1. Organic Chemistry
Organic chemistry is the study of carbon-based molecules.
Nearly all of the compounds that a cell makes are composed of carbon bonded to other carbon atoms and to atoms of other elements. 1

2. Organic Chemistry
Carbon is unparalleled in its ability to form large, diverse molecules.
Recall that carbon has six electrons:
2 in its innermost shell and 4 in its outermost shell C
Carbon completes its outer shell by sharing electrons with other atoms in 4 covalent bonds. 2

3. Organic Chemistry
The diversity of carbon molecules is the driving force behind the myriad of molecules and chemical processes required for life, and explains the great diversity of life on Earth! 3

4. Organic Chemistry
Carbon can share its electrons with four hydrogen atoms, creating CH4 or methane.
Methane is an example of an organic compound and is the simplest of all organic compounds. C H 4

5. Organic Compunds
When Carbon shares electrons with Hydrogen atoms, a hydrocarbon results
Hydrocarbons are the major components of petroleum
Petroleum (crude oil) consists of the partially decomposed remains or organisms that lived millions of years ago
This is why the burning of fossil fuels increases carbon dioxide into our atmosphere
CH4 + 2O2 → 2H2O + CO2 + Energy 5

6. Organic Chemistry
The unique properties of an organic compound depend upon the size and shape of its carbon skeleton (the chain of carbon atoms in an organic molecule) and the groups of atoms that are attached to that skeleton.
Functional groups are smaller portions of a larger molecule affect a molecule’s function by participating in chemical reactions in characteristic and predictable ways.
Of the six functional groups of atoms that are essential to life, five are polar and one is nonpolar. 6

7. 7

8. Same carbon skeleton, but different functional groups
Estradiol female sex hormone
Female Lion
Testosterone male sex hormone
Male Lion 8

9. Besides water, all biological molecules are organic, or carbon-based.
There are many organic molecules, but most of the organism is made up of just four types: carbohydrates, lipids, proteins and nucleic acids. 9

10. Carbohydrates, lipids, proteins and nucleic acids are called macromolecules, and are the building blocks of cells and their chemical machinery.
Cells make most of these large molecules by joining together smaller molecules, or monomers, into chains called polymers.
Cellular structure
Polymer
Monomer
Chromosome
DNA strand
Nucleotide
Nucleic Acid 10

11. The key to the great diversity of macromolecules is in the arrangement of its monomers.
DNA is built up of only four monomers (nucleotides), and proteins are made with only twenty monomers (amino acids), but both macromolecules are incredibly diverse.
The DNA and proteins in you and a fungus are made with the same 4 nucleotides and 20 amino acids! 11

12. A cell links monomers together to form polymers by way of a dehydration reaction.
A dehydration reaction is so named because it results in the removal of a water molecule from the 2 reacting monomers.
An unlinked monomer has a hydroxyl group (--OH) at one end and a hydrogen at the other end, with will react with another unlinked monomer or a polymer that is increasing in size.
Hydroxyl group 12

13. Dehydration Reaction
polymer
monomer
Hydroxyl group
By removing the hydroxyl group of the polymer, and the hydrogen atom of the monomer that is being added, a water molecule is released. 13

14. Dehydration Reaction
Water molecule 14

15. The process of breaking up polymers is called hydrolysis.
Just as removing a water molecule links monomers together (to form polymers), the addition of a water molecule breaks a polymer chain apart (releasing a monomer).
The process of breaking up polymers is called hydrolysis.
Hydrolysis is essentially the reverse of a dehydration reaction.
Hydrolysis is necessary to break down polymers that are too large to be used by the organism.
digestion of food 15

16. Hydrolysis shorter polymer monomer Water molecule Hydrogen atom
Hydroxyl group
shorter polymer
monomer 16

17. Hydrolysis
Note that the addition of a water molecule results in the reinstatement of a hydroxyl group at the detached end of the polymer, and the hydrogen atom at the detached end of the newly formed monomer.
Hydroxyl group
Hydrogen atom
shorter polymer
monomer 17

