SYLLABUS

INTRO TO ORGANIC & BIOCHEMISTY LECTURE & LABORATORY

CH133/CL131

Spring 2009

NAME OF SCHOOL: PresentationCollege

NAME OF DEPARTMENT: College of Arts & Sciences – Department of Chemistry

SEMESTER/YEAR: Spring 2009

CLASS DAY: Lecture (AB) – Monday, Wednesday, & Friday

Laboratory (AB) – Tuesday, Wednesday, & Thursday

CLASS HOURS: Lecture – 1:00 am until 1:50 pm (MWF)

Laboratory – Tuesday (CL131A) 10:00 am until 12:00 pm

Wednesday (CL131B) 3:00 am until 5:00 pm Thursday (CL131C) 8:00 am until 10:00 pm

MEETING ROOM: Lecture – Nursing Building NU27

Laboratory – Main Building E106 & E111

CAMPUS SITE: Aberdeen

INSTRUCTOR NAME: Dr. James Johnson (Lecture)

INSTRUCTOR OFFICE: E-360

INSTRUCTOR CONTACT INFORMATION:

Office phone: 229-8360 or email:

You may also contact me anytime at home (cell: 216-0117).

INSTRUCTOR OFFICE HOURS:

Monday: 10:00 am to 11:00 am and from 2:00 pm to 3:00 pm

Tuesday: 1:00 pm to 3:00 pm

Wednesday: 11:00 am to 12:00 pm

Thursday: 10:30 am to 11:30 am

Friday: 9:00 am to 10:00 am

Please note: I have an open door office policy

If the above mentioned times will not work please schedule a time with me that will 216-0117

COURSE NUMBER: CH133 and CL131

COURSE TITLE: Intro to Organic & Biochemistry – Lecture and Laboratory

COURSE DESCRIPTION: CH133 & CL131 (Intro to Organic & Biochemistrywith Lab – 3,1 credits). This is a one-semester course that offers and introduction to the chemical principles important to biological systems. It is designed mainly for students of nursing, health sciences, and those not planning to take additional chemistry courses. Topics covered are those especially important for health-related majors with special emphasis placed on examples illustrating the relevance of organic and biochemical principles to medical applications. It will involve approximately five weeks of organic chemistry and ten weeks of biochemistry. This course includes 3 hours of lecture plus 2 hours of laboratory and/or recitation weekly.

Prerequisite: “C” or above in CH123/CL121 or its equivalent, or a satisfactory score on the departmental-approved placement exam. The lab may only be taken if previously or concurrently enrolled in CH133. (Foundational Science course).

CHANGES: Any and/or all parts of this syllabus are subject to change at any time. Students will be notified in class of any changes made to the syllabus prior to taking effect. Updated versions of the syllabus will be posted on WebCT

CLASS CANCELLATION POLICY: When class is canceled, an email message will be sent to all students via your Presentation College email address (PLEASE CHECK YOU EMAIL DAILY)

CLASS NOTIFICATIONS: Check email and website daily for class relocations, assignments and relevant course information.

TEXTBOOK: “Organic & Biochemistry for Today, 6thEdition,”Seager and Slabaugh; ThomsonLearning, Inc. (Lachina Publishing Services) – 2008(REQUIRED)

SOFTWARE: GOB Chemskills 3000 for General, Organic, and Biochemistry (Version 3.4), by

Spain, Garmon, and Peters; Electronic Homework Systems, Inc. – 2007 (REQUIRED)

Laboratory Supplies:

1. Safety goggles or glasses will be required for admission to the laboratory and may be purchased at the bookstore. It is departmental policy that no one will be permitted to work in a chemistry laboratory without eye protection. If you wear prescription glasses, you still have to have safety glasses that have side-shield protection.

2. Scientific calculator – scientific notation and log functions.

3. Composition notebook for homework and laboratory assignments.

4. A lab coat or apron to protect your clothing (optional).

COURSE OBJECTIVES/OUTCOMES:

COURSE OBJECTIVES

Course objectives for lecture and laboratory:

  • Develop a working vocabulary and knowledge of the two major fields discussed in this course (Organic Chemistry & Biochemistry)
  • Understand the basic scientific theories and principles of chemistry (General Chemistry, Organic Chemistry, and Biochemistry).
  • Develop a systematic approach to problem-solving.
  • Prepare for advanced learning in physiology, nutrition, and/or human chemistry.
  • To fulfill PC’s general education goal (#6) in that students will be able to:
  • Demonstrate knowledge of a natural science’s focus
  • Demonstrate the ability to apply the scientific method
  • Demonstrate skills in scientific problem solving, critical thinking and reading
  • PLEASE NOTE: in order to fulfill goal #6, students may be required to take and successfully pass an additional science exit exam in order to pass CH133.

