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Organic Chemistry Outline Organic vs Inorganic Functional Groups and Isomers Macromolecules Carbohydrates Lipids Proteins Nucleic Acids 1 Organic Chemistry 2 Organic Molecules Inorganic – Chemistry of elements other than carbon Organic – Carbon-based chemistry Inorganic Organic Usually with + & - ions Always contain carbon and hydrogen Usually ionic bonding Always covalent bonding Always with few atoms Often quite large, with many atoms Often associated with nonliving matter Usually associated living systems Organic Chemistry 3 Carbon Atom Carbon atoms: Contain a total of 6 electrons Only four electrons in the outer shell Very diverse as one atom can bond with up to four other atoms Often bonds with other carbon atoms to make hydrocarbons Can produce long carbon chains like octane Can produce ring forms like cyclohexane Organic Chemistry 4 Functional Groups and Isomers Functional groups: Specific combinations of bonded atoms Attached as a group to other molecules - Always react in the same manner, regardless of where attached - Determine activity and polarity of large organic molecules Many functional groups, but only a few are of major biological importance Biologically Important Functional Groups Organic Chemistry 5 Group Structure Compound Significance forms H-bonds; some sugars R OH Hydroxyl Alcohols Polar, and amino acids Example: Ethanol O some sugars Aldehydes Polar; R C Example: Formaldehyde H Carbonyl O Polar; some sugars Ketones Example: Acetone R CR O Carboxylic Polar, acidic; fats and amino acids R Carboxyl Example: Acetic acid C Acids OH H Polar, basic; amino acids R N Amino Amines Example: Tryptophan H R SH O Phosphate R C R OH Sulfhydryl Thiols Disulfide Bonds; some amino acids Example: Ethanethiol Organic Polar, acidic; some amino acids Example: Adenosine triphosphate Phosphates Organic Chemistry Isomers Isomers - organic molecules that have: Identical molecular formulas, but Differing internal arrangement of atoms 6 Organic Chemistry 7 Macromolecules Some molecules called macromolecules because of their large size Usually consist of many repeating units Resulting molecule is a polymer (many parts) Repeating units are called monomers Some examples: Category Example Subunit(s) Lipids Fat Glycerol & fatty acids Carbohydrates Polysaccharide Monosaccharide Proteins Polypeptide Amino acid Nucleic Acids DNA, RNA Nucleotide Common Foods 8 Organic Chemistry 9 Dehydration and Hydrolysis Dehydration - Removal of water molecule Used to connect monomers together to make polymers Polymerization of glucose monomers to make starch Hydrolysis - Addition of water molecule Used to disassemble polymers into monomer parts Digestion of starch into glucose monomers Specific enzymes required for each reaction Accelerate reaction Are not used in the reaction Synthesis and Degradation of Polymers 10 Four Classes of Organics: 1 - Carbohydrates Organic Chemistry Monosaccharides: Single sugar molecule Glucose, ribose, deoxyribose Disaccharides: Contain two monosaccharides joined during dehydration reaction Sucrose Polysaccharides: Polymers of monosaccharides Starch, cellulose, chitin 11 Popular Models for Representing Glucose Molecules 12 Synthesis and Degradation of Maltose, a Disaccharide 13 Carbohydrates Examples: Monosaccharides Organic Chemistry 14 Single sugar molecules Quite soluble and sweet to taste Examples Glucose (blood), fructose (fruit) and galactose - Hexoses - Six carbon atoms - Isomers of C6H12O6 Ribose and deoxyribose (in nucleotides) - Pentoses – Five carbon atoms - C5H10O5 & C5H10O4 Carbohydrates Examples: Disaccharides Organic Chemistry Contain two monosaccharides joined by dehydration reaction Soluble and sweet to taste Examples Sucrose - Table sugar, maple sugar - One glucose and one fructose joined by dehydration Maltose - Malt sugar - Two glucoses joined by dehydration 15 Carbohydrates Examples: Polysaccharides (1) Organic Chemistry Polymers of monosaccharides