1. Ms. Napolitano Honors Biology
Organic Chemistry
Ms. Napolitano
Honors Biology

3. Introduction to Orgo
Organic chem – the study of C based compounds (must have both C & H)
Why Carbon?
It’s versatile!
4 valence electrons (4 covalent bonds)
Form simple or complex compounds
C chains form backbone of most biological molecules (straight, bent, double bond, rings)

4. Hydrocarbons Hydrocarbons ONLY consist of C & H
Importance – store energy
Hydrophobic

5. Organic Shorthand

6. Isomers
Isomers – same number of atoms per element, different arrangement
3 types:
Structural – differ in covalent partners
Geometric – differ in arrangement around a double bond
Enantiomers – mirror images of each other
Different structure means different function!

7. Functional Groups
Functional groups – parts of organic molecules that are most commonly involved in chemical reactions
replace H in hydrocarbons
Most are hydrophilic
Variation of life is due to molecular variation

8. Functional Groups

9. Isomers
Geometric Isomers
Structural Isomers
cis
trans
Enantiomers

10. 10/29 – Do Now
Draw the following compounds using organic shorthand.
Draw out all hydrogens and carbons for the following compounds. What is the chemical formula? 1. 2. 3.
C4H9OH
4. C4H8 5. 6. 7. 8.

11. Practice Problem
Draw the following compound (Retinol – Vitamin A) using organic shorthand.

12. Isomers
Isomers – same number of atoms per element, different arrangement
3 types:
Structural – differ in covalent partners
Geometric – differ in arrangement around a double bond
Enantiomers – mirror images of each other
Different structure means different function!

13. Cyanide is an organic compound.
True
False

14. What kind of isomers are these?
Structural
Geometric
Enantiomers

15. This is a fatty acid. What type of isomer would you expect to see?
Structural
Geometric
Enantiomers

16. Functional Groups
Functional groups – parts of organic molecules that are most commonly involved in chemical reactions
replace H in hydrocarbons
Most are hydrophilic
Variation of life is due to molecular variation

17. Functional Groups

18. Macromolecules Huge biological molecules! 4 classes:
Carbohydrates
Lipids
Proteins
Nucleic Acids
Polymers – long molecule made of monomers

19. Polymerization Building dimers or polymers
Condensation rxn AKA dehydration synthesis:
Monomer-OH + monomer-H  dimer + H2O
Breaking down dimers or polymers
Reverse rxn called hydrolysis
Dimer + H2O  monomer-OH + monomer-H

21. The breaking down of foods during digestion is an example of dehydration synthesis.
True
False

22. The breaking down of foods during digestion is an example of dehydration synthesis.
True
*False

23. Amino acids (shown below) are linked together to form proteins
Amino acids (shown below) are linked together to form proteins. This is an example of dehydration synthesis.
True
False

24. Amino acids (shown below) are linked together to form proteins
Amino acids (shown below) are linked together to form proteins. This is an example of dehydration synthesis.
*True
False

25. Carbohydrates Cells get most of their energy from carbs
Carbs are sugars, most end in “-ose”
Multiple of molecular formula: CH2O
Glucose: C6H12O6
Carbonyl group
Multiple hydroxyl groups

26. Carbohydrates Monosaccharides
Monomers: simple sugars w/ 3-7 carbons
Ex. (C6H12O6): Glucose, Fructose, Galactose
Disaccharide – formed by 2 monosaccharides forming a glycosidic linkage by dehydration synthesis
Ex:
glucose + glucose  maltose + H2O
glucose + fructose  sucrose + H2O
glucose + galactose  lactose + H2O

27. Carbohydrates

28. Carbohydrates
Polysaccharides: 100’s – 1000’s of monosaccharides joined by glycosidic linkages
Storage polysaccharides
Starch
Plants – stored in plastids
Made entirely of glucose - helical
Glycogen
Animals – stored in liver & muscle (in vertebrates)
Made entirely of glucose - branched
Structural polysaccharides
Cellulose – plant cell walls
Made of glucose – linear
Chitin
Exoskeleton of arthropods & fungi cell walls

