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~ /Jfle < :!,inceton Review MCAT ORGANIC CHEMISTRY Peter J Alaimo Copyright© 2001 by Princeton Review, lnc All rights reserved Contributors Peter J Alaimo, Ph.D Senior Author and Editor DouglasS Daniels, Ph.D Senior Editor Daniel J Pallin, M.D Adam Johnson Stefan Loren, Ph.D Christopher Volpe, Ph.D Steven A Leduc Production, Design, and Copy Editor National Director of MCAT Research, Production, and Development, The Princeton Review Copyright© 2001, 2000, 1999, 1998, 1997 by Princeton Review, Inc All rights reserved Version 3.1 MCAT is a registered trademark of the Association of American Medical Colleges (AAMC) The Princeton Review is not affiliated with Princeton University or AAMC This manual is for the exclusive use of Princeton Review course students, and is not legal for resale ~ /J.IJe ~inceton Review 011001 348 MCAT ORGANIC CHEMISTRY Table of Contents Below each chapter title are listed the MCAT topics covered in that chapter "These topics correspond to those given in the AAMC's MCAT Student Manual, in the section entitled MCAT Biological Sciences Topics, Organic Chemistry Structure and Bonding Topic XVI Substitution and Elimination Reactions Topics XIIIA, XIV; XVA Electrophilic Addition Reactions Topic XV Nucleophilic Addition and Cycloaddition Reactions Topic XIII Lab Techniques and Spectroscopy Topics XVII and XVIII Biologically-Important Organic Chemistry Topic XII 349 PERIODIC TABLE OF THE ELEMENTS - He H 1.0 Li 6.9 11 Na B Be 10.8 9.0 13 12 Mg 23.0 24.3 19 20 21 22 23 24 Ti v 1~0 1fo 16.0 AI Si 14 15 16 27.0 28.1 31.0 31 32 33 Fe 27 Co 28 Ni Cu Zn Ga Ge Cr 25 Mn 26 29 30 p s F 19.0 17 4.0 10 Ne 20.2 18 Cl Ar 32.1 35.5 39.9 As 34 Se 35 36 Br Kr Ca Sc 39.1 37 40.1 38 45.0 39 47.9 40 52.0 42 54.9 43 55.8 44 58.9 45 58.7 46 63.5 47 65.4 48 69.7 49 74.9 51 79.0 52 79.9 53 83.8 54 y 72.6 50 8~~5 Zr 50.9 41 87.6 88.9 57 91.2 92.9 95.9 (98) 101.1 102.9 106.4 107.9 112.4 114.8 118.7 121.8 127.6 126.9 131.3 73 74 76 77 78 80 81 82 83 K Sr 55 La* Cs (223) 226.0 227.0 Fr Ra Hf 138.9 178.5 104 89 132.9 87 88 72 Act Rf {261) Nb Ta w 180.9 183.9 105 106 Db Sg (262) (263) 58 59 Ce 140.1 t Mo 90 Th 232.0 Pr Tc 75 Re 186.2 (231) 190.2 192.2 109 ~ 60 Nd u 238.0 Rh lr Os (2 140.9 144.2 91 92 Pa Ru ) 61 Pm (145) Ag 79 Cd Pt Au Hg 195.1 197.0 200.6 In Tl Sn Pb 204.4 207.2 Sb Te I Xe Bi Po 84 85 At Rn 86 209.0 (209) (210) (222) 70 71 Mt {267) 62 Sm 63 Eu 150.4 152.0 93 94 (237) (244) Np Pd Pu 95 Am (243) 350 64 Gd 157.3 65 66 67 69 Tb Dy 158.9 162.5 164.9 167.3 168.9 Ho Tm Yb Lu 173.0 175.0 96 97 98 99 100 101 102 103 (247) (247) {251) {252) (257) (258) (259) {260) Cm Bk Cf Es Fm Md No Lr MCAT ORGANIC CHEMISTRY TABLE OF CONTENTS STRUCTURE AND BONDING 357 BACKGROUND AND INTRODUCTION 358 Basic 1\Jomenclature 358 Principal Classes of Organic Compounds 359 BONDING IN ORGANIC MOLECULES 360 Hybridization 360 a Bonds 363 n Bonds 363 STRUCTURAL FORMULAS 364 BOND LENGTH AND BOND DISSOCIATION ENERGY 365 ISOMERISM AND CHIRALITY 367 Constitutional Isomerism 367 Conformational Isomerism 367 Stereoisomerism 368 Chirality 369 Absolute Stereocenter Configuration 372 Enantiomers 377 Diastereomers 378 Epimers 382 Anomers 383 Geometric Isomers 383 Summary of Isomers 385 OPTICAL ACTIVITY 386 Racemic Mixtures and Meso Compounds 387 PHYSICAL PROPERTIES OF HYDROCARBONS 391 Melting and Boiling Points 391 Solubility 392 THE ORGANIC CHEMIST'S TOOLBOX 393 Nucleophiles and Electrophiles 393 Reaction Intermediates 393 Inductive Effects 394 Electron Delocalization and Resonance Stabilization 395 351 