1. BIOCHEMISTRY
AP BIOLOGY

2. I. Atoms in Organic Molecule
Organic = molecules with carbon and found in living things
Common Atoms = C, O, H, N
Other Atoms = S, P

3. II. Importance of Carbon
Valence number of 4 – forms four bonds
Backbone of all organic molecules
Functional groups attach to form specific properties

4. Four Valence electrons means four bonds…

5. Hydrocarbons
Contain only carbon & hydrogen atoms

6. Carbon can form an endless diversity of carbon skeletons

7. Large Hydrocarbons:
Are the main molecules in the gasoline we burn in our cars
The hydrocarbons of fat molecules provide energy for our bodies

8. Shape of Organic Molecules
Each type of organic molecule has a unique three-dimensional shape
The shape determines its function in an organism

9. Functional Groups
Groups of atoms that give properties to the compounds to which they attach

11. Phosphate group
Used to transfer energy

12. III. Bonding Organic Molecules
Covalent bonds are used to form the backbone of organic molecules
Formed by dehydration synthesis (removal of water to make room for new bonds)
Broken by hydrolysis (replacing the water as bonds are broken apart)

13. Giant Molecules - Polymers
Large molecules are called polymers
Polymers are built from smaller molecules called monomers
Biologists call them macromolecules

14. Examples of Polymers
Proteins
Lipids
Starch
Nucleic Acids

15. Most Macromolecules are Polymers
Polymers are made by stringing together many smaller molecules called monomers
Nucleic Acid Monomer

16. Linking Monomers
Cells link monomers in the process of dehydration synthesis (removing a molecule of water)
Remove OH
Remove H
H2O Forms

17. Breaking Down Polymers
Cells break down macromolecules by a process called hydrolysis (adding a molecule of water)
Water added to split a double sugar

18. IV. Types of Organic Molecules
Carbohydrates – energy formation – sugars and starches
Lipids – storage and insulation – fats and oils
Proteins – enzymes run all body reactions
Nucleic acids – store genetic information – DNA and RNA

19. V. Carbohydrates

20. A. General Information Made of C, H, O
Basic shape is a ring of carbons with –OH and –H groups attached to the carbons
Isomers = same number of C, O, and H but arranged differently
Grouped based on number of rings in molecule

21. B. Monosaccharides Mono = one - one ring
Many isomers (glucose, alpha and beta; fructose; galactose) which react differently in the body
Function – used in energy releasing reactions

22. Glucose – the most common monosaccharide

23. Isomers
Glucose & fructose are isomers because they’re structures are different, but their chemical formulas are the same

24. In aqueous (watery) solutions, monosaccharides form ring structures

25. C. Dissacharides H2O + Formed from two monosaccharides
Glycosidic bonds = covalent bonds in carbs formed by dehydration synthesis
Found mostly in plants – common example is sucrose – used as a transport sugar + OH HO
H2O

27. D. Polysaccharides Many rings (100’s)
Purposes depend on way the rings are constructed
Storage = starch in plants and glycogen in animals
Structure = cellulose in plant cell walls and chitin in fungus cell walls or insect exoskeletons

28. Examples of Polysaccharides
Glucose Monomer
Starch
Glycogen
Cellulose

29. Starch Starch is an example of a polysaccharide in plants
Plant cells store starch for energy
Potatoes and grains are major sources of starch in the human diet

30. Glycogen Glycogen is an example of a polysaccharide in animals
Animals store excess sugar in the form of glycogen
Glycogen is similar in structure to starch

31. Cellulose Cellulose is the most abundant organic compound on Earth
It forms cable-like fibrils in the tough walls that enclose plants
It is a major component of wood
It is also known as dietary fiber

32. Cellulose
SUGARS

33. Dietary Cellulose Most animals cannot derive nutrition from fiber
They have bacteria in their digestive tracts that can break down cellulose

34. Sugars in Water
Simple sugars and double sugars dissolve readily in water
WATER MOLECULE
They are hydrophilic, or “water-loving”
SUGAR MOLECULE

35. Lipids

36. VI. Lipids General Information Fats and oils are triglycerides.
Constructed of a 3 carbon alcohol called glycerol and three long chains of hydrocarbons called fatty acids.

37. Lipid structure H H - C – O - fatty acid H - C – O - fatty acid
Dehydration synthesis removed –OH and –H as bond forms H
H - C – O - fatty acid
H - C – O - fatty acid
H - C – O - fatty acid H

38. Fats
Dietary fat consists largely of the molecule triglyceride composed of glycerol and three fatty acid chains
Fatty Acid Chain
Glycerol
Dehydration links the fatty acids to Glycerol

39. B. Functions of Triglycerides
Storage of chemical energy
Insulation
Padding

40. C. Types of Fatty Acids
Unsaturated fatty acids have less than the maximum number of hydrogens bonded to the carbons (a double bond between carbons)
Saturated fatty acids have the maximum number of hydrogens bonded to the carbons (all single bonds between carbons)

41. Single Bonds in Carbon chain
Double bond in carbon chain

42. Triglyceride
Fatty Acid Chains
Glycerol

43. Fats in Organisms
Most animal fats have a high proportion of saturated fatty acids & exist as solids at room temperature (butter, margarine, shortening)
Saturated fats stack and block arteries.