29. A compound has the molecular formula C5H10O5. Is it a carbohydrate?
Yes No

30. A compound has the molecular formula C5H10O5. Is it a carbohydrate?
*Yes No

31. Two monosaccharides are joined together by hydrolysis to form a disaccharide.
True
False

32. Two monosaccharides are joined together by hydrolysis to form a disaccharide.
True
*False

33. Which of the following is only made in animals?
Collagen
Glycogen
Starch

34. Which of the following is only made in animals?
Collagen
*Glycogen
Starch

35. Which of the following is only made by fungi?
Collagen
Glycogen
Starch
Chitin

36. Which of the following is only made by fungi?
Collagen
Glycogen
Starch
*Chitin

37. 11/6 - Do Now Grab your clickers! Take out your carbohydrates lab.
Draw the dehydration synthesis reaction that joins the following two molecules:

38. Lipids No polymers! Hydrophobic (mostly hydrocarbons)
Store energy efficiently (2x more than carbs!)
Types :
Fats & oils
Phospholipids
Steroids
Waxes

39. Fats & Oils Fat = dehydration synthesis of:
Glycerol C3H5(OH)3
Fatty acid: 16 or 18 carbon hydrocarbon chain w/ carboxyl group
Glycerol + 3 fatty acid chains = triglyceride + 3 H2O
Function:
Energy storage
Insulation
Protective cushioning around organs

40. Saturated Fats No double bonds between carbons
Saturated with hydrogens
Solid at room temperature
Mostly animal fat
Ex: butter, lard, adipose

41. Unsaturated Fats 1 or more double bonds between carbons
Bent or kinked chains
Liquid at room temperature
Mostly plant or fish fat
Ex: olive oil, cod liver oil, corn oil

42. Phospholipids Glycerol + 2 fatty acids + phosphate
Phosphate head = hydrophilic
Fatty acid tails = hydrophobic
Form a bilayer in water
Makes up cell membranes

43. Phospholipids

44. Steroids 4 fused carbon rings with various functional groups
Ex: cholesterol
Component of cell membrane & many hormones

45. 11/12 – Do Now Take out your lipids HW from the weekend.
Grab your clickers!
Fill out the the Venn Diagram comparing carbs and lipids.
Carbs
Lipids

46. Which of the following is a class of molecules that encompasses all of the other molecules listed?
Triglycerides
Waxes
Lipids
Fatty acids
Sterols
Phospholipids

47. Which of the following is a class of molecules that encompasses all of the other molecules listed?
*Triglycerides
Waxes
Lipids
Fatty acids
Sterols
Phospholipids

48. One molecule of fat is made by joining three molecules of _________ to one molecule of _________ .
Glycerol, fatty acid
Sterols, phosphate
Phosphate, sterols
Fatty acid, glycerol

49. One molecule of fat is made by joining three molecules of _________ to one molecule of _________ .
Glycerol, fatty acid
Sterols, phosphate
Phosphate, sterols
*Fatty acid, glycerol

50. Which of the following is most likely to have all single bonds in its fatty acid chain?
Coconut oil
Sunflower oil
Canola oil
Olive oil

51. Which of the following is most likely to have all single bonds in its fatty acid chain?
*Coconut oil
Sunflower oil
Canola oil
Olive oil

52. Which of the following statements about saturated fats is true?
They contain 1+ double bonds in the hydrocarbon tail.
They contain the maximum number of hydrogens in the hydrocarbon tail
They make up the majority of plant oils.
They are healthier for you then unsaturated fats.

53. Which of the following statements about saturated fats is true?
They contain 1+ double bonds in the hydrocarbon tail.
*They contain the maximum number of hydrogens in the hydrocarbon tail
They make up the majority of plant oils.
They are healthier for you then unsaturated fats.

54. Little Debbie Swiss Rolls
Hostess Cupcakes

55. 11/14 – Do Now + Get your clickers! Answer the following questions:
Which two amino acids are shown as the reactants?
Draw the product.
What type of reaction is this?
What is the name of the newly formed bond?
Predict the following: The long chain made by the joining of MANY amino acids using the newly formed BONDS is called a _____________.

56. Proteins
Functions: enzymes, structural support, storage, transport, cellular communication, movement, defense
Monomer = amino acid
Short C chain
Amino group
Carboxylic acid group
“R” group determines type
Cells use 20 different amino acids to build 1000’s of different proteins
Amino acids linked by peptide bonds via dehydration synthesis to form polymers – polypeptides
Chaperonins assist in protein folding

58. Protein Structure 10 Structure 20 Structure
- Sequence of amino acids (length vary)
- Determined by genes
20 Structure
How polypeptide folds or coils
Α helix
β pleats
30 Structure - 3D (fold onto itself)
H bonds
Hydrophobic interaction
Disulfide bridges
40 Structure – bonds to other polypeptides
2 or more polypeptide chains bonded together

