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1.3: Functional groups and organic nomenclature

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  • Functional groups in organic compounds

    Functional groups are structural units within organic compounds that are defined by specific bonding arrangements between specific atoms. The structure of capsaicin, the compound discussed in the beginning of this chapter, incorporates several functional groups, labeled in the figure below and explained throughout this section.

    A capsaicin molecule in bond-line molecule. It has an ether, aromatic/phenol, amide, and alkene functional group.

    As we progress in our study of organic chemistry, it will become extremely important to be able to quickly recognize the most common functional groups, because they are the key structural elements that define how organic molecules react. For now, we will only worry about drawing and recognizing each functional group, as depicted by Lewis and line structures. Much of the remainder of your study of organic chemistry will be taken up with learning about how the different functional groups behave in organic reactions.

    The 'default' in organic chemistry (essentially, the lack of any functional groups) is given the term alkane, characterized by single bonds between carbon and carbon, or between carbon and hydrogen. Methane, CH4, is the natural gas you may burn in your furnace. Octane, C8H18, is a component of gasoline.

    Alkanes

    Examples of alkanes. A methane molecule which is one carbon and four hydrogens. An octane molecule with eight carbons and 18 hydrogens written in structural and bond-line form. Molecules only contain single bonds.

    Alkenes (sometimes called olefins) have carbon-carbon double bonds, and alkynes have carbon-carbon triple bonds. Ethene, the simplest alkene example, is a gas that serves as a cellular signal in fruits to stimulate ripening. (If you want bananas to ripen quickly, put them in a paper bag along with an apple - the apple emits ethene gas, setting off the ripening process in the bananas). Ethyne, commonly called acetylene, is used as a fuel in welding blow torches.

    Alkenes and alkynes

    On left: Ethene molecule with two carbons and four hydrogens. The carbons are attached by double bonds so it's an alkene. On right: Ethyne molecule with two carbons and two hydrogens. Carbons are attached by a triple bond so it's an alkyne.

    In chapter 2, we will study the nature of the bonding on alkenes and alkynes, and learn that that the bonding in alkenes is trigonal planar in in alkynes is linear. Furthermore, many alkenes can take two geometric forms: cis or trans. The cis and trans forms of a given alkene are different molecules with different physical properties because, as we will learn in chapter 2, there is a very high energy barrier to rotation about a double bond. In the example below, the difference between cis and trans alkenes is readily apparent.

    Two alkene functional groups. Left is in cis so the hydrogens are on the same side of the double bond. Right is in trans so the hydrogens are on opposite sides of the double bond.

    We will have more to say about the subject of cis and trans alkenes in chapter 3, and we will learn much more about the reactivity of alkenes in chapter 14.

    Alkanes, alkenes, and alkynes are all classified as hydrocarbons, because they are composed solely of carbon and hydrogen atoms. Alkanes are said to be saturated hydrocarbons, because the carbons are bonded to the maximum possible number of hydrogens - in other words, they are saturated with hydrogen atoms. The double and triple-bonded carbons in alkenes and alkynes have fewer hydrogen atoms bonded to them - they are thus referred to as unsaturated hydrocarbons. As we will see in chapter 15, hydrogen can be added to double and triple bonds, in a type of reaction called 'hydrogenation'.

    The aromatic group is exemplified by benzene (which used to be a commonly used solvent on the organic lab, but which was shown to be carcinogenic), and naphthalene, a compound with a distinctive 'mothball' smell. Aromatic groups are planar (flat) ring structures, and are widespread in nature. We will learn more about the structure and reactions of aromatic groups in chapters 2 and 14.

    Aromatics

    Aromatic functional groups. On left: A benzene molecule which is a ring with 6 carbons, 6 hydrogens and 3 double bonds. On right: A Napthalene molecule which is two six-carbon rings attached with 5 double bonds.

    When the carbon of an alkane is bonded to one or more halogens, the group is referred to as a alkyl halide or haloalkane. Chloroform is a useful solvent in the laboratory, and was one of the earlier anesthetic drugs used in surgery. Chlorodifluoromethane was used as a refrigerant and in aerosol sprays until the late twentieth century, but its use was discontinued after it was found to have harmful effects on the ozone layer. Bromoethane is a simple alkyl halide often used in organic synthesis. Alkyl halides groups are quite rare in biomolecules.