SUBSTITUTION AND ELIMINATION REACTIONS 405 STRUCTURE AND REACTIVITY OF ALKANES AND CYCLOALKANES 406 Common Structural Notations for Alkanes 406 Conformational Analysis of Alkanes and Cycloalkanes 407 Combustion Reactions of Hydrocarbons 417 Free-Radical Halogenation of Alkanes 417 ALCOHOLS 425 Structure, Hydrogen Bonding, and Acidity in Alcohols and Phenols 425 Hydrogen Bonding in Alcohols 425 Acidity of Alcohols 427 Substitution Reactions of Alcohols 430 The Details of SN2 Reactions 430 The Details of SN Reactions 432 Elimination Reactions of Alcohols: Dehydration 435 HALO ALKANES 439 Formation of Haloalkanes 439 Reactions of Alcohols with Phosphorus Halides 439 Reactions of Alcohols with Thionyl Chloride 440 Substitution Reactions of Haloalkanes 440 Elimination Reactions of Haloalkanes 441 E1 Reactions 441 E2 Reactions 443 Summary of Substitutions and Eliminations 445 ETHERS 445 AMINES 446 Alkylation 447 352 ELECTROPHILIC ADDITION REACTIONS 449 ALKEN ES 450 Structure and Nomenclature 450 Isomerism in Alkanes 450 The CisfTrans Convention 450 The (Z)/(E) Convention 451 Electrophilic Addition Reactions to Alkenes and Alkynes 451 H-X Addition Across an Bond 452 H-Br and Peroxides Addition Across a n Bond 454 Acid-Catalyzed Hydration of Alkanes 455 Oxymercuration-Demercuration 457 Hydroboration-Oxidation 458 Hydrogenation 459 Addition of Halogens (X2 ) to a n Bond 460 Epoxide Formation and Hydrolysis 462 Oxidation of n Bonds with Dilute KMnO 463 Ozonolysis 464 AROMATIC COMPOUNDS 468 Aromaticity Defined 468 Nomenclature of Substituted Benzenes 470 Reactivity of Aromatic Compounds: Electrophilic Aromatic Substitution 470 353 NUCLEOPHILIC ADDITION AND CYCLOADDITION REACTIONS 475 ALDEHYDES AND KETONES 476 Reactivity: Acidity and Enolization 476 Keto-Enol Tautomerism 479 Nucleophilic Addition Reactions to Aldehydes and Ketones 479 Acetals and Hemiacetals 480 Imine Formation 484 The Aldol Condensation 486 Conjugate Addition to a,~-Unsaturated Carbonyl Corn pounds 490 CARBOXYLIC ACIDS 493 Acidity and Hydrogen Bonding 493 Inductive Stabilization of Carboxylate Ions by Electron-Withdrawing Groups 493 Hydrogen Bonding in Carboxylic Acids 495 Decarboxylation Reactions of ~-Keto Acids 495 Esterification Reactions 495 CARBOXYLIC ACID DERIVATIVES 497 Acidic and Basic Hydrolysis of Esters 498 Saponification 501 Synthesis of the Carboxylic Acid Derivatives 502 Acid Halides 502 Carboxylic Acid Anhydrides 502 Esters 503 Amides 503 Carboxylic Acids 503 Relative Reactivity of Carboxylic Acid Derivatives 503 CONCERTED REACTIONS 505 Diels-Aider 505 354 LAB TECHNIQUES AND SPECTROSCOPY 507 SEPARATIONS 508 Extractions 508 Crystallization and Precipitation 512 Chromatography 512 Thin-Layer Chromatography 512 Gas Chromatography 514 Distillations 515 Simple Distillation 515 Fractional Distillation 515 SPECTROSCOPY 516 Infrared (IR) Spectroscopy 517 Important Stretching Frequencies 518 Summary of Infrared {IR) Stretching Frequencies 521 Proton CH) Nuclear Magnetic Resonance (NMR) Spectroscopy 522 Chemically Equivalent Protons 522 The Chemical Shift 523 Electronegativity Effects on Chemical Shift Values 524 Hybridization Effects on Chemical Shift Values 524 Acidity and Hydrogen Bonding Effects on Chemical Shift Values 525 Integration 527 Splitting 527 355 BIOLOGICALLY-IMPORTANT ORGANIC CHEMISTRY 531 AMINO ACIDS 532 Amino Acid Structure and Nomenclature 532 Amino Acid Reactivity 535 Classification of Amino Acids 539 Hydrophobic Amino Acids 540 Hydrophilic Amino Acids 541 Sulfur-Containing Amino Acids 543 Proline 543 PROTEINS 545 The Peptide Bond 545 The