Mastery of Organic Chemistry

For many pre-medical students, Organic Chemistry represents a monumental hurdle that must be crossed painfully. This need not be the case if you can change your “thinking” about organic Chemistry. I will be the first person to say with great conviction that I was not a “carbon-friendly” chemistry major but I had a passionate love of the subject matter of chemistry and organic chemistry was but one more course that added to my knowledge of the subject matter that I loved. I ended up performing very well in Organic chemistry even though it wasn’t my favorite course in chemistry.

Organic Chemistry is the chemistry of carbon-containing compounds. It is not the basis of Biochemistry, though both chemical disciplines share carbon as a component for many of the compounds that are studied within each discipline. O-Chem is centered around carbon and the special characteristics of carbon-containing compound families while B-Chem generally looks as structure, function and characteristic reactivity of macromolecules that contain carbon. This is why I could happily study B-Chem in graduate school and not be a particularly “carbon-friendly” chemist.

O-Chem starts out with the special atomic characteristics of carbon that are responsible for it’s bonding and reactivity. There are plenty of explanations of reaction mechanisms that must be mastered and absorbed as these basic reaction mechanisms will present themselves repeatedly as you move through the course. Rather than look at them as abstract and in isolation, learn them and be able to recognize them as a recurring theme as new carbon-containing families are presented. In short, you should be able to look at the way electrons behave in the various mechanistic schemes and apply that knowledge to new reactions as you encounter them.

O-Chem has a specific vocabulary that includes terms like nucleophile, electrophile, substitution, replacement, degradation etc. It is a very good idea to keep a list of the new terms as you encounter them and make sure that you understand them within the context of your o-chem study. One of my techniques was to take class notes on the left side of my spiral notebook. The right side was reserved for adding notes from my textbook and for working problems. I also kept a running tally of terms by leaving the last ten pages of my spiral notebook clear and using those for listing new terms and their definitions. I would circle in red, the new terms that I had defined in my notebook glossary as they were mentioned in my notes.

O-Chem requires daily study while you are taking the course. You need to review the previous lectures and notes, preview the next lecture and study the current lecture notes within the context of how they fit with the assigned reading and problems. Always look at an o-chem problem by making a note of the concept that the problem will be illustrating. Every o-chem problem or synthetic scheme has a concept behind it. Make a practice of noting these as you work the problems and studying the concepts as you work the problems.

O-chem also builds upon previous principles. For example, as you are introduced to the simple alkane family of compounds, the characteristics of this family should be compared and contrasted to the alkenes, alkynes, aromatics and other families as they are introduced. Make yourself get into the habit of reviewing summaries and characteristics of each old family as new families are introduced. This will greatly help you with synthetic schemes and problem-solving.

Before you go to lab, you should sit down with your lab book, write out a simple outline of each experiment with a listing of the steps that you will be doing. You should do any pre-lab exercises and review any topics in your text as they relate to your experiment. Many organic labs require that you answer post lab exercises, write up a report and submit these for grade. Look over your post experiment questions before you begin the lab so that you can be sure that you have obtained the proper observations that will enable you to answer these questions easily.

If you are required to keep a laboratory notebook, make sure that you include the following:

• The purpose of the experiment
• The experimental procedure
• Your data (tabular form is a good way to present this
• An explanation of your data that includes possible errors
• Any spectra (NMR, GC, Mass Spect that you obtained
• A summary of your observations

Don’t record data on little scraps of paper! Those little paper scraps can get lost and your grade will suffer. Get used to preparing for each experiment and recording your data directly into your laboratory notebook. I used to take photos of my experiments as I went along and pasted these directly into my laboratory notebook so that my instructor knew exactly what my reaction setup looked like as I progressed through an experiment. I also pasted my NMR spectra and GC results directly into my lab notebook with annotations and directions to my conclusions about their appearance.

As you encounter a new family of compounds, look at their reactions and usefulness in synthetic schemes. Again, you may want to keep a running list of characteristic reactions of each family as they are presented. With each lecture, link to the previous lecture and study a whole weeks worth of material and data on the weekend.

