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Chapter 3 The Chemistry of Organic Molecules
AP Biology
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Definitions Organic Molecules Inorganic Molecules
Bonding of H, O, N, and other molecules to carbon. Characterize the structure and function of living things Inorganic Molecules Do not contain C and H together Nonliving matter; however they play important roles in living things
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Functional Groups Functional groups are the parts of molecules involved in chemical reactions Give organic molecules distinctive chemical properties (ex. Polarity, hydophobic/philic, acidic, etc.)
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Six functional groups are important in the chemistry of life: (see Figure 3.2, pg 35)
Hydroxyl Carbonyl Carboxyl Amino Sulfhydryl Phosphate
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Isomers Isomers are molecules with the same molecular formula but different structures (different functional groups) and properties
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Macromolecules Are large molecules composed of smaller molecules
Are complex in their structures
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Macromolecules Macromolecules are polymers, built from monomers
Four classes of life’s organic molecules are polymers Carbohydrates Proteins Nucleic acids Lipids
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The Synthesis and Breakdown of Polymers
Monomers form larger molecules by condensation reactions called dehydration synthesis (a) Dehydration reaction in the synthesis of a polymer HO H 1 2 3 4 H2O Short polymer Unlinked monomer Longer polymer Dehydration removes a water molecule, forming a new bond Figure 5.2A
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The Synthesis and Breakdown of Polymers
Polymers can disassemble by Hydrolysis (addition of water molecules) (b) Hydrolysis of a polymer HO 1 2 3 H 4 H2O Hydrolysis adds a water molecule, breaking a bond Figure 5.2B
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Carbohydrates Monosaccharides Disaccharides Polysaccharides Glucose
Fructose Ribose/Deoxyribose Disaccharides Lactose Maltose Sucrose Polysaccharides Starch Glycogen Cellulose Chitin
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Lipids Lipids are a diverse group of hydrophobic molecules (nonpolar and insoluble) Lipids Are the one class of large biological molecules that do not consist of polymers Provide energy storage Act as cell messengers
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Fats Are constructed from two types of smaller molecules, a single glycerol and usually three fatty acids Vary in the length and number and locations of double bonds they contain
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(a) Saturated fat and fatty acid
Saturated fatty acids Have the maximum number of hydrogen atoms possible Have no double bonds (a) Saturated fat and fatty acid Stearic acid Figure 5.12
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(b) Unsaturated fat and fatty acid
Unsaturated fatty acids Have one or more double bonds (b) Unsaturated fat and fatty acid cis double bond causes bending Oleic acid Figure 5.12
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Waxes Chains of fatty acids bonded to an alcohol chain. Solid
Protective
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Phospholipids Have only two fatty acids
Have a phosphate group instead of a third fatty acid
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(a) Structural formula (b) Space-filling model
Phospholipid structure Consists of a hydrophilic “head” and hydrophobic “tails” CH2 O P CH C Phosphate Glycerol (a) Structural formula (b) Space-filling model Fatty acids (c) Phospholipid symbol Hydrophobic tails Hydrophilic head Hydrophobic tails – Hydrophilic head Choline + Figure 5.13 N(CH3)3
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The structure of phospholipids
Results in a bilayer arrangement found in cell membranes Hydrophilic head WATER Hydrophobic tail Figure 5.14
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Steroids Steroids Are lipids characterized by a carbon skeleton consisting of four fused rings Differ with functional groups
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One steroid, cholesterol
Is found in cell membranes Is a precursor for some hormones HO CH3 H3C Figure 5.15
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Proteins Support Enzymes Transport Defense Hormones Motion
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Amino acids Are organic molecules possessing both carboxyl (acidic) and amino groups Differ in their properties due to differing side chains, called R groups
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Amino Acid Polymers Amino acids Are linked by peptide bonds (covalent)
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Protein Structure A protein’s specific conformation (shape) determines how it functions
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Four Levels of Protein Structure
Primary structure Is the unique sequence of amino acids in a polypeptide Figure 5.20 – Amino acid subunits +H3N Amino end o Carboxyl end c Gly Pro Thr Glu Seu Lys Cys Leu Met Val Asp Ala Arg Ser lle Phe His Asn Tyr Trp Lle
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Secondary structure Is the folding or coiling of the polypeptide into a repeating configuration Includes the helix and the pleated sheet O C helix pleated sheet Amino acid subunits N H R H Figure 5.20
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Is the overall three-dimensional shape of a polypeptide
Tertiary structure Is the overall three-dimensional shape of a polypeptide Results from interactions between amino acids and R groups CH2 CH O H O C HO NH3+ -O S CH3 H3C Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hyrdogen bond Ionic bond Disulfide bridge
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Quaternary structure Results when two or more polypeptide chains combine. Polypeptide chain Collagen Chains Chains Hemoglobin Iron Heme
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Protein Structure http://www.stolaf.edu/people/giannini/
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Denaturation is when a protein unravels and loses its native conformation (shape)
Renaturation Denatured protein Normal protein Figure 5.22
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Nucleic Acids Made of nucleotide monomers Two Types: DNA & RNA
Differences in structure
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ATP A nucleotide of ribose and adenine 5-C sugar and 3 phosphates
High energy (bonds)
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