1. Chemistry for Bio 9
Spring 2011

3. Which of the following is/are properties of life?
a complex organization  
the ability to take in energy and use it  
the ability to respond to stimuli from the environment  
the ability to reproduce  
All of the choices are correct.  

4. Lecture outline Chemistry- definition, scope, and relevance to biology
Classification of matter
The atom and subatomic particles
Chemical bonding & reactions
Chemistry of water
Acids, Bases, and the pH scale

5. Chemistry is relevant to Biological Concepts
Chemistry is the study of matter and its interactions
All Living things are made of matter
Biolgists are interested in:
Complex biological molecules
Chemical energy
Biochemical reactions
The chemical environment

6. Complex biological molecules
All living things are made of complex macromolecules
Chemical principles rule their assembly

7. Chemical energy Photosynthesis creates molecules rich in energy:
6CO2(g)+ 6H2O(l) + hν  C6H12O6(s) + 6O2(g)
Earth has been transformed by chemical reactions peformed by living things

8. Biochemical reactions
All living things are collections of a vast number of chemical reactions
Even the simplest living things contain impossibly complex pathways

10. The Chemical Environment
The physical properties of water determine the fate of life on earth
pH, salinity and other chemical factors influence
Living things are profoundly influenced by their chemical environment

11. Chemical reactions performed by living things have transformed earth over billions of years of its history

12. Classification of matter

13. Classification of matter
Mixtures can be homogeneous or heterogeneous
Mixtures can vary in composition of their ingredients
Compounds are defined substances with proportional amounts of ingredients: water, carbon dioxide, etc.
Elements cannot be broken down into ingredients by chemical processes

14. Basic principles of chemistry

15. The periodic table is an organized display of all the elements in the universe
This is so interesting! Wow!

16. The Structure of the Atom
Subatomic particles- protons, neutrons electrons
Orbitals and the nucleus

17. All matter is comprised of atoms
Atoms themselves are made of 3 kinds of subatomic particles
Protons
Neutrons
Electrons
Protons and neutrons reside in the nucleus

18. All matter is ultimately comprised of atoms
Atoms are the smallest individual unit of matter
Atoms are comprised of protons, neutrons and electrons
Proton: Charge= +1, Mass= 1
Neutron: Chg= 0, mass= 1
Electron: Chg = -1, mass= ~0
Mass= p + n
Charge = p - e

19. Electron cloud 6e– 2e– Nucleus 2 6 2 6 2 6
LE 2-4a
Electron
cloud
6e–
2e–
Nucleus 2
Protons 6
Protons
Mass
number = 4
Mass
number = 12 2
Neutrons 6
Neutrons 2
Electrons 6
Electrons
Helium atom
Carbon atom

20. Reading the Periodic Table

21. Elements are defined by the number of their protons
There are 92 naturally occurring elements
Many others have been synthesized
Atomic number = # protons
Atomic mass (mass number) = protons + neutrons of an individual atom
Atomic weight= Naturally occurring average of isotopes of a substance

22. The number of neutrons in atoms of a single element is variable
Isotopes are variants of an element, differentiated by numbers of neutrons
Some isotopes are stable, others are radioactive (radioisotopes)

23. Some isotopes are common, others rare

24. Many Isotopes for an element can exist; radioisotopes are radioactive

25. Radioisotopes can be used as tracers in medical diagnosis- Radioisotopes of iodine target the thyroid gland

26. How is atomic weight different from atomic mass?

27. How is atomic weight different from atomic mass?
All carbon atoms have 6 protons
Most, but not all, carbon atoms have 6 neutrons, and weigh 12 AMU (atomic mass units)
Carbon atoms with 7 neutrons weigh 13 AMU
Carbon atoms with 8 neutrons weigh 14 AMU (and are radioactive)

28. The sodium atom contains 11 electrons, 11 protons, and 12 neutrons
The sodium atom contains 11 electrons, 11 protons, and 12 neutrons. What is the mass number (atomic mass) of sodium?
 0  
11  
22  
23  
34  

29. 96% of human tissue is comprised of 6 elements
Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorous, Sulfur (CHNOPS)
25 elements serve known functions in the body, incl. Ca, K, Na, Cl, Mg, Fe
Trace elements are essential, but in small quantities

30. A compound A) is a pure element.
B) is less common than a pure element.  
C) contains two or more elements in a fixed ratio.  
D) is exemplified by sodium.  
E) is a solution.  