After attending lecture and studying the assigned materials, the student will:

  • Recognize the molecular formulas of organic and inorganic compounds.
  • Be able to explain some general differences between inorganic and organic compounds.
  • Be able to use structural formulas to identify compounds that are isomers of each other.
  • Assign IUPAC names and draw structural formulas for alkanes and cycloalkanes.
  • Be able to name and draw structural formulas for geometric isomers.
  • Be able to classify unsaturated hydrocarbons as alkenes, alkynes, or aromatics.
  • Be able to write IUPAC names of alkenes from their molecular structures.
  • Be able to write equations for addition reactions of alkenes, and use Markovnikov’s rule to predict the major products of certain reactions.
  • Be able to write IUPAC names of alkynes from their molecular structures.
  • Classify organic compounds as aliphatic or aromatic.
  • Recognize uses for specific aromatic compounds.
  • Be able to name and draw structural formulas for alcohols and phenols.
  • Be able to classify alcohols as primary, secondary, or tertiary on the basis of their structures.
  • Be able to write equations for alcohol dehydration and oxidation reactions.
  • Recognizes uses for specific alcohols and phenols.
  • Be able to name and draw structural formulas for ethers.
  • Be able to assign IUPAC names to aldehydes and ketones.
  • Be able to write key reactions for aldehydes and ketones.
  • Be able to give specific uses for aldehydes and ketones.
  • Be able to assign IUPAC names and draw structural formulas for carboxylic acids.
  • Recognize and write key reactions of carboxylic acids.
  • Recognize and write key reactions for ester formation.
  • Be able to assign common and IUPAC names to esters.
  • Recognize and write key reactions of esters.
  • Be able to classify amines as primary, secondary, or tertiary.
  • Be able to assign common and IUPAC names to amines.
  • Recognize and write key reactions for amines.
  • Be able to name amines used as neurotransmitters.
  • Be able to give uses for specific biological amines.
  • Be able to assign IUPAC names for amides.
  • Be able to show the formation of hydrogen bonds with amides.
  • Be able to describe the four major functions of carbohydrates in living organisms.
  • Be able to classify carbohydrates as mono-, di-, or polysaccharides.
  • Be able to identify molecules possessing chiral carbon atoms.
  • Be able to use Fischer projections to represent D and L compounds.
  • Be able to classify monosaccharides as aldoses or ketoses and classify them according to the number of carbon atoms they contain.
  • Be able to describe the uses for important monosaccharides.
  • Be able to list sources and uses for important disaccharides.
  • Be able to describe the structures and list sources and uses for important polysaccharides.
  • Be able to classify lipids as saponifiable or nonsaponifiable and list major functions of lipids.
  • Be able to describe four general characteristics of fatty acids.
  • Be able to describe the structural similarities and differences of fats and oils.
  • Be able to describe uses for phosphoglycerides.
  • Be able to describe uses for sphingolipids.
  • Be able to describe the major features of cell membrane structure.
  • Be able to identify the structural characteristics typical of steroids and list important groups of steroids in the body.
  • Be able to name the major categories of steroid hormones.
  • Be able to describe the biological importance and therapeutic uses of the prostaglandins.
  • Be able to identify the characteristic parts of alpha-amino acids.
  • Be able to write reactions to represent the formation of peptides and proteins.
  • Be able to describe the uses for important peptides.
  • Be able to describe proteins in terms of the following characteristics: size, function, classification as fibrous or globular, and classification as simple or conjugated.
  • Be able to explain what is meant by the terms primary, secondary, tertiary, and quaternary regarding the structure of proteins.
  • Be able to describe the conditions that can cause proteins to hydrolyze or become denatured.
  • Be able to describe the general characteristics of enzymes and explain why enzymes are vital in body chemistry.
