Organic Chemistry (of Biological Systems)

Part II: Sections V-VIII

(Emphasis is on Lipids, Carbonyls and Alcohols, Carbohydrates, and Nitrogen Compounds)


At the beginning of each of the 8 sections in the Organic Chemistry Review Books (2017 edition) is a page listing the "Key Goals" for that particular section. After reading the text in each section and completing the accompanying MCAT-style passages, we feel that you will have a better conceptual understanding of the material important to the organic chemistry found in the Chemical and Physical Foundations of Biological Systems and the Biological and Biochemical Foundations of Living Systems sections of the MCAT.

Section V: Lipids

Section Goals

  1. Know the typical classes of lipids and their chemical properties and biological usages. Passages may present a typical biological lipid, such as a phospholipid, and then ask about its synthesis pathway or its biological use. Questions could focus on the impact of pi-bonds and chain length on the biological applications.

  2. Know how natural fatty acids are made and what biological molecules incorporate them. Passages may present the syntheic pathway of a fatty chain and ask you about the pathway, the energetics, and the stereochemistry. Once the fatty acid is synthesized, it has a few potential destinations, which may or may not become questions.

  3. Know basic information about eicosanoids, steroids, and fat-soluble vitamins. Passages may present a biologically interesting lipid, such as a prostaglandin or steroid, and then ask you about its structure and its transport pathway through the body. Questions may center around the impact of stereochemistry and reactivity of the compound.

  4. Be able to recognize the isoprene subunits in naturally occuring terpenes. Passages may present some terpenes isolated from various plants or animals and tell you about their utility to the plant or animal from which they were extracted. Questions may ask about the skeletal makeup of a given terpene in terms of 5-carbon isoprene units or terpene properties.

  5. Be aware of biological hydrocarbons and their physical properties in vivo. Passages could present a biologically significant hydrocarbon and information on its pathway of activity. Questions may focus on what would result if the molecule were treated with a given chemical reagent or if its environment was altered in some way.

Passages and Solutions

Section V includes 14 MCAT-style passages with detailed solutions. Passage topics are centered around information important to carbonyls and alcohols.


Section VI: Carbonyls and Alcohols

Section Goals

  1. Recognize the carbonyl functional groups and types of compounds. Be able to recognize functional groups such as amides, anhydrides, acid halides, especially ketones and aldehydes. Know which compounds are most reactive towards substitution (which is based on the leaving group strength), and most electrophilic (which is based on the electron withdrawing or donating capacity of the functional group).

  2. Be able to identify infrared peaks for carbonyl compounds. Carbonyl compounds will have a peak in the infrared spectrum in the area of 1700 cm-1. This will most likely be useful when comparing two carbonyl compounds, or identifying an unknown carbonyl compound. Know roughly where esters, aldehydes, and ketones fall in the IR range.

  3. Be able to identify common name reactions involving carbonyl compounds. Recognize common name reactions from carbonyl chemistry. Included in this group should be the aldol reaction, Grignard reaction, Wittig reaction, and the Claisen reaction. The aldol and Claisen reactions have biological significance, because they play a role in select biochemical pathways such as glycolysis and beta oxidation.

  4. Be able to recognize the acidity of alpha carbons. The carbon alpha to the carbonyl can be deprotonated, if it has a proton bonded to it. The pKa of a standard ketone is near 17 2. Once deprotonated, an enolate is formed. The enolate has an equilibrium of its own with the enol structure. The conversion of a ketone into an enol is referred to as tautomerization.

  5. Be able to identify ketals, hemiketals, acetals and hemiacetals. Although current accepted nomenclature does not distinguish between ketals and acetals, you should be aware of the functional group. Acetals and ketals are best described as "double ethers." They play a major role in sugar chemistry and protecting groups in carbonyl synthesis.

  6. Understand the difference between thermodynamic and kinetic enolates. The thermodynamic enolate is formed under conditions of higher temperature where the pathway of greater activation energy may be chosen. The thermodynamic enolate is the more substituted and thus more stable intermediate which will lead to the more stable final product. The kinetic enolate is formed under conditions of lower temperature and greater steric hindrance where the pathway of lower activation energy must be chosen. The kinetic enolate is the less substituted and thus less stable intermediate which will lead to the less stable final product.

  7. Know the mechanism for basic carbonyl reactions. The mechanism for transesterification is present in biochemistry and organic chemistry, so it is important that you recognize the steps. Also recognize what catalyst is necessary to carry out the process.

  8. Recognize common oxidizing and reducing agents. In a nutshell, oxidation is defined as the gain of bonds to oxygen and/or the loss of bonds to hydrogen. Oxidizing agents include KMnO4 and K2Cr2O7. Reduction is defined as the loss of bonds to oxygen and/or the gain of bonds to hydrogen. Reducing agents include LiAlH4 and NaBH4.

  9. Know the acidity associated with phenols and alcohols. Phenols are acidic, because the phenoxide has resonance stabilization from the aromatic ring. You should know that phenols have pKa values in the 10 1 range.

Passages and Solutions

Section VI includes 14 MCAT-style passages with detailed solutions. Passage topics are centered around information important to carbonyls and alcohols.


Section VII: Carbohydrates

Section Goals

  1. Be able to recognize common monosaccharides. There are certain monosaccharides that recur in both organic chemistry and biochemistry that you should recognize and be able to draw. These include glucose, ribose, fructose, mannose, and galactose. It may be easiest to recall how the other sugars relate to glucose. For instance, mannose is the C-2 epimer of glucose.

  2. Be able to interconvert between Fischer and Haworth Projections. Some passages and questions will assume that you can translate between structures. For instance, the Fischer projection may be given in the passage, but the question may center around the structure in a Haworth projection. In translating structures, there are three separate points to observe. The chirality of the anomeric carbon is dependent on the direction of the attack. The chirality of the penultimate carbon (carbon five in aldohexoses) is constant according to the D or L status, and the backbone carbons will go from left in the Fischer projection to up in the Haworth projection.

  3. Be able to solve the chirality of an unknown sugar from reaction data. From organic chemistry class, you may recall solving the identity of a sugar by evaluating the reaction data presented. This makes for an ideal passage. You may recall evaluating whether a sugar would oxidize into an optically active or inactive diacid.

  4. Be able to recognize the chirality of cyclic and linear sugars. It is rather simple to solve for the chirality of selected carbons in both the Fischer and Haworth projections, after you have done this once. The rules are the same, so determine a quick way to identify the R and S configuration of each hydroxyl group of the sugar.

  5. Be able to identify common disaccharides. As with the monosaccharides, there are certain disaccharides that recur in organic chemistry and biochemistry. The disaccharides you must recognize include sucrose, lactose, and maltose. Know the monosaccharides that form the disaccharide and the glycosidic linkage.

  6. Be able to recognize the linkage associated with a given disaccharide. The linkage of a disaccharide is defined by the chirality of the anomeric carbon and the carbon of the sugar containing oxygen of the linkage. The disaccharide that presents the greatest difficulty is sucrose, which is composed of two anomeric carbons (one that is alpha-1 and the other that is beta-2).

  7. Be able to distinguish epimers and anomers. You must be able to identify the difference in chirality between diastereomers, which in the sugar questions are commonly presented as either alpha or beta in regards to an anomer and epimers.

  8. Know the common reactions involving sugars and sugar derivatives. This section contains a large number of sugar reactions, perhaps more than you need. Key reactions include the Kiliani-Fischer synthesis, Ruff degradation, and nitric acid oxidation. The passage usually provides plenty of reactions, so don't memorize them, understand them.

  9. Know the common polysaccharides and their biological significance. You must recognize the difference between glycogen and cellulose. The structural difference simply involves the linkage, but the difference in reactivity is significant.

Passages and Solutions

Section VII includes 14 MCAT-style passages with detailed solutions. Passage topics are centered around information important to carbohydrates.


Section VIII: Nitrogen Compounds

Section Goals

  1. Know the amino acids that affect the secondary structure of proteins. You must know the structures for cysteine and proline. You should know that cysteine forms disulfide bridges that result in cross-linking within proteins. Proline, because of its cyclic structure, will cause structural abnormalities likes bends, kinks, and turns. You should have an idea of what structural features are most affected.

  2. Be able to recognize and classify amino acids according to their side chain. Amino acids are classified as hydrophobic, hydrophilic, acidic, basic, polar, and aromatic. Each of the classifications gives you information about the reactivity of the amino acid side chain. With proteins, the side chain is most important because the amino and carboxyl terminals are involved in the peptide linkage.

  3. Be able to determine the isoelectric point for amino acids and proteins. The isoelectric pH is the pH at which the compound carries no net charge. For all amino acids except those with a basic side chain, it can be determined by averaging the values for pKa1 and pKa2. For proteins and the basic amino acids (histidine, lysine, and arginine), you must average the two pKa values that involve the zwitterion (neutral molecule). This is most easily found by first determining the charge of the protein (or amino acid) when it is fully protonated.

  4. Have an understanding of lab techniques such as gel electrophoresis. The basics of gel electrophoresis and isoelectric focusing involve placing the protein or amino acid between the charged plates of a capacitor, and allowing the compound to migrate through a viscous gel that offers resistance. The nature of the charge on the compound is determined by the migration features.

  5. Know the structural definitions and structural features. It is important to know what is meant by primary, secondary, tertiary, and quaternary structure, although some definitions overlap. You should recognize beta-pleated sheets and how they are arranged (parallel or anti-parallel). Have a basic idea of alpha-turns and alpha-helices.

  6. Be able to determine the sequence of a peptide from chemical information. Sequencing a protein involves treating the protein with denaturing reagents, and then sequentially determining the component amino acids or peptides that fragment from the protein when it is treated with a sequencing enzyme (restriction enzyme). You don't necessarily need to memorize the reagents, but you must be able to sequence a protein when provided with the reagent (or enzyme) and its function.

  7. Know the basicity of amines and the effects of alkyl substituents. Perhaps the most common weak base in organic chemistry is the amine. The pKa of a standard protonated alkyl amine is in the range of 8 to 10. This makes the amine a weak base, and the ammonium cation a weak acid.

  8. Know that amine compounds can exist in either the free base or acid salt form. There are several common amine compounds used for medicinal purposes as antibiotics, antipyretics, and analgesics. The MCAT likes to present organic molecules that have a definite biological application.

  9. Know how amines react to form amides. There are several instances in biochemistry where an amine will react with a carbonyl compound to form an amide bond. The most obvious case is the formation of proteins from amino acids. For in vitro reactions, you must be aware of the solvent, because of the acid/base properties of the amines.

Passages and Solutions

Section VIII includes 14 MCAT-style passages with detailed solutions. Passage topics are centered around information important to amino acids and amines.

SAMPLE PASSAGE




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