Introduction to organic chemistry chem 106

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Chemistry for Allied Health II


Spring , 2011

Instructor: Shirish K. Shah, Ph.D.

Office: Smith Hall, Room 539B

Office Phone: 410-704-2720

Home Phone: 410-323-0803

E-mail: or

Internet Address:






Introduction to Organic Chemistry presents the basic principles of Organic Chemistry, the identification, and reactions of functional groups, nomenclature, and stereochemistry. The properties and reactions of some complex compounds, such as carbohydrates, lipids, and proteins will be investigated. The laboratory includes techniques and methods used by organic chemists to identify, synthesize, separate, and purify organic compounds.



Text: Denniston, Topping and Caret General, Organic and Biochemistry,

McGraw-Hill 6th Edition.

Laboratory Manual: Chemistry for Allied Health Professionals II - Frank Milio and Shirish Shah

Chemistry 106 notes Dr. Shah from the Copy Center.

Calculator: For homework, lab reports, quizzes, and exams. Strongly recommend one with

scientific (exponential) notation and logarithms.

Study Guide: To go with text - not required but highly recommended, it contains

answers to problems in the text and extra practice questions.

Safety Goggles are required by law.

All syllabi are required to include numbers 1 - 9 below - as stated in the TU Faculty Handbook:

1.    Course Catalog Description, including prerequisites (required for 300 level and above, may be used for 200 level (not required))

2.    Learning Goals,

 Courses meeting University Core requirements must include the

  1. relevant University learning outcomes and related course goals;

  2. instructor-determined or department determined for multi-section courses

3.    Course Content

a.    course content, usually in the form of a schedule of topics and assignments that explicate and justify both the catalog title and level (lower division, upper division, graduate);

4.    Statement of Requirements

a.    For example, readings/assignments/tests/finals

5.    Instructor’s Grading Scheme or Policy

a.    For example, (a) work/assignments required, (b) percentage/numeric value for each assignment, (c) range of values that forms the course’s plus/minus grading policy (Note: There is noA+ or C-grade at TU) and (d) policies and/or penalties regarding late assignments

6.    Course Policies (a) on Academic Dishonesty (including plagiarism, as relates to grades) and (b) on Attendance (as relates to grades), both consistent to TU Policy on Academic Integrity.  How attendance (and participation) is graded must be spelled out clearly so that students cannot question the grade.

7.    Statement of Additional Work (amount and type) Required of Graduate Students (if course is offered for graduate as well as undergraduate credit)

8.    Bibliography (for upper-level undergraduate and graduate courses)

9.    Statements regarding course policies on:

                                Class attendance, participation, absence and assessment make up

                                Penalties for late assignments

Personal honesty, integrity, cheating, and plagiarizing—may refer to the Student handbook

                                Students with disability policy—may refer to the Student Handbook                      

Writing Skills

Repeated Course

Course Withdrawal


Course Content:

  1. General Course objectives

1. The course should help each student become more aware of the role that

chemistry plays in our immediate environment at home and in the workplace.


2. The course will increase the student's ability to solve and analyze word

problems in the class.


3. The course will provide the opportunity for students to develop competence

in the laboratory methodology and its relationship to the underlying concepts.


4. The course should provide the necessary background for a student to further

Investigate related scientific disciplines if he or she chooses to do so.


B. Learner Objectives:

The student is expected to know:

1. covalence of carbon, hydrogen, oxygen, and nitrogen; functional groups; structural isomers and covalent bond formation by overlap of atomic orbitals.


2. structures of alkanes, nomenclature of alkanes - IUPAC system, common

names of alkanes, cycloalkanes, confirmations of alkanes and cycloalkanes,

configuration (cis-trans) isomers, physical and chemical properties of alkanes.


3. structure and bonding in alkenes. Nomenclature of alkenes, cis- tran isomers in alkenes, addition, reduction and oxidation reactions of alkenes and overview of polymerization of substituted ethylene and aromatic hydrocarbons.


4. structures of alcohols and ethers; nomenclature of alcohols and ether; physical properties of alcohols; reaction of alcohols; comparison between alcohols, ethers, phenols and thiols.


5. structure classification and nomenclature of amines, physical and chemical properties of amines.


6. structure of aldehydes and ketones; nomenclature of aldehydes and ketones; physical and chemical properties of aldehydes and ketones and properties of alpha- hydrogens.


7. structure of carboxycylic acids, physical and chemical properties of carboxylic acids and preparation of carboxylic acids.


8. structure and nomenclatures of esters, anhydrides and amides: reactions of

anhydrides, esters and amides, preparation of esters and the Claisen condensation.


