1. Organic Molecules

2. Carbon: The Backbone of Life
cells are 70–95% water
Remainder is carbon-based compounds
Carbon accounts for the diversity of molecules
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

3. Organic chemistry is the study of carbon compounds
Organic compounds range from simple molecules to colossal ones
Simple: CO2: 3 atoms
Complex: proteins: 1000’s of atoms
Most organic compounds contain:
hydrogen atoms in addition to carbon atoms
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

4. Some question molecules present in early earth’s atmosphere
EXPERIMENT
1953
Stanley Miller
“Atmosphere”
CH4
Water vapor
Electrode
NH3 H2
Condenser
Cooled water
containing
organic
molecules
Cold
water
Figure 4.2 Can organic molecules form under conditions believed to simulate those on the early Earth?
Some question molecules present in early earth’s atmosphere
H2O
“sea”
Sample for
chemical analysis

5. Formation of bonds with carbon
electron configuration
4 electrons
Tends to share electrons
COVALENT BONDS
Double
Single
Acts as an intersection
Branches in many directions

6. Versatility of carbon Acts as an intersection
Branches in many directions
Up to 4
tetravalence

7. 4 major components of organic molecules
Fig. 4-4
Elements most frequently partnered with
Hydrogen
(valence = 1)
Oxygen
(valence = 2)
Nitrogen
(valence = 3)
Carbon
(valence = 4) H O N C
Figure 4.4 Valences of the major elements of organic molecules
4 major components of organic molecules

8. Molecular diversity in carbon chains (skeletons)
Straight branched rings

9. Hydrocarbons organic molecules consist of only carbon and hydrogen
Covalent bonds
Nonpolar/hydrophobic
Many organic molecules, such as fats, have hydrocarbon components
Hydrocarbons can undergo reactions that release a large amount of energy

10. Fat droplets (stained red)
Fig. 4-6
Fat droplets (stained red)
Figure 4.6 The role of hydrocarbons in fats
100 µm
(a) Mammalian adipose cells
(b) A fat molecule

11. C6 H12 O6 Isomers compounds with:
same number of atoms of the same elements
different structures
Different properties
C6 H12 O6

12. 3 types of Isomers Structural isomers Geometric isomers Enantiomers
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

13. May also differ in the location of their double bonds
Structural isomers
have different covalent arrangements of their atoms
# of possibilities increase as carbon skeleton increases
C5 H12 – 3 forms
C8 H18 – 18 forms
C20 H42 – 366,319 forms
May also differ in the location of their double bonds

14. Structural isomers same number of atoms of the same elements
different covalent arrangements
different structures

15. Geometric isomers have SAME covalent partnership of their atoms
Differ in SPATIAL ARRANGMENT around a double bonded Carbon
Inflexible double bonds (single bonds rotate more freely)

16. Enantiomers Are mirror images Middle carbon is an asymmetrical,
Attached to 4 different atoms

17. Enantiomers Left handed and right handed Distinguishable by shape
One is biologically active other is inactive

18. Enantiomers are important in the pharmaceutical industry
Two enantiomers of a drug may have different effects
Differing effects of enantiomers demonstrate that organisms are sensitive to even subtle variations in molecules

19. Effective Enantiomer Ineffective Enantiomer Drug Condition Pain;
Fig. 4-8
Effective
Enantiomer
Ineffective
Enantiomer
Drug
Condition
Pain;
inflammation
Ibuprofen
S-Ibuprofen
R-Ibuprofen
Figure 4.8 The pharmacological importance of enantiomers
Albuterol
Asthma
R-Albuterol
S-Albuterol

20. Thalidomide 1953-1962 dysmelia, morning sickness, teratogen Lupus HIV
Chron’s
racemizing

21. A small number of chemical groups are key to the functioning of biological molecules
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

22. Distinctive properties of organic molecules depend on:
carbon skeleton
molecular components attached to it
A number of characteristic groups are often attached to skeletons of organic molecules
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

23. The Chemical Groups Most Important in the Processes of Life
Functional groups
are the components of organic molecules most commonly involved in chemical reactions
number and arrangement of functional groups give each molecule its unique properties
Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

