1. Bio 11 Lecture- Chemistry II
Chemical reactions, Ions, pH, functional groups, organic molecules

2. Lecture outline Chemical Bonds review 5. Ions 6. pH
7. Functional groups
8. Organic molecules
4. Chemical Reactions
9. Carbohydrates

3. What part(s) of an element’s atoms determines its mass?
A. Protons
B. Neutrons
C. Electrons
D. Protons + Neutrons
E. Electrons/Protons

4. What part(s) of an element’s atoms define the element?
A. Protons
B. Neutrons
C. Electrons
D. Protons + Neutrons
E. Electrons/Protons

5. What part(s) of an element’s atoms differentiate its isotopes?
A. Protons
B. Neutrons
C. Electrons
D. Protons + Neutrons
E. Electrons/Protons

6. What part of atoms determine how they bond with other atoms?
A. Protons
B. Neutrons
C. Electrons
D. Protons + Neutrons
E. Electrons/Protons

7. Basic atomic structure- protons, neutrons, and electrons

8. The periodic table logically arranges and describes all matter

9. Molecules, compounds, chemical reactions, and bonding

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

11. Valence electrons determine bonding

12. Atoms seek complete valence electron shells (the octet rule)

13. In Ionic bonding, atoms strip valence electrons from partners, forming ions

14. Atoms are stable when their outer shells are filled with electrons
Shell 1: Holds 2 electrons
Shell 2: Holds 8
Shell 3: Holds 8
Hydrogen- 1p, 1e, seeks a second electron in its outermost shell
Carbon seeks 4
The electrons in the outermost shell are called valence electrons

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

16. Sodium chloride (NaCl)
LE 2-7
In ionic bonding, an atom takes an electron from another atom, forming 2 ions
Transfer of
electron
Na+
Sodium ion
Cl-
Chloride ion
Sodium chloride (NaCl) Na
Sodium atom Cl
Chlorine atom

17. 5. Ions Ions- Charged atoms or molecules Anion- negative ion
Cation- positive ion
Ionization- reaction producing ions
Salt- a neutral compound comprised of ions

18. Sodium chloride (NaCl)
LE 2-7a-2
Na+
Sodium ion
Cl-
Chloride ion
Sodium chloride (NaCl)

19. LE 2-7b
Na+
Cl-

20. Water dissolves many ionic compounds (“like dissolves like”)
Individual soluble ions are not physically bound to each other

21. In covalent bonding, pairs of valence electrons are shared, and molecules are formed

22. LE 2-17a +
2 H2 + O2
2 H2O

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

24. In neutral molecules, carbon always forms 4 bonds
Structural
formula
Ball-and-stick
model
Space-filling
model
Methane
The 4 single bonds of carbon point to the corners of a tetrahedron.

25. Carbon skeletons vary in length.
LE 3-1b
Ethane
Propane
Carbon skeletons vary in length.

26. Skeletons may be unbranched or branched.
LE 3-1c
Butane
Isobutane
Skeletons may be unbranched or branched.
Butane and Isobutane are _______________of each other.

27. Skeletons may have double bonds, which can vary in location.
LE 3-1d
1-Butene
2-Butene
Skeletons may have double bonds, which can vary in location.

28. Skeletons may be arranged in rings.
LE 3-1e
Cyclohexane
Benzene
Skeletons may be arranged in rings.

29. Organic Chemistry The chemistry of carbon
Hydrocarbons are the most basic example
Combustible
Can form rings

30. The variety of carbon compounds is limitless
inorganic - lack carbon atoms
organic - with carbon (plus hydrogen)
biochemical - organic molecule in life
• carbohydrates • proteins
• lipids • nucleic acids

31. Covalent bonds hold together the macromolecules of life
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

32. Electronegativity determines properties of covalently bonded molecules

33. Electronegativity = “electron greediness”
Atoms in covalently bonded molecules do not always share electrons equally
This creates polar molecules
Polar regions of water molecules interact to form hydrogen bonds
Hydrogen bonds: weak/temporary intermolecular forces

34. Some electronegativity values
Hydrogen: 2.20
Oxygen:
Carbon: 2.55
Chlorine: 3.16
Sodium: 0.93
Difference between:
H and O: 1.22
H and C: 0.35

35. Hydrogen bonding in water determine many of water’s unique properties
H-bonds can form a lattice (ice)
H-bonds require much energy to break
H-bonds give water surface tension
Hydrogen bond

