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Chem 131 Final Exam Review: Roadmap

Chem 131 Final Exam Review: Roadmap. Learning Objectives Functional Groups Nomenclature Organic Reactions Drawing Molecules Isomers Chirality Acetals & Hemiacetals Carboxylic Acid acid/base chemistry Alkaloids Types of Lipids Carbohydrates: chirality & cyclic forms

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Chem 131 Final Exam Review: Roadmap

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  1. Chem 131 Final Exam Review: Roadmap Learning Objectives Functional Groups Nomenclature Organic Reactions Drawing Molecules Isomers Chirality Acetals & Hemiacetals Carboxylic Acid acid/base chemistry Alkaloids Types of Lipids Carbohydrates: chirality & cyclic forms Amino Acids & Proteins Nucleotides & Nucleic Acids Protein synthesis Coenzymes Citric Acid Cycle Metabolism Overview Glycolysis

  2. Learning Objectives Chapter 11-15 • Difference between organic and inorganic molecules • Name characteristic features of organic compounds • Draw organic compounds, including skeletal structures • Identify common bond types, angles, and molecule shapes • Name functional groups • Understand polarity and its effect on solubility and boiling point • Explain the difference between fat and water soluble vitamins • Describe alkane characteristics • Draw alkanes as full, condensed, and skeletal structures • Bond angle around alkane carbons • Draw constitutional isomers and ID longest carbon chain • ID 1°, 2°, 3°, 4° carbons • Name simple alkanes and cycloalkanes • Predict products of combustion & balance reaction equations • Identify unsaturated hydrocarbons: alkenes, alkynes, aromatic compounds • Alkene, Alkyne, Aromatic nomenclature • Stereoisomers • Addition Reactions • Polymers • Substitution Reactions • Name organic compounds with carbon-heteroatom single bonds (oxygen, halogens, sulfur) • Identify 1°, 2°, 3° alcohols and alkyl halides • Predict the products or reactants for following reactions: • Alcohol dehydration • Alcohol oxidation • Sulfur oxidation • Sulfur reduction • Understand the difference between Chiral and Achiral molecules • Identify chiral centers • Draw the enantiomers & diastereomers of a chiral molecule (using dashes & wedges to show geometry) • Draw fischer projections of chiral molecules • Explain the relevance of chiral centers in Biochemistry

  3. Learning Objectives Chapter 16-20 • Nomenclature for aldehydes & ketones • Identify structure and describe bonding of aldehydes & ketones • Aldehyde oxidation without alcohol oxidation • Addition reactions at C – O double bond • Hemiacetal & acetal formation • Identify cyclic hemiacetals • Acid-base chemistry of amines • Neurotransmitter amines • Amines and common drugs • Identify basic structure & function of lipids: • Hydrolyzable Lipids: • Waxes • Triglycerols • Phospholipids (and phospholipid bilayers) • Nonhydrolyzable Lipids • Steroids • Fat soluble vitamins (A, D, E, K) • Eicosanoids • Nomenclature for carboxylic acids, esters, & amides • Identify and describe structure of carboxylic acids, esters & amides • Acid-base chemistry of carboxylic acids (think soap!) • Substitution reactions of carboxylic acids • Formation of esters • Formation of amides • Hydrolysis of acyl compounds • Ester hydrolysis • Amide hydrolysis • Structure & formation of polyamides & polyesters • Identify carbohydrates • Draw Fischer projections of carbohydrates • Classify as D or L • ID multiple chiral center and draw enantiomers • Draw common monosaccharides: glucose, galactose, fructose • Draw cyclic monosaccharides & identify hemiacetal •  &  isomers • draw Haworth projections • Reduction & oxidation of monosaccharides • Describe & draw polysaccharides • Identify amines and describe bonding & structure • (1°, 2°, 3°) • Nomenclature for amines • Amine hydrogen bonding • Alkaloids & Nitrogen heterocycles

  4. Learning Objectives Chapter 21-24 • The 20 common, naturally occurring Amino Acids • stereochemistry • acid/base chemistry • Peptide Formation • Proteins • Primary, Secondary, Tertiary, Quaternary structure • Hydrolysis and denaturation • Enzymes: Catalysis & Inhibition • Stages of Metabolism • ATP: structure, hydrolysis, & formation • Coupling reactions • Coenzymes • NAD+ & NADH • FAD & FADH2 • Coenzyme A • Citric Acid Cycle: all 8 steps • Electron Transport Chain • ATP synthesis by Oxidative Phosphorylation • Nucleosides & Nucleotides: structure • DNA & RNA base pairs: names & structures • Phosphate addition • Nucleic Acids • Formation & primary structure • DNA double helix structure, hydrogen bonding • Replication, Transcription, Translation • RNA • rRNA, mRNA, tRNA • Genetic Code: codon & anticodon • Protein Synthesis: initiation, elongation, termination • Mutations • Recombinant DNA: formation & use • Role in Metabolism of fatty acid oxidation, glycolysis, & Amino acid catabolism • Reactions catalyzed by: kinase, isomerase, dehydrogenase, decarboxylase, carboxylase • Glycolysis: steps & net reaction • Pyruvate conversion to acetyl Coenzyme A