O-chem is a preview and practice course for many of the courses in medical school. The manner in which you approach your o-chem will be good practice for medical biochemistry, pharmacology, microbiology and pathology. These medical school courses build heavily on their introductory concepts just as o-chem builds upon the concepts that are presented at the beginning of the course. Like o-chem, these courses require daily mastery and will increase your vocabulary exponentially.

What you cannot do with o-chem or any other pre-med course is decide mentally that you cannot master this course or that it’s a “weed out” course in which the professor is out to “destroy your career”. No professor has the time or energy to care about working to destroy any particular student. While there are good professors and poor professors, the material to be mastered in o-chem or any other subject, does not change. Don’t let your feelings about a particular professor distract you from the business of learning.

Learning to tune out your fellow classmates i.e. those who whine, complain and otherwise attempt to distract you, is another good characteristic to develop. Some immature folks are going to brag that they “never study and get As” or that “the professor doesn’t give As” or my personal favorite, “you can’t possibly earn an A because you are not that smart”. Don’t buy into any of this stuff. Look at the course syllabus as soon as you get it. Look at the requirements for each grade and decide that you will meet them. At the first sign of trouble, get some help.

Check out the O-Chem help site at Frostburg State University. This site is under construction but can be an excellent adjunct to any o-chem coursework. Use the site as a tool not as a substitute for attending class and working your assigned problems. The URL for the site is: http://www.chemhelper.com/ This site requires registration but has a message board, discussion forums and plenty of resources for any o-chem student. In addition to this site, there are likely others too including possibly one at your school so utilize them as you need them.

Don’t underestimate the value of attending recitation sections and tutorial sessions. These sections/sessions are great opportunities to get your questions answered or reinforcement of your knowledge of the material as you learn it. Don’t skip these sessions and don’t skip class. Utilize the office hours of your professor and make an appointment for a consultation at the first sign of trouble. Don’t wait until a couple of days before the exam to seek help.

Keep up with your homework and studies. Again, I cannot overemphasize the importance of keeping up and not getting behind. Few people fail or do poorly in o-chem because they cannot understand the material. Most people struggle because they get behind and cannot catch up. Don’t get behind and don’t skip class. If possible, get ahead of the class and stay ahead. If something comes up that takes time away from your daily study, take care of it quickly and get back on track. If you are taking o-chem during the summer, skipping even one day of study can be a “deathblow” to your total course performance.

Finally, get a copy of the Biological Science Topics for the MCAT(o-chem starts on page 12 of this document) and make sure that you are systematically checking the topics off from both your General Biology and o-chem course as you go along. This document can be downloaded at : http://www.aamc.org/students/mcat/preparing/start.htm Go to the Tests Sections and download the topic lists (pdf documents) for Biological Sciences, Physical Sciences and Verbal Reasoning. These three documents can help to keep you on track as you move through all of your pre-med coursework.

Keeping up with your undergraduate coursework

If you have “taken the plunge” and decided that you want to pursue medical school, no doubt, you are taking or have taken some science courses. Most pre-medical students will start with General Biology or General Chemistry as General Chemistry is a prerequisite for Organic Chemistry. General Biology is one of the ultimate “survey” courses. A good General Biology course should contain a thorough introduction to the upper-division courses in the major while providing enough depth to cover the subject matter on the Medical College Admissions Test (MCAT). The bottom line is that General Biology can introduce hundreds of terms and concepts that are the basis for your major (if you decide on Biology).

Your General Biology course should have a very strong laboratory component. These labs should be designed to demonstrate and emphasize the terms and concepts that you studied in the lecture portion of your course. In general, these labs should occupy about 3 hours one time per week in order for you to make the most of your experiences here. My General Biology course was my only study of botany and I totally enjoyed the afternoon field trips that we were able to take. One of our instructors walked us around campus and explained just about every tree, shrub and flower in the springtime. It was a wonderful experience.

My method of mastering General Biology lecture was to scan the syllabus and figure out how much reading I needed to accomplish before each lecture. I would make a list of terms that needed to be remembered and put this list next to my notes. I would also take notes on one half of a notebook sheet leaving the other half of the paper for summary or notes from my text. By the time I had finished my text reading before a lecture, I would have a sheet of paper with a list of topics and terms that I would listen for during the lecture.