  • Be able to identify the general function of cofactors.
  • Be able to list two ways of describing enzyme activity and identify the factors that affect enzyme activity.
  • Be able to describe the three methods of cellular control over enzyme activity.
  • Be able to describe the importance of measuring enzyme levels in the diagnosis of disease.
  • Be able to identify the components of nucleotides and correctly classify the sugar and bases.
  • Be able outline the process of DNA replication.
  • Be able to describe the structures of DNA and RNA and list the function of the three types of cellular RNA.
  • Be able to describe what is meant by the terms transcription and translation.
  • Be able to describe the process by which RNA is synthesized in cells.
  • Be able to explain how the genetic code functions in the flow of genetic information.
  • Be able to explain the process by which proteins are synthesized in cells.
  • Be able to describe how genetic mutations occur and how they influence organisms.
  • Be able to describe the difference between macronutrients and micronutrients in terms of amounts required and their function in the body.
  • Be able to describe the primary functions in the body of each macronutrient and for each major mineral.
  • Be able to distinguish between and classify vitamins as water-soluble or fat-soluble on the basis of name and behavior in the body.
  • Be able to differentiate among metabolism, anabolism, and catabolism.
  • Be able to describe the three stages in the extraction of energy from food.
  • Be able to explain the role of coenzymes in the common catabolic pathway.
  • Be able to identify the products of carbohydrate digestion.
  • Be able to explain the importance of maintaining proper blood sugar levels in the body.
  • Be able to list the starting material and products of the glycolysis pathway.
  • Be able to describe how the glycolysis pathway is regulated in response to cellular needs.
  • Be able to describe the three fates of pyruvate.
  • Be able to identify the two major functions of the citric acid cycle and describe how the citric acid cycle is regulated in response to cellular energy needs.
  • Be able to explain the function of the electron transport chain and describe how electrons move down the chain.
  • Be able to list the major features of the chemiosmotic hypothesis.
  • Be able to calculate the amount of ATP produced by the complete oxidation of a mole of glucose.
  • Be able to explain the importance of the processes of glycogenesis and glycogenolysis.
  • Be able to describe gluconeogenesis and the operation of the Cori cycle.
  • Be able to describe how hormones regulate carbohydrate metabolism.
  • Be able to describe the digestion, absorption, and distribution of lipids in the body.
  • Be able to explain what happens during fat mobilization.
  • Be able to outline the steps of -oxidation for fatty acids.
  • Be able to calculate the amount of ATP produced by the complete catabolism of a fatty acid.
  • Be able to name the ketone bodies and list the conditions that cause their overproduction.
  • Be able to describe the pathway for fatty acid synthesis.
  • Be able to describe the source and function of the body’s amino acid pool.
  • Be able to write equations for transamination and deamination reaction and explain the overall results of the urea cycle.
  • Be able to describe how amino acids can be used for energy production, the synthesis of triglycerides, and gluconeogensis.
  • Be able to outline the relationship between intermediates of carbohydrate metabolism and the synthesis of nonessential amino acids.
  • Be able to describe the chemical compositions of plasma, interstitial fluid, and intracellular fluid.
  • Be able to explain how oxygen and carbon dioxide are transported within the bloodstream.
  • Be able to explain how materials move from the blood into the body cells and from the body cells into the blood.
  • Be able to list the normal and abnormal constituents of urine.
  • Be able to explain how proper fluid and electrolyte balance is maintained in the body.
  • Be able to explain how acid-base balance is maintained in the body and how buffers work to control blood pH.
  • Be able to describe respiratory and urinary control of blood pH.
  • Be able to list the causes of acidosis and alkalosis.

