1. Chapter 2: Chemistry (!)
In many ways, life can be viewed as a complicated chemical reaction.
Modern models of how life works at all levels typically have at least some aspect of chemistry as a major component or underpinning.
Therefore….
You must understand chemistry to understand life (and to pass this course)!

2. Chapter 2: Chemistry Elements and Atoms Describing Atomic Combinations
Chemical Bonds Hold Molecules Together and Store Energy
Chemical Equations Describe Chemical Reactions
Oxidation-Reduction Reactions (redox reactions) Are Common in Biological Systems

3. Chapter 2: Chemistry Elements and Atoms Describing Atomic Combinations
Chemical Bonds Hold Molecules Together and Store Energy
Chemical Equations Describe Chemical Reactions
Oxidation-Reduction Reactions (redox reactions) Are Common in Biological Systems

4. Describe the difference between the terms “element” and “atom”.
What are chemical symbols, and what is the periodic table?
Draw a model of a neutral atom with atomic number 6 and atomic mass 12.

5. Elements and Atoms

6. Elements and Atoms
elements – substances that cannot be further broken down into other substances (at least by ordinary chemical reactions)
every element has a chemical symbol (H for hydrogen, O for oxygen, etc.); this is most familiar from the periodic table
there are 92 naturally occurring elements, from hydrogen up to uranium

7. Elements and Atoms O, C, H, N ~ 96% of living mass
Ca, P, K, S, Na, Cl, Mg, Fe - consistently present in small amounts
several trace elements

9. Elements and Atoms atom = smallest unit of an element
electron: little mass; -1
proton: ~1 mass unit; +1
neutron : ~1 mass unit
nucleus: protons and neutrons

10. Elements and Atoms atomic number = # of protons
periodic table arranged largely according to atomic number

11. Elements and Atoms atomic mass ≈ protons + neutrons
isotopes:# of protons same, # of neutrons different

12. Describe the difference between the terms “element” and “atom”.
What are chemical symbols, and what is the periodic table?
Draw a model of a neutral atom with atomic number 6 and atomic mass 12.

13. Draw a model of a neutral atom with atomic number 6 and atomic mass 14.
Compare with the previous atom that you drew and discuss isotopes.

14. Fig. 2.3

15. Elements and Atoms atomic decay alpha, beta, and/or gamma radiation
many uses and dangers
DNA mutations
decay rates are averages
used for measuring time
radioisotopes: most unstable isotopes

16. Draw a model of a neutral atom with atomic number 6 and atomic mass 14.
Compare with the previous atom that you drew and discuss isotopes.

17. What are electron orbitals?
What is the valence shell?
How does the valence shell relate to chemical reactivity of an atom?

18. Elements and Atoms electrons occupy orbitals
ATOMS: # of electrons = # of protons
orbitals: electrons energy levels, location probabilities
electron shell: orbitals with similar energies

19. Elements and Atoms

20. Elements and Atoms valence shell: filled by highest-energy electrons
valence electrons involved in chemical interactions
“rule of eight”

21. What are electron orbitals?
What is the valence shell?
How does the valence shell relate to chemical reactivity of an atom?

22. Chapter 2: Chemistry Elements and Atoms Describing Atomic Combinations
Chemical Bonds Hold Molecules Together and Store Energy
Chemical Equations Describe Chemical Reactions
Oxidation-Reduction Reactions (redox reactions) Are Common in Biological Systems

23. Draw a Venn diagram for the following terms:
molecule
compound
Then place the following in the diagram:
O2 NaCl H2O

24. Describing Atomic Combinations
molecule – has covalent bonds
one or more elements
examples: O2, H2O
smallest unit of a molecular substance
differs in properties from its elements

25. Describing Atomic Combinations
compound - two or more different elements combined
may just be ratios, not fixed numbers
differs in properties from its elements
may have ionic bonds

26. Describing Atomic Combinations
chemical formula - number of atoms of each element
molecular formula for molecules
examples: H2O, CO2, O2, C6H12O6
simplest ratio for ionic compounds (NaCl, etc.)
structural formula - arrangement of atoms
examples:
water H─O─H
carbon dioxide O═C═O
molecular oxygen O═O

27. Draw a Venn diagram for the following terms:
molecule
compound
Then place the following in the diagram:
O2 NaCl H2O

28. Discuss moles, atomic mass units, and Avogadro’s number.
Why use moles instead of just mass?
Discuss the water and glucose problem (will be given in class).

29. Describing Atomic Combinations
molecular mass = sum of the atomic masses in molecule
mole: # molecules for gram amount to = atomic mass
Example:
water has molecular mass = 18
mole of water has a mass of 18 g
mole is simply a conversion factor
Avogadro’s number, is 6.02 x 1023 atoms or molecules

30. Discuss moles, atomic mass units, and Avogadro’s number.
Why use moles instead of just mass?
Discuss the water and glucose problem (will be given in class).