Disulfide Bond 548 Protein Structure in Three Dimensions 549 Primary Structure 549 Secondary Structure 549 Tertiary Structure 550 Quaternary Structure 552 CARBOHYDRATES 553 Structure and Nomenclature of Monosaccharides 553 Structure and Nomenclature of Disaccharides 559 Reducing Sugars 562 LIPIDS 563 STEROl DS 569 NUCLEIC ACIDS 570 Phosphorus-Containing Compounds 570 Nucleotides 571 A APPENDIX 573 SUMMARY OF REACTIONS 574 356 566 MCAT Organic Chemistry Chapter6 Triacylglycerols (TG) The storage form of the fatty acid is the fat The technical name for fat is triacylglycerol (shown below) The triglyceride is composed of three fatty acids esterified to a glycerol molecule Glycerol is a three-carbon triol with the formula HOCH 2-CHOH-CH 20H As you can see, it has three hydroxyl groups that can be esterified to fatty acids It is necessary to store fatty acids in the relatively inert form of fat because free fatty acids are reactive chemicals A Triglyceride (Fat) II H2C-0-C-Rl ~~ H 2C - - C - R / R-groups may be the same or different II H2C-O-C-R3 The triacylglycerol undergoes reactions typical of esters, such as base-catalyzed hydrolysis Soap is economically produced by base-catalyzed hydrolysis of triglycerides from animal fat into fatty acid salts (soaps) This reaction is called saponification and is illustrated below Saponification oAR1 + II H C-O-C-R NaOH + oAR2 II + H2C-O-C-R3 Triacylglycerol Glycerol oAR3 Fatty acids Lipases are enzymes that hydrolyze fats Triacylglycerols are stored in fat cells as an energy source Fats are more efficient energy storage molecules than carbohydrates for two reasons: packing and energy content MCAT Organic Chemistry Biologically-Important Organic Chemistry 567 1) Packing Their hydrophobicity allows fats to pack together much more closely than carbohydrates Carbohydrates carry a great amount of water-of-solvation (water molecules hydrogen bonded to their hydroxyl groups) In other words the amount of carbon per unit area or unit weight is much greater in a fat droplet than in dissolved sugar If we could store sugars in a dry powdery form in our bodies, this problem would be obviated 2) Energy content All packing considerations aside, fat molecules store much more energy than carbohydrates In other words, regardless of what you dissolve it in, a fat has more energy carbonfor-carbon than a carbohydrate The reason is that fats are much more reduced Remember that energy metabolism begins with the oxidation of foodstuffs to release energy Since carbohydrates are more oxidized to start with, oxidizing them releases less energy Animals use fat to store most of their energy, storing only a small amount as carbohydrates (glycogen) Plants such as potatoes commonly store a large percentage of their energy as carbohydrates (starch) Introduction to Lipid Bilayer Membranes Membrane lipids are phospholipids derived from diacylglycerol phosphate or DG-P For example, phosphatidyl choline is a phospholipid formed by the esterification of a choline molecule [HO(CH2) 2N+(CH 3) 3] to the phosphate group of DG-P Phospholipids are detergents, substances that efficiently solubilize oils while remaining highly water-soluble Detergents are like soaps, but stronger A Phosphoglyceride (Diacylglycerol Phosphate, or DGP) Diacylglycerol phosphate We saw above how fatty acids spontaneously form micelles Phospholipids also minimize their interactions with water by forming an orderly structure-in this case it is a lipid bilayer (below) Hydrophobic interactions drive the formation of the bilayer, and once formed, it is stabilized