1. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings PowerPoint Lectures for Biology, Seventh Edition Neil Campbell and Jane Reece Lectures by Chris Romero Chapter 2 The Chemical Context of Life

2. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Overview: Chemical Foundations of Biology

3. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The bombardier beetle uses chemistry to defend itself Figure 2.1

4. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 2.1: Matter consists of chemical elements in pure form and in combinations called compounds

5. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Elements and Compounds Organisms are composed of matter, which is anything that takes up space and has mass

6. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Matter is made up of elements, substances that cannot be broken down to other substances by chemical reactions

7. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings SodiumChloride Sodium Chloride + A compound – Is a substance consisting of two or more elements combined in a fixed ratio – Has characteristics different from those of its elements Figure 2.2

8. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings About 25 of the 92 natural elements are known to be essential for life. – Four elements - carbon (C), oxygen (O), hydrogen (H), and nitrogen (N) - make up 96% of living matter. – Most of the remaining 4% of an organism’s weight consists of phosphorus (P), sulfur (S), calcium (Ca), and potassium (K). 2. Life requires about 25 chemical elements Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

9. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings A few other elements – Make up the remaining 4% of living matter Table 2.1

10. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Trace elements are required by an organism but only in minute quantities. – Some trace elements, like iron (Fe), are required by all organisms. – Other trace elements are required only by some species. For example, a daily intake of 0.15 milligrams of iodine is required for normal activity of the human thyroid gland. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2.4

11. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Atomic number= number of protons Atomic mass= atomic weight= protons + neutrons – measured in daltons Helium= 4.003 daltons

12. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Nucleus (a) (b) In this even more simplified model, the electrons are shown as two small blue spheres on a circle around the nucleus. Cloud of negative charge (2 electrons) Electrons This model represents the electrons as a cloud of negative charge, as if we had taken many snapshots of the 2 electrons over time, with each dot representing an electron‘s position at one point in time. Simplified models of an atom Figure 2.4

13. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Atoms with different amounts of neutrons are isotopes

14. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Nonradioactive carbon-12Nonradioactive carbon-13Radioactive carbon-14 6 electrons 6 protons 6 neutrons 6 electrons 6 protons 8 neutrons 6 electrons 6 protons 7 neutrons Section 2-1 Figure 2-2 Isotopes of Carbon

15. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Radioactive isotopes have many applications in biological research. – Radioactive decay rates can be used to date fossils. – Radioactive isotopes can be used to trace atoms in metabolism. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

16. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2.6

17. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Radioactive isotopes are also used to diagnose medical disorders. – For example, the rate of excretion in the urine can be measured after injection into the blood of known quantity of radioactive isotope. – Also, radioactive tracers can be used with imaging instruments to monitor chemical processes in the body. Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 2.7 Cancerous throat tissue Figure 2.6

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19. While useful in research and medicine, the energy emitted in radioactive decay is hazardous to life. – This energy can destroy cellular molecules. – The severity of damage depends on the type and amount of energy that an organism absorbs. Fig. 2.8

20. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The Energy Levels of Electrons An atom’s electrons – Vary in the amount of energy they possess

21. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Energy – Is defined as the capacity to cause change Potential energy – Is the energy that matter possesses because of its location or structure

22. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The electrons of an atom – Differ in the amounts of potential energy they possess A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons, because the ball can only rest on each step, not between steps. (a) Figure 2.7A

23. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Atoms have different energy levels or shells Moving electrons to outer orbitals increases the atom’s potential energy The 3D space where an electron is found 90% of the time is called an orbital

24. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Electron Configuration and Chemical Properties The chemical behavior of an atom – Is defined by its electron configuration and distribution

25. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings The periodic table of the elements – Shows the electron distribution for all the elements Second shell Helium 2 He First shell Third shell Hydrogen 1 H 2 He 4.00 Atomic mass Atomic number Element symbol Electron-shell diagram Lithium 3 Li Beryllium 4 Be Boron 3 B Carbon 6 C Nitrogen 7 N Oxygen 8 O Fluorine 9 F Neon 10 Ne Sodium 11 Na Magnesium 12 Mg Aluminum 13 Al Silicon 14 Si Phosphorus 15 P Sulfur 16 S Chlorine 17 Cl Argon 18 Ar Figure 2.8

26. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Valence electrons – Are those in the outermost, or valence shell – Determine the chemical behavior of an atom

27. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Each electron shell – Consists of a specific number of orbitals Electron orbitals. Each orbital holds up to two electrons. 1s orbital2s orbitalThree 2p orbitals 1s, 2s, and 2p orbitals (a) First shell (maximum 2 electrons) (b) Second shell (maximum 8 electrons) (c) Neon, with two filled shells (10 electrons) Electron-shell diagrams. Each shell is shown with its maximum number of electrons, grouped in pairs. x Z Y Figure 2.9

28. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 2.3: The formation and function of molecules depend on chemical bonding between atoms

29. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Covalent Bonds A covalent bond – Is the sharing of a pair of valence electrons

30. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 2.10 Formation of a covalent bond Hydrogen atoms (2 H) Hydrogen molecule (H 2 ) + + + + ++ In each hydrogen atom, the single electron is held in its orbital by its attraction to the proton in the nucleus. 1 When two hydrogen atoms approach each other, the electron of each atom is also attracted to the proton in the other nucleus. 2 The two electrons become shared in a covalent bond, forming an H 2 molecule. 3

31. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings A molecule – Consists of two or more atoms held together by covalent bonds A single bond – Is the sharing of one pair of valence electrons A double bond – Is the sharing of two pairs of valence electrons

32. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings (a) (b) Name (molecular formula) Electron- shell diagram Structural formula Space- filling model Hydrogen (H 2 ). Two hydrogen atoms can form a single bond. Oxygen (O 2 ). Two oxygen atoms share two pairs of electrons to form a double bond. HH O O Figure 2.11 A, B Single and double covalent bonds

33. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Name (molecular formula) Electron- shell diagram Structural formula Space- filling model (c) Methane (CH 4 ). Four hydrogen atoms can satisfy the valence of one carbon atom, forming methane. Water (H 2 O). Two hydrogen atoms and one oxygen atom are joined by covalent bonds to produce a molecule of water. (d) H O H HH H H C Figure 2.11 C, D Covalent bonding in compounds

34. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Electronegativity – Is the attraction of a particular kind of atom for the electrons in a covalent bond The more electronegative an atom – The more strongly it pulls shared electrons toward itself

35. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings In a nonpolar covalent bond – The atoms have similar electronegativities – Share the electron equally

36. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Figure 2.12 This results in a partial negative charge on the oxygen and a partial positive charge on the hydrogens. H2OH2O –– O H H ++ ++ Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen. In a polar covalent bond – The atoms have differing electronegativities – Share the electrons unequally

37. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Ionic Bonds In some cases, atoms strip electrons away from their bonding partners

38. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Electron transfer between two atoms creates ions Ions – Are atoms with more or fewer electrons than usual – Are charged atoms

39. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings An anion – Is negatively charged ions A cation – Is positively charged

40. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Cl – Chloride ion (an anion) – The lone valence electron of a sodium atom is transferred to join the 7 valence electrons of a chlorine atom. 1 Each resulting ion has a completed valence shell. An ionic bond can form between the oppositely charged ions. 2 Na Cl + Na Sodium atom (an uncharged atom) Cl Chlorine atom (an uncharged atom) Na + Sodium on (a cation) Sodium chloride (NaCl ) Figure 2.13 An ionic bond – Is an attraction between anions and cations

41. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Na + Cl – Figure 2.14 Ionic compounds – Are often called salts, which may form crystals

42. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Weak Chemical Bonds Several types of weak chemical bonds are important in living systems

43. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Hydrogen Bonds  – –  + +  + + Water (H 2 O) Ammonia (NH 3 ) O H H  + +  – – N H H H A hydrogen bond results from the attraction between the partial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia. ++ ++ Figure 2.15 A hydrogen bond – Forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom

44. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Van der Waals Forces Electrons may gather on one side of an atom momentarily by chance causing one side to become slightly positive and the other negative

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46. Weak chemical bonds – Reinforce the shapes of large molecules – Help molecules adhere to each other

47. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Strength of Bonds Ionic (dry) -110 kcals/mole Covalent – 50 kcals/mole Hydrogen – 5 kcals/mole Ionic (aqueous) – 5 kcals/mole Vander waals – 1-2 kcals/mole Weak bonds help to shape the molecule

48. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Molecular Shape and Function The precise shape of a molecule – Is usually very important to its function in the living cell – Is determined by the positions of its atoms’ valence orbitals

49. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings s orbital Z Three p orbitals X Y Four hybrid orbitals (a) Hybridization of orbitals. The single s and three p orbitals of a valence shell involved in covalent bonding combine to form four teardrop-shaped hybrid orbitals. These orbitals extend to the four corners of an imaginary tetrahedron (outlined in pink). Tetrahedron Figure 2.16 (a) In a covalent bond – The s and p orbitals may hybridize, creating specific molecular shapes

50. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Space-filling model Hybrid-orbital model (with ball-and-stick model superimposed) Unbonded Electron pair 104.5° O H Water (H 2 O) Methane (CH 4 ) H H H H C O H H H C Ball-and-stick model H H H H (b) Molecular shape models. Three models representing molecular shape are shown for two examples; water and methane. The positions of the hybrid orbital determine the shapes of the molecules Figure 2.16 (b)

51. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Molecular shape – Determines how biological molecules recognize and respond to one another with specificity

52. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Molecules such as neural transmitters must have a specific shape to fit in the receptor molecule

53. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Morphine Carbon Hydrogen Nitrogen Sulfur Oxygen Natural endorphin (a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds to receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close match. (b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell recognize and can bind to both endorphin and morphine. Natural endorphin Endorphin receptors Morphine Brain cell Figure 2.17

54. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Concept 2.4: Chemical reactions make and break chemical bonds

55. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings A Chemical reaction – Is the making and breaking of chemical bonds – Leads to changes in the composition of matter

56. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings ReactantsReactionProduct 2 H 2 O2O2 2 H 2 O + + Chemical reactions – Convert reactants to products

57. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Photosynthesis – Is an example of a chemical reaction Figure 2.18

58. Copyright © 2005 Pearson Education, Inc. publishing as Benjamin Cummings Chemical equilibrium – Is reached when the forward and reverse reaction rates are equal