18. Enzymes
Both dehydration reactions and hydrolysis require the help of enzymes to make and break bonds
Enzymes are specialized proteins that speed up the chemical reactions in cells
Enzymes are extremely important – without them, many reactions cannot take place. If you lack lactase, you cannot hydrolyze the bond in lactose (lactose intolerant) 18

19. Carbohydrates are polymers made up of carbon, hydrogen, and oxygen atoms.
Carbohydrates play important roles in the energy storage and structural support of organisms, and are themselves an excellent source of energy. 19

20. The monomers that make up carbohydrates are called monosaccharides.
A monosaccharide is a small sugar, that can link together to form larger, more complex sugars.
Monosaccharides generally contain carbon, hydrogen and oxygen in a ratio of 1:2:1.
Glucose, the sugar that carries energy to the cells of your body, is a monosaccharide with the chemical formula of C6H12O6. 20

21. When two monosaccharides are linked together by dehydration synthesis, they form a disaccharide.
Examples of disaccharides include the table sugar sucrose, the milk sugar lactose, and maltose which is formed by linking two glucose molecules together. 21

22. Recall that all polymers are built by a dehydration reaction.
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23. Monosaccharides can also be linked together to form polysaccharides.
A polysaccharide is a large polymer consisting of hundreds or thousands of monosaccharides linked by dehydration reactions.
Polysaccharides function as storage molecules or structural compounds.
The most common types of polysaccharides are starch, glycogen, cellulose, and chitin. 23

24. Polysaccharide: Starch
Starch (amylose) is an energy storage polysaccharide used by plants. Starch consists entirely of repeating glucose monomers.
glucose
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25. Through the process of photosynthesis, plants produce glucose as an energy source. Often, a plant produces more glucose than is readily needed, so the plant stores this energy as long chains of glucose molecules, or starch! Starch is found in potatoes and grains, such as wheat, corn and barley. 25

26. Polysaccharide: Glycogen
Glycogen is an energy storage polysaccharide used by animals. Glycogen also consists entirely of repeating glucose monomers, but is much longer and more branched than starch. Glycogen is broken down into glucose as energy is needed. 26

27. Polysaccharide: Cellulose
Cellulose is a structural polysaccharide used by plants. Cellulose is the most abundant organic compound on Earth, forming the cell walls of all plant cells. 27

28. Polysaccharide: Cellulose
Cellulose consists of long chains of glucose molecules linked in such a way that they can not be broken down easily. Humans are unable to digest cellulose and it makes up the fiber in our diets. Certain microbes can digest cellulose, and reside in the guts of herbivores, such as cows, sheep, and even termites! 28

29. Polysaccharide: Chitin
Chitin is a structural polysaccharide used by animals. Animals that use chitin for external skeletons include insects and crustaceans. Chitin attaches to proteins forming a tough and resistant protective material. 29

30. Chitin forms the exoskeleton of crustaceans such as crabs and lobsters, as well as insects and spiders!
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31. Animals Plants Storage Glycogen Starch Structure Chitin Cellulose 31
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32. Lipids
For short-term energy storage, animals convert glucose into glycogen.
For long-term storage, however, organisms usually convert sugars into fats, or lipids.
Lipids are a diverse group of molecules that includes oils, fats, waxes, phospholipids, and steroids.
All lipids are insoluble in water because they are non-polar. 32

33. Lipids
Lipids are important for energy storage because they contain many more energy-rich C-H bonds than carbohydrates.
A gram of lipids contains twice as much energy as a gram of polysaccharides, such as starch. 33

34. Lipids: Fats
Fats are made up of 2 smaller molecules: glycerol and fatty acids.
A fat molecule contains 1 glycerol and 3 fatty acids.
For this reason, fats are called triglycerides. 34