by van der Waals forces between the long tails Chapter6 568 MCAT Organic Chemistry A Small Section of a Lipid Bilayer Membrane 56) Would a saturated or an unsaturated fatty acid residue have more van der Waals interactions with neighboring alkyl chains in a bilayer membrane?56 A more precise way to give the answer to the above question is to say that double bonds (unsaturation) in phospholipid fatty acids tend to increase membrane fluidity Unsaturation prevents the membrane from solidifying by disrupting the orderly packing of the hydrophobic lipid tails This decreases the melting point The right amount of fluidity is essential for function Decreasing the length of fatty acid tails also increases fluidity The steroid cholesterol (discussed below) is a third important modulator of membrane fluidity At low temperatures, it increases fluidity in the same way as kinks in fatty acid tails; hence it is known as a membrane antifreeze At high temperatures, however, cholesterol attenuates (reduces) membrane fluidity Don't ponder this paradox too long; just remember that cholesterol keeps fluidity at an optimum level Remember, the structural determinants of membrane fluidity are: degree of saturation, tail length, and amount of cholesterol The lipid bilayer acts like a plastic bag surrounding the cell in the sense that it seals the interior of the cell from the exterior However, the cell membrane is much more complex than a plastic bag Since the plasma bilayer membrane surrounding cells is impermeable to charged molecules such as Na+, protein gateways such as ion channels are required for these molecules to enter or exit cells Proteins that are integrated into membranes also transmit signals from the outside of the cell into the interior For example, certain hormones (peptides) cannot pass through the cell membrane due to their charged nature, instead, protein receptors in the cell membrane bind these hormones and transmit a signal into the cell in a second messenger cascade 56 The bent shape of the unsaturated fatty acid means that it doesn't fit in as well and has less contact with neighboring groups to form van der Waals interactions Unsaturations make the membrane less stable, less solid MCAT Organic Chemistry 569 Biologically-Important Organic Chemistry 6.5 Steroids Steroids are included here because of their hydrophobicity, and hence similarity to fats Their structure is otherwise unique All steroids have the basic tetracyclic ring system (see below), based on the structure of cholesterol, a polycyclic amphipath (Polycyclic means several rings, and amphipathic means displaying both hydrophilic and hydrophobic characteristics.) As discussed above, the steroid cholesterol is an important component of the lipid bilayer It is obtained from the diet and synthesized in the liver It is carried in the blood packaged with fats and proteins into lipoproteins One type of lipoprotein has been implicated as the cause of atherosclerotic vascular disease, which refers to the build-up of cholesterol "plaques" on the inside of blood vessels Cholesterol-Derived Hormones tetracyclic ring system cholesterol HO testosterone estrogen Steroid hormones are made from cholesterol Two examples are testosterone (an androgen or male sex hormone) and estradiol (an estrogen or female sex hormone) There are no receptors for steroid hormones on the surface of cells If this is true, how can they exert an influence on the cell? Because steroids are highly hydrophobic, they can diffuse right through the lipid bilayer membrane into the cytoplasm The