31. Chapter 2: Chemistry Elements and Atoms Describing Atomic Combinations
Chemical Bonds Hold Molecules Together and Store Energy
Chemical Equations Describe Chemical Reactions
Oxidation-Reduction Reactions (redox reactions) Are Common in Biological Systems

32. What is a covalent bond?
What do polar and nonpolar mean for covalent bonds?
Give an example of each.

33. Chemical Bonds Hold Molecules Together and Store Energy
outermost shell (valence electrons) determine chemistry
filled shells: rule of 8

34. Chemical Bonds Hold Molecules Together and Store Energy
chemical bonds are based on filling valence shells
reduced energy state
bond energy amount required to break bond

35. Chemical Bonds Hold Molecules Together and Store Energy
strong chemical bonds
covalent bonds – electrons shared
ionic bonds – ions of opposite charge

36. Chemical Bonds Hold Molecules Together and Store Energy
covalent bonds
electrons shared in pairs
1 pair is a single covalent bond
double and triple also possible
carbon forms four total

37. Chemical Bonds Hold Molecules Together and Store Energy
covalent bonds
give definite shapes
spacial arrangements of shared orbitals

38. Chemical Bonds Hold Molecules Together and Store Energy
covalent bonds
nonpolar: equal sharing
polar: unequal sharing
polar if one nucleus holds a stronger attraction on the electron pair
polar molecules have regions with partial charges

39. What is a covalent bond?
What do polar and nonpolar mean for covalent bonds?
Give an example of each.

40. What are ions?
What are cations and anions?
What is an ionic bond?
Give an example of an ionic bond.

41. Chemical Bonds Hold Molecules Together and Store Energy
ionic bonds
ion: atom that has gained or lost at least one net electron
cations - lost one or more; +charge
anions - gained one or more; -charge
–ide indicates an anion
polyatomic ions can also form
covalently bound atoms that lose or gain electrons or protons
only polyatomic ions can lose or gain protons

42. Chemical Bonds Hold Molecules Together and Store Energy
ionic bonds
ionic bond: cation/anion attraction
ionic compound: substance with ionic bonds

43. Chemical Bonds Hold Molecules Together and Store Energy
ionic bonds
polar substances, such as water, tend to dissolve ionic compounds
hydration – surrounding ions with the ends water molecules with the opposite (partial) charge

44. What are ions?
What are cations and anions?
What is an ionic bond?
Give an example of an ionic bond.

45. What are hydrogen bonds?
Draw an example.

46. Chemical Bonds Hold Molecules Together and Store Energy
hydrogen bonds
d+ with d-
d+ charge is usually H
weak interaction

47. Chemical Bonds Hold Molecules Together and Store Energy
hydrogen bonds
common and important in living things
water forms them
weak means relatively easy to manipulate
collectively, hydrogen bonds can be very strong – they hold together the two strands of DNA, for example

48. What are hydrogen bonds?
Draw an example.

49. Chemical Bonds Hold Molecules Together and Store Energy
In aqueous systems (such as living organisms), the effective relative bond strengths are:
covalent bond > ionic bond > hydrogen bond

50. Chapter 2: Chemistry Elements and Atoms Describing Atomic Combinations
Chemical Bonds Hold Molecules Together and Store Energy
Chemical Equations Describe Chemical Reactions
Oxidation-Reduction Reactions (redox reactions) Are Common in Biological Systems

51. Discuss the chemical equations in the notes and the terms there (reactant, product, equilibrium).

52. Chemical Equations Describe Chemical Reactions
Reactants are written on the left
Products are written on the right
an arrow ( ) is used to show the direction the reaction proceeds
C6H12O O CO H2O + Energy
double arrows ( ) indicate equilibrium reactions - i.e. reactions proceeding at simultaneously in both directions
N H NH3
Sometimes, different lengths of double arrows are used to indicate which direction is favored
CO2 + H2O H2CO3

53. Discuss the chemical equations in the notes and the terms there (reactant, product, equilibrium).

54. Chapter 2: Chemistry Elements and Atoms Describing Atomic Combinations
Chemical Bonds Hold Molecules Together and Store Energy
Chemical Equations Describe Chemical Reactions
Oxidation-Reduction Reactions (redox reactions) Are Common in Biological Systems

55. What gets oxidized/reduced in the following:
What is a redox reaction, and how does it relate to movement of electrons and movement of energy?
What gets oxidized/reduced in the following:
making NaCl
rusting iron
What gains/loses energy in each case?

58. Oxidation-Reduction Reactions Are Common in Biological Systems
example: rusting
4 Fe O Fe2O3
during the process iron atoms (Fe) become iron ions (Fe3+):
4 Fe Fe e-
on the flip side, the oxygen atoms gain electrons
3 O e O2-

59. Oxidation-Reduction Reactions Are Common in Biological Systems
oxygen is common oxidizing agent (hence “oxidation”)
redox in biological systems
very important in photosynthesis, respiration, more
electrons are less easily lost from molecules than from atoms
molecules typically will lose the equivalent of a complete hydrogen atom when oxidized (proton as well as electron)
counting charge changes alone is not sufficient – look for movement of electrons , includes complete H equivalent

60. What gets oxidized/reduced in the following:
What is a redox reaction, and how does it relate to movement of electrons and movement of energy?
What gets oxidized/reduced in the following:
making NaCl
rusting iron
What gains/loses energy in each case?