35. Lipids: Fats
A fatty acid consists of a long chain of carbon and hydrogen atoms.
The arrangement of these atoms can vary, affecting the fat molecule’s physical properties.
Fats whose fatty acids contain the maximum number of hydrogen atoms that can fit are called saturated fats. 35

36. Lipids: Fats
Fats whose fatty acids contain double bonds between some of the carbon atoms are called unsaturated fats because they contain fewer than the maximum amount of hydrogen atoms.
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37. Lipids: Fats
The double bonds (C=C) in unsaturated fats cause kinks, or bends, in the carbon chains of the fatty acids.
These kinks prevent the molecules from packing tightly together so unsaturated fats (like corn oil) remain liquid at room temperature.
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38. Lipids: Fats
In contrast, saturated fats have no double bonds (or kinks).
The molecules can then pack more tightly together, so saturated fats (like butter) are solid at room temperature.
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39. Triglycerides (fats and oils): Store energy Insulate (blubber, etc)
Provide cushioning
Prevent dehydration
Help to maintain internal temperature 39

40. Lipids: Phospholipids
Phospholipids are structurally similar to fats, but contain only 2 fatty acids attached to a glycerol molecule.
Each phospholipid molecule has a polar, or hydrophilic end, and a non-polar, or hydrophobic end.
Phospholipids are the main component of cellular membranes. 40

41. Lipids: Phospholipids
The polar, or hydrophilic end of a phospholipid is “water-loving” and water soluble.
The non-polar, or hydrophobic end of a phospholipid is “water-fearing” and water insoluble.
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42. Lipids: Phospholipids
The membranes of all cells are composed of two layers of phospholipids, called a bi-layer.
The polar, hydrophilic ‘heads’ face outward and are in contact with the aqueous environment on either side of the membrane.
The non-polar, hydrophobic ‘tails’ cluster together in the middle of the membrane. 42

43. Lipids: Phospholipids
Hydrophilic head
Hydrophobic tails
Water (outside of cell)
Water (inside of cell)
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44. Lipids: Steroids
A steroid is a type of lipid that does not contain fatty acids.
Instead, steroids are composed of 4 carbon rings fused together.
4 Carbon rings 1 2 3 4 44

45. Lipids: Steroids
Cholesterol is a common steroid found in animal cell membranes.
Cholesterol is also part of some sex hormones like testosterone, estrogen and progesterone.
Cholesterol
Testosterone
Estrogen 45

46. Proteins
Proteins are a very diverse group of organic molecules. The many shapes of protein molecules allow them to perform a variety of functions.
In living organisms, they are used for transport, structure, metabolism, communication, and even to detect stimuli such as light.
The protein hemoglobin carries oxygen in your blood, and the protein keratin helps support your skin, hair and nails. 46

47. Amino Acids
Like other organic polymers, proteins are made of many monomers bonded together.
These monomers are called amino acids, and there are 20 different kinds found in protein molecules.
Every amino acid molecule contains an amino group (--NH2) and a carboxyl group (--COOH). 47

48. Amino acids are linked together via dehydration synthesis.
The bonds between amino acid monomers are called peptide bonds.
Peptide bond
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49. Proteins
A polypeptide contains hundreds or thousands of amino acids linked together by peptide bonds.
The unique combination of amino acids in a protein molecule determines its specific shape, or structure.
The shape of a protein determines its specific function. 49

50. Every protein has four levels of structure:
Primary
Secondary
Tertiary
Quaternary
Proteins have different levels of structure. 50

51. Primary Structure
The primary structure of a protein describes its unique sequence of amino acids.
The primary structure is determined by the cell’s genetic information (DNA).
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52. Secondary Structure
The secondary structure of a protein describes its folding pattern.
Chains of polypeptides may fold into shapes like a beta pleated sheet or an alpha helix
Theses secondary structures are stabilized by hydrogen bonds between spatially nearby amino acids 52