60. Protein Conformation
Structure of a protein is directly related to function
Protein conformation is determined when it is synthesized, and it is maintained by chemical interactions
Protein conformation also depends on environmental factors: pH, salt concentration, temp…etc
Protein can be denatured – unravel and lose conformation, therefore biologically inactive.
When conditions change again, protein can be renatured (restored to normal)

61. 11/18 – Do Now Happy Monday! Please get your clickers!
Take out your lipids & proteins lab.
Add proteins to your Venn Diagram! Draw & fill in the following:
Carbs
Lipids
Proteins

62. All of the following are true about both amino acids and monosaccharides EXCEPT:
They are monomers.
The are linked to other amino acids & monosaccharides (respectively) by dehydration synthesis.
They are organic molecules.
They are always arranged in a ring.

63. All of the following are true about both amino acids and monosaccharides EXCEPT:
They are monomers.
The are linked to other amino acids & monosaccharides (respectively) by dehydration synthesis.
They are organic molecules.
*They are always arranged in a ring.

64. All amino acids contain all of the following groups EXCEPT:
hydroxyl
carboxyl
central carbon between 2 functional groups

65. All amino acids contain all of the following groups EXCEPT:
*hydroxyl
carboxyl
central carbon between 2 functional groups

66. All proteins have a primary structure.
True
False

67. All proteins have a primary structure.
*True
False

68. The helix that forms in a protein chain as a result of hydrogen bonds & other weak forces is an example of:
Primary structure
Secondary structure
Tertiary structure
Nonlinear structure

69. The helix that forms in a protein chain as a result of hydrogen bonds & other weak forces is an example of:
Primary structure
*Secondary structure
Tertiary structure
Nonlinear structure

70. In the stable form of a protein, what is generally oriented to the interior of the protein molecule?
Hydrophilic portions
Hydrophobic portions
Large portions
Random portions

71. In the stable form of a protein, what is generally oriented to the interior of the protein molecule?
Hydrophilic portions
*Hydrophobic portions
Large portions
Random portions

72. Nucleic Acids 2 types: DNA (deoxyribonucleic acid)
Found in nucleus of eukarya
Double stranded helix
Provides directions for its own replication
Also directs RNA synthesis
Though RNA controls 10 structure of proteins
RNA (ribonucleic acid)
Single stranded, variety of shapes
Transfers information from nucleus to cytoplasm (where proteins are made)
DNA RNA Proteins

73. Structure of Nucleic Acids
Monomers – nucleotides composed of 3 parts:
Pentose (ribose or deoxyribose)
Phosphate group
Nitrogenous base
Pyrimidines – 6 membered rings of C & N
Cytosine (C)
Thymine (T)….DNA only
Uracil (U)… RNA only
Purines – 6 membered ring fused to 5 membered ring of C & N
Adenine (A)
Guanine (G)

74. Nucleotide Structure

75. Bonding of Nucleotides

76. Bonding of Nucleotides

77. Write the complementary DNA strand for the following:
CGTAAGCGCTAATTA
TCTTAAATGATCGATC
AATGAATAGCTAGCTT
GGCATTCGCGATCATG
CGTTAGCATGCTTCAT

78. Write the complementary DNA strand for the following:
CGTAAGCGCTAATTA
GCATTCGCGATTAAT
TCTTAAATGATCGATC
AGAATTTACTAGCTAG
AATGAATAGCTAGCTT
TTACTTATCGATCGAA
GGCATTCGCGATCATG
CCGTAAGCGCTAGTAC
CGTTAGCATGCTTCAT
GCAATCGTACGAAGTA

79. Write the complementary RNA strand for the following:
CGTAAGCGCTAATTA
TCTTAAATGATCGATC
AATGAATAGCTAGCTT
GGCATTCGCGATCATG
CGTTAGCATGCTTCAT

80. Write the complementary RNA strand for the following:
CGTAAGCGCTAATTA
GCAUUCGCGAUUAAU
TCTTAAATGATCGATC
AGAAUUUACUAGCUAG
AATGAATAGCTAGCTT
UUACUUAUCGAUCGAA
GGCATTCGCGATCATG
CCGUAAGCGCUAGUAC
CGTTAGCATGCTTCAT
GCAAUCGUACGAAGUA

81. ATP Not a macromolecule, but still important for life!
Adenosine Triphosphate (ATP) – primary energy transferring molecule in the cell
ATP   ADP + Pi + Energy