44. Fats in Organisms
Most plant oils tend to be low in saturated fatty acids & exist as liquids at room temperature (oils)

45. D. Other types of Lipids Found in this group because they are insoluble in water.
Phospholipids – a phosphate group replaces one fatty acid. Found in cell membranes.
Terpenes = pigments such as chlorophyll
Prostaglandins = chemical messengers
Steroids = parts of hormones

46. Steroids
The carbon skeleton of steroids is bent to form 4 fused rings
Cholesterol
Cholesterol is the “base steroid” from which your body produces other steroids
Estrogen
Testosterone
Estrogen & testosterone are also steroids

47. Synthetic Anabolic Steroids
They are variants of testosterone
Some athletes use them to build up their muscles quickly
They can pose serious health risks

48. Lipids Lipids are hydrophobic –”water fearing”
Nonpolar bonds on hydrophobic fatty acids.
Polar bonds on hydrophilic glycerol.
This means that lipids do not dissolve in water.
Includes fats, waxes, steroids, & oils
FAT MOLECULE

50. VII. Protein H H2N – C – COOH R Building Blocks
Composed of chains of amino acids H
H2N – C – COOH R

51. 2. Amino acids come in 20 types and only the R groups vary
2. Amino acids come in 20 types and only the R groups vary. R groups fall into three categories – nonpolar, polar, and ionized.
3. R groups interact and form bonds with one another.

52. Structure of Amino Acids
Amino acids have a central carbon with 4 things boded to it:
Amino
group
Carboxyl
group
Amino group -NH3
R group
Carboxyl group –COOH
Hydrogen -H
Side group -R
Side groups
Serine-polar
Leucine -nonpolar

53. Linking Amino Acids Cells link amino acids together to make proteins
Carboxyl
Side Group
The process is called dehydration synthesis
Dehydration Synthesis
Peptide bonds form to hold the amino acids together
Peptide Bond

54. Nonpolar
(hydrophobic)
Polar
(hydrophilic)
Charged
(Negative/Positive)

55. B. How to build a protein
1. PRIMARY STRUCTURE Straight chain of amino acids
or a polypeptide
(A peptide bond is a dehydration synthesis bond between two amino acids)

56. B. How to build a protein
2. SECONDARY STRUCTURE - Chain forms helix or pleated sheet. (Motif = some parts are helix and some parts are sheet)

57. motif

58. B. How to build a protein
3. TERTIARY STRUCTURE – Helix forms three dimensional shape as R groups interact.
Hydrophobic
interactions

59. What holds the tertiary structure?
Disulfide bridges
Ionic bonds
Hydrogen bonds
between polar R groups
Hydrophobic
interactions

60. 4. QUATERNARY STRUCTURE – not always present – two or more tertiary structures bond together, usually with a metal atom as the center

62. Types of Proteins
Storage
Structural
Contractile
Transport

63. Functions of Proteins Structural – support, tendons & ligaments
Storage – egg whites store amino acids
Transport – carry substances, hemoglobin
Hormones – coordinate body, insulin
Receptors – built into membranes
Contractile – movement, muscle fibers
Defensive – antibodies fight disease
Enzymes – accelerate reactions, digest molecules

64. Denaturating Proteins
Changes in temperature & pH can denature (unfold) a protein so it no longer works
Cooking denatures protein in eggs
Milk protein separates into curds & whey when it denatures

65. Denaturalization
Proteins are denatured when their 3-D shape changes. An incorrect shape can not bond with other molecules correctly and the enzyme does not function.
Denaturalization occurs by
Temperature / heat
pH changes
Excessive salts

66. VIII. Nucleic Acids General notes
Two basic types – DNA (long molecules which store all of our genetic information and never leave the nucleus) and RNA (short molecules that are copies of one gene of the DNA and used to direct protein synthesis)
The organelle chromatin is composed of DNA wrapped around proteins to form a double helix.

68. B. Structure
A nucleotide has three parts – a sugar (monosaccharide), a phosphate functional group, and a nitrogen base.
Nitrogen bases are rings of carbon, nitrogen, and hydrogen. They come in five major types (A, T, C, G, and U).

69. Nucleic acids are polymers of nucleotides
Nitrogenous base
(A,G,C, or T)
Phosphate
group
Thymine (T)
Sugar
(deoxyribose)
Phosphate
Base
Sugar
Nucleotide

70. Bases Each DNA nucleotide has one of the following bases: Adenine (A)
Thymine (T)
Cytosine (C)
Adenine (A)
Guanine (G)
Thymine (T)
Cytosine (C)
Adenine (A)
Guanine (G)

71. RNA – Ribonucleic Acid Ribose sugar has an extra –OH or hydroxyl group
Nitrogenous base
(A,G,C, or U)
Ribose sugar has an extra –OH or hydroxyl group
Uracil
Phosphate
group
It has the base uracil (U) instead of thymine (T)
Sugar (ribose)

72. C. Functions Storage of genetic instruction
Using genetic instructions to create proteins.