As I said before, I would take notes on the right half of a piece of 8 X 10 inch narrow-ruled looseleaf notebook paper. The left half would be for summary so that I could cover the right half and quiz myself on the concepts. I might also jot down a note or two from the text if there was something that was particularly helpful to the understanding of the lecture.

I would study my lecture as soon as I could. Usually this would be the afternoon after morning lecture. I would study a week’s worth of lecture material every weekend paying close attention to how one lecture was related to the next lecture. In terms of the laboratory, I never went to lab unprepared. I would preview the lab; have a list of the procedures that we would be doing and then look at the questions that needed to be answered for the write-up. Since every lab required a written report, I was able to do half of my report before I actually performed the lab experiments or dissection.

I tackled General Chemistry in much the same manner as General Biology except for solving problems. I always made sure that I completely understood the concept that each problem involved. I kept a running list of formulas that needed to be mastered or memorized. When I had a spare moment, I could pull out my index card of formulas and do some memorization. Again, I would keep at least one lecture ahead of the rest of my class.

An ability to use algebra as a tool is essential for General Chemistry. If your math is weak, definitely shore up your deficiencies before you tackle General Chemistry. There are several short books around with titles like “Math for General Science” or “Math For General Chemistry”. Check out these books and do some math practice if your skills are rusty. If you were required to take College Algebra, make sure that you complete it before you take General Chemistry. You can substitute some General educational requirements and take your Chemistry after you have completed your College Algebra course. General Chemistry can be quite “unforgiving” if you math is rusty or not up to level. The same is true of General Physics.

Your grades in your premedical courses are vitally important for entrance into medical school. Make sure that you thoroughly master this coursework (for the MCAT) and that you keep the highest GPA possible. Doing GPA “damage-control” is very difficult. If you get off to a slow start, figure out your problems and get your grades up as soon as possible. One low grade will not “tank” your application but repeated courses with multiple “Cs” will.

Keep up! Shore up! and Stay Up!

Going Premed…

(The above photo is me in front of a poster as a graduate student)

At some point in your life, you have made a conscious decision to pursue medicine as a career. For me, that decision came after spending a couple of years doing research with and attending grand rounds with a very high-output cardiologist. At the time, I was far older than many of the professors in most medical schools yet alone the students but I was intrigued by the science and craft of medicine. My cardiologist mentor encouraged me to apply to medical school (after a bachelors degree in chemistry&biology + graduate study in biochemistry) as I definitely had more than mastered the pre-med coursework and had a strong interest in the direct application of my then research (ischemia/reperfusion effects on cell-cell communication).

For most medical students, the decision to pursue medical school comes in high school (or early undergraduate). They sign up for the pre-med classes: one year of general biology with lab; one year of general chemistry with lab; one year of organic chemistry with lab and one year of general physics with lab. In addition, most universities require humanities in addition to science in order to receive a degree. Biology is by far, the most popular major for most pre-med students but definitely not a necessity. Any major (from music to American studies) is a good major for pre-med as long as you are interested in the subject matter and as long as you thoroughly master the pre-med sciences.

For most pre-medical students, freshman year is occupied with General Biology, General Chemistry, English, History, math and a foreign language. Sophomore year is occupied with Organic Chemistry, General Physics and other general education requirements. Sometime during the sophomore year, a major is declared and so forth. The important things to consider are getting your general education requirements out of the way and doing exceptionally well in your coursework.

I was very fortunate to have attended a very strong secondary school. When I entered university, I had already taken Differential and Integral Calculus. My math course freshman year was Differential Equations. I had decided to pursue a double major in Biology with Math as a minor since I was interested in the subject matter. My interests in Biology were along the lines of organismal biology (comparative anatomy, parasitology, histology, cell physiology, biochemistry) and my math interests were very strong. I ended up taking Differential Equations, Applied Differential Equations, Advanced Calculus and Higher Algebra in addition to seminar. The bottom line was that I was passionately interested in this coursework because I was interested in being an excellent scientist and researcher.

At the time, I had no interest in medical school but a huge interest in the subject matter of science. This interest coupled with my study skills, enabled me to thoroughly master the subject matter of my coursework. I cared less about my grades and more about making sure that I knew everything that had been presented in these classes. It was during my freshman and sophomore years that I began to hone my study methods that would later serve me well in both graduate and medical school.

In organic chemistry, my performance in this class was not about getting an “A” but about making sure that I learned the theory and craft of organic chemistry. I made sure that I knew as much about the chemistry of carbon-containing compounds as possible in addition to the basics that I needed to devise synthetic themes. Organic chemistry started with an overview of types of bonding that carbon would participate in along with the introduction of families of compounds. Each family had their own synthetic reactions which intertwined to give more and more synthetic possibilities. My favorite means of devising a synthetic scheme was to take the final compound and work backward to the starting material. I was especially adept at anything that contained an alcohol (-OH) group.

In terms of organic chemistry and other coursework, I did not learn in isolation. All of my coursework was interrelated and contained valuable tools for my future work as a researcher. I never considered any course in isolation. General Chemistry contained principles that were useful in Organic. My math courses were quite useful in Physics for understanding how these principles were studied and developed. For some reason, I always saw the big picture.

Later on, as I moved from pre-clinical to clinical medical student, I could see how my ability to apply the principals of Organic Chemistry to the development of synthetic themes was just practice for applying the principles of my pre-clinical sciences to clinical problems. If I am treating a patient with Peripheral Arterial Occlusive Disease, I have to understand the science of how atherosclerosis is a complex disease process that involves inflammation (chronic) and epidemiology (risk factors). Nothing in medicine is studied in isolation. The nature of the pathological changes that I see in the arterial wall directly affect the physiology of the vessel and the progression of the disease. Organic Chemistry was my launch pad in the sense that it was a course that honed my ability to apply the concepts that I was learning to problem solving from many angles.

When I obtained my second bachelors in Analytic Chemistry (I was passionately interested in this subject matter), I found the ultimate outlet for my interest in problem-solving. My coursework for this degree consisted of Quantitative Analysis, Qualitative Analysis, Advanced Inorganic Chemistry (graduate course), Advanced Analytical Chemistry (grad course in electro-chemistry and mass spectrometry), Advanced Organic Chemistry and Synthesis, Instrumentation, Advanced Spectroscopy (grad course) and one year of Physical Chemistry. In addition, I took an undergraduate research course, Atomic Physics, Nuclear Physics and Analytical Biochemistry. When I began my chemistry degree, I had already taken the freshman and sophomore coursework (transferred in from my first university). I was in heaven in the chemistry lab and in class with graduate students.

Armed with a second bachelor’s degree, I applied for graduate school in Biochemistry and was accepted with full departmental funding. I was assigned to a research lab and began the work that would lead to my graduate degree in Biochemistry and Molecular Biology. My mentor was a cardiologist whose research interests were ischemia/reperfusion and low magnesium states. He was the ultimate mentor in that he was a fierce collaborator and Renaissance man. He had two research labs that contained a powerful group of basic scientists with broad research interests. I was fortunate to become associated with this principle investigator who encouraged me to master and study everything that was of interest to me. These broad interests later led to my application to medical school.

Your premed coursework is not torture (shouldn’t be anyway) but an opportunity for you to lean and master some fascinating studies. It is also where you set your groundwork for medical school. Your pre-med coursework is where you hone your study skills that will enable you to master large amounts of material in a short period of time. Undergraduate pre-med coursework moves at a very slow pace compared to medical school and thus you have an opportunity to build a solid knowledge base that you can apply (especially on the MCAT).

The whole study of medicine involves development of a solid knowledge base and application of that knowledge base to the treatment of your patients. There are few shortcuts to mastery of the materials that you will need for your day to day practice. If you think of your mastery of your pre-med coursework as the training ground for mastery of the study skills that will enable you to obtain your knowledge base, you will be well on you way to becoming an excellent physician. Medicine is the ultimate problem-solving profession which, makes medicine ultimately quite interesting.