31. Atomic structure Protons and electrons in the nucleus
Electrons orbit around
Bohr atom- classic model featuring electrons in “planetary” orbitals
Each orbit holds a determined number of electrons (first holds two, 2nd and 3rd hold eight)

32. The second electron shell can hold a maximum of_____ electrons.

33. Electrons in the outermost shell of an atom are called valence electrons

34. Atoms are stable when their outer valence shells are filled with electrons
The first valence shell holds 2 electrons
The 2nd and 3rd shells hold 8 electrons each

35. Intramolecular Chemical Bonds: Ionic bonds, Covalent bonds, formation of molecules

36. Noble gases have a stable electron structure
Their outer orbitals have a full complement of electrons
Noble gases are very unreactive

37. Atoms are stable when their valence shells are filled with electrons
What atoms are these?
How could they satisfy their valence shells?

38. Elements combine in chemical reactions to form compounds
Molecules- 2 or more atoms combined in specific ways
Compounds- different elements in a molecule, in exact, whole-number ratios, joined by a chemical bond
2 major kinds of intramolecular chemical bonds: Covalent (incl. polar and nonpolar) and Ionic

39. In ionic bonding, an atom takes an electron from another atom
Transfer of
electron
Na+
Sodium ion
Cl-
Chloride ion
Sodium chloride (NaCl) Na
Sodium atom Cl
Chlorine atom

40. Ions are charged atoms
Ionic compounds are held together by the attraction of opposite charges
Positive ion- cation (sodium)
Negative ion- anion (chloride)
Neutral ionic compounds are called “salts” (NaCl is one kind of salt)
Ionic comounds often form crystals

41. LE 2-7b
Na+
Cl-

42. The nucleus of an atom contains
protons and neutrons.  
protons and electrons.  
only neutrons.  
only protons.  
only electrons.

43. What about two hydrogen atoms?

44. In covalent bonding, electrons are shared
Atoms form as many bonds as they have vacancies in their outermost electron orbitals
Atoms are bound together by the sharing of electrons
Chemical reactions often involve the exchange of covalent bonds

45. LE 2-6b
Nitrogen (N)
Atomic number = 7
Oxygen (O)
Atomic number = 8

46. Single, double and even triple bonds can be formed
Bonds can be formed between two of the same atoms, or two different atoms
Covalent bonds fix two atoms together to form a molecular compound

47. In this way, a few elements can form all the molecules of the world

48. Covalent bonds hold together the macromolecules of life
DNA, proteins, carbohydrates, etc- All held together by covalent bonds

49. Many chemical reactions solely involve exchange of covalent bonding partners+

50. Living things create macromolecular products for structure:
6CO2(g)+ 6H2O(l) + hν  C6H12O6(s) + 6O2(g)
Macromolecules as reactants are broken down for energy:
C6H12O6(s) + 6O2(g)  6CO2(g)+ 6H2O(l)
All the reactions of a living thing are called its metabolism

51. Electronegativity and its effect on chemical bonds
Polar and nonpolar molecules
Hydrogen bonds

52. Electronegativity values can predict how atoms will bond

53. In covalent bonds, electrons do not always share time between bond partners equally
Comparisions of electronegativity
Na: 0.9
H: 2.1
C: 2.5
N: 3.0
Cl: 3.0
O: 3.5

54. Electronegativity = “electron greediness”
Large differences in polarity of atoms in a bond creates polar molecules
Relative electronegativity of Hydrogen and oxygen makes water a very polar molecule
Polar- regions of positivity and negativity
By Oxygen, water is (slightly) negative
By Hydrogens, water is (slightly) positive

55. Intermolecular forces and the chemistry of water
Polarity and hydrophilicity,
Nonpolarity and hydrophobicity, hydrogen bonding, and the chemistry of water

56. The polarity of water allows hydrogen bonding
Polar regions of water molecules interact to form hydrogen bonds
Hydrogen bonds: weak/temporary intermolecular forces between positive and negative regions
Inter- “between”
Intra- “within”

