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Study Guide to Organic Compounds_6ec7aa2419bd18706ac0a2b6d5c52753 Flipbook PDF
Study Guide to Organic Compounds_6ec7aa2419bd18706ac0a2b6d5c52753
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CHEM 18: GENERAL CHEMISTRY LABORATORY MODULE 3. INTRODUCTION TO ORGANIC CHEMISTRY Introduction
“You will die but [the] carbon will not; its career does not end with you. It will return to the soil, and there a plant may take it up again in time, sending it once more on a cycle of plant and animal life.” – Jacob Bronowski, mathematician and historian “…There would come a day when the sun exploded like a red balloon, and everyone on earth would be reduced in less than a camera flash to carbon. Didn't Genesis say as much? For dust thou art, and unto dust shalt thou return. This was far more than dull old theology: It was precise scientific observation! Carbon was the Great Leveler--the Grim Reaper…” – Alan Bradley, The Weed That Stings the Hangman’s Bag
These remarks have imposed upon us the superiority of carbon, dubbed as the “King of the Elements” due to its ability to form extensive bonds with many atoms, its importance in life applications, and its property to exist in various forms. Due to this, a field of chemistry is solely dedicated to the study of the structure, properties, and reactions of compounds containing carbon, termed as organic chemistry. There are nearly ten million known organic compounds, many of them being essential for biological processes and for perpetuation of life. Since carbon is the “star” of organic compounds, we should have a great knowledge of its properties and its chemical behavior. Carbon, aside from being bonded to hydrogen, when bonded to itself and to other atoms or group of atoms forms a characteristic feature of organic compounds called functional groups. These groups render such carbon compounds their primary structural composition, their physical and chemical properties, and their behavior in chemical reactions. Objectives At the end of this module, the students should be able to: 1. Explain the chemical bonding and hybridization in carbon using the Valence Bond Theory; and 2. classify the organic compounds and biomolecules based on their structure and functional groups.
3.1 Versatility of Carbon In 1807, Jöns Jacob Berzelius gave names to two kinds of compounds namely Organic and Inorganic. As stated, • Organic – compounds derived from living organisms (believed to contain immeasurable vital force • Inorganic – compounds derived from minerals (believed to be lacking of those vital force)
In 1828, Friedrich Wöhler produced urea – a compound excreted by mammals – by heating ammonium cyanate, an inorganic mineral
Organic compounds are compounds that contain carbon atom covalently linked to other elements. The following are notable characteristics of C atom: • Carbon is tetravalent • Carbon can form bonds with C and other atoms • Carbon can form single ang multiple bonds • Carbon is in the center of 2nd row elements in the periodic table • Carbon neither readily gives up nor readily accepts electrons – it shares electrons Learning Resource: Classes of Organic Compounds (URL Link: https://courses.lumenlearning.com/boundless-chemistry/chapter/classes-oforganic-compounds/) Annotation: In the latter part of this resource, the properties of carbon will be explained that allow it to serve as the building block for biomolecules. 3.2 Hybridization of Carbon Atom Chemical bonding can be explained by valence bond theory (VBT), along with molecular orbital theory (MOT), that chemical bonds are formed via physical overlap of half-filled valence orbitals between two atoms. This physical overlap arises to sigma (σ) and pi (π) bonds. Recall: • σ bond occurs when atomic orbitals overlap between the nuclei of two atoms known as internuclear axis • π bonds occur when two unhybridized p-orbitals located above and below the nuclei of the atoms overlap.
Figure 1. Illustration of sigma (σ) and pi (π) bonds respectively. Learning Resource: Valence Bond Theory (URL Link: https://courses.lumenlearning.com/boundless-chemistry/chapter/valencebond-theory/)
Annotation: This Learning Resource explains the process of hybridization as it applies to the formation of sp3 hybridized atoms, recognize the role of sp2 atoms in sigma and pi bonding, and describe the bonding geometry of an sp hybridized atom. Hybridization in carbon atom can be reinforced using this resource. Practice Questions (10 minutes) Access Practice Problem and fill your answers in the boxes provided. Click “Check Answers” to verify if you got the correct answers. You may try to answer the practice problem twice to view the correct answer by clicking “View Answers”.