Laboratory Practices

1. Students will work in the laboratory in accordance with good laboratory practices.

A) No eating or drinking in the laboratory.

B) Dress appropriately on lab days (wear long pants and shoes with enclosed

toes). Hair must be tied back.

C) Safety goggles or glasses are required for admission to the laboratory. Wear safety goggles when anyone in the laboratory is using chemicals. (If caught not wearing your safety goggles, you will lose 5 points for the respective lab). If you wear prescription glasses, you still have to have safety glasses that have side-shield protection. Contact lenses are not acceptable eye protection and you are strongly encouraged not to wear contact lenses to the laboratory. It is departmental policy that no one will be permitted to work in a chemistry laboratory without eye protection.

D) Follow written/verbal directions accurately.

E) Work safely, effectively, and correctly when using equipment and chemicals.

F) Demonstrate use of required techniques.

G) Obtain samples from stock reagents that are the correct substance, concentration, & sample size

H) Dispose of waste products appropriately.

2. Students Will Gather and Record Qualitative and Quantitative Data Accurately.

A) Keep notebooks and worksheets that are neat, clean, understandable and

accurately represent work done.

B) Display computer data in a spreadsheet or graphically, as is relevant.

Course objectives for lab in addition to the above mentioned objectives for lecture

1. Learn how to reason and solve scientific problems.

2. Learn to communicate effectively.

3. Learn about chemicals and their properties.

4. Learn various laboratory techniques involved in collecting and analyzing data.

5. Learn to draw conclusions from experiments and evaluate the validity of the data.

INSTRUCTIONAL METODS: A variety of instructional techniques will be used in this course. These may include, but are not limited to, class lectures, small group work, out-of-class assignments, in-class assignments, and quizzes.

METHODS OF COURSE ASSESSMENT/EVALUATION: PLEASE NOTE: in order to fulfill Presentation College’s General Education Program goal #6(located on page 42 of the 2008-2009 College Catalog), students will be required to take and successfully pass an additional science exit exam in order to be eligible to pass CH133.

GRADING SCALE:

Lecture: You are expected to attend all lecture sessions. The letter grade, which you will earn for the lecture portion of this course, will be determined as follows: (1) The “Lecture assignments” total points you earned (i.e. in-class assignments, handouts, unannounced quizzes, etc…) will be divided by the total possible “Lecture assignments” points and then multiplied by 20(these “Lectureassignments” points are worth 20% of your Overall Lecture %), (2) The total points you earned fromfour exams will be divided by the total possible exam points and then multiplied by 70 (exams points are worth 70% of your Overall Lecture %), and (3) The total points you earned from the American Chemical Society Standardized Exam (ACS Exam) and Assessment Exams will be divided by the total possible points for the ACS and Assessment exams and then multiplied by 10 (the ACS and Assessment exams are worth 10% of your Overall Lecture %). The three calculated percentages (Lecture assignments %, Exam %, and ACS/Assess %) will be added together to obtain your Overall Lecture Percentage for CH133. Final Lecture Grades will be distributed as outlined below (please see Final Grades).

Laboratory: The laboratory portion of the course is designed to supplement various lecture topics and provide you with some experience in conducting experiments. Each laboratory activity (handout and/or experiment) is worth 25 points. These points will be incorporated into your Laboratory grade. The laboratory activities (a combination of dry and wet labs) are due at the end of the lab period unless otherwise indicated. Please note: CL131 labs will consist of approximately 4 dry labs and 7 wet labs. However, the number of dry or wet labs may vary if students elect (vote) to have a review session(s) as opposed to a scheduled lab or additional lecture material needs to be covered. The dry labs will consist of computer based projects that are designed to enhance various concepts covered in lecture. The wet labsare designed to enhance various lecture concepts and/or provide insight into concepts not covered in lecture. You will not be tested on specific material or concepts that were introduced in a wet lab but were not covered during lecture. I solicit and appreciate your comments, suggestions and feedback for helping me refine labs for yourselves and future students. The letter grade, which you will earn for the laboratory portion of this course, will be determined as follows: (1) The “Lab Assignments” total points you earned from laboratory experiments will be divided by the total possible “Lab Assignments” points and then multiplied by 100% (these “Lab Assignments” points are worth 100% of your Overall Laboratory %). Final Laboratory Grades will be distributed as outlined below (please see Final Grades).

Attendance: You are expected to attend all lecture and laboratory sessions. I do not give make-up exams, and/or lecture/lab assignments. If you are unable to attend lecture/lab you should contact me as soon as you possibly can in order to discuss your situation. Those who may miss class because of illness, family emergency, or weather must hand in a signed paper (or e-mail) stating the date and reason for the absence. However, an excused absence does not automatically entitle you to make-up a missed exam and/or lecture/lab assignments; only that you have asked me to provide you an opportunity to make-up the points for the work you missed. The validity of the excuse(s) is totally up to the instructor’s discretion. Exams and/or lecture/lab assignments missed for compelling reasons may be rescheduled; however, the student must take the initiative in rescheduling the missed activity. Rescheduling a missed exam is done at the instructor's convenience. The make-up exam is similar to the classroom exam but it is never the same exam. These exams are written such that the level of difficulty is on par with the classroom exam, though some students may perceive them as more difficult. Unexcused absences for any activity (i.e. exam, quiz, in-class activity, etc…) will result in a grade of zero.