36. Water dissolves many ionic compounds (“like dissolves like”)

37. Intermolecular Hydrogen bonds give water its surface tension

38. Intermolecular Hydrogen bonds require much heat in order to be broken

39. 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-]
salt - neutral molecule releases ions
acid releases hydrogen H+, burns
base releases hydroxide OH–, slimy

40. pH is a measure of acidity/basicity
pH = -log [H+] (logarithmic scale)
pH 1 6.9: acid
pH 7.114: base
pH 7 neutral
buffers - absorb excess H+ or OH–
- stomach 2, urine 5-7.8, blood 7.4
Acids donate [H+] to water
Bases remove [H+] from water (or donate [OH-] to water)
Proteins are very sensitive to small changes in pH

41. (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

42. 7. FUNCTIONAL GROUPS
hydroxide group – OH amino group – NH2 carboxyl group – COOH phosphate group – PO4 methyl group – CH3

43. The physical/ chemical properties of carbon skeletons can be modified by functional groups

44. figure 02-20b.jpg
2.20 – Part 2
Figure 2.20 – Part 2

45. Functional groups can radically change the function of a molecule
Estradiol
Female lion
Testosterone
Male lion

46. The six functional groups that are most important in the chemistry of life:
Hydroxyl group (alcohols)*
Carbonyl group
Carboxyl group (carboxylic acids)*
Amino group*
Sulfhydryl group
Phosphate group*
Methyl group

47. FUNCTIONAL PROPERTIES
LE 4-10aa
STRUCTURE
(may be written HO—)
Ethanol, the alcohol present in
alcoholic beverages
NAME OF COMPOUNDS
FUNCTIONAL PROPERTIES
Alcohols (their specific names
usually end in -ol)
Is polar as a result of the
electronegative oxygen atom
drawing electrons toward itself.
Attracts water molecules, helping
dissolve organic compounds such
as sugars (see Figure 5.3).

48. STRUCTURE EXAMPLE NAME OF COMPOUNDS LE 4-10ab
Acetone, the simplest ketone
STRUCTURE
EXAMPLE
Acetone, the simplest ketone
Propanal, an aldehyde
NAME OF COMPOUNDS
Ketones if the carbonyl group is
within a carbon skeleton
FUNCTIONAL PROPERTIES
Aldehydes if the carbonyl group is
at the end of the carbon skeleton
A ketone and an aldehyde may
be structural isomers with
different properties, as is the case
for acetone and propanal.

49. LE 4-10ac STRUCTURE EXAMPLE Acetic acid, which gives vinegar
its sour taste
NAME OF COMPOUNDS
FUNCTIONAL PROPERTIES
Carboxylic acids, or organic acids
Has acidic properties because it is
a source of hydrogen ions.
The covalent bond between
oxygen and hydrogen is so polar
that hydrogen ions (H+) tend to
dissociate reversibly; for example,
Acetic acid
Acetate ion
In cells, found in the ionic form,
which is called a carboxylate group.

50. LE 4-10ba STRUCTURE EXAMPLE Glycine Because it also has a carboxyl
group, glycine is both an amine and
a carboxylic acid; compounds with
both groups are called amino acids.
NAME OF COMPOUNDS
FUNCTIONAL PROPERTIES
Amine
Acts as a base; can pick up a
proton from the surrounding
solution:
(nonionized)
(ionized)
Ionized, with a charge of 1+,
under cellular conditions

51. STRUCTURE EXAMPLE NAME OF COMPOUNDS
LE 4-10bb
STRUCTURE
EXAMPLE
(may be written HS—)
Ethanethiol
NAME OF COMPOUNDS
FUNCTIONAL PROPERTIES
Thiols
Two sulfhydryl groups can
interact to help stabilize protein
structure (see Figure 5.20).

52. STRUCTURE EXAMPLE NAME OF COMPOUNDS
LE 4-10bc
STRUCTURE
EXAMPLE
Glycerol phosphate
NAME OF COMPOUNDS
FUNCTIONAL PROPERTIES
Organic phosphates
Makes the molecule of which it
is a part an anion (negatively
charged ion).
Can transfer energy between
organic molecules.

53. Organic molecules are good energy sources
Energy is required to form covalent bonds; energy is released when bonds are broken

54. Most molecules in living things fall into four categories
Carbohydrates
Lipids
Proteins
Nucleic acids
These all exhibit modular construction

55. Made of interchangeable parts
Modular housing
Made of interchangeable parts

56. Freight trains have modular assembly

57. Modular assembly allows a wide variety of products from a few pieces

58. Most biopolymers of life are formed by dehydration synthesis

59. Hydrolysis is the reverse reaction (Catabolic)

60. 4. CHEMICAL REACTIONS  
metabolism - all chemical reactions in body - reactants ‹ products    synthesis - build larger molecule   CH3-OH + H-CH3 ‹ CH3-CH3 + H2O    hydrolysis - break down molecule    CH3-CH3 + H2O ‹ CH3-OH + H-CH3   exchange reaction - example: AB + CD ‹ AD + CB

61. Carbohydrates “Carbon” + “Hydro” Formula (CH2O)n
Different from hydrocarbons
Soluble in water
Includes: table sugar, honey, starch, glycogen, cellulose, high fructose corn syrup
Glucose is the monomer

62. Glucose can cyclize to form a ring structure
Atoms in bonds are free to rotate around the bonds

63. Glucose + Glucose = Maltose (A Sugar dimer)

64. Chain can be extended to thousands

65. 9. Carbohydrates functions - principle source of energy (4 kcal/g)
- structure & energy storage in plants
 atoms - C H O
structure - ring or chain of 5-6 C’s
 monosaccharide
- single sugars (example: glucose) disaccharide - double sugars (example: sucrose) polysaccharide - polymer or chain of 100’s sugars - starch & cellulose (mostly plants) - glycogen (animals, esp. liver)

66. Proteins are polymers made of 20 different kinds of amino acid monomers

67. table 03-02bc.jpg
Table 3.2 – Part 2
Table 3.2 – Part 2

68. table 03-02d.jpg
Table 3.2 – Part 3
Table 3.2 – Part 3

69. Proteins: Polymers of Amino Acids
Amino acids are covalently bonded together by peptide linkages. Review Figure 3.4

70. 3.4 Modular assembly of amino acids through dehydration synthesis
figure jpg
Modular assembly of amino acids through dehydration synthesis
3.4

71. Proteins have an incredible variety of structures

72. Proteins have an incredible variety of functions
Hair, skin, fingernails, muscles, eye pigments, are all made of protein

73. 11. Proteins functions - energy (4 kcal/g)
- structure in animals (meat)
- enzymes (speed up & reg chem rxs) 
atoms - C H O N
amino acid
- central C, hydrogen –H
- amino group –NH2
- carboxyl group –COOH
- R-group (20 different)
polypeptide - polymer of amino acids
 protein - 1 or more polypeptides
4 levels of structure - necessary
for protein function, esp. enzymes
I° primary structure - sequence of
amino acids in polypeptide chain
II° secondary structure
- coiling or folding of chain
- hydrogen bonds between regions
III° tertiary structure
- folding of coiled-folded chain
IV° quaternary structure
- linkage to other polypeptides

74. Lipids Non-polar High-energy molecules For energy storage
Forms cell membranes
Hormones
Members of family include oils, fats, waxes, and cholesterol (steroids)

75. Lipids are non-polar
Therefore, they are hydrophobic

76. Triglycerides are a primary lipid structure

77. Dehydration synthesis links fatty acids to glycerol

78. Fatty acids can be saturated and unsaturated (cis and “trans”)

79. 10. Lipids functions - energy storage (9 kcal/g)
- also animal structure (blubber)
atoms - C H O
structure - glycerol + 3 fatty acids
oil - liquid, unsaturated (missing H’s)
fat - solid, saturated (maximum H’s)
- promotes heart disease
others
- steroids, phospholipids, waxes

80. Nucleic acids Informational molecules in cells
Include DNA, RNA, and ATP/ADP
Have other functions

81. Nulceotides are the subunits of nucleic acids
Consist of a sugar, a phosphate, and a nitrogen-containing base
Sugar can be deoxygenated

82. 12. Nucleic Acids function - not energy
- genetics (genes & chromosomes)
atoms - C H O N P S
structure - chain of 100’s nucleotides
examples - DNA, RNA, ATP

83. Review Atomic structure- protons, neutrons electrons Valence electrons
Carbon
Functional groups
Carbohydrate structure
Protein structure
Lipid structure

84. Things left unsaid
Isotopes of all elements exist (some of these are radioactive)
Electronegativity determines polarity of covalent bonds, and thus solubility
Water has important physical properties essential to life on earth
Isomers have the same molecular formula but not the same shape in space
Nucleic acids are comprised of nucleotide monomers