1. Chemical Basis of Life

2. Outline: The Chemical Basis of Life
Chemistry of Carbon
Polymers & Monomers
Biologically Important Compounds
Carbohydrates
Lipids
Proteins
Nucleic Acids

3. Carbon Chemistry Protons Neutrons Electrons
1. Carbon has 4 valence electrons
2. Each carbon atom  four covalent bonds

4. Covalent Bonds in Carbon
Electron Pair
Covalent Bond

5. Carbon Chemistry
Molecular Formula
CH4
C2H6

6. Carbon Chemistry
C4H10
C4H10
C4H8
C4H8

7. Carbon Chemistry

8. Summary: Carbon Chemistry Unbranched or Branched
Structural formula
Methane H
Ball-and-stick model
Space-filling model C
The 4 single bonds of carbon point to the corners of a tetrahedron.
Ethane
Propane
Carbon skeletons vary in length.
Butane
Isobutane
Skeletons may be unbranched or branched.
1-Butene
2-Butene
Skeletons may have double bonds, which can vary in location.
Cyclohexane
Benzene
Skeletons may be arranged in rings.
4 Covalent Bonds
Variable Length
Unbranched or Branched
Single or Double Bonds
Rings

9. HYDROXYL Carboxyl FUNCTIONAL GROUPS Melting Point (C) C2H6O -114
Structural Formula
FUNCTIONAL GROUPS H H
Hydroxyl OH H C C OH
HYDROXYL
Melting Point (C)
C2H6O
-114
C2H5O2 17 H H C H O
Carbonyl O H C C H H O H O
Carboxyl C H C C OH H OH H O H H
C2H6O 78
Boiling Point (C)
C2H5O2
118
Amino N HO C C N
Carboxyl H H
CH3 H H
Sulfhydryl S H HO C C S H H H O– OH OH H O
Phosphate O P O– H C C C O P O– O H H H O– H O O H
Methyl C H O– C C C H H H

10. Figure 3. Functional groups of male and female sex hormonesOH
Estradiol HO
Female lion OH
Testosterone O
Male lion

11. Dehydration synthesis is
Polymer Building
Unlinked monomer H OH OH H
Short polymer
H2O
Dehydration reaction H OH
Longer polymer

12. Hydrolysis is Polymer Breaking
H2O OH H
Hydrolysis H OH OH H

13. Classes of Biologically Important Compounds
Carbohydrates
Lipids
Proteins
Nucleic Acids

14. Carbohydrates
Monosaccharides
Disaccharides
Polysaccharides

15. Figure 3.4B Structure of MonosaccharidesHO O OH
Glucose
Fructose
C6H12O6
Carboxyl
Groups
Carbonyl
Group

16. Three representations of glucose6
CH2OH 6
CH2OH 5 C O H O O 5 H H H H H 4 C C 1 4 1 OH OH H H OH OH HO OH 3 C C 2 3 2 H OH H OH
Simplified structure
Structural formula
Abbreviated structure

17. Figure 3.5 Disaccharide formation
CH2OH
CH2OH O O H H H H H H OH H HO OH H OH HO OH H OH H OH
Glucose
Glucose
H2O
CH2OH
CH2OH O O H H H H H H OH H O OH H HO OH H OH H OH
Maltose

18. Lactose – A Disaccharide
CH2OH O
CH2OH H H H OH O OH H O H OH OH H H H H OH
Glucose H OH
Galactose

19. Polysaccharides – Complex Carbohydrates
Starch
Glycogen
Cellulose
Glucose monomer
Starch in potato cells
STARCH O O O O O O O O O O O
Glycogen in muscle tissue
GLYCOGEN O O O O O O O O O O O O O
CELLULOSE
plant cell wall O O
Cellulose molecules O O O OH O O O O O OH O O O O O O
Figure 3.7 O O O O O O O

20. Functions of Carbohydrates
Energy Source e.g. blood sugar
Energy Storage e.g. starch
Structural Material e.g. cellulose