  5. Functional Groups Overview Alkane Alkene Alkyne Aromatic C − C C = C C = C Hydrocarbon Functional Groups Smith. General Organic & Biolocial Chemistry 2nd Ed.

  6. Functional Groups Overview Alkyl halides Alcohols Ethers Amines Thiols Single Bond to a Heteroatom Functional Groups Smith. General Organic & Biolocial Chemistry 2nd Ed.

  7. Functional Groups Overview Aldehydes Carboxylic Acids Esters Ketones Amides Carbonyl Functional Groups Smith. General Organic & Biolocial Chemistry 2nd Ed.

  8. Nomenclature Alkanes 6 4 2 3 5 1 + + prefix parent suffix What, where are the substituents? Example: 2,4- dimethyl prefix How many carbons in longest chain? Example: hex parent What is the functional group? Example: ane suffix 2,4-dimethylhexane Smith. General Organic & Biolocial Chemistry 2nd Ed.

  9. Nomenclature Cycloalkanes 6 5 1 4 2 3 + cyclo- prefix + suffix + parent What, where are the substituents? Example: 1,3- dimethyl prefix How many carbons in the ring? Example: hex parent What is the functional group? Example: ane suffix 1,3-dimethylcyclohexane Smith. General Organic & Biolocial Chemistry 2nd Ed.

  10. Nomenclature Alkenes & Alkynes 6 4 2 3 5 1 + + prefix parent suffix First give location and type of substituents Second give location of double bond prefix How many carbons in longest chain? parent How many of the functional group and what is it? Alkene = ene; Alkyne = yne suffix 2,4-dimethyl 1,5- hexa diene * Note: when we have more then 1 multiple bond the parent name has an “a” added on: hexa instead of hex Smith. General Organic & Biolocial Chemistry 2nd Ed.

  11. Nomenclature Alkenes & Alkynes 1 3 2 4 5 + + prefix parent suffix First give location and type of substituents Second give location of double bond prefix How many carbons in longest chain? parent How many of the functional group and what is it? Alkene = ene; Alkyne = yne suffix 4-methyl 2- pent yne Smith. General Organic & Biolocial Chemistry 2nd Ed.

  12. Nomenclature Cyclo Alkenes & Alkynes 4 5 3 2 1 + + prefix parent suffix First give location and type of substituents Second give location of double bond prefix How many carbons in longest chain? parent How many of the functional group and what is it? Alkene = ene; Alkyne = yne suffix cyclo pent ene 3-methyl 1- Smith. General Organic & Biolocial Chemistry 2nd Ed.

  13. Nomenclature Aromatics: Benzene 5 6 o - m - p - 1 2 4 3 + prefix parent Give location, number, and type of substituent. You can also replace location & number with o, m, p prefix parent “Benzene” Polysubstituted Benzenes: Number to give lowest #s around ring Alphabetize substituents If part of common root name the molecule as a derivative of a monosubstituted benzene with common root at C1. 1,2-dimethyl benzene o-dimethyl benzene Smith. General Organic & Biolocial Chemistry 2nd Ed.

  14. Nomenclature Alcohols OH 6 4 2 3 5 1 + + prefix parent suffix First give location and type of substituents Second give location of double bond prefix How many carbons in longest chain? parent How many of the functional group and what is it? Alcohol = “ol” suffix 2-methyl 4- hexan ol *Note: after the greek root of the parent use “an”, iehexan * Second Note: when we have more then 1 multiple bond the parent name has an “a” after the greek root: hexa Smith. General Organic & Biolocial Chemistry 2nd Ed.

  15. Nomenclature Ethers 1 4 2 O 3 + + prefix parent suffix Use alkyl substitutant naming roots, but drop the “yl” and use “oxy” for the simplest alkyl group bonded to the ether oxygen. prefix parent How many carbons in longest chain? suffix Use alkane ending: ane 2-ethoxy but ane Smith. General Organic & Biolocial Chemistry 2nd Ed.

