The Chemistry of Organic and Biochemical Molecules II - Chem 112


Dr. Henry Jakubowski


TEXT: Chemistry, 4th Edition, by McMurry and Fay (same book used in the first semester of Gen. Chemistry.

TIME: 11:20-12:30 pm, Days 2-4-6


LAB: Day 5, 1:00-5:00 am, ASC 202/4

OFFICE: Ardolf Science Center, 245

OFF. HRS: 1:00 to 2:00 p.m, Days 1, 3, and 6, by appointment, or whenever you can find me


Organic Chemistry

Introduction to Organic Chem

Functional Groups

  1. Acids and Bases - A review

  2. Animation:  Reaction of HCl and water.
  3. Formation of Molecular Ions from Acids
  4. HCl + H20: Space fill model, electron density model, and reaction mechanism.
  5. Reaction Mechanism:  CO2, NO2, SO3: Interactions with water
  6. Ordering Strong and Weak Acids
  7. Animation:  Reaction of HCl and water.
  8. Reaction Mechanism:  CO2, NO2, SO3: Interactions with water
  9. Ordering Strong and Weak Acids

Organic Molecules as Acids: pKa's

4 Rules of Chemical Reactivity

Drawing Reaction Mechanisms

Chemistry: of Carbonyls

  1. Aldehydes, Ketones

  2. Carboxylic Acid Derivatives

  3. Protonation/Deprotonation of Intermediates


Chemistry of Alkenes, Aromatics, Alcohols

Redox Reactions

  1. Review Oxidation/Reduction

  2. Counting Electrons:  Oxidation Numbers

  3. Oxidation Organic Molecules: Problem Set

  4. Oxidation of Alchols - Oxidizing Agents and Identification

  5. Oxidation of Alkenes and Aldehydes - Oxidizing Agents and Identification

Reaction Rates and Equilibrium


The Meaning of ΔG, ΔGostab, and Δa Gconc

Example: ΔG and the reactions of hydrochloric acid and acetic acid


Phosphoesters, Phosphoanhydrides, and ATP

Driving Unfavorable Reactions

Biological Molecules and the Central Dogma of Biology


  1. straight chain and cyclic sugars

  2. 5 and 6 C sugars to know

  3. hemiacetals, acetals, and dissacharides

  4. polysaccharides: starch, glycogen, and cellulose


  1. Fatty Acids

  2. Phospholiids

  3. Micelles and Bilayers

  4. single chain amphiphile | micelle
  5. micelle
  6. double chain amphiphile | bilayer membranes
  7. bilayer


  1. 20 naturally occuring amino acids

  2. Primary structure of proteins

  3. Secondary Structure - alpha helix and beta sheets

  4. Tertiary Structure - 3D structure of proteins


  1. The Structure of DNA

  2. The Central Dogma of Biology

  3. Control of Gene Transcription

Carbohydrate Metabolism

  1. Glycolysis

  2. Cori Cycle

  1. Gluconeogenesis

  1. Pyruvate Dehydrogenase

  2. Kreb's Cycle - TCA CYCLE

  1. Glycogen Breakdown - Glycogenolysis

  2. Glycogen Synthesis

    • Glycogen Synthesis - detailed highlights

  3. ATP as Substrate, Allosteric Activator/Inhibitor, and Covalent Regulator of Enzyme Activity

Oxidative Phosphorylation: ATP synthesis

  1. mitochondrial electron transport/proton gradient

  2. mitochondria ATP synthesis

  3. substrate-level ox-phos in glycolysis

Lipid Metabolism

Fatty Acid Oxidation

Fatty Acid Synthesis

  1. Ketone Body Synthesis - Ketogenesis

  2. Ketone Body Utilization

Triacylglyceride Metabolism

Lipoprotein metabolism

Integration of Metabolism

Organ Specialization and Hormone Signaling
Kinases and Phosphatases




  1. to learn and understand some of the chemistry of organic functional groups which predominate in biological molecules
  2. to understand the role of enzymes in the catalysis and regulation of metabolic reactions
  3. to understand the central dogma of biology
  4. to understand how the products of enzyme-catalyzed reactions are controlled by the interplay between thermodynamics, which determines the extent of chemical reactions and kinetics, which determines the rate of the reactions


  1. to apply the principles of organic chemistry to the degradative (catabolic) and synthetic (anabolic) reactions which occur in the body
  2. to understand how metabolic reactions are grouped into pathways and how these pathways are regulated
  3. to integrate the various metabolic pathways and be able to understand how the chemistry of the body responds to various conditions and diseases.