3.3. Classification of Organic Compounds Based on Functional Group Organic compounds can be classified according to two categories – arrangement of carbon chain and presence of functional groups. This course will focus more on the classification based on the functional group(s) present on organic compounds. 3.3.1. Functional groups Functional groups are atoms or small group of atoms with a common and specific arrangement, exhibiting characteristic chemical behaviors. They allow for the grouping of organic compounds into different classes, not only based on the structural features but also on the different chemical reactions they undergo. Moreover, functional groups are the basis of the naming of organic compounds. Organic molecules primarily contain C—C and C—H σ bonds, which are strong, nonpolar, and not readily broken. Well then, what features exactly make the functional groups reactive? These are the presence of heteroatoms and pi (π) bonds. •
•
Heteroatoms – atoms other than carbon and hydrogen. For organic compounds, the common heteroatoms include oxygen, nitrogen, sulfur, phosphorus, and halogens. They have lone pairs and create electron-deficient sites on carbon. pi (π) bonds – these create the double and triple bonds in organic compounds. The most common π bonds occur in C-C and C-O double bonds. These types of bonds are easily broken in chemical reactions.
The C-C and C-H σ bonds in organic molecules are the composition of the carbon backbone or skeleton to which the functional groups are bonded. The carbon and hydrogen portion or the
carbon skeleton of these compounds is often abbreviated by a capital letter R, which usually refers to the Rest of the molecule.
This downloadable infographic (https://edu.rsc.org/download?ac=14658) shows the most common functional groups that you will surely encounter in your study of the diverse collection of organic compounds. In this illustration, you can see that a certain functional group can have unique elements in its structure, have single or multiple bonds, or have different arrangement of its atoms. These variances in the features of functional groups differentiate and expand their physical and chemical properties. We will briefly discuss each of these functional groups later in this module. To facilitate the discussion on functional groups, we will organize them according to whether they only contain carbon and hydrogen (hydrocarbons) or have atoms or elements other than these two (organic compounds with heteroatoms). This classification of organic compounds according to functional groups can be seen in the following diagram. Take note that in our discussion, what is of utmost importance is that you learn how to identify functional groups in various organic compounds and determine to what class they belong.
Key Questions: What are functional groups? How are they integral to the overall properties of organic compounds?
3.3.2. Hydrocarbons Hydrocarbons, from the name itself, are organic compounds with functional groups containing only the elements carbon and hydrogen. They may be aliphatic (alkanes, alkenes, alkynes), alicyclic (cyclic analogs of aliphatic), or aromatic, depending on the functional group present. Aliphatic hydrocarbons are those that are present in open-chain forms, meaning that only linear and branched chains of carbon atoms are present. Alicyclic hydrocarbons are those compounds whose carbon atoms are present in a cyclic ring form. Aromatic hydrocarbons are those that contain one or more aromatic or benzene rings in their structures. Hydrocarbons can also be distinguished based on the presence of single or multiple bonds. Saturated hydrocarbons are those that only contain single bonds since they already contain the maximum number of hydrogen atoms that they can possess. On the other hand, unsaturated hydrocarbons are those that may have double or triple bonds since they possess fewer number of hydrogens than the maximum, and they can react with hydrogen under the proper conditions.
3.3.2.1. Alkanes Alkanes are the first and simplest class of organic compounds under hydrocarbons. These saturated organic compounds have no functional group because they only contain carboncarbon single (or σ) bonds. They are distinguished through their names by having -ane as suffix. All carbon atoms in an alkane are surrounded by four atoms or groups of atoms, making them sp3 hybridized and tetrahedral, and all bond angles are near 109.5°. Alkanes are sufficiently present in fossil fuels. The simplest alkane with only four carbons, methane (CH4), is the most abundant alkane present in natural gas and petroleum (about 70-90%). The bond length of the C—H bonds in CH4 is 109 pm. The structural formula and 3D ball-and-stick model of methane is shown as follows.
Methane, along with alkanes with two to four carbons, exists as gas, those with five to 35 carbons exist as liquids, while those with greater than 35 carbons can be found as viscous liquids. The structures and names of the two-, three-, and four-carbon alkanes are shown as follows.
Key Questions: a) What are the structural features of alkanes? Do they have a functional group? b) What is the hybridization of the carbons in alkanes?
3.3.2.2. Alkenes Alkenes are unsaturated hydrocarbons containing at least one carbon-carbon double bond in their structure. They are named with a suffix of -ene. The functional group then, for alkenes, is the double bond connecting two carbon atoms.
In this figure, the R and R’ are the carbon skeletons or longer chains of hydrocarbons or other groups of atoms containing other functional groups. The location of the double bond determines whether the alkene is terminal or internal. A terminal alkene has the double bond on either end of the organic compound while an internal alkene has the double bond within any part of the molecule but not at the opposite ends. This difference is illustrated in the examples below.
The compound with the terminal alkene is 1-butene while that with the internal alkene is 2butene. There are special names for alkenes with multiple double bonds. An alkene with two, three, and four π bonds is referred to as diene, triene, and tetraene, respectively.
The double bond of an alkene consists of one σ bond and one π bond. Each carbon is sp2 hybridized and trigonal planar, and all bond angles are approximately 120°. Shown below is the structure and hybridization of the simplest alkene, ethylene or ethene.