receptors for steroid hormones are located within cells rather than on the cell surface This is an important point You must be aware of the contrast between peptide MCAT Organic Chemistry Chapter6 570 hormones such as insulin, which exert their effects by binding to receptors at the cell-surface, and steroid hormones such as estrogen, which diffuse into cells to find their receptors 57) Would a saturated or an unsaturated fatty acid residue have more van der Waals interactions with neighboring alkyl chains in a bilayer membrane?57 6.6 Nucleic Acids Before we can talk about nucleic acids, we must first briefly review some background 6.6.1 Phosphorus-Containing Compounds Phosphoric acid is an inorganic acid (it does not contain carbon) with the potential to donate three protons The Kas for the three acid dissociation equilibria are 2.1, 7.2, and 12.4 Therefore at physiological pH, phosphoric acid is significantly dissociated, existing largely in anionic form Phosphoric Acid II HO-P-OH I OH II HO-P-00 l OH II HO-P-00 ~0 A._ II -u-P-00 ~0 Phosphate is also known as orthophosphate Two orthophosphates bound together via an anhydride linkage form pyrophosphate The P-0-P bond in pyrophosphate is an example of a high energy phosphate bond This name is derived from the fact that the hydrolysis of pyrophosphate is thermodynamically extremely favorable (shown below) The D.Go' for the hydrolysis of pyrophosphate is about -7 kcal/mol This means that it is a very favorable reaction The actualD.G in the cell is about -12 kcal/mol, which is even more favorable There are three reasons that phosphate anhydride bonds store so much energy: 1) When phosphates are linked together their negative charges repel each other strongly 2) Orthophosphate has more resonance forms and thus a lower free energy than linked phosphates 3) Orthophosphate has a more favorable interaction with the biological solvent (water) than linked phosphates The details are not cruciaL What is essential is that you fix the image in your mind of linked phosphates acting like compressed springs, just waiting to fly open and provide energy for an enzyme to catalyze a reaction 57 The bent shape of the unsaturated fatty acid means that it doesn't fit in as well and has less contact with neighboring groups to form van der Waals interactions Unsaturations make the membrane less stable, less solid 571 Biologically-Important Organic Chemistry MCAT Organic Chemistry The Hydrolysis of Pyrophosphate 0 e0 - P II - - PII - e 6e + be II Ho 2 HO-P-0 e 6e 6.6.2 Nucleotides Nucleotides are the building blocks of nucleic acids (RNA and DNA) Each nucleotide contains a ribose (or deoxyribose) sugar group, a purine or pyrimidine base joined to carbon number one of the ribose ring, and one, two or three phosphate units joined to carbon five of the ribose ring The nucleotide Qdenosine triphosphate (ATP) plays a central role in cellular metabolism in addition to being an RNA precursor ATP is the universal short-tenn energy storage molecule Energy extracted from the oxidation of foodstuffs is immediately stored in ATP' s phosphoanhydride bonds This energy will later be used to power cellular processes; it may also be used to synthesize glucose or fats, which are longer-term energy storage molecules This applies to all living organisms, from bacteria to humans Even some viruses carry ATP with them outside the host cell, though viruses cannot make their own ATP Adenosine Triphosphate (A TP) NH2 e 0 II II II le le 0- le s' 0-P - - P - -P-0-CH2 4' H OH
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