chapter 3 the chemistry of organic molecules. figure 4.3 valences for the major elements of organic...
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Chapter 3
The Chemistry of Organic Molecules
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Figure 4.3 Valences for the major elements of organic molecules
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Why Carbon?
• Most versatile building blocks of molecules– Tetravalence– Can link together– Covalent compatibility with variety of elements
• Variation in carbon skeletons contributes to the diversity of organic molecules– Hydrocarbons– Isomers – shape can dramatically alter activity
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Figure 4.4 Variations in carbon skeletons
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Figure 4.2 The shapes of three simple organic molecules
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Figure 4.6 Three types of isomers
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Figure 4.6ax Structural isomers
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Figure 4.7 The pharmacological importance of enantiomers
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Functional Groups
• A specific configuration of atoms commonly attached to C-skeletons, usually involved in chemical reactions
• Behave consistently from one organic molecule to the next
• Contribute to distinctive properties of organic molecules
• Most molecules have two or more
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Table 4.1 Functional Groups of Organic Compounds
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Functional Groups cont.
• Hydroxyl– Alcohols
– Polar
– Increase solubility
• Carbonyl
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Functional Groups cont.
• Carboxyl– Carboxylic acids
– Very polar
• Amino– Amines
– Basic
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Functional Groups Cont.
• Sulfhydryl– Thiols
– Can interact to help stabilize structures
• Phosphate– One fxn includes
energy transfer
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Recap
• Emergent properties of organic compounds due to:– Arrangement of carbon skeleton– Functional groups added to skeleton
• Variation at molecular level underlies biological diversity
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Macromolecules
• Large biological molecules formed from small organic molecules
• Polymers…made up of monomers
• Synthesized by cells…how?
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Figure 5.2 The synthesis and breakdown of polymers
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Carbohydrates
• Sugars• End in -ose
• CH2O
• Carbonyl group and multiple hydroxyl groups
• Monosaccharides and disaccharides = fuel and carbon sources
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Figure 5.3 The structure and classification of some monosaccharides
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Figure 5.3x Hexose sugars
Glucose Galactose
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Figure 5.4 Linear and ring forms of glucose
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Figure 5.5 Examples of disaccharide synthesis
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Figure 5.5x Glucose monomer and disaccharides
Glucose monomer
Sucrose
Maltose
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Polysaccharides
• thousands of monosaccharides
• Storage and structural roles
• Glycogen, starch, cellulose, peptidoglycan (sugars + amino acids), and chitin (contains nitrogen)
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Figure 5.7a Starch and cellulose structures
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Figure 5.7b,c Starch and cellulose structures
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Figure 5.7x Starch and cellulose molecular models
Glucose Glucose
Starch
Cellulose
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Figure 5.6 Storage polysaccharides
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Figure 5.8 The arrangement of cellulose in plant cell walls
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Figure 5.x1 Cellulose digestion: termite and Trichonympha
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Figure 5.x2 Cellulose digestion: cow
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Chitin
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Figure 5.9 Chitin, a structural polysaccharide: exoskeleton and surgical thread
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Peptidoglycan
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Lipids
• Diverse group of nonpolymers
• Share one trait: hydrophobic
• Consist mainly of hydrocarbons
• Fats, phospholipids, waxes, steroids
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Fats
• Glycerol + fatty acids• Fatty acids: carbon
chain with carboxyl group at end
• Triglycerols• Saturated vs
unsaturated
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Figure 5.11 Examples of saturated and unsaturated fats and fatty acids
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Fats cont.
• Functions:– Energy (2x a
polysaccharide)
– Storage – adipose tissue – swells and shrinks
– Cushions
– Warmth
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Artherosclerosis
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Phospholipids
• Glycerol + 2 fatty acids + phosphate group
• Amphipathic
• Major components of cell membranes
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Figure 5.12 The structure of a phospholipid
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Figure 5.13 Two structures formed by self-assembly of phospholipids in aqueous environments
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Steroids
• Carbon skeletons consisting of four fused rings
• Hormones (many produced from cholesterol)
• Vary in their functional groups
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Figure 4.8 A comparison of functional groups of female (estradiol) and male (testosterone) sex hormones
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Waxes
• Protectant
• Water-proofing
• Corrosion prevention
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Proteins
• Greek: “first place”
• 50% + of dry weight of most cells
• Instrumental in activities
• Structural support, storage, transport, signaling within organism, movement of organism, defense against foreign substances, enzymes (help regulate metabolism)
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Proteins cont.
• Vary extensively in structure
• Unique 3d shape
• Polymers of amino acids: polypeptides
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Figure 5.15 The 20 amino acids of proteins: nonpolar
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Figure 5.15 The 20 amino acids of proteins: polar and electrically charged
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Peptide Bonds
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Proteins cont.
• A functional protein consists of 1+ polypeptides precisely twisted, folded, and coiled into a precise 3d conformation
• Globular vs fibrous
• Function depends on ability to recognize and bind to some other molecule
• Determined by amino acid sequence
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Figure 5.18 The primary structure of a protein
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Figure 5.20 The secondary structure of a protein
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Figure 5.22 Examples of interactions contributing to the tertiary structure of a protein
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Figure 5.23 The quaternary structure of proteins
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Figure 5.24 Review: the four levels of protein structure
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Figure 5.17 Conformation of a protein, the enzyme lysozyme
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Figure 5.19 A single amino acid substitution in a protein causes sickle-cell disease
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Fibrous vs globular
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Figure 5.21 Spider silk: a structural protein
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What determines protein conformation?
• Amino acid sequence• pH• Salt concentration• Temperature• Chaperonins – protein
molecules that assist the proper folding other proteins; keep it away from “bad influences”
• If environment is changed or altered from “native” conditions = denatured
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Figure 5.25 Denaturation and renaturation of a protein
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Figure 5.27 X-ray crystallography
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Table 5.1 An Overview of Protein Functions
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Nucleic Acids
• DNA and RNA
• Genetic material
• DNA directs the synthesis of RNA, which then directs the ribosomes to make proteins
• Polymers of nucleotides
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Figure 5.29 The components of nucleic acids
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Figure 5.x3 James Watson and Francis Crick
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Figure 5.x4 Rosalind Franklin
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Erwin Chargaff
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3’ and 5’ ends
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Genetic Material
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Figure 5.30 The DNA double helix and its replication
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DNA and proteins as tape measures of evolution
• Two species that are more closely related share a greater proportion of their DNA and protein sequences than do distantly related species
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ATP
• RNA nucleotide + • 2 more P groups• Energy transfer!