  16. Nomenclature Thiols SH 2 4 5 3 1 + + prefix parent suffix Give location and type of substituents, then give location of thiolgroup. prefix How many carbons in longest chain? parent Hydrocarbon functional group suffix + “thiol” suffix 2,4-dimethyl 1- pent anethiol Smith. General Organic & Biolocial Chemistry 2nd Ed.

  17. Nomenclature Alkyl Halides 1 2 6 4 Cl 3 5 + + prefix parent suffix Give location and type of substituents. Replace “ine” in halide name with “o”, ie Chlorine = chloro prefix parent How many carbons in longest chain? What is the hydrocarbon functional group? If alkane then “ane” suffix suffix 2-chloro 4-methyl hex ane Smith. General Organic & Biolocial Chemistry 2nd Ed.

  18. Nomenclature Aldehydes O 4 2 5 1 3 + + prefix parent suffix prefix First give location and type of substituents. How many carbons in longest chain? Aldehyde @ C1, Ketone @ lowest # C parent What is the functional group? How many? Aldehyde = -al; Ketone = -one suffix al 2,4-dimethyl petan * Note: when we have more then 1 aldehyde or ketone the parent name has an “a” added on: hexa instead of hex Smith. General Organic & Biolocial Chemistry 2nd Ed.

  19. Nomenclature Ketones O O • Ketone is C1 in cyclic ketones • then number to make the first substituent on the smallest C # • Common names for ketones: • Name both alkyl groups • Order alphabetically • Add the work ketone 2 6 4 1 5 3 + + prefix parent suffix First give location and type of substituents. Then the location of the ketone prefix How many carbons in longest chain? Aldehyde @ C1, Ketone @ lowest # C parent What is the functional group? How many? Aldehyde = -al; Ketone = -one suffix dione 2,3 - hexa * Note: when we have more then 1 aldehyde or ketone the parent name has an “a” added on: hexa instead of hex Smith. General Organic & Biolocial Chemistry 2nd Ed.

  20. Nomenclature Carboxylic Acids O 4 2 1 5 3 OH + + prefix parent suffix prefix First give location and type of substituents. How many carbons in longest chain? Carboxylic acid @ C1 parent What is the functional group? How many? Carboxylic acid: “-oic acid” suffix 2,4-dimethyl oic acid petan * Note: when we have more then 1 functional group the parent name has an “a” added on: hexa instead of hex Smith. General Organic & Biolocial Chemistry 2nd Ed.

  21. Nomenclature Esters O 3 1 O 2 4 + + prefix parent suffix First give location and type of substituents. Then give the name of the alky group bonded to the ester functional group prefix How many carbons in longest chain? Carbonyl carbon @ C1 parent What is the functional group? How many? Ester: “-oate” suffix oate butan methyl * Note: when we have more then 1 functional group the parent name has an “a” added on: hexa instead of hex Smith. General Organic & Biolocial Chemistry 2nd Ed.

  22. Nomenclature Amide O H 3 1 N 2 4 H + + prefix parent suffix prefix First give location and type of substituents. How many carbons in longest chain? Carbonyl carbon @ C1 parent What is the functional group? How many? Amide: “-amide” suffix 3-methyl amide butan * Note: when we have more then 1 functional group the parent name has an “a” added on: hexa instead of hex Smith. General Organic & Biolocial Chemistry 2nd Ed.

  23. Nomenclature Amide O 3 1 N 2 4 + + prefix parent suffix prefix Use “N” to indicate naming amide R groups How many carbons in longest chain? Carbonyl carbon @ C1 parent What is the functional group? How many? Amide: “-amide” suffix NN-dimethyl amide butan * Note: when we have more then 1 functional group the parent name has an “a” added on: hexa instead of hex Smith. General Organic & Biolocial Chemistry 2nd Ed.

  24. Nomenclature Amines 3 1 2 4 N + + prefix parent suffix prefix Give location and type of substituents. Indicate naming the amine R groups with “N” How many carbons in longest chain? Amine @ C1 parent What is the functional group? How many? Amine = “amine” suffix N,N-dimethyl butan amine * Note: when we have more then 1 functional group the parent name has an “a” added on: hexa instead of hex Smith. General Organic & Biolocial Chemistry 2nd Ed.