Low solubility; not sweet to taste Examples Starch -Polymer of glucose -Used for short-term energy storage Plant starch Often branched chain Amylose, corn starch Animal starch Unbranched Glycogen in liver and muscles 16 Carbohydrates Examples: Polysaccharides (2) More polysaccharide examples Organic Chemistry Cellulose - Long, coiled polymer of glucose - Glucoses connected differently than in starch - Structural element for plants - Main component of wood and many natural fibers - Indigestible by most animals Chitin - Polymer of glucose - Each glucose with an amino group - Very resistant to wear and digestion - Arthropod exoskeletons, cell walls of fungi 17 Starch Structure and Function 18 Glycogen Structure and Function 19 Cellulose Structure and Function 20 Organic Chemistry Four Classes of Organics: 2 - Lipids 21 Insoluble in water Long chains of repeating CH2 units Renders molecule nonpolar Types of Lipids Type Organismal Uses Fats Long-term energy storage & thermal insulation in animals Butter, lard Oils Long-term energy storage in Cooking oils plants and their seeds Component of plasma Phospholipids membrane Human Uses No-stick pan spray Steroids Component of plasma membrane; hormones Waxes Wear resistance; retain water Candles, polishes Medicines Blubber 22 Types of Lipids: Triglycerides 23 Types of Lipids: Triglycerides (1) Organic Chemistry 24 Triglycerides (Fats) Long-term energy storage Backbone of one glycerol molecule - Three-carbon alcohol - Each has an OH- group Three fatty acids attached to each glycerol molecule - Long hydrocarbon chain Saturated - no double bonds between carbons Unsaturated - 1 double bonds between carbons - Carboxylic acid at one end - Carboxylic acid connects to –OH on glycerol in dehydration reaction Dehydration Synthesis of Triglyceride from Glycerol and Three Fatty Acids 25 Types of Lipids: Phospholipids (2) Organic Chemistry 26 Phospholipids Derived from triglycerides Glycerol backbone Two fatty acids attached instead of three Third fatty acid replaced by phosphate group - The fatty acids are nonpolar and hydrophobic - The phosphate group is polar and hydrophilic Molecules self arrange when placed in water Polar phosphate “heads” next to water Nonpolar fatty acid “tails” overlap and exclude water Spontaneously form double layer & a sphere Phospholipids Form Membranes 27 Types of Lipids: Steroids & Waxes (3) Organic Chemistry 28 Steroids Cholesterol, testosterone, estrogen Skeletons of four fused carbon rings Waxes Long-chain fatty acid bonded to a long-chain alcohol - High melting point - Waterproof - Resistant to degradation Steroid Diversity 29 Waxes 30 Four Classes of Organics: 3 -Proteins Organic Chemistry 31 Functions Support – Collagen Enzymes – Almost all enzymes are proteins Transport – Hemoglobin; membrane proteins Defense – Antibodies Hormones – Many hormones; insulin Motion – Muscle proteins, microtubules Organic Chemistry 32 Protein Subunits: The Amino Acids Proteins are polymers of amino acids Each amino acid has a central carbon atom (the alpha carbon) to which are attached a hydrogen atom, an amino group –NH2, A carboxylic acid group –COOH, and one of 20 different types of –R (remainder) groups There are 20 different amino acids that make up proteins All of them have basically the same structure except for what occurs at the placeholder R Structural Formulas for the 20 Amino Acids 33 Synthesis and Degradation of a Peptide 34 Protein Molecules: Levels of Structure Organic Chemistry 35 Primary: Literally, the sequence of amino acids A string of beads (up to 20 different colors) Secondary: The way the amino acid chain coils or folds Describing the way a knot is tied Tertiary: Overall three-dimensional shape of a polypeptide Describing what a knot looks like from the outside Quaternary: Consists of more than one polypeptide Like several completed knots glued together Levels of Protein Organization 36 Examples of Fibrous Proteins 37 Four Classes of Organics: 4 -Nucleic Acids