21. End
Carbohydrates

22. Start Fri 9/15/06

23. Classes of Biologically Important Compounds
Carbohydrates
Lipids
Proteins
Nucleic Acids

24. Dissolve in nonpolar solvents
Lipids
Properties
Non-polar molecules
Not Water soluble
Dissolve in nonpolar solvents

25. Types of Lipids Fatty acids Triglycerides or neutral fats
Phospholipids
Steroids, prostaglandins and waxes

26. Fatty Acid Structure
Hydrocarbon chain
Carboxyl
Group

27. Saturated & Unsaturated Fatty Acids

28. Cis & Trans Unsaturated Fatty Acids

29. Trans Fatty Acids Increase LDL levels (bad cholesterol)
Decrease HDL levels (good cholesterol)
Increase heart attack risk

31. Omega Numbering System for Fatty Acids

32. Unsaturated Fatty Acids
Linoleic Acid
An omega-6 fatty acid

33. Beneficial Fatty Acids
1. Monounsaturated and Polyunsaturated fatty acids
MONO  ONE double bond
POLY  more than one double bond
2. Essential fatty acids – All unsaturated
A. linoleic acid… Omega-6 fatty acid
sources: canola, soybean, corn, flaxseed
1. heart protective
B. alpha linolenic acid … Omega-3 fatty acid
sources: canola, olive oil, flax seed oil
1. heart protective
2. Reduce triglycerides
Source:
Omega-3 fatty acids are derived from Linolenic Acid, Omega-6 from Linoleic Acid.
An ideal intake ratio of Omega-6 to Omega-3 fatty acids is between 1:1 and 4:1, with most Americans only obtaining a ratio between 10:1 and 25:1.
Imbalance of too much omega-6 (linoleic acid) to omega-3 (linolenic acid) in diet.

34. Fatty Acids - Summary 1. Saturated 2. Unsaturated A. monounsaturated
B. polyunsaturated
Types of polyunsaturated fatty acids
1. omega-3 alpha linolenic acid
2. omega-6 linoleic acid
3. Trans fatty acids...products of food processing

35. Triglyceride Synthesis

36. Triglyceride or Neutral Fat

37. Structure of a TriglycerideH H C
Fatty acid H C
Fatty acid H C
Fatty acid H

38. Phospholipid Structure
Hydrophilic Polar Head
Hydrophobic
Nonpolar Tails

39. Membrane Structure Phospholipid bilayer
Water

40. Steroids Cholesterol Hydrocortisone
The main glucocorticoid secreted by the ADRENAL CORTEX. Its synthetic counterpart is used, either as an injection or topically, in the treatment of inflammation, allergy, collagen diseases, asthma, adrenocortical deficiency, shock, and some neoplastic conditions.
Cholesterol

41. Steroids
Digitoxin

42. Other Lipids Waxes Terpenes Prostaglandins Citronellol Taxol
Source:
Prostaglandins are unsaturated carboxylic acids, consisting of of a 20 carbon skeleton that also contains a five member ring and are based upon the fatty acid, arachidonic acid. There are a variety of physiological effects including:
1. Activation of the inflammatory response, production of pain, and fever. When tissues are damaged, white blood cells flood to the site to try to minimize tissue destruction. Prostaglandins are produced as a result.
2. Blood clots form when a blood vessel is damaged. A type of prostaglandin called thromboxane stimulates constriction and clotting of platelets. Conversely, PGI2, is produced to have the opposite effect on the walls of blood vessels where clots should not be forming.
3. Certain prostaglandins are involved with the induction of labor and other reproductive processes. PGE2 causes uterine contractions and has been used to induce labor.
Prostaglandin functions:
cause the arteries to widen or constrict  
 influence blood clotting  
 stimulate pain nerve endings  
 reduce stomach acid secretion  
 relieve asthma
Citronellol:
Citronella is the common name for a grass, Cymbopogon nardus, which is native to India and southeast Asia. Citronella oil is a yellowish essential oil distilled from the leaves of either of two grasses, Cymbopogon nardus or C. winterianus. This aromatic oil is inexpensive, and widely used in cheap perfumes and as a fragrance in soaps. It is also best known as an insect repellent. Citronellol, derived form citronella oil, is a chief constituent of geranium oil, another is geraniol. Both are used in the production of perfumes. (sweet, rose, lilac, geranium )
Taxol is a terpene:

43. Waxes, Sperm Whales & Jojoba oil

44. Examples of Waxes, Terpenes and Prostaglandins
Jojoba oil
Beeswax
Carnauba wax
Terpenes
Citronellol
Taxol
Menthol
Camphor oil
Prostaglandins
Thromboxane – stimulates blood clotting
PGE2 – stimulates uterine contractions/labor
Inflammation/pain
Control of blood pressure
The Sperm Whale, considered an endangered species under the parameters set up by this Act, became protected to the extent that no sperm whale oil could be imported into the US.  Up until then we had been importing 55 million gallons of the oil each year.  Sperm whale oil is currently stockpiled, for use in national emergencies.  The head of the Sperm Whale contains vast quantities of sperm oil (actually an unsaturated wax) and a solid white wax called spermaceti.  The Sperm Whale’s blubber contains ever more sperm oil.  A large Sperm Whale can yield several tons of the oil and the wax.
Without the Sperm Whale as a source of these materials, a search for substitutes began.  Synthetic substitutes are difficult to produce, so other natural sources were investigated.  A fish known as the Orange Roughy makes a similar oil, but it has been so overfished that it could not be counted on as a long term solution.  The Jojoba plant was considered too.
Today there are an amazing number of potential uses for Jojoba oil.  They include: cosmetics, lubricants for everything from artificial hearts to watches, motors, and transmissions, low-calorie cooking oil that does not become rancid, antifoaming agents in fermentation, candle wax, polishes, coatings for fruits and pills, insulation for batteries and wires, varnishes and paints, detergents, plastics and resins, leather softeners, transformer coolants, and more.

45. Lipid Functions Long term energy storage Protection
Triglycerides
Protection
Fat deposits around kidneys
Prostaglandin thromboxane induces clotting
Waxes on leaf surface
Synthesis: hormones
Cholesterol

46. Classes of Biologically Important Compounds
Carbohydrates
Lipids
Proteins
Nucleic Acids

47. Fig. 3.4

48. Protein = chain of amino acids
Protein Structure
Protein = chain of amino acids H O R C C OH N
Amino acid
Carboxyl group
H H
Amino
group

49. Amino acid Amino acid H H H N C C OH H N C C OH H O H O H2OR H R H N C C OH H N C C OH H O H O
H2O
Peptide Bond
Polypeptide chain H R H R H N C C N C C OH H O H O

50. Amino Acid Structure
Nonpolar Amino Acids

51. Amino Acid Structure

52. Amino Acid Structure
Polar Charged

53. Amino Acid Structure

54. Special Function Amino Acids
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Special Function Amino Acids
CH3 S SH
CH2
CH2
CH2
CH2
CH2
CH2 CH C O–
H3N+ C C O– +
H3N+ C C O–
NH2 O H O H O
Proline
(Pro)
Cysteine
(Cys)
Methionine
(Met)

55. Types of Amino Acid Side Groups - Summary
1. Non-Polar
2. Polar – Uncharged
3. Polar – Charged
4. Aromatic
5. Special Function