Ethylene is used as the starting material for the synthesis of many industrial compounds. It also occurs as a natural plant hormone as it is produced by fruits such as tomatoes and bananas and is involved in the ripening process of these fruits.
Key Questions: a) What is the functional group present in alkenes? How are alkenes structurally different from alkanes? b) Can an alkene have more than one of its functional group in its structure? 3.3.2.3. Alkynes Another unsaturated hydrocarbon are the alkynes, which have one or more triple bonds in their chemical structure. Organic compounds under the class of alkynes have names with a suffix of -yne. The functional group then, for alkynes, is the triple bond connecting two carbon atoms.
Similar to alkenes, alkynes can be categorized as terminal or internal depending on the location of the triple bond. A terminal alkyne has the triple bond at the end of the carbon chain, so that a hydrogen atom is directly bonded to a carbon atom of the triple bond. An internal alkyne has a carbon atom bonded to each carbon atom of the triple bond. Between the two compounds shown as follows, 1-hexyne is a terminal alkyne while 3-heptyne is an internal alkyne.
An alkyne has the general molecular formula CnH2n-2, giving it four fewer hydrogens than the maximum number possible. The presence of a triple bond in a compound causes removal of two hydrogens from an alkene, making alkynes relatively more unsaturated than alkenes. Each carbon of a triple bond is sp hybridized and linear, and all bond angles are 180°.
Acetylene (C2H2), the simplest alkyne, is an explosive gas and an important industrial raw material in the production of solvents and alkenes. Like ethylene, acetylene is used to ripen fruits and mature trees or flowers. The triple bond of an alkyne consists of one σ bond and two π bonds. The σ bond in alkynes is formed from the end-on overlap of two sp hybrid orbitals while each π bond is formed by side-by-side overlap of two 2p orbitals. The hybridization in alkynes is visualized as follows.
Key Questions: What is the functional group present in alkynes? How are alkynes structurally different from alkanes and alkenes?
3.3.2.4. Aromatic hydrocarbons Aromatic hydrocarbons, or simply aromatics, are a class of organic compounds which contain the aromatic or benzene ring. Benzene (C6H6) is the simplest aromatic hydrocarbon, consisting of a six-membered ring with alternating single and double bonds, which can be represented through a Kekulé structure. It has three additional degrees of unsaturation due to the presence of three double bonds. In most books and other references, benzene is mostly written in its bond line representation. The benzene ring (or aromatic ring) or phenyl group is the functional group for aromatic hydrocarbons.
In a benzene ring, the pi electrons are delocalized over the six carbon atoms due to the overlapping of the six adjacent p orbitals. We can say that the π electrons of benzene are roaming all throughout the six carbon atoms. Because of this, all of the carbon-carbon bonds in benzene are one and one-half bonds, have similar bond lengths with values in between that of a single bond and a double bond, and have bond angles of 120°. Due to this delocalization
of electrons, the structure of benzene is usually represented as a resonance hybrid shown below.
Key Question: What is the functional group present in aromatic hydrocarbons? How are they structurally different from alkanes, alkenes, and alkynes?
3.3.2.5. Alicyclic Hydrocarbons Alicyclic hydrocarbons, also called cyclic analogs, are simply alkanes, alkenes, and alkynes which themselves are structurally occurring as ring compounds or are containing cyclic systems. In general, the naming of alicyclic hydrocarbons involves the addition of cyclo- before the name of the carbon chain. Alicyclic alkanes or cycloalkanes, just like aliphatic ones, do not have any functional groups and are only composed of single bonds. The common monocyclic (only one cyclic ring) cycloalkanes include cyclopropane, cyclobutane, cyclopentane, and cyclohexane.
Alicyclic alkenes or cycloalkenes have the alkene or the C—C double bond as functional group. They may also have one or more double bonds in their cyclic structure just like aliphatic alkenes. Like cycloalkanes, there are also existing bicyclic cycloalkenes. Cycloalkenes are perhaps among the most important organic substances for biological and industrial purposes
because they are used in the production of molecules essential to a broad spectrum of applications. Alicyclic alkynes or cycloalkynes have the alkyne or the C-C triple bond as functional group. Similar to aliphatic alkynes, they may have more than one triple bonds in their cyclic structure. Cyclooctyne and cyclononyne are the only cycloalkynes that can be isolated, although they are very reactive. Cycloalkynes of lower number of carbons only exist as transient reaction intermediates or as ligands coordinating to a metal center.
Key Questions: How are cyclic analogs of alkanes, alkenes, and alkynes different from the acyclic hydrocarbons? Do they contain the same functional group?
3.3.2.6. