2.  Section 2.3

3. Lipids Fats/Oils/Steroids/Wax 4 Categories of Organic Molecules Molecules of Life Biochemicals (CHON) Proteins Enzymes/Structure/ Movement/Protection Nucleic Acids (DNA/RNA) Carbohydrates Glucose/Fructose Starch/Cellulose

4. Organic Compounds Carbohydrates Monomer: Monosaccharide Made up of: Carbon, Hydrogen, Oxygen (H:O in 2:1 ratio) Lipids Monomer: Glycerol and Fatty Acids Made up of: Carbon, Hydrogen, Oxygen (H:O not in 2:1 ratio) Proteins Monomer: Amino Acid Made up of: Carbon, Hydrogen, Oxygen, Nitrogen Nucleic Acids Monomer: Nucleotide 1) 5 Carbon sugar, 2) phosphate group 3)nitrogenous base Made up of: Carbon, Hydrogen, Oxygen, Nitrogen and Phosphorus

5. ORGANIC INORGANIC  All compounds are either ORGANIC, containing carbon bonded to hydrogen and oxygen, or INORGANIC.  The chemistry of carbon is the chemistry of life.

6.  >11 million compounds  Contain a C-C or C-H bond in combination with N, O, S, P or halogens  Simplest = CH 4  Most complex = DNA

7. Allotropes of carbon Allotropes: Different forms of an element in same physical state Catenation: ability of an element to form chains and/or rings of covalently bonded atoms Carbon has high bond energies C-C 346 kJ/mol C-H 418 kJ/mol

8.  tetrahedral array of C atoms o sp 3 hybridized  high mp (>3500°C)  hardest material known to man  brittle  most dense (3.5x that of H 2 O)  Industrial uses: cutting, drilling, grinding

9.  layers of hexagonal arrays of C atoms o sp 2 hybridized (planar)  high mp  no covalent bonds between layers – C atoms too far apart from each other (London Dispersion forces)  layers slip past one another  lubricant and pencil “lead”  Graphite fibers (stronger and less dense than steel)- sporting goods and aircraft

10.  amorphous form of carbon (no structure)  impure carbon particles resulting from incomplete combustion

11.  How many protons does carbon have? Electrons? FOUR valence  Carbon has FOUR valence electrons o Needs eight electrons to be stable four covalent  Carbon readily forms four covalent bonds with other atoms, including carbon

12.  Carbon can form straight chains, branched chains, or rings o Leading to a great variety of organic compounds Isomers

13.  Isomers – compounds that have the same molecular formula but different structures  More C atoms in formula, more isomers o 18 isomers for C 8 H 18 o 35 isomers for C 9 H 20 o 75 isomers for C 10 H 22 Isomers of C 6 H 14

14. Ex #1) Butane, C 4 H 10 Ex #2) Butene, C 4 H 8 Ex #3) 2-Butene, C 4 H 8 Ex #4) methyl propene, C 4 H 8 ISOMERS

15.  Indicates the number and types of atoms present in a molecule and also shows the bonding arrangement of the atoms  One possible isomer of C 4 H 10  Does not show 3D shape

16.  Isomers in which the atoms are bonded together in different orders.  C 4 H 10 (note continuous chain of C atoms) butane methylpropane

17. Melting Point (°C) Boiling Point (°C) Density at 20°C Butane -138.4-0.50.5788 Methylpropane -159.4-11.6330.549

18.  Only have carbon and hydrogen  Simplest organic compounds  From petroleum (crude oil)

20. Single BondSharing 2 electronsA single line Double BondSharing 4 electronsTwo parallel lines Triple BondSharing 6 electronsThree parallel lines

21.  Organic P REFIXES  Indicates the number of carbon atoms in the hydrocarbon chain  Hydrocarbon : any organic compound that contains only the elements, hydrogen and carbon # of Cprefix# of Cprefix 1 Meth- 6 Hex- 2 Eth- 7 Hept- 3 Prop- 8 Oct- 4 But- 9 Non- 5 Pent- 10 Dec-

22.  Prefixes for alkanes that have 1-4 carbons are rooted historically. o These are methane, ethane, propane, and butane, respectively. o An easy way to remember the first four names is the anagram M ary E ats P eanut B utter (methane, ethane, propane, butane)  Prefixes for 5 carbons and up are derived from the Greek language.

23. SeriesEnding Formula determines the # H atoms Type of Bond(s) Alkane- a neC n H 2n+2 Single Alkene- e neC n H 2n Double Alkyne- y neC n H 2n-2 Triple  Organic S UFFIXES  Indicates the types of covalent bonds that are present in the hydrocarbon chain o Identifies the series to which it belongs

24. Saturated Hydrocarbons: compounds that contain all SINGLE bonds Alkanes Alkanes: each carbon is bonded to 4 atoms – Only contain single bonds – Skeleton: C-C Molecular formula: C n H 2n+2

26. Compounds that contain at least one double bond or triple bond 1. Alkenes : compounds that contain a double bond Skeleton: C=C Molecular formula = C n H 2n

27. 2. Alkynes : compounds that contain a triple bond –Skeleton: C  C –Molecular formula = C n H 2n-2

28.  To give an alkane a name, a prefix indicating the number of carbons in the molecule is added to the suffix ane o identifies both the kind of molecule (an alkane) and how many carbons the molecule has (the prefix).  The name pentane tells you that the molecule is an alkane (- ane ending) and that it has 5 carbons (pent- indicates 5)

29. 1. Locate the carbon atoms in the longest carbon chain that contains the double bond. Use the stem with the ending –ene. 2. Number the carbon atoms of this chain sequentially, beginning at the end nearer the double bond. If the parent chain has more than 3 carbons, insert the number describing the position of the double bond (indicated by its 1 st carbon location) before the base name. 1-butene2-butene

30. http://wps.prenhall.com/wps/media/objects/476/488316/index.html

31.  Named just like the alkenes except the suffix –yne is added 1-butyne 2-butyne ethyne propyne

32. methanepropyne 1-pentene 2-pentene nonane 3-hexene 2-butyne

33. 1. ethene 2. heptane 3. 3-decyne 4. butane 5. 2-octene

34.  An atom or group of atoms, that replaces hydrogen in an organic compound and that defines the structure of a family of compounds and determines the properties of the family.

35. Female lion Estradiol (estrogen) HO OH O Testosterone Male lion Hydroxyl Carbonyl (middle) Carboxyl Lactic Acid { Amino Urea Wohler 1828  FUNCTIONAL GROUP - a cluster of atoms that influence the properties of the molecules that they compose, and determine the characteristics of the compound.

36. Structure Compound Name Alcohols Properties Polar, attracts water (good solvent) Naming -ol

38. Structure Compound Name Aldehydes Properties Structural isomers with different properties Naming -al

39. Structure Compound Name Ketones Properties Structural isomers with different properties Naming -one

40. Structure Compound Name Carboxylic acid (organic acids) Properties Acidic properties Naming -oic acid

41. Structure Compound Name Amines Properties Basic properties Naming -amine

42. Structure Compound Name Phosphates Properties Makes the molecule and anion Transfer energy DNA

43. Structure Compound Name Methylated compounds Properties May affect gene expression

44. Structure Compound Name Thiols Properties Stabilize proteins Some can have a stinky odor – skunk, rotten eggs, garlic Naming -thiol Methanethiol - It is a colorless gas with a distinctive putrid smell. It is a natural substance found in the blood and brain of humans and other animals as well as plant tissues. It occurs naturally in certain foods, such as some nuts and cheese. It is also one of the main compounds responsible for bad breath and the smell of flatus. bloodbrainnutscheese bad breathflatus

45.  In many carbon compounds, the molecules are built up from smaller, simpler molecules known as MONOMERS.  Monomers can bind to one another to form complex molecules known as POLYMERS. o Large polymers are also called MACROMOLECULES o The process of reacting monomer molecules together in a chemical reaction to form polymer chains or three-dimensional networks - POLYMERIZATION

46.  WATER  WATER is the most important inorganic compound in the body and it participates in two biological reactions: o Hydrolysis o Dehydration Synthesis

47.  Breaking down polymers by adding a water molecule.

48. C 12 H 22 O 11 + H 2 O  C 6 H 12 O 6 + C 6 H 12 O 6

49. Polymers are broken down to monomers Animation: Hydrolysis of sucroseHydrolysis of sucrose H H2OH2O OH H H Hydrolysis

50.  Build up large molecules by releasing a molecule of water.

51. C 6 H 12 O 6 + C 6 H 12 O 6  C 12 H 22 O 11 + H 2 O

52. o Cells make most of their large molecules by joining smaller organic molecules into chains called polymers o Cells link monomers to form polymers H OHH H Unlinked monomer Dehydration reaction Longer polymer Short polymer OH H H Unlinked monomer Dehydration reaction Short polymer H2OH2O

53.  Energy necessary for processes is available in the form of certain compounds that contain a large amount of energy in their overall structure.  One of these is adenosine triphosphate or ATP

54.  ATP has three linked phosphate groups ( PO 4 -2 ) attached to one another by covalent bonds.  The bond holding the last one is easily broken and when broken much more energy is released then was required to make the bond.  This conversion of energy is used by cells to drive chemical reactions that enable organisms to function.

