Advanced Chemistry Objectives

Textbook: Fundamentals of General, Organic and Biological Chemistry. McMurry, J. & Castellion, M. 1996          

Unit I.  General Chemistry Overview

Chapters 1-10

1.      Use the Scientific Method to employ scientific research procedures.

2.      Explain John Dalton’s Atomic Theory in terms of accepted and non-accepted claims.

3.      Describe the Modern View of the Atom in terms of subatomic particles.

4.      Describe how isotopes differ by defining atomic number, mass number, & atomic mass.

5.      Describe the electronic structure of the atom by using the Quantum Mechanical Model.

6.      Correctly write electron configurations and orbital diagrams of a specific atom’s electrons.

7.      Describe how Mendeleev and Moseley designed the periodic table.

8.      Describe what periodicity is and rationalize the periodic trend of specific elemental properties.

9.      Explain the difference between ionic and covalent compounds.

10.  Use the VSEPR model to predict molecular geometries.

11.  Describe how hybridization changes the atomic orbitals of bonded atoms.

12.  Predict molecular structures using available valence electrons and bond orders.

    a. Utilize molecular structures to describe resonance of pi electrons through valence shells of bonded atoms

13.  Describe how coordinate covalent bonds are formed.

14. Identify molecules that possess a dipole moment from molecular formulas

15. Describe the intermolecular attractions that occur between molecules:

    a. dipole/dipole

    b. hydrogen bonding

    c. London dispersion forces

Unit II. Organic Chemistry:  Alkanes, Alkenes & Alkynes

Chapter 12. Alkanes

1.      Describe how hydrocarbons can differ by parent chain modifications and functional groups.

2.      Identify an organic family by the correct identification of specific functional groups.

3.      Correctly name simple alkanes that differ by parent chain structures and functional groups.

4.      Identify common alkyl groups that can be added to existing parent chains and correctly name them.

5.      Correlate the staggered and eclipsed conformations of single covalent bonds in alkanes.

6.      Predict the products from the combustion and halogenation reactions associated with alkanes.

    a. identify the initiation, propagation & termination steps in a radical chain mechanism.

7.      Correctly draw and name specific cycloalkanes.

Chapter 13. Alkenes, Alkynes & Aromatics

1.      Identify alkenes and alkynes by the degrees of unsaturation.

2.      Correctly name specific alkenes and alkynes by type of unsaturation, parent chain and functional groups.

3.      Differentiate the types of isomerization found in alkenes. (Constitutional, Stereoisomers: diastereomers, and enantiomers)

4.      Identify what a chiral center is and why they exist.

5.      Employ the Cahn-Ingold-Prelog convention to identify the type of enantiomer

6.      Differentiate between D- and L- enantiomers

7.      Predict the products of the following alkene and alkyne reactions:

    a.    Hydrogenation

    b.   Halogenation

    c.    Hydrohalogenation

    d.   Hydration

    e.    Halohydrin formation

    f.     Oxymercuration/Reduction

8.      Utilize Markovnikov’s rule for predicting products for hydrohalogenation & hydration reactions

9.      Predict if reactants function as nucleophiles or electrophiles in specific reactions

10.  Explain why Benzene is the functional precursor for aromatic molecules.

11.  Correctly name mono-substituted aromatics and di-substituted aromatics using ortho-, meta-, & para- prefixes where necessary.

12.  Correctly identify and name specific polynuclear aromatic hydrocarbons and some heterocyclic aromatic compounds.

13.  Differentiate between the properties of aromatic compounds and their polyunsaturated hydrocarbon analogs.

14.  Predict the products of the following aromatic compound reactions

    a.    Halogenation

    b.   Nitration

    c.    Sulfonation

    d.   Friedel-Crafts Alkylation

Unit III. Organic Chemistry: Functional Group Families

Chapter 14. Oxygen, Sulfur, or Halogen containing compounds

    1. List the functional groups that contain either oxygen or sulfur.  Be sure to include the name of the functional group and the name of the family of    

        compounds that contain each functional group

    2. List the rules that one should follow when naming alcohols, phenols & thiols

    3. Identify the common name for a diol is? Examples

    4. Compare/Contrast the properties of the alcohols to that of the parent alkanes

    5. Identify what chemical property causes the change in properties between alkanes and their alcohols? Explain

    6. In aqueous solutions, determine if alcohols behave more as an acid or more as a base? Explain

    7. Explain how alcohols function as bases in the presence of strong acids

    8. Write a mechanism for the dehydration of an alcohol via acid catalysis

    9. Explain why there is a specificity about the product formed via acid catalyzed dehydration of an alcohol

    10. Describe the reaction between an alcohol and an active metal (Na, Li, K, etc.). 

    11. Predict the products by writing the mechanism for the reaction between an alcohol and a haloacid. 

       a. differentiate between S_N1 and S_N2 mechanisms by product formation

    12. Demonstrate what specificity is seen in the production of the alkyl halide from #11

    13. Describe the oxidation of 1^o, 2^o, & 3^o alcohols with chromic acid

    14. Describe how a thiol is produced using hydrogen sulfide and NaOH_(aq)

    15. Compare the acidity of thiols versus an alcohol

    16. Describe how two thiols are oxidized forming a disulfide   

    17. Draw the general structure for an ether and give the rules for naming them   

    18. Explain how do the properties of ethers compare to the properties of alcohols

    19. Describe how an ether can be synthesized from each of the following pathways

        a. Williamson Ether synthesis                       

 b. Acid-Catalyzed Dehydration of an Alcohol

 c. Acid-Catalyzed Addition of Alcohols to Alkene

    20. Describe the general mechanisms and predict products for ethers (sulfides) that undergo

        a. Acid-Catalyzed Cleavage by Concentrated HX

        b. Oxidation of Ethers

        c. Oxidation of Sulfide

    21. Describe the general structure of an epoxide

Chapter 15. Amines

1.      Identify and correctly name the four classes of amine containing compounds.

2.      Describe some common properties of amines

3.      Explain why most amines function as organic bases

4.      List specific amines that are essential in living systems

Chapter 16. Aldehydes and Ketones

1.      Differentiate between an aldehyde and ketone by the position of the carbonyl functional group

2.      Correctly name specific aldehydes and ketones

3.      Describe some common properties of aldehydes and ketones

4.      Predict the products from certain reactions of aldehydes and ketones

    a. Oxidation of aldehydes: formation of a carboxylic acid

    b.   Reduction of aldehydes and ketones to alcohols

    c.    Addition of alcohols to produce acetals or hemiacetals

    d.   Aldol formation of Aldehydes and Ketones

Chapter 17. Carboxylic Acids and Their Derivatives

1.      Correctly identify and name specific carboxylic acids.

2.      Describe some specific properties of carboxylic acids.

3.      Explain the formation of the following:

    a.    Acid Anhydrides

    b.   Esters

    c.    Amides

4.      Describe how a phosphate ester is formed

Chapter 18. Amino Acids and Proteins

    1.   Describe the general composition of biomolecule.

    2.   Identify the general types of proteins that are found in organisms.

    3.   Correctly name the 20 common amino acids by distinguishing side chain characteristics.

    4.   Explain why amino acids typically occur as zwitterions at biological pH conditions.

           a. Identify the pKa values for a-COOH, a-NH2, & side chain functional groups. 

    5.   Solve for pH conditions knowing acid and conjugate base concentrations using Henderson-Hasselbalch.

    6.   Identify the isoelectric points for the titrations of amino acids.

    7.   Differentiate between enantiomeric forms of amino acids by using Cahn-Ingold-Prelog nomenclature (R,S).

    8.   Correctly draw Fisher Projections models to demonstrate biomolecules with multiple chiral centers.

    9.   Describe the formation of a peptide bond.

    10. Contrast the four levels of protein structure: primary, secondary, tertiary & quaternary .

           a. Identify the structure of alpha-helices .

           b. Compare parallel and anti-parallel beta sheets .

           c. Compare the side chain bonding associated tertiary structuring .