Organic Chemistry 38 Polymers of nucleotides Very specific cell functions DNA (deoxyribonucleic acid) - Double-stranded helical spiral (twisted ladder) - Serves as genetic information center - In chromosomes RNA (ribonucleic acid) - Part single-stranded, part double-stranded - Serves primarily in assembly of proteins - In nucleus and cytoplasm of cell The Nucleotides of Nucleic Acids Organic Chemistry 39 Three components: - A phosphate group, - A pentose sugar (ribose or deoxyribose), and - A nitrogenous base (4 kinds in DNA, 3 kinds in RNA, 3 common to both Nucleotide subunits connected end-to-end to make nucleic acid Sugar of one connected to the phosphate of the next Sugar-phosphate backbone Nucleotides 40 DNA Structure 41 RNA Structure 42 Organic Chemistry Comparison of DNA & RNA Table 3.4 Feature DNA Sugar Deoxyribose Bases Strands Cytosine, guanine; Cytosine, guanine; adenine, thymine adenine, uracil Double-stranded; Pairing across strands Mostly single stranded Helix Yes cellular Function Heredity; control center Where RNA Ribose No Interprets genetic info; protein synthesis Chromosomes of cell Cell nucleus and nucleus cytoplasm 43 Organic Chemistry 44 Other Nucleic Acids ATP (adenosine triphosphate) is composed of adenine, ribose, and three phosphates In cells, one phosphate bond is hydrolyzed – Yields: The molecule ADP (adenosine diphosphate) An inorganic phosphate molecule pi Energy Other energy sources used to put ADP and pi back together again ATP 45 Organic Chemistry Review Organic vs Inorganic Functional Groups and Isomers Macromolecules Carbohydrates Lipids Proteins Nucleic Acids 46 Cells and Energy Organic Chemistry 47 Metabolic Reactions and Energy Transformations Organic Chemistry 48 Metabolism: Sum of cellular chemical reactions in cell Reactants participate in reaction Products form as result of reaction Free energy is the amount of energy available to perform work Exergonic Reactions - Products have less free energy than reactants Endergonic Reactions - Products have more free energy than reactants Metabolic Reactions and Energy Transformations Organic Chemistry 49 Metabolism: Sum of cellular chemical reactions in cell Reactants participate in reaction Products form as result of reaction Free energy is the amount of energy available to perform work Exergonic Reactions - Products have less free energy than reactants Endergonic Reactions - Products have more free energy than reactants Organic Chemistry 50 Enzymes Enzymes Protein molecules that function as catalysts The reactants of an enzymatically accelerated reaction are called substrates Each enzyme accelerates a specific reaction Each reaction in a metabolic pathway requires a unique and specific enzyme End product will not appear unless ALL enzymes present and functional E1 E2 E3 E4 E5 E6 A B C D E F G Enzymes: Energy of Activation Organic Chemistry 51 Reactants often “reluctant” to participate in reaction Energy must be added to at least one reactant to initiate the reaction Energy of activation Enzyme Operation: Enzymes operate by lowering the energy of activation Accomplished by bringing the substrates into contact with one another Energy of Activation Organic Chemistry 52 Organic Chemistry 53 Enzyme-Substrate Complex The active site complexes with the substrates Causes active site to change shape Shape change forces substrates together, initiating bond Induced fit model Induced Fit Model Organic Chemistry 54 Organic Chemistry 55 Factors Affecting Enzyme Activity (1) Substrate concentration Enzyme activity increases with substrate concentration More collisions between substrate molecules and the enzyme Temperature Enzyme activity increases with temperature Warmer temperatures cause more effective collisions between enzyme and substrate However, hot temperatures destroy enzyme pH Most enzymes are optimized for a particular pH Factors Affecting Enzyme Activity: Organic Chemistry 56 Temperature Factors Affecting Enzyme Activity: Organic Chemistry 57 pH
