compound 17 https: //commons. wikimedia. org/wiki/File: Water_molecule_3 D. 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

Copyright © The Mc. Graw-Hill Companies, Inc. Permission required for reproduction or display. covalent bond Single covalent bond Hydrogen gas H H H 2 Double covalent bond oxygen gas O O N H O O N N O 2 Triple covalent bond Nitrogen gas N H N 2 20

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

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

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 (C 6 H 12 O 6) 23 http: //www. nutritionalhq. com/wp-content/uploads/2011/08/Glucose-moleculemodel. 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/p. H/section 10/eshift 1. 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 6 H 2 O + 6 CO 2 reactants → C 6 H 12 O 6 + 6 O 2 products 27

Chemical reactions • Extent of chemical reaction influenced by 1. Temperature 2. Concentration of reactants and products 3. 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 Mc. Graw-Hill Companies, Inc. Permission required for reproduction or display. a. Solid b. Liquid a: © Glen Allison/Getty Images RF; b: © Photo. Link/Getty Images RF; c: © Jeff Vanuga/Corbis c. Gas 30

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+ http: //academic. brooklyn. cuny. edu/biology/bio 4 fv/page/image 15. gif 31

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

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

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

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 35 http: //www. baltimoresun. com/media/photo/2012 -05/70086876. jpg

Properties of water 3. Solid water is less dense than liquid water - Bodies of water freeze from the top down http: //www. hdwallpapersplus. com/wpcontent/uploads/2012/10/iceberg_2. jpg 36

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

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

4. Water is a good solvent – When H 2 O dissolves a polar or ionic compounds like Na. Cl – water is the solvent – Na. Cl is the solute • Both solvent and solute make up a solution 39 http: //bio 1151. nicerweb. com/Locked/media/ch 03/03_07 Dissolving. Salt-

5. Water organizes nonpolar molecules – Hydrophilic “water-loving” – Hydrophobic “water-fearing” – Water causes hydrophobic molecules to aggregate or assume specific shapes Hydrophobic molecule http: //www. uic. edu/classes/bios 100/lecturesf 04 am/hydrophobic. jpg 40

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

Acids and Bases - p. H • Acid (p. H < 7) – Any substance that dissociates in water to increase the [H+] (and lower the p. H) – The stronger an acid is, the more hydrogen ions it produces and the lower its p. H • Base (p. H > 7) – Substance that combines with H+ dissolved in water, and thus lowers the [H+] 43

Buffers • Substance that resists changes in p. H • 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 p. H Changes Copyright © The Mc. Graw-Hill Companies, Inc. Permission required for reproduction or display. p. H 9 8 7 6 5 4 3 2 1 0 Buffering range 0 1 X 2 X 3 X 4 X Amount of base added 5 X 46

Buffers • Most biological buffers consist of a pair of molecules, one an acid and one a base Copyright © The Mc. Graw-Hill Companies, Inc. Permission required for reproduction or display. – + Water Carbon (H 2 O) + dioxide (CO 2) + Carbonic acid (H 2 CO 3) + Bicarbonate Hydrogen ion + ion (H+) (HCO 3–) 47