     11. Describe the differences in general structures of the 3 major shapes of proteins.

Chapter 19. Enzymes, Vitamins and Chemical Messengers

    1. Describe the three features of enzymes as catalysts in biochemical reactions: Catalytic power, specificity and regulation.

    2. Correctly use Enzyme Classification designations to identify enzymes.

    3. Explain what Cofactors are in biochemical reactions.

    4. Define the factors that affect enzyme kinetic rates.

    5. Utilize rate law equations to identify the enzymatic rate order.

    6. Graphically identify where V_max and K_m exist.

    7. Employ Michaelis-Menten & Lineweaver-Burk equations to calculate V_max and K_m.

    8. Define the different types of inhibitors of enzyme-catalzyed reactions.

    9. Use Lineweaver-Burk graphs to identify the types of inhibitors.

Chapter 21 Carbohydrates

    1. Identify the functionality of carbohydrates in living organisms.

    2. Correctly identify certain monosaccharides by structure and name.

    3. Describe the formation of a monosaccharide hemiacetal or hemiketal structure from ring formation.

    4. Utilize Haworth projection modeling to identify enantiomeric isomerization of chiral carbons.

    5. Identify the structures & functions of sugar derivatives:

        a. reducing sugars

        b. sugar alcohols

        c. deoxy sugars

        d. sugar esters

        e. amino sugars

    6. Describe the formation of a glycosidic linkage via dehydration synthesis mechanisms.

    7. Discriminate between alpha & beta linkages in glycosidic linkages.

    8. Identify certain disaccharide & polysaccharides by structure and name.

Chapter 23 Lipids

    1. Identify the fundamental properties of all lipid molecules

    2. Classify lipids by name into classes based on molecular structures and physical/chemical properties

        a. fatty acids (saturated & unsaturated)

        b. triacylglycerols

        c. glycerophosholipids (with varying polar head groups)

        d. sphingolipids

        e. waxes

        f. terpenes

        g. steroids

        h. eicosanoids

Chapter 26 Nucleic Acids & Protein Synthesis

    1. Describe the fundamental composition of DNA & RNA:

        a. nitrogen base structures (purine vs. pyrimidine)

        b. nucleoside structures

        c. nucleotides structures

        d. cyclic nucleotide structures

    2. Structurally discriminate between DNA & RNA.

    3. Employ Chargaff's rule to explain the conservation of pyrimidine & purine numbers in DNA.

    4. Describe the nucleotides in DNA form a double helix structure.

    5. Identify the roles of DNA & RNA in a living system.

        a. Name and identify the structures/roles for mRNA, rRNA, & rRNA.

    6. Discriminate between the modes of DNA replication.

    7. Explain how Messelsen & Stahl concluded Semi-Conservative replication as a mode for DNA replication.

    8. Describe the general mechanism, with specific factors, of DNA replication

    9. Relate the processes associated with initiation, elongation & termination within DNA replication.

    10. Describe the general scheme for protein synthesis.

    11. Relate the processes associated with initiation, elongation & termination within protein synthesis.

Chapter 20. The Generation of Biochemical Energy

    -In development

Chapter 22. Carbohydrate Metabolism

    -In development

Unit VII. Laboratory Practices

    1. Correctly set-up a hot water bath and employ reactions vials for organic reactions

    2. Properly separate aqueous and non-aqueous layers using decanting or other separation techniques

    3. Identify potential unknown organic molecules from melting/boiling points and densities.

    4. Use bromine water and/or potassium permanganate to identify the existence of an alkene/alkyne

    5. Use thin-layer chromatography in order to separate molecules from crude extracts

        a. correctly measure retention times as means of labeling extracted molecules

    6. Set up and utilize column chromatography in order to purify organic extracts

    7. Identify the differences between TLC, column chromatography and gas chromatography

    8. When possible, be able to run a gas chromatograph and identify unknown elutants from standard retention times

    9. When possible, be able to run a gas chromatograph/mass selective detector and verify unknown from a spectrum