57. Water is a “universal solvent” and dissolves many polar and ionic compounds (“like dissolves like”)

58. Other molecules can engage in H-bonding, w/ water or other substances

59. Hydrogen bonds hold together the two strands of a DNA double helix

60. Hydrogen bonding in water is the cause of many of water’s critical properties

61. Hydrogen Bonds help to make water cohesive, allowing water surface tension- water sticks to itself, holding droplets together and surfaces taut
When water H-bonds with other substances (like glass), adhesion results, causing capillary action

62. Capillary action allows redwoods to grow to heights over 300 feet

63. Just as heat breaks H-bonds, as water cools, more H-bonds form
Hydrogen bond
Ice
Liquid water
Hydrogen bonds are stable
Hydrogen bonds
constantly break and re-form
Because H-bonds have a fixed distance, the crystal lattice of water makes ice less dense

64. Hydrogen bonds require energy to break- water has a high specific heat
Water’s high specific heat allows evaporative cooling
-and makes sweating an effective cooling mechanism

65. Due to water’s high specific heat, proximity to water has a stabilizing effect on regional temperature

66. Water and hydrogen bonding
Polar molecules are dissolved easily in water
High specific heat allows evaporative cooling
Crystal lattice of H-bonds causes ice to be less dense than liquid water, not more
Hydrogen bonds give water surface tension
Hydrogen bonds with other substances allow adhesion

67. Since ions do not share electrons, they may separate in solution

68. Water is a universal solvent, allowing many polar compounds to dissolve

69. Nonpolar molecules are mostly neutral
C: 2.5, H: 2.1
Very few positive or negative regions, if any
Hydrocarbons- compounds solely made of hydrogen and carbon, e.g. fats, oils, & gas
Nonpolar substances are hydrophobic and do not mix well with water

70. Acids, bases, and the pH scale

71. Ionic compounds dissolve in water, forming ions
Many ionize completely
Salt: NaCl  Na+ + Cl-
Hydrochloric acid: HCl  H+ + Cl-
Sodium Hydroxide: NaOH Na+ + OH-
Some (not all) substances which ionize affect the pH of a water solution

72. Like ionic compounds, water also forms ions sometimes
H2O ↔ H+ + OH-
Spontaneously happens to water molecules
1/ 107 water molecules are ionized in distilled water
In dH2O, [H+ ]= [OH-]

73. Hydrogen [H+] and Hydroxide [OH-] do not stay ionized for long, and quickly re-form into water

74. [H+] ions in solution is the cause of acidity [OH-] ions are the cause of basicity
Because pure H2O always forms [H+] ions and [OH-] in equal amounts, water is a neutral compound, neither acidic or basic

75. pH is a measure of acidity/basicity
pH = -log [H+] (logarithmic scale)
pH 1 6.9: acid
pH 7.114: base
Acids donate [H+] to water
Bases remove [H+] from water – often have a slimy feel
Strong acids & bases are ~equally nasty
Proteins are sensitive to small changes in pH

76. pH is a measure of acidity/basicity
Acids donate [H+] to water
Bases remove [H+] from water
Sodium Hydroxide:
NaOH Na+ + OH-
Hydrogen chloride:
HCl  H+ + Cl-
Which is acidic? Which is basic?

77. (Higher concentration of H+) (Lower concentration of H+)
LE 2-15
pH scale H+ H+
OH H+ H+
Lemon juice, gastric juice
OH H+ H+ H+ H+
Grapefruit juice, soft drink
(Higher concentration of H+)
Increasingly ACIDIC
Acidic solution
Tomato juice
Human urine
OH
OH
NEUTRAL
[H-]
Pure water H+ H+
OH
OH
OH
Human blood H+ H+ H+
Seawater
Neutral solution
(Lower concentration of H+)
Increasingly BASIC
Milk of magnesia
Household ammonia
OH
OH
OH H+
OH
Household bleach
OH
OH H+
Oven cleaner
Basic solution

78. Acid rain pollution can cause tremendous ecological damage
SO2 (g)+ H2O SO2·H2O
SO2·H2O H++HSO3-
HSO3- H++SO32-

79. Mechanism of acid rain

80. More effects of acid rain

81. Buffers can help control changes in pH

82. Water's surface tension and heat storage capacity is accounted for by its
 orbitals.  
weight.  
hydrogen bonds.  
mass.  
size.