56. Four Levels of Protein Structure
Primary
Secondary
Tertiary
Quaternary

57. Levels of Protein Structure
Leu
Met
Asn
Pro
Val
Primary structure
Val
Ile
Ala
Cys
Glu
Lys
Val
Arg
Gly
Ala
His
Phe
Thr
Ser
Lys
Val
Gly
Val
Leu
Asp
Ala
Val
Arg
Gly
Ser
Pro
Amino acids O H H C C C O C C N N C C C H O C O C N H H R N C N H C N H O H C C N C O N H H C N H N H C N O C O H C C N C C N
Secondary structure O C O C C H C R O C H O O H C C C N H C H O C N C O N H O C N C N H H C C O N C H C O N C N H O C N H C C N C H O O C O C N C H C C C H O N C N
Alpha helix
Pleated sheet H O C
Tertiary structure
Domains
Quaternary structure
Two or more
Polypeptides

58. Humans: Creutzfeldt Jacob Disease
What is it?
Humans: Creutzfeldt Jacob Disease
Cattle: Bovine Spongiform encephalopathy
(Mad cow disease)
Deer: Chronic Wasting Disease
Human brain section with spongiform encephalopathy
Creutzfeldt Jacob Disease
The propagation of infectious prion protein occurs via conversion of normal prion protein (PrPc, left) to a disease-causing form (PrPSc, right). In the refolding process, some of the -helical regions (purple coils) in PrPc unfold, forming an extended ß-sheet region (flat blue arrows).

59. Normal Protein Folding is Critical to Function
Normal (Good) PrPC
43% a-helix
Prion (Bad) PrPSc
30% a-helix
43% b-sheet
Prions, Mad Cow Disease. Creutzfeldt Jacob Disease. Bovine Spongiform Encephalopathy (BSE) or mad cow disease

60. Protein Functions Function Class Examples Use Enzyme catalysis Enzymes
Proteases
Break down protein
Defense
Immunoglobulins
Antibodies
Mark foreign substances
Transport
Long distance transporters
Hemoglobin
Transport O2 and CO2
Short distance transporters
Proton pump
Transports protons across membranes

61. Protein Functions Function Class Examples Use Support Fibers Collagen
Forms cartilage
Motion
Muscle
Actin & Myosin
Muscle Contraction
Regulation
Hormones
Insulin
Glucose Transport
Storage
Ion Binding
Ferritin
Calmodulin
Stores Iron
Binds Calcium

62. Classes of Biologically Important Compounds
Carbohydrates
Lipids
Proteins
Nucleic Acids

63. Nucleic Acids Deoxyribonucleic Acid = DNA Genetic Material
Ribonucleic Acid = RNA
Protein Synthesis

64. A Nucleotide is a monomer of a nucleic acid
Fig. 3.14(TE Art)
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
A Nucleotide is a monomer of a nucleic acid
Nitrogenous base
NH2 N N
Phosphate group O N N –O P O
CH2 O– O
OH in RNA OH R
H in DNA
Sugar

65. NH2
Adenine
NH2
Cytosine
(both DNA
and RNA) N C C C N H C N P U R I N E S H C P Y R I M D N E S C H C H C N C O N N H H O
Guanine O
Thymine
(DNA only) N C C N H C
H3C C N H H C C N
NH2 C H N C C O N H H O
Uracil
(RNA only) C H C N H H C C O N H

66. Sugar-phosphate "backbone"
Fig. 3.16(TE Art)
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
DNA Structure
Sugar-phosphate "backbone" O P O
Hydrogen bonds between
nitrogenous bases C G P O O C P P G O O P A P T O O P G P C O O T OH
3’ end A P
Phosphodiester
bond O P
5’ end

67. RNA Structure P P P Ribose-phosphate P backbone C A G P U A Bases P U
Fig. 3.17b(TE Art)
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
RNA Structure P P P
Ribose-phosphate
backbone P C A G P U A
Bases U P P G

68. Nucleic Acid Functions
DNA – Genetic material
RNA – Protein synthesis

69. END

70. END Carbohydrates Lipids Proteins Nucleic Acids
Fig. 3.13
END
Carbohydrates
Lipids
Proteins
Nucleic Acids
Scanning Tunneling micrograph of DNA