55.  The four main classes of organic compounds essential to all living things are made from CARBON, HYDROGEN, and OXYGEN atoms, but in different ratios giving them different properties.

56.  Made of carbon, hydrogen, and oxygen with H to O in a 2:1 ratio MONOMER  Monosaccharides are a single sugar - MONOMER  Source of energy  Can be in straight or ring form  -ose ending for sugars Glucose (C 6 H 12 O 6 ) Ribose (C 5 H 10 O 5 )

57.  Glucose, galactose, and fructose all have the same molecular formula but differ in the arrangement of atoms = ISOMERS  General formula for the monomer = (CH 2 O) n o Molecular formula = C 6 H 12 O 6 (hexoses) C 5 H 10 O 5 (pentoses)

58. Type of Sugar Name of Sugar Description of Sugar PentoseriboseFound in RNA PentosedeoxyriboseFound in DNA Hexoseglucose In blood; cell’s main energy source (ATP) Hexosefructose In fruit; sweetest of monomers (honey) HexosegalactoseIn milk

59.  Disaccharides are double sugars  Two monosaccharides condense to form disaccharides dehydration o Formed by dehydration synthesis o Molecular formula = C 12 H 22 O 11

60.  Bond that joins monosaccharides (carbohydrates) = glycosidic bond

61. A disaccharide is produced by joining 2 monosaccharide (single sugar) units. In this animation, 2 glucose molecules are combined using a condensation reaction, with the removal of water. Glucose molecules joining to form a disaccharide Glucose molecules joining to form a disaccharide Condensation of Monosaccharides

63. Name of Disaccharide 2 single sugars that join to form the disaccharide Description of Sugar SucroseGlucose + Fructose Table Sugar; transportable energy (sugar beets, sugar cane) LactoseGlucose + Galactose In milk of mammals; provides energy for suckling animals MaltoseGlucose + Glucose In malt (grains) From starches (cereal, pasta, potatoes)

64.  Polysaccharides many sugars:  General formula – (C 6 H 10 O 5 ) n plus H 2 O (n = # monomers)  Formed by dehydration synthesis  Long chains of glucose molecules

65. Name of Polysaccharide Description of Sugar Glycogen (animal starch) Animal polysaccharide - stores excess sugar Stored in liver and muscles Muscle contraction & movement Broken down into glucose and released into blood for quick energy Starch Plant polysaccharide Stores excess sugar Cellulose Gives plants strength and rigidity Major component of wood and paper Component of cell wall

66. o Starch and glycogen are polysaccharides That store sugar for later use o Cellulose is a polysaccharide found in plant cell walls – provides structure Starch granules in potato tuber cells Glycogen granules in muscle tissue Cellulose fibrils in a plant cell wall Glucose monomer Cellulose molecules STARCH GLYCOGEN CELLULOSE O O O O OOO O OOO O O O O O O O O O O O O O O O O O O O O O OO OOOOO O O OO O OO O OH Figure 3.7

67.  Elements – carbon, hydrogen, and oxygen ( NOT a 2:1 H:O ratio)  Do not dissolve in water  Lipids contain a large number of C-H bonds which store more energy than C-O bonds in carbohydrates  Monomers: glycerol and fatty acid

68.  Fatty Acids: o Fatty acids are unbranched C-chains  (12-28 C) with a carboxyl group (acid) at one end POLAR HYDROPHILIC The carboxyl end is POLAR and attracted to water – HYDROPHILIC NONPOLAR HYDROPHOBIC The hydrocarbon end is NONPOLAR and does not interact with water – HYDROPHOBIC

69. General Structure Saturated (single bonds) Unsaturated (double bonds)

70.  Lipids can be used to store energy – long term E storage  Lipids are important parts of biological membranes  Lipids are waterproof coverings – nonpolar  Heat insulation and protection around internal organs  Steroids and hormones are lipids that send messages to cells (eg. estrogen, progesterone, testosterone) o anabolic steroids - synthetic  Cholesterol, an important steroid, is an important component of the animal cell wall Steroid – 4 fused rings

71.  Long fatty acid chain joined to an alcohol chain  Highly waterproof o Plant parts (leaves, fruit) form a protective coating on the outer surface (reduce transpiration)  In animals  ear wax

72. Look at the structures of the fatty acids and explain the differences between saturated, unsaturated and polyunsaturated fats.

