organic chemistry functional group pre-med bio MCAT

Functional Groups for Health and Bio Majors

Modern biology is inescapably dependent on organic chemistry.  From macro to micro, ecology to quantum biology, everything we know about life is built on an understanding of events happening at a molecular scale.  This is especially true for healthcare and medicine.  Drug design targets neurological and metabolic pathways with chemicals designed to patch malfunctioning chemical circuits.  Germ Theory permeates nearly every aspect of clinical culture.  Gene Therapy is coming into its own as a branch of medicine.  Every CNA, nurse, and doctor could perform their job better with a deeper understanding of chemistry.  So, it is especially tragic that most biology and pre-health majors are taught chemistry from the chemist’s perspective, rather than the biologist or a medic point of view.  Thus, what most students see in a chemistry class, doesn’t prepare them for the chemistry they will see in their biology classes, and in their professional capacity.

Most molecular biology and pre-health degrees require two semesters of organic chemistry.  The objective for the students is to develop systematic thinking, and to learn how to “read” biological molecules.  This is all well and good, except that most organic chemistry classes are designed based on the generalized “one size fits all” curriculum, or more tailored towards chemistry students.  Either way most of the material is still irrelevant to biology and health majors.

Another big problem that most students face is the general reputation of organic chemistry.  the course is often referred to as a “weeder” class or a “gatekeeper.”  And there’s a good reason for it.  The material comes fast and hard, and the people who can’t keep up often drop out or, in more severe cases, change their majors.  Biology and health majors are smart, and there is certainly nothing wrong with expecting them to keep up with a hard class.  However, the problem arises when there is so much focus on outcomes and so much of the material is irrelevant to our profession.  Within the vastness of the material covered in a typical organic chemistry course, only a fraction is vitally important to the health and bio majors, and none of it is covered in the depth that biology and health students require.  If you want to learn the kind of chemistry that will help you in your career, then you are going to have to put in the effort to sort the useful kernels of knowledge and be willing to dive into those topics deeper than your teacher will take you.

This unfortunate design leaves students in a lurch.  The combination of overwhelming amounts of material, and high emphasis on GPA, students cannot give themselves enough breathing room to take risks, or the time grow with the material to discover what is important to their future.  These factors often lead students to the awful strategy of trying to memorize each of the hundreds of equations presented in organic chemistry.  This is an overwhelming and stressful task, especially when most of the equations will never be relevant after they appear on the test.  Unless you are planning to take the MCAT exam, which does cover lots of reactions that you go over in your typical organic chemistry class, memorizing equations is the worst way to learn chemistry.  In my opinion, learning functional groups rather than equations will save you a lot of stress and leave you with usable skills after the class (memorization won’t).  It is a much better idea to develop a deep understanding of a handful of functional groups and their behaviors, rather than having a shallow understanding of a hundred equations.  Most of the time you can predict the outcomes of an unknown reaction just by understanding how functional groups behave.  Of course, there will be some specific and obscure reactions that don’t follow the general logic.  But who cares if you miss one reaction on the test and get the rest right?  There always going to be one of those questions.  It’s just unavoidable.

What’s more, the major part of biochemistry relies only on a very small number of functional groups.  So, by knowing which ones are important, students can recognize and focus on them when they show up in class.  By focusing on functional groups, biology and health students can cut down on the amount of chemistry they have to memorize, still achieve a good grade in the class, and be confident that they have learned something that will help them in the future.  And by the future I mean outside the chemistry classroom because it will help you “read” biochemical reactions you see!  Even when you have never seen those reactions before!

Organic Functional Groups That Are Relevant For Health And Bio Majors

Below is a list of some of the most common functional groups in biology and a brief description of their character.  This list is by no means comprehensive and is only intended as a starting point for biology and health students entering organic chemistry.

Hydroxyl Group
hydroxyl group

Hydroxyl groups consist of an oxygen and a hydrogen (-OH).  In organic chemistry they get a lot of attention because they can be converted to many other functional groups.  Esterification, oxidation, and combustion are important for sugars but many other reactions, especially with halides, are unlikely to come up again.  In biology the important role of hydroxyl groups mostly has to do with their ability to form hydrogen bonds.  The polarity of the functional group and the ability to form two simultaneous H-bonds increase the water solubility of any molecule that has a hydroxyl group attached to it.  This is why sugar is soluble in water despite being a large carbon-based molecule.

Carbonyl Group
carbonyl group

Carbonyl groups include aldehydes and ketones, which consist of an oxygen double bonded to a primary or secondary carbon.  Every sugar has a carbonyl group, and they are often targeted by enzymes as the site for making or breaking carbon-carbon bonds.  Carbonyl groups have a large partial positive charge on the carbon attached to the oxygen which makes it susceptible to nucleophilic attack.  This is a mechanism that is worth remembering after it is taught to you.

Carboxyl Group (Carboxylic Acid)
carboxyl group carboxylic acid

Carboxyl groups consist of a carbon double bonded to an oxygen, and an -OH group.  They are weak acids and donate protons off the -OH group.  Carboxylic acids are ubiquitous in biology and include amino acids, fatty acids, acetic acid, and many others.  Carboxyl groups are also susceptible to nucleophilic attack, especially when modified in an enzymatic pocket. This is what allows amino acids to chain together into proteins. Carboxylic acids are usually dissociated in physiological conditions and thus are negatively charged.

Amino Group
amino group

Amino groups consist of a nitrogen and one, two, or zero hydrogens.  Amino group is always connected to a carbon and have a total of 3 bonds.  Pretty much all biological nitrogen is contained in amino groups, so they occur commonly and are worth getting to know their behavior.  Amines function as bases by accepting protons which gives them a positive charge.  Amines are important for maintaining the structure of many macromolecules through electrostatic interactions and H-bonding.  Amines can be found in the backbone, and positively charged (when protonated, which is most of the time) R-groups of amino acids, as well as in neurotransmitters and the base pairs of nucleic acids.

Thiol Group
thiol group

Thiol groups consist of a sulfur and a hydrogen (-SH) and undergo similar reactions to hydroxyl groups.  The thiol group is nucleophilic and readily undergo redox reactions, giving it a variety of biological functions. The most common place students will see thiols is in the amino acid cysteine.  Two cysteines can form a sulfur-sulfur bonds which give additional 3D structure to the protein.  Not all organic chemistry classes will talk about sulfur bridges, and enzymatic functions of thiols will only be covered in biochemistry.  If you don’t have the good fortune to learn about thiols in class I think it is important enough to merit independent research.

Phosphate Group
phosphate group

Phosphate groups consist of a phosphorous atom attached to four oxygen, with a net negative charge ranging from -1 to -2 depending on what it is attached to, or -3 when in a free form.  Phosphate groups are hugely important to biological systems for many reasons:  They are vital structural units for nucleic acids, and biological membranes; they have a perfectly balanced reduction potential to make them excellent intermediaries in red-ox reactions; Their large size, and electronegativity can cause deformations in the 3D structure of proteins which make them the primary way to control enzymatic function, and cell signaling.  Unfortunately, it is unlikely that this functional group will even be mentioned in your organic chemistry class.  I highly recommend spending some time outside of class to learn a little about the mechanisms and reactions that this functional group can undergo.

Chemistry classes are important to the craft of biology and health.  Sound understand of chemistry can be the difference between a good biologist and an exceptional one.  Unfortunately, the classes are an ocean of irrelevant, or unhelpful facts.  For biology and health majors to succeed in chemistry the first skill they must learn is to sort out the information that is ok to forget after the test, and the information that will be useful in their carriers.  These functional groups are what I consider to be a good starting place for biology/health majors looking to learn useful chemistry but is by no means the end of the journey.  Pay attention to the overlap between your biology and chemistry classes and never be afraid to dig a little deeper into a subject after it has been presented.

In Summary

organic chemistry functional group pre-med bio MCAT functional groups

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