24. Functional Groups 24

25. Hydroxyl
Polar
Forms H bonds with water…helps dissolve organic compounds

26. Carbonyl
Found in sugars

27. Carboxyl
-COOH
Organic ACID
Is polar

28. Amino
NH2
Acts as BASE

29. Sulfhydryl -SH Found in cysteine 2 can from bridges
Stabilize proteins (tertiary)
Break and reform bridges

30. Phosphates OPO3 -2 P Phospholipids (cell membrane)
Potential to react with water releasing energy P

31. Methyl
Addition affects gene expression
Male v. female

32. Ch 5

33. Monomers and Polymers
Condensation
hydrolysis

34. 4 Categories Carbohydrates Lipids (not considered polymer) Proteins
Nucleic Acids

35. 1. Carbohydrates
Elements Present?
Function?
Building blocks:

36. Glucose
Hexose sugar

37. Alpha & Beta Glucose
Functional groups?

40. Kind of Isomer?
structural
Major nutrients
respiration

41. 5-carbons sugar has the formula: C5H10O5

42. The synthesis and breakdown of polymers

43. Dissacharides

44. Table sugar
Covalent bonds
Glycosidic linkages
Milk sugar
Malt sugar
beer
malt

45. Table sugar
Enzyme:
sucrase
Milk sugar
Enzyme:
lactase
Malt sugar
maltase
Enzyme:
All digested in small intestine

46. Storage polysaccharides

47. Starch and cellulose structures
Structural polysaccharide

48. The arrangement of cellulose in plant cell walls
fiber
Provides strength

49. fiber

50. Cellulose digestion: termite and Trichonympha

51. Cellulose digestion: cow
R rumen
R reticulum
O omasum
A abomasum
fistulated cow

52. Chitin, a structural polysaccharide: exoskeleton and surgical thread
Does contain some nitrogen

53. Chitin- Exoskeleton

54. Chitin- Exoskeleton

55. fungus

56. 2. Lipids Not true polymers
Not large enough to be considered macromolecule
Hydrocarbon chains
Hydrophobic- nonpolar

57. Ester bond between alcohol (glycerol) and acid (fatty acid)
Lipids
Elements Present?
Function?
Building blocks:
Ester bond between alcohol (glycerol) and acid (fatty acid)

58. possess both hydrophobic and hydrophilic parts
Functional groups?
Amphipathic:
possess both hydrophobic and hydrophilic parts

59. Saturated fatty acid
single

60. unsaturated fatty acid
double

61. Examples of saturated and unsaturated fats and fatty acids

62. Purpose of lipids?

63. The structure of a phospholipid
amphipathic

64. Two structures formed by self-assembly of phospholipids in aqueous environments   

65. Cholesterol, a steroid lipid
Amphipathic
Maintain membrane fluidity

66. Signaling molecule

68. 3. Proteins
Elements Present?
Function?
Building blocks:

69. The 20 amino acids of proteins: polar and electrically charged

70. The 20 amino acids of proteins: nonpolar

71. Proteins.. Enzymes, Antibodies

72. Proteins..Spider silk: a secondary structural protein

73. Silk drawn from the spinnerets at the rear of a spider

74. Proteins….hemoglobin, insulin

75. Protein… Hair, Albumin

76. Protein Functions

77. Making a polypeptide chain

78. the four levels of protein structure

79. primary structure of a protein
Peptide bonds
Due to genetic code

80. Sickle Cell- association with primary structure

81. A single amino acid substitution in a protein causes sickle-cell disease

82. secondary structure of a protein
H bonds
Weak bond
slightly - charge atom attracted to slightly + charge H
Usually O &N

83. Interactions contributing to the tertiary structure of a protein
NONPOLAR
Weak bond
slightly - charge atom attracted to slightly + charge H
Usually O &N
Covalent bond
cysteine
Attraction of opposite charged ions

84. The quaternary structure of proteins
Fibrous:
Insoluble
Structural, support, protection
Ex:skin, hair, nuclear membrane, red blood cell collagen, elastin, keratin etc.  
Globular:
Water soluble
Catalytic
Ex: insulin, myoglobin, hemoglobin,&immunoglobulins

85. the four levels of protein structure
4 levels of protein structure video

86. Denaturation and renaturation of a protein
denaturing a protein

87. chaperonin in action

88. 4. Nucleic Acids
Elements Present?
Function?
Building blocks:

89. Nucleic Acids

90. The components of nucleic acids

91. James Watson and Francis Crick

92. X-ray crystallography

93. Rosalind Franklin

94. DNA RNA protein: a diagrammatic overview of information flow in a cell

95. Polypeptide Sequence as Evidence for Evolutionary Relationships