73. Lipids (4:52)

74. Saturated Fatty Acids Carbon atoms with 4 atoms covalently bonded All single bonds High melting points Solid @ room temperature Ex.) animal fat, shortening Unsaturated Fatty Acids Carbon not bonded to the maximum # of atoms There are double bond(s) polyunsaturated Liquid @ room temperature Primarily in plants Energy storage in animals

76.  A diet rich in saturated fats may contribute to cardiovascular disease through plaque deposits  Hydrogenation – process of converting unsaturated fats to saturated fats by adding hydrogen  Hydrogenating vegetable oils also creates unsaturated fats with trans double bonds o These trans fats may contribute more than saturated fats to cardiovascular disease

79.  Lipids ( fats, oils, and waxes ) are formed by a glycerol molecule bonding to fatty acid(s) o formed by dehydration synthesis

82.  Three fatty acids attached to glycerol

84.  Two fatty acids joined to a glycerol PHOSPHOLIPID BILAYER  Makes up cell membrane - PHOSPHOLIPID BILAYER

86.  Elements: Carbon, Hydrogen, Oxygen, Nitrogen  Monomer: AMINO ACID (20 different kinds)  Each amino acid has a central carbon atom bonded to 4 other atoms or functional groups

88.  Essential Amino Acids : Cannot be synthesized in the animal body and should be obtained from diet  Nonessential Amino Acids: Can be synthesized in the animal body o Some may be conditionally essential in newborns or during illness o Amino acids absorbed from food are used to synthesize structural proteins, functional proteins, protein hormones, carrier proteins, and proteins essential for growth, development and tissue repair.

90.  Bond that joins amino acids (protein) = PEPTIDE BOND

91. amino acid 1 amino acid 2dipeptidewater Peptide bond Formation of a peptide bond

93. 1. Structural component of cell 2. Transport substances into or out of cells 3. Regulate cell processes 4. Control the rate of reactions - enzymes 5. Skin, hair, muscles, parts of skeleton (structural proteins – collagen and elastin in tissue) 6. Help to fight disease – antibodies 7. Hemoglobin – transport O 2

94. TypeExample(s)Description Enzymes Ligase Pepsin Lactase Speed up reactions (catalyst) Have a specificity for one substance Antibodies (Immunoglobulins) IgM IgA IgG IgD Highly specific Bind to foreign antigens First line of defense against disease-causing organisms Hormones Insulin Thyroxin Epinephrine Produced at one site – function at another Small amount to bring about a response Structural Proteins Keratin Collagen Actin & Myosin Build body and cell parts

95. Structural Protein Description/Function Tubulin Found in microtubules – cell skeleton Actin & Myosin In muscle for contraction Keratin In hair and nails Collagen Elasticity of skin Histones Proteins in chromosomes for support

96. Protein Structure: Proteins can only function properly if they have the proper shape Levels of Protein Structure:  Primary Structure: the sequence of amino acids.  Secondary Structure: the folding or coiling of the polypeptide chain.  Tertiary Structure: the complete 3D arrangement of polypeptide chain.  Quaternary Structure: the arrangement of the different polypeptide in a protein.

97. Groove A protein’s specific shape determines its function o A protein consists of one or more polypeptide chains folded into a unique shape that determines the protein’s function

98. Primary Structure The way the amino acids are lined up Dictated by your genes Secondary Structure Alpha Helix - coil/spiral Beta Pleated - formed due to hydrogen bonding between functional groups Tertiary Structure Determines protein’s function – Active Conformation Bonds between R groups: Ionic, Hydrogen, Hydrophobic, Disulfide Quaternary Structure Only get this if there is more than 1 polypeptide chain Ex.) Collagen (makes skin elastic) – 3 chains; Hemoglobin 2  & 2 

100. Primary Structure Levels of Protein Structure Primary structure Gly Thr Gly Glu SerLys Cys Pro LeuMet Val Lys Val Leu Asp AlaVal Arg Gly Ser Pro Ala Ile Asn Val Ala Val His Val Amino acids Phe Arg Secondary structure C N O C C N H O C C H Hydrogen bond O C N H C C O N H O C C N H C N O C C N H O C C N H C O C H N H C O H C R H N Alpha helix C N H C C H H O N R CC O N H O C C N H CC O N H O C C N H C O C N H O C CN H C O O C C N H C C O N H C C O N H C C O N H C C O N H C C O N H C C O N H C C O H N C Pleated sheet Amino acids Secondary structure Tertiary structure Polypeptide (single subunit of transthyretin) Tertiary Structure Quaternary structure Transthyretin, with four identical polypeptide subunits Quaternary Structure

102. Enzyme + Substrate = ES complex  EP complex = Enzyme + product(s)

105. Got Lactase? o Many people in the world suffer from lactose intolerance Lacking an enzyme (lactase) that digests lactose, a sugar found in milk “ase” = enzyme “ose” = sugar

106. Each enzyme is the specific helper to a specific reaction o each enzyme needs to be the right shape for the job o enzymes are named for the reaction they help sucrase breaks down sucrose proteases breakdown proteins lipases breakdown lipids DNA polymerase builds DNA Catalase breaks down hydrogen peroxide Enzymes Enzymes - a fun intro (4:46)

107.  Most enzymes work the best at certain pH and temperature.  Denaturation: a change in the shape of the enzyme. o Cause the enzyme to ineffective because the active site and the substrate no longer fit together. o Changes in pH and increases in temperature can denature enzymes. Regulation of Enzyme Activity Animation

108.  Protein that has lost its active conformation, or shape  Denaturing caused by: o Temperature o Solute (salt) Concentration o pH

109. amount of enzyme reaction rate http://www.kscience.co.uk/animations/anim_ 2.htm

110. amount of substrate reaction rate

111. 37°C temperature reaction rate

112.  Temperature effect on rates of enzyme activity o Optimum temperature greatest number of collisions between enzyme & substrate human enzymes = 35°- 40°C (body temp = 37°C) o Raise temperature denature protein = unfold = lose shape o Lower temperature molecules move slower decrease collisions

113. 7 pH reaction rate 20134568910 stomach pepsin intestines trypsin 11121314 Pepsin breaks down proteins in stomach Trypsin is produced in the pancreas and breaks down proteins in the small intestine

114.  pH effects on rates of enzyme activity o pH changes protein shape o most human enzymes = pH 6-8 depends on where in body pepsin (stomach) = pH 3 trypsin (small intestines) = pH 8  Some enzymes can be turned on and off by regulator molecules that bind to the enzyme causing the active site to change shape. Enzyme function and inhibition (1:07)

115.  Large, complex organic compounds that store information in cells, using a system of four compounds to store hereditary information, arranged in a certain order as a code for genetic instructions of the cell.  Elements: Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus  Monomer: Nucleotide 1. Phosphate group (Phosphoric Acid) 2. 5-carbon (pentose) sugar (Deoxyribose or Ribose) 3. Nitrogenous Base

116. Polymer : polynucleotide  Polynucleotides are formed when the phosphate group of one nucleotide binds to the sugar of another nucleotide. Function:  Provides instructions to the cell on how to make proteins - Dictates the amino acid sequence which controls protein synthesis  Stores and transmits genetic information - allows genetic information to be passed on from one generation to the next.  Specificity determined by the fact that only certain bases bond with each other o Said to be complementary A –T C-G

117. There are FOUR Nitrogen bases

118.  Purines - 2 ring base Adenine (A) Guanine (G)  Pyrimidines - 1 ring base Cytosine (C) Thymine (DNA) (T), Uracil (RNA) (U)

119.  Nucleotides combine, in DNA to form a double helix, and in RNA a single helix  The sides of the ladder are made up of the phosphate group and the sugar and the rungs of the ladder are nitrogen bases  Examples of Nucleic Acids: 1. Deoxyribonucleic Acid (DNA) 2. Ribonucleic Acid (RNA) Nucleic Acids and Dehydration Synthesis

120. Type of BondBond Between…… phosphodiester phosphate group and sugar N-glycosidic sugar (glycosidic) and nitrogen base hydrogen nitrogen bases

121.  Dictate the amino acid sequence – controls protein synthesis  Stores and transmits genetic information  Specificity determined by the fact that only certain bases bond with each other o Said to be complementary A –T C-G

122.  The glue contains long strands of molecules like spaghetti.  If the long molecules slide past each other easily, then the substance acts like a liquid because the molecules flow.  If the molecules stick together at a few places along the strand, then the substance behaves like a rubbery.  Borax is the compound that is responsible for hooking the glue’s molecules together to form the putty-like material

123. 1. Measure 20 ml of solution a into a small beaker 2. Use a graduated cylinder to measure 10 ml of solution B, add it to the beaker. Add food coloring if you want 3. Stir with a glass rod and knead with fingers 4. Put it into a plastic cup and cap. Label with your name and pick up at the end of the day