    Haloalkanes

    Three examples of haloalkanes. Trichloromethane or chloroform: carbon bonded to three chlorine atoms and one hydrogen atom. Dichlorodifluoromethane or Freon-12: carbon bonded to two chlorine atoms and two fluorine atoms. Bromoethane: two carbons with one bromine atom and five hydrogen atoms.

    In the alcohol functional group, a carbon is single-bonded to an OH group (the OH group, by itself, is referred to as a hydroxyl). Except for methanol, all alcohols can be classified as primary, secondary, or tertiary. In a primary alcohol, the carbon bonded to the OH group is also bonded to only one other carbon. In a secondary alcohol and tertiary alcohol, the carbon is bonded to two or three other carbons, respectively. When the hydroxyl group is directly attached to an aromatic ring, the resulting group is called a phenol. The sulfur analog of an alcohol is called a thiol (from the Greek thio, for sulfur).

    Alcohols, phenols, and thiols

    Alcohols, phenols, and thiols. Methanol: O H or hydroxy group attached to methane. Primary alcohol: Hydroxy group attached to a carbon attached to one methyl group. Secondary alcohol: Hydroxy group group attached to a carbon attached to two methyl groups. Tertiary alcohol: Hydroxy group attached to a carbon attached to three methyl groups. Phenol: O H group attached to a benzene ring. Thiol: an S H group attached to a carbon attached to a methyl group.

    Note that the definition of a phenol states that the hydroxyl oxygen must be directly attached to one of the carbons of the aromatic ring. The compound below, therefore, is not a phenol - it is a primary alcohol.

    Primary alcohol attached to a benzene ring. Not a phenol because hydroxy group is not attached to a carbon in the benzene ring.

    The distinction is important, because as we will see later, there is a significant difference in the reactivity of alcohols and phenols.

    The deprotonated forms of alcohols, phenols, and thiols are called alkoxides, phenolates, and thiolates, respectively. A protonated alcohol is an oxonium ion.

    Deprotonated forms of functional groups. Alkoxide: alcohol whose hydroxy group is missing a hydrogen. Phenolate: phenol group whose hydroxy group is missing a hydrogen. Thiolate: Thiol with no hydrogen attached to the sulfur. All three have an overall negative charge. Oxonium ion: Protonated alcohol whose hyroxy group has an extra hydrogen. Overall positive charge.

    In an ether functional group, a central oxygen is bonded to two carbons. Below is the structure of diethyl ether, a common laboratory solvent and also one of the first compounds to be used as an anesthetic during operations. The sulfur analog of an ether is called a thioether or sulfide.

    Ethers and sulfides

    Ethers and sulfides. Ether: an oxygen atom attached to two carbon chains. Sulfide: a sulfur atom attached to two carbon chains.

    Amines are characterized by nitrogen atoms with single bonds to hydrogen and carbon. Just as there are primary, secondary, and tertiary alcohols, there are primary, secondary, and tertiary amines. Ammonia is a special case with no carbon atoms.

    One of the most important properties of amines is that they are basic, and are readily protonated to form ammonium cations. In the case where a nitrogen has four bonds to carbon (which is somewhat unusual in biomolecules), it is called a quaternary ammonium ion.

    Amines

    Amines. Ammonia: Nitrogen with a lone pair bonded to three hydrogens. Primary amine: Nitrogen with a lone pair bonded to one methyl group and two hydrogens. Secondary amine: Nitrogen with a lone pair bonded to two methyl groups and a hydrogen. Tertiary amine: Nitrogen with a lone pair bonded to three methyl groups. Ammonium ion: Nitrogen bonded to four hydrogens. Has a positive charge. Primary ammonium ion: Nitrogen bonded to three hydrogens and a methyl group. Positively charged. Quaternary ammonium ion: Nitrogen bonded to four methyl groups. Positively charged.

    Note

    Do not be confused by how the terms 'primary', 'secondary', and 'tertiary' are applied to alcohols versus amines - the definitions are different. In alcohols, what matters is how many other carbons the alcohol carbon is bonded to, while in amines, what matters is how many carbons the nitrogen is bonded to.

    On left: a tertiary alcohol. Carbon is bonded to three carbons. On right: a primary amine. Nitrogen is bonded to one carbon.

    Phosphate and its derivative functional groups are ubiquitous in biomolecules. Phosphate linked to a single organic group is called a phosphate ester; when it has two links to organic groups it is called a phosphate diester. A linkage between two phosphates creates a phosphate anhydride.

    Organic phosphates

    Organic phosphates. Phosphate: Phosphorus double bonded to one oxygen atom and single bonded to three oxygen atoms with negative charges. Phosphate anhydride: two phosphate groups linked together by an oxygen. A phosphate ester: A phosphate where one oxygen is bonded to a methyl group. Phosphate diester: A phosphate where two different oxygen atoms are bonded to a methyl group.

    Chapter 9 of this book is devoted to the structure and reactivity of the phosphate group.

    There are a number of functional groups that contain a carbon-oxygen double bond, which is commonly referred to as a carbonyl. Ketones and aldehydes are two closely related carbonyl-based functional groups that react in very similar ways. In a ketone, the carbon atom of a carbonyl is bonded to two other carbons. In an aldehyde, the carbonyl carbon is bonded on one side to a hydrogen, and on the other side to a carbon. The exception to this definition is formaldehyde, in which the carbonyl carbon has bonds to two hydrogens.

    A group with a carbon-nitrogen double bond is called an imine, or sometimes a Schiff base (in this book we will use the term 'imine'). The chemistry of aldehydes, ketones, and imines will be covered in chapter 10.

    Aldehydes, ketones, and imines

    Aldehydes, ketones and imines. Formaldehyde: carbon doubled bonded to an oxygen and single bonded to two hydrogens. Aldehyde: carbon doubled bonded to oxygen and single bonded to one methyl group and one hydrogen. Ketone: Carbon double bonded to oxygen and single bonded to two carbon chains. Imine: Carbon single bonded to two carbon chains and double bonded to a nitrogen. The nitrogen is either bonded to a carbon or hydrogen.

    When a carbonyl carbon is bonded on one side to a carbon (or hydrogen) and on the other side to an oxygen, nitrogen, or sulfur, the functional group is considered to be one of the ‘carboxylic acid derivatives’, a designation that describes a set of related functional groups. The eponymous member of this family is the carboxylic acid functional group, in which the carbonyl is bonded to a hydroxyl group. The conjugate base of a carboxylic acid is a carboxylate. Other derivatives are carboxylic esters (usually just called 'esters'), thioesters, amides, acyl phosphates, acid chlorides, and acid anhydrides. With the exception of acid chlorides and acid anhydrides, the carboxylic acid derivatives are very common in biological molecules and/or metabolic pathways, and their structure and reactivity will be discussed in detail in chapter 11.

    Carboxylic acid derivatives

    Carboxylic acid derivatives. Carboxylic acid: Carbon double bonded to oxygen and single bonded to one carbon and one hydroxy group. Carboxylate ion: Carbon double bonded to oxygen and single bonded to one carbon and one oxygen. The oxygen is not bonded to a hydrogen so it has a negative charge. Carboxylic ester: carbon double bonded to oxygen and single bonded to one carbon and one oxygen. The oxygen is bonded to another carbon. Thioester: Carbon double bonded to oxygen and single bonded to one carbon and one sulfur. The sulfur is bonded to another carbon. Amide: Carbon double bonded to oxygen and single bonded to one carbon and one nitrogen. The nitrogen is bonded to another carbon and a hydrogen. Acyl phosphate: carbon double bonded to oxygen and single bonded to one carbon and one oxygen. The oxygen is part of a phosphate group. Acid chloride: Carbon double bonded to oxygen and single bonded to one carbon and one chlorine. Acid anhydride: Carbon double bonded to one oxygen and single bonded to one carbon and one oxygen. The oxygen is bonded to another carbon with a double bonded oxygen.

    Finally, a nitrile group is characterized by a carbon triple-bonded to a nitrogen.

    Nitriles

    Acetonitrile: Carbon triple bonded to a nitrogen with a lone pair and single bonded to another carbon.

    A single compound often contains several functional groups, particularly in biological organic chemistry. The six-carbon sugar molecules glucose and fructose, for example, contain aldehyde and ketone groups, respectively, and both contain five alcohol groups (a compound with several alcohol groups is often referred to as a ‘polyol’).

    On left: A glucose molecule. Six carbon atoms. Five form alcohols and one forms an aldehyde. On right: A fructose molecule. Six carbon atoms. Five form alcohols and one forms a ketone.

    The hormone testosterone, the amino acid phenylalanine, and the glycolysis metabolite dihydroxyacetone phosphate all contain multiple functional groups, as labeled below.

    Top left: Testosterone molecule contains cycloalkane, secondary alcohol and ketone functional groups. Top right: phenylaniline molecule contains primary ammonium ion, carboxylate ion and aromatic ring functional groups. Bottom: dihydroxyacetone phosphate molecule contains primary alcohol, ketone and phosphate functional groups.

    While not in any way a complete list, this section has covered most of the important functional groups that we will encounter in biological organic chemistry. Table 9 in the tables section at the back of this book provides a summary of all of the groups listed in this section, plus a few more that will be introduced later in the text.

    Exercise 1.12

    Identify the functional groups (other than alkanes) in the following organic compounds. State whether alcohols and amines are primary, secondary, or tertiary.

    Solutions to exercises

    Exercise 1.13

    Draw one example each of compounds fitting the descriptions below, using line structures. Be sure to designate the location of all non-zero formal charges. All atoms should have complete octets (phosphorus may exceed the octet rule). There are many possible correct answers for these, so be sure to check your structures with your instructor or tutor.

    a) a compound with molecular formula C6H11NO that includes alkene, secondary amine, and primary alcohol functional groups

    b) an ion with molecular formula C3H5O6P 2- that includes aldehyde, secondary alcohol, and phosphate functional groups.

    c) A compound with molecular formula C6H9NO that has an amide functional group, and does not have an alkene group.

    Naming organic compounds

    A system has been devised by the International Union of Pure and Applied Chemistry (IUPAC, usually pronounced eye-you-pack) for naming organic compounds. While the IUPAC system is convenient for naming relatively small, simple organic compounds, it is not generally used in the naming of biomolecules, which tend to be quite large and complex. It is, however, a good idea (even for biologists) to become familiar with the basic structure of the IUPAC system, and be able to draw simple structures based on IUPAC names.

    Naming an organic compound usually begins with identify what is referred to as the 'parent chain', which is the longest straight chain of carbon atoms. We’ll start with the simplest straight chain alkane structures. CH4 is called methane, and C2H6 ethane. The table below continues with the names of longer straight-chain alkanes: be sure to commit these to memory, as they are the basis for the rest of the IUPAC nomenclature system (and are widely used in naming biomolecules as well).

    Names for straight-chain alkanes:

    1 carbon: methane

    2 carbons: ethane

    3 carbons: propane

    4 carbons: butane

    5 carbons: pentane

    6 carbons: hexane

    7 carbons: heptane

    8 carbons: octane

    9 carbons: nonane

    10 carbons: decane

    Substituents branching from the main parent chain are located by a carbon number, with the lowest possible numbers being used (for example, notice in the example below that the compound on the left is named 1-chlorobutane, not 4-chlorobutane). When the substituents are small alkyl groups, the terms methyl, ethyl, and propyl are used.

    From left to right: 1-chlorobutane; a chlorine atom bonded to the first carbon of a four-carbon chain. 2-methylpentane; a methyl group attached to the second carbon of a five-carbon chain. 4-ethylheptane; an ethyl group attached to the fourth carbon of a seven-carbon chain.

    Other common names for hydrocarbon substituent groups are isopropyl, tert-butyl and phenyl.

    Top left: 4-tert-butylheptane; tert-butyl group (carbon bonded to three methyl groups) attached to the fourth carbon of seven-carbon chain. Top right: 5-isopropylnonane: Isopropyl group (carbon bonded to two methyl groups) attached to the fifth carbon of a nine-carbon chain. Bottom are non-IUPAC examples. Bottom left: alanine, an amino acid with a carboxylate ion and primary ammonium ion functional group. Bottom right: phenylalanine, alanine with a phenyl group (a benzene ring) attached to the methyl group of the amino acid.

    Notice in the example below, an ‘ethyl group’ (in blue) is not treated as a substituent, rather it is included as part of the parent chain, and the methyl group is treated as a substituent. The IUPAC name for straight-chain hydrocarbons is always based on the longest possible parent chain, which in this case is four carbons, not three.

    Four carbon chain with a methyl group attached to the second carbon. Named 2-methylbutane, not 2-ethylpropane.

    Cyclic alkanes are called cyclopropane, cyclobutane, cyclopentane, cyclohexane, and so on:

    From left to right: cyclopropane, a three carbon ring. Cyclobutane, a four carbon ring. Cyclopentane, a five carbon ring. Cyclohexane, a six carbon ring.

    In the case of multiple substituents, the prefixes di, tri, and tetra are used.

    Left: 2,5-dimethylhexane; one methyl group on the 2nd carbon and one on the fifth carbon of a six-carbon chain. Right: 1,2,2-trifluoropentane; one fluorine on the first carbon and two on the second carbon of a five carbon chain.

    Functional groups have characteristic suffixes. Alcohols, for example, have ‘ol’ appended to the parent chain name, along with a number designating the location of the hydroxyl group. Ketones are designated by ‘one’.

    Left: 3-pentanol; a hydroxy group on the third carbon of a five-carbon chain. Right: 3-pentanone; a ketone group on the third carbon of a five-carbon chain.

    Alkenes are designated with an 'ene' ending, and when necessary the location and geometry of the double bond are indicated. Compounds with multiple double bonds are called dienes, trienes, etc.

    From left to right: Ethene; two methyl groups linked with a double bond. Cyclohexene: a six-carbon ring with one double bond. 1-pentene: a five-carbon chain with a double bond between the first and second carbon. Trans-2-pentene: a five-carbon chain with a double bond between the second and third carbon. In trans so the hydrogen are on opposite sides of the double bond. 1,3-butadiene; four-carbon chain with double bonds between the first and second carbon and third and fourth carbon.

    Some groups can only be present on a terminal carbon, and thus a locating number is not necessary: aldehydes end in ‘al’, carboxylic acids in ‘oic acid’, and carboxylates in ‘oate’.

    From left to right: Hexanal; a six carbon chain with an aldehyde at the sixth carbon. Hexanoic acid: a six carbon chain with a carboxylic acid on the sixth carbon. Hexanoate; a six carbon chain with a carboxylate ion on the sixth carbon.

    Ethers and sulfides are designated by naming the two groups on either side of the oxygen or sulfur.

    From left to right: diethyl ether; two ethyl groups attached to an oxygen. Ethyl methyl ether: An oxygen bonded to one methyl group and one ethyl group. Dimethyl sulfide: Sulfur bonded to two methyl groups.

    If an amide has an unsubstituted –NH2 group, the suffix is simply ‘amide’. In the case of a substituted amide, the group attached to the amide nitrogen is named first, along with the letter ‘N’ to clarify where this group is located. Note that the structures below are both based on a three-carbon (propan) parent chain.

    Left: Propanamide; three carbon chain with an amide on the first carbon. Right: N-methylpropanamide; Three carbon chain with a secondary amide on the first carbon. A methyl group attached to the nitrogen.

    For esters, the suffix is 'oate'. The group attached to the oxygen is named first.

    Left: ethyl propanoate; three carbon chain with an ester on the first carbon. Ethyl group attached to the oxygen in the ester group. Right: methyl butanoate; a four-carbon chain with an ester on the first carbon. Methyl group attached to the oxygen in the ester group.

    All of the examples we have seen so far have been simple in the sense that only one functional group was present on each molecule. There are of course many more rules in the IUPAC system, and as you can imagine, the IUPAC naming of larger molecules with multiple functional groups, ring structures, and substituents can get very unwieldy very quickly. The illicit drug cocaine, for example, has the IUPAC name 'methyl (1R,2R,3S,5S)-3-(benzoyloxy)-8-methyl-8-azabicyclo[3.2.1] octane-2-carboxylate' (this name includes designations for stereochemistry, which is a structural issue that we will not tackle until chapter 3).

    Cocaine molecule. IUPAC name: methyl (1 R, 2 R, 3 S, 5 S)-3-(benzoyloxy)-8-methyl-8-azabicyclooctane-2-carboxylate

    You can see why the IUPAC system is not used very much in biological organic chemistry - the molecules are just too big and complex. A further complication is that, even outside of a biological context, many simple organic molecules are known almost universally by their ‘common’, rather than IUPAC names. The compounds acetic acid, chloroform, and acetone are only a few examples.

    From left to right: Acetic acid; Two carbon chain with a carboxylic acid on the first carbon. Chloroform; Carbon attached to three chlorine atoms. Acetone; Carbon double bonded to oxygen and single bonded to two methyl groups.

    In biochemistry, nonsystematic names (like 'cocaine', 'capsaicin', 'pyruvate' or 'ascorbic acid') are usually used, and when systematic nomenclature is employed it is often specific to the class of molecule in question: different systems have evolved, for example, for fats and for carbohydrates. We will not focus very intensively in this text on IUPAC nomenclature or any other nomenclature system, but if you undertake a more advanced study in organic or biological chemistry you may be expected to learn one or more naming systems in some detail.

    Exercise 1.14

    Give IUPAC names for acetic acid, chloroform, and acetone.

    Exercise 1.15

    Draw line structures of the following compounds, based on what you have learned about the IUPAC nomenclature system:

    a) methylcyclohexane

    b) 5-methyl-1-hexanol

    c) 2-methyl-2-butene

    d) 5-chloropentanal

    e) 2,2-dimethylcyclohexanone

    f) 4-penteneoic acid

    g) N-ethyl-N-cyclopentylbutanamide

    Solutions to exercises

    Drawing abbreviated organic structures

    Often when drawing organic structures, chemists find it convenient to use the letter 'R' to designate part of a molecule outside of the region of interest. If we just want to refer in general to a functional group without drawing a specific molecule, for example, we can use 'R groups' to focus attention on the group of interest:

    From left to right: Primary alcohol; Carbon bonded to a hydroxy group and an R-group; Secondary alcohol; Carbon attached to two R-groups and one hydroxy group. Ketone; Carbon double bonded to oxygen and single bonded to two R-groups. Aldehyde; Carbon double bonded to oxygen and single bonded to one R-group and one hydrogen.

    The 'R' group is a convenient way to abbreviate the structures of large biological molecules, especially when we are interested in something that is occurring specifically at one location on the molecule. For example, in chapter 15 when we look at biochemical oxidation-reduction reactions involving the flavin molecule, we will abbreviate a large part of the flavin structure which does not change at all in the reactions of interest:

    On left: flavin molecule with the complex carbon chain attached to a nitrogen abbreviated as R. On right: the flavin molecule with the complex carbon chain attached to a nitrogen written out in red.

    As an alternative, we can use a 'break' symbol to indicate that we are looking at a small piece or section of a larger molecule. This is used commonly in the context of drawing groups on large polymers such as proteins or DNA.

    On left: an adenine base with a break and "DNA" written indicating a small portion of the large molecule. On right: a small section of protein with two breaks with "protein" written.

    Finally, 'R' groups can be used to concisely illustrate a series of related compounds, such as the family of penicillin-based antibiotics.

    Top left: penicillin framework with a red R attached to the top left. Top right: benzyl penicillin; same penicillin framework but with a benzyl group instead of an R. Bottom row shows different groups R could be. Benzyl penicillin; R = benzyl group. Ampicillin: R = benzyl group with an amino group. Amoxicillin: R = benzyl group with an amino group and hydroxy group.

    Using abbreviations appropriately is a very important skill to develop when studying organic chemistry in a biological context, because although many biomolecules are very large and complex (and take forever to draw!), usually we are focusing on just one small part of the molecule where a change is taking place.

    As a rule, you should never abbreviate any atom involved in a bond-breaking or bond-forming event that is being illustrated: only abbreviate that part of the molecule which is not involved in the reaction of interest.

    For example, carbon #2 in the reactant/product below most definitely is involved in bonding changes, and therefore should not be included in the 'R' group.

    Reaction of a six carbon chain with five hydroxy groups and one carbonyl group. Part of molecule involved in R abbreviation colored red. Carbon #2 is involved in reaction events  so is not included in abbreviation. Appropriate abbreviation: carbon 2 is not involved in abbreviation. Inappropriate abbreviation: carbon 2 in R abbreviation. Bonding transformation at carbon #2 is not shown in the inappropriate abbreviation example.

    If you are unsure whether to draw out part of a structure or abbreviate it, the safest thing to do is to draw it out.

    :

    a) If you intend to draw out the chemical details of a reaction in which the methyl ester functional group of cocaine (see earlier figure) was converted to a carboxylate plus methanol, what would be an appropriate abbreviation to use for the cocaine structure (assuming that you only wanted to discuss the chemistry specifically occurring at the ester group)?

    b) Below is the (somewhat complicated) reaction catalyzed by an enzyme known as 'Rubisco', by which plants 'fix' carbon dioxide. Carbon dioxide and the oxygen of water are colored red and blue respectively to help you see where those atoms are incorporated into the products. Propose an appropriate abbreviation for the starting compound (ribulose 1,5-bisphosphate), using two different 'R' groups, R1 and R2.

    Ribulose-1,5-biphopshate plus water and carbon dioxide react to form two phosphoglycerate molecules.

    Solutions to exercises

    Kahn Academy video tutorial on functional groups

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