9. how to predict optical isomers. Racemic mixtures, molecules that contain two or more chiral centers and the significance of the chirality in the biological world.


10. how to recognize carbohydrates, and amino acids, and how to identify them.


11. about lipids, protein structures, enzymes, DNA, hormones and their role in Biochemistry.


For the regular schedule during a traditional semester, the course is composed of lecture/lab combination. The class is conducted in a lecture and group discussion mode. Students use the class notes and homework to study. Overhead projector, VCR, and conceptual questions are used to stimulate the students. Bi-Weekly labs provide the reinforcement for the students. A feedback mechanism is established through quizzes test and small study groups. The students are asked to present their findings from the INTERNET PROJECTS that relates to organic or biochemistry topics. Students are encouraged to use tutorial assistance and communication with the instructor by using appointment opportunities.

Course Requirements:

1. Attendance at all classes is strongly recommended.


2. Completion of all required experiments and lab reports in a timely manner.


3. Internet project requires the evaluation of the web site as well as the scientific content, and how it relates to the college students.


4. Some Problem assignments from chapters and quizzes will be during the class activities.


5. Completion of all tests, quizzes and final examination.


Grading Policy:

  • There will be four major exams, including the final.


  • We will cover mainly chapters 11-20. Final grade will be determined as follows:

Four exams in class 72%

Homework & class projects 8%

Lab Average 20%


94-100 A

90-94 A-

86-90 B+

82-86 B

78-82 B­-


74-78 C+

70-74 C

60-70 D

Below 60 F






Chemistry for Allied Health II



Spring, 2011



For Test I

Chapter 10 Intro to Organic Chemistry (Alkanes)

#Examples from 10.1-10.8; Figures 10.2,10.3,10.4, Tables 1,2,3,4,5,6,7,8

Articles on pages 323,325,335,339 (Write 1 paragraph summary for each article)

P 340; Summary of Reactions


Chapter 11 Alkenes, Alkynes and Aromatic Compounds Figures 11.1-11.3; Tables 1and 2

#Examples from 11.1-11.10;

Articles on pages 354 &373- 375 (same as above)

P 382; Summary of Reactions

For Test II

Chapter 12 Alcohols, Phenols and Ethers Example 12.1-12.12


Article pages 395,401,407,413

(same as above) Summary of reactions on page 415


Chapter 15 Amines and Amides Figures 15.1,15.2,15.4,15.5,15.6,15.9 Tables 15.1,15.2,15.3,15.4

# Examples from 15.1-15.4

Article pages 505, 513, 518,

(same as above) Summary of reactions on page 522


Chapter 13 Aldehydes and ketones Examples 13.1-13.9 Table13.1

Articles pages 433, 436, 438

Summary of Reactions pages 444-445


For test III


Chapter 14 Carboxylic Acid and Derivatives Figures 14.1,14.2, Table 14.1 Examples 14.1-14.13,

Article Pages 458, 460, 470, 484

Summary of reactions pages 485 -486




Chapter 16 carbohydrates Figures 16.1-16.13 Examples 16.1-16.5 ;

Article pages 533, 551, 555,

(same as above Summary on pages 556-557)




Chapter 17 Lipids Figures 17.1, to 17.13 Table 17.1,17.2

Examples 17.1-17.5

Article pages 577, 581, 582,590,

(same as above Summary 592-593)




Chapter 18 Amino Acids, Protein Structue Figures 18.1-18.16

Tables 18.1,18.2 Examples18.1

Article pages 602, 610, 618

Summary & Key Terms page 621-622




Presentations of the Articles

Final Exam (Comprehensive)

The instructor reserves the right to change the schedule of the labs and tests, depending upon the availability of resources and the weather.





Chemistry for Allied Health II


Spring 2011,

Title Page

a. experiment title

b. student names

c. date submitted



A one-or-two sentence statement of the objectives, goals or purposes of the experiment.



It is necessary only to provide an explicit reference to the source(s) of the procedure; it is not necessary to include the complete procedure. For example, Colligative Properties of Solutions, Chemistry 116 Laboratory Manual 1999.


Experimental Details

This section should describe what was actually done. It is a succinct exposition of the laboratory notebook, describing procedures, techniques, instrumentation, special precautions, and so on. It should be sufficiently detailed that other experienced researchers would be able to repeat the work and obtain comparable results.


If the experiment is performed without modification using a published procedure, it is necessary only to provide an explicit reference to the source(s) of the procedure. For example, Colligative Properties of Solutions, Chemistry 106 Laboratory Manual.



Sample calculations should be shown for each type of calculation requested in the experiment. Calculations can sometimes be organized into a table.