  25. Nomenclature Amines

  26. Reactions Summary H OH H2O Hydration H2SO4 H OH Dehydration H2SO4 H2O RO OR Hydrolysis of Acetals & Hemiacetals H2O/H2SO4 2 eq ROH (alcohol) H2SO4 Acetal & Hemiacetal formation RO OR H2O ROH (alcohol) H2SO4 Esterification H2O OR HNR2 Amide Formation NR2 Δ Ester/Amide Hydrolysis H2O/H2SO4 NR2 Ester/Amide Hydrolysis H2O/NaOH OR O- Na+

  27. Reactions Summary Nucleophilic Substitution Nucleophile Nuc H2SO4 HX (X = Br or Cl) X H Hydrohalogenation [O] Oxidation Ag2O Selective Oxidation NH4OH Oxidation [O] 2 RSH RS SR [H] Reduction RS SR 2 RSH [H] or H2 Hydrogenation Pd, Pt, or Rh catalyst

  28. Reactions Summary [H] or H2 Reduction Pd, Pt, or Rh catalyst Cl X2 Chlorination or Bromination FeX3 (X = Cl or Br) NO2 HNO3 Nitration H2SO4 SO3H SO3 Sulfonation H2SO4 HCl NaOH Amine Acid/Base NH3 NH4 NH3

  29. Drawing Chemical Structures .. Lewis Dot Structures Structural Formula or Complete Structure Structural Formula or Complete Structure with Geometry Indicated Condensed Structure Skeletal Structure H H H H H C C C C H H H H H H H H C C H C C H H H CH3CH2CH2=CH2

  30. Alkanes Longest Carbon Chain 1 2 1 1 3 3 4 2 2 4 5 3 5 6 4 6 7 5 Longest Carbon Chain Smith. General Organic & Biolocial Chemistry 2nd Ed.

  31. Alkanes 1°, 2°, 3°, 4° R H R R C C C C H R H R R R R R H H H R 1° 2° 3° 4° R = a Carbon atom Smith. General Organic & Biolocial Chemistry 2nd Ed.

  32. Alcohols & Alkyl Halides 1°, 2°, 3°

  33. Structure Amines

  34. Structure Amides Smith, Janice Gorzynski. General, Organic, & Biological Chemistry 2nd Ed.

  35. ISOMERS Same chemical formula Stereoisomers Spatial Isomers Constitutional Isomers Structural Isomers Different connectivity between atoms Different spatial arrangement of atoms but with the same connectivity Enantiomers Diastereomers Mirror images of a chiral molecule that are not superimposable All stereoisomers that are not mirror images of one another Cis/Trans Isomers Conformational Isomers Rotation around C-C single bonds R R R R

  36. Chiral Molecules Fischer Projections A Fischer Projection takes a 3D tetrahedral shape, and re-draws it: Smith. General Organic & Biological Chemistry 2nd Ed.

  37. Stereo- isomers Multiple Chiral Centers chemwiki.ucdavis.edu

  38. Ketones & Aldehydes Acetal Formation Smith, Janice Gorzynski. General, Organic, & Biological Chemistry 2nd Ed.

  39. Ketones & Aldehydes Acetal Hydrolysis Smith, Janice Gorzynski. General, Organic, & Biological Chemistry 2nd Ed.

  40. Carboxylic Acids Acid/Base Chemistry

  41. Amines Alkaloids Alkaloids are compounds that contain an amine. Cocaine

  42. Biochemistry Neurotransmitters Serotonin is important in mood, sleep, perception, and temperature regulation. Dopamineaffects the brain processes that control movement, emotions, and pleasure When norepinephrinelevels increase, a person feels elated, and then manicif levels go too high. Acetylcholineis a quaternary ammonium ion that serves as a neurotransmitter between neurons and muscle cells

  43. Lipids Categories of Lipids

  44. Lipids Categories of Lipids

  45. Carbohydrates Monosaccharides Aldehyde monosaccharides are aldoses ketone monosaccharides are ketoses. generally have 3 to 6 C atomsin a chain with an aldehyde or ketoneending and many –OH groups. Smith, Janice Gorzynski. General, Organic, & Biological Chemistry 2nd Ed.

  46. Carbohydrates D vs L Monosaccharides The configuration of the chirality center farthest from the carbonyl group determines whether a monosaccharide is D or L. All naturally occurring sugars are D sugars. Smith, Janice Gorzynski. General, Organic, & Biological Chemistry 2nd Ed.

  47. Carbohydrates Cyclic Monosaccharides The C atom that is part of the hemiacetal is a new chirality center, called the anomer carbon. Haworth projections Smith, Janice Gorzynski. General, Organic, & Biological Chemistry 2nd Ed.

  48. Carbohydrates Disaccharides Smith, Janice Gorzynski. General, Organic, & Biological Chemistry 2nd Ed.

  49. Amino Acids Basic Structure Smith, Janice Gorzynski. General, Organic, & Biological Chemistry 2nd Ed.

  50. Peptides Amide Bond Formation Smith, Janice Gorzynski. General, Organic, & Biological Chemistry 2nd Ed.

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