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Chapter 03 Organic Chemistry Organic Chemistry Outline Organic vs Inorganic Functional Groups and Isomers Macromolecules Carbohydrates Lipids Proteins Nucleic Acids 2 Organic Chemistry 3 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 Carbohydrates as structural materials 4 Organic Chemistry 5 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 Octane & Cyclohexane 6 Organic Chemistry 7 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 8 Group Structure Compound Significance forms H-bonds; some sugars R OH Hydroxyl Alcohols Polar, and amino acids Example: Ethanol O Polar, formsRH-bonds; some sugars Polar; some sugars Aldehydes Example: Formaldehyde C and amino acids;HExample: Ethanol Carbonyl O some sugars Polar; some sugars Polar; Ketones Example: Acetone Example: Formaldehyde R CR O Carboxylic Polar; some sugars Polar, acidic; fats and amino acids R Carboxyl CExample:Acids AcetoneExample: Acetic acid OH H and amino acids Polar, basic; amino acids Polar, acidic; fats R N Amino Amines Example: Tryptophan H Example: Acetic acidamino acids Polar, acidic; some Disulfide Bonds; some amino acids R SH Sulfhydryl Thiols Polar, basic; amino acids Example: Ethanethiol Example: Adenosine triphosphate Example: Tryptophan Disulfide Bonds; amino acids O some Organic Polar, acidic; some amino acids Example: Ethanethiol R C R Phosphates Example: Adenosine triphosphate Phosphate OH Organic Chemistry Isomers Isomers - organic molecules that have: Identical molecular formulas, but Differing internal arrangement of atoms 9 Organic Chemistry 10 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 11 Organic Chemistry 12 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 13 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 14 Popular Models for Representing Glucose Molecules 15 Synthesis and Degradation of Maltose, a Disaccharide 16 Carbohydrates Examples: Monosaccharides Organic Chemistry 17 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 18 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 19 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 20 Starch Structure and Function 21 Glycogen Structure and Function 22 Cellulose Structure and Function 23 Organic Chemistry Four Classes of Organics: 2 - Lipids 24 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 25 Types of Lipids: Triglycerides 26 Types of Lipids: Triglycerides (1) Organic Chemistry 27 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 28 Types of Lipids: Phospholipids (2) Organic Chemistry 29 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 30 Types of Lipids: Steroids & Waxes (3) Organic Chemistry 31 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 32 Waxes 33 Four Classes of Organics: 3 -Proteins Organic Chemistry 34 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 35 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 36 Proteins: The Polypeptide Backbone Organic Chemistry 37 Amino acids joined together end-to-end COOH of one AA covalently bonds to the NH2 of the next AA Special name for this bond - Peptide Bond - Two AAs bonded together – Dipeptide - Three AAs bonded together – Tripeptide - Many AAs bonded together – Polypeptide Characteristics of a protein determined by composition and sequence of AA’s Virtually unlimited number of proteins Synthesis and Degradation of a Peptide 38 Protein Molecules: Levels of Structure Organic Chemistry 39 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 40 Examples of Fibrous Proteins 41 Organic Chemistry 42 Protein-folding Diseases Assembly of AA’s into protein extremely complex Process overseen by “chaperone” molecules Inhibit incorrect interactions between R groups as polypeptide grows Defects in these chaperones can corrupt the tertiary structure of proteins Mad cow disease could be due to mis-folded proteins Four Classes of Organics: 4 -Nucleic Acids Organic Chemistry 43 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 44 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 45 DNA Structure 46 RNA Structure 47 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 48 Organic Chemistry 49 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 50 Organic Chemistry Review Organic vs Inorganic Functional Groups and Isomers Macromolecules Carbohydrates Lipids Proteins Nucleic Acids 51 Ending Slide Chapter 03 Organic Chemistry