In this section, relevant data, observations, and findings are summarized. Tabulation of data, equations, charts, and figures can be used effectively to present results clearly and concisely. Schemes to show reaction sequences may be used here or elsewhere in the report.



The crux of the report is the analysis and interpretation of the results. What do the results mean? How do they relate to the objectives of the project? To what extent have they resolved the problem? This is the place to prove, in your own words, that you understand the concepts

included in the laboratory experiment. This section should be written assuming the reader is not familiar with the laboratory experiment.


Conclusions & Summary

A separate section outlining the main conclusions of the project is appropriate if conclusions have not already been stated in the "Discussion" section. A lengthy report, or one in which the findings are complex, usually benefits from a paragraph summarizing the main features of the report - the objectives, the findings, and the conclusions.



Why work in a group?

Throughout the semester your lab work will be completed in a group. Why do we put so much emphasis on group work? Our reasons are really twofold. First, both you and the other members of your lab. group will understand the labs better. Educational research has shown that cooperative group work is an effective means for teaching/learning science (and almost any other subject) and can help increase your understanding of the material. Every time you have to explain something to a group mate, the better you will understand the concept. Second, for those times when you find yourself clueless (it happens to all of us from time to time), group work gives you the opportunity to have someone besides your Graduate Instructor or professor explain the concept to you. Sometimes your group mates will have a common experience that will make a great memory association or analogy for you that is unknown to the staff. This means there are benefits for all group members, if the group is functioning properly.



Building a working group

Although most humans are by nature social creatures, cooperative group work is not something that comes without effort. Such group activities require that a sense of trust be built between members, as well as a feeling of shared responsibility. This means a responsibility to carry your own weight in the group, as well as a responsibility to all of the other members of the group. In such a case, no one group member gets frustrated and rushes on ahead of the

group, and the group NEVER leaves any of its members behind. This may not always be easy. What do you do when you have someone in your group that you don't like? Or who doesn't like you? How do you deal with group members who refuse to help you out when you are confused?


Some words of advice: slow down and remember that your group members are just as new at this as you are. Learning to be a member of the group, rather than a competing individual in the learning process is a new experience for nearly everyone in this class. Second, this should be seen as a professional experience, not a time for making social contacts. It does not matter whether or not your group mates are the kind of people you would most likely choose to socialize with on Friday night. You will find that you can still work with these individuals.

  Finally, remember that in group work we expect all group members to take responsibility for keeping all of their group mates up to speed and to take personal responsibility for contributing their maximum effort. "The whole is greater than the sum of its parts" is especially true when working in groups. "My group can't get along." Very rarely do we find a group that actually cannot work. What we do find are groups with members who are not communicating effectively. If you think your group is having problems, sit down and talk things over as a group. Agree on some basic rules of conduct and responsibility within your group, and make a commitment to each other. Then try again. If you find you are still having problems, you may need help from someone with an "outside" perspective. Make an appointment when your entire group can meet with your Graduate Instructor, course supervisor, or professor to talk things over. Don't let problems linger or fester, but do try to work things out among yourselves first. Most of all, relax and enjoy interacting with new people. Think of this as preparation for the "real" world where you will be required to work closely with people in many different settings. You will not always like all of those people, but you may find that you enjoy interacting with people who are very different from yourself. Relax, enjoy yourself, and have fun exploring the world around you.


Working as a team

Working as a team requires that different members assume different responsibilities. There are many ways to divide responsibility of work in a project and one suggested way is to assign roles, which rotate among group members from week-to-week.




Quality Control Officer

Safety Officer


While each member of the group helps with the lab work, each individual accepts the major responsibility for ensuring that a portion of the project is done properly. Even though the data and the design of the experiment(s) are done collectively, each individual will write a separate lab report. The lab report should not exceed three pages. (excluding the data and graphs and questions from the assigned lab)

Laboratory Reports

You will be working in teams of 2-3 for all of the laboratory experiments (unless otherwise stated). Each individual will submit a single laboratory report for each experiment. While we encourage you to discuss concepts with other members of your class, each written laboratory report must represent the unique effort of each team. All laboratory reports must be typed. All graphs should be generated using a spreadsheet program such as Microsoft Excel.

Abstracted in part from: Guidelines for Preparing a Research Report, The American Chemical Society, 2000 (

Spring 2011 Schedule for Labs

Week Of


Experiment Title


1/31 and 2/7


Lewis Structures; Molecular Models / Check-In/Safety Procedures




Melting Point








Fats & Oils




Dehydration of Alcohols




Gas Chromatography & Review




Paper Chromatography








Aspirin Synthesis




Vitamin C Tablet Analysis




Macromolecules (selected parts only) and Biuret Experiment for Proteins




Enzyme Kinetics & An Acid tablet reaction






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