53. Tertiary Structure
The tertiary structure of a protein describes its overall 3-dimensional shape.
This includes all of the pleated sheets and alpha helixes and is the active form of the protein.
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54. Quaternary Structure
The quaternary structure of a protein describes the complex association of multiple polypeptide chains.
Each polypeptide chain in the association has its own primary, secondary, and tertiary structures. 54

55. Quarternary Structure
Polypeptide
chain
Collagen is formed by several polypeptide chains in a rope-like arrangement
Gives connective tissue, bone, tendons, and ligaments its strength!
Hemoglobin is another example of a quarternary structure protein (transports oxygen in blood)
Collagen 55

56. Quaternary Structure Tertiary structure Primary structure
Secondary structure
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57. Protein shape determines function
When exposed to excessive heat, or changes in salinity or pH, a protein can denature.
Denaturation causes the polypeptide chains in a protein to unravel, and lose their specific shape.
Properly-folded protein
Denaturation
When this happens, a protein will no longer function normally.
Denatured protein
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58. Enzymes
Enzymes are proteins that increase the rate of chemical reactions and so are called catalysts.
Like other proteins, the structure of enzymes determines what they do.
Since each enzyme has a specific shape, it can only catalyze a specific chemical reaction.
The digestive enzyme pepsin, for example, breaks down proteins in your food, but can’t break down lipids or carbohydrates.
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59. Nucleic Acids
Nucleic acids are molecules, like DNA, that store genetic information - the instructions cells need to build proteins.
A nucleic acid contains information on what type of amino acids are needed to make a protein and in what order they should be linked to give the protein its structure, and function.
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60. Nucleotides
The monomers that are linked together to form a nucleic acid polymer are called nucleotides.
Every chromosome in our cells contains nucleic acids
Chromosome
Polymer = nucleic acid
Nucleic acids are polymers
Monomer = nucleotide
Many nucleotide monomers make up each nucleic acid 60

61. Nucleotides Every nucleotide has three parts: 5-carbon sugar
Phosphate group
Nitrogenous base
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62. Nucleotides
Nucleotides can encode information because they contain more than one type of nitrogenous base.
There are 5 different nitrogenous bases: 62

63. Nucleotides Pyrimidines Cytosine Thymine Uracil Purines Adenine
Guanine
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64. Nucleic Acids
There are two types of nucleic acids:
RNA
DNA 64

65. Nucleic Acids There are two types of nucleic acids:
RNA = ribonucleic acid
DNA = deoxyribonucleic acid
Both are nucleotide polymers but they differ in both their structures and their functions. 65

66. RNA Ribonucleic acid contains the sugar ribose.
RNA is composed of 4 nucleotides
RNA contains:
adenine (A)
uracil (U)
cytosine (C)
guanine (G) 66

67. RNA
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68. RNA RNA exists as a long, single strand of nucleotides. 68
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69. DNA Deoxyribonucleic acid contains the sugar deoxyribose.
DNA also is composed of 4 nucleotides
DNA contains:
adenine (A)
thymine (T)
cytosine (C)
guanine (G)
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70. DNA
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71. DNA
DNA exists as a two strands of nucleotides wound around each other to form a double helix.
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72. The Double Helix
DNA’s double helix results from hydrogen bonds formed between its nitrogenous bases.
Large nitrogenous bases or purines (adenine and guanine) pair with smaller bases pyramidines (thymine and cytosine).
Adenine bonds with thymine (A-T) and guanine bonds with cytosine (G-C). 72

73. The Double Helix
Because of its A-T, G-C pairing, each DNA strand is complimentary to the other.
If the sequence of one strand is ATCGAT, the sequence of the other strand must be TAGCTA because A always bonds to T, and C always bonds to G.
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74. DNA Double Helix
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75. DNA Double Helix
The 2 DNA chains are held in a double helix by hydrogen bonds between their paired bases
Most DNA molecules have thousands or millions of base pairs
(A and T would be considered a base pair; as would C and G) 75

76. Hydrogen bonds (dotted lines)76