Three exams (not counting the final) will be given during the semester. The exams will be a combination of multiple choice, short answers, and/or longer problems. The exams might include a combination of take-home, group, out-of-class, and in-class exams. Make-ups will only be allowed for certified emergencies. The makeup will be more difficult than the original, and consist of in depth essay questions or problems. The problems may be any combination of oral or written. The final exam will emphasize the material presented after the last exam, but will also be cumulative.


Many quizzes will be given during the semester. Some may cover assigned readings which were not covered in class. The quizzes will take about 10 minutes. Often times, one group grade will be given for quizzes. The grade may be determined by randomly grading one group member's quiz and assigning that grade to all members of the group. All the quizzes count the equivalent of 1 exam. Take them seriously!


In almost every class we will do group work. Because of this, ATTENDANCE IS MANDATORY! The group work will vary from informal, ungraded exercises to formal, graded problems. Several homework problem sets will be assigned, which will also be done in groups. All homework will not be graded. Sometimes, random questions will be assigned a grade. Correct answers will be posted on the due date for the homework.


The final exam counts 20% toward the final grade.  Its structure will be explained later on in the semester.    Further details will be given in class..


Four  exams are scheduled for this class (three regular exams and one final exam). I will replace your lower regular exam score with your score on the final exam if the final exam score is higher than your lower regular exam score.  In that case, your final exam will count twice, once as a regular exam and once for the final. This policy is designed to help you if you had a bad day on one exam and to give you motivation to study hard for the final exam.


What does it take to get an A?


The lab will count 20% of the grade and attendance is mandatory. Failure to complete a lab or labs, without a valid reason, will have the following consequences on the FINAL COURSE GRADE in all lower division chemistry courses with a laboratory component: 1 unexcused absence - not eligible for S/U grading in the course. Each additional unexcused absence will result in a final course grade reduction equivalent to half a grade, e.g., from AB to B. Completion of a lab or lab equivalent is defined as both attendance at the lab and completion of the requisite written report. NOTE: An unexcused lab will result in an F (0 points) grade for that lab. This grade will be averaged in with the student's other lab grades for the semester when calculating the final laboratory grade. It is this final course grade which will then be lowered by unexcused absences. Students having a valid excuse may reschedule the lab, if possible, only if they notify the laboratory coordinator BEFORE the scheduled lab.


I will not lecture directly from the book, which is well written. Use the book as an additional way to understand the material presented in class and lab. I will supplement the book extensively, especially in the areas of carbohydrate and lipid metabolism. You will receive many handouts in class which will be your responsibility to organize.


Attendance at lecture is expected. If you miss a class, it is your responsibility to find out what you missed and to be prepared for the next class. If you miss too many classes, your grade will be affected and/or you will be asked to drop the class.


We will use computers extensively in this class. This use will include the following applications.

Email: I will use the campus email system to send you announcements concerning the course throughout the semester. Sometimes I will email assignments to you that will be due at the next class period. Since people check their email frequently each day, I will assume that you have all read the messages in a timely fashion.

On-Line Study Guide - OLSG/Class Schedule: I have a web-based schedule and study guide (accessible through the course main web page) during the semester. It will review the main contents we discussed in class. It is meant as an ancillary way to understand the material and is not a substitute for class attendance.   Also some online multiple choice quizzes (ungraded) may  be available through Web CT.  More on this in class.


Your final grade can  be influenced by the extent and quality of your participation in the course.  If you participate in a significant way in the course, AND if your grade is close to a cutoff for a higher grade, I will boost your grade to that higher level (for example from a BC to a B).    Participation suggests interest and effort. It is not limited to just asking/answering questions in class.  It includes not just doing the absolute minimum of work. It includes showing some interest in the course.


To be successful in the class, you will need to study regularly and diligently.  Click the link below to find out some proven ways to study successfully that were compiled by Ronald Ragsdale, University of Utah..



I reserve the right to make changes to the syllabus in order to facilitate better learning in the class. Any changes will be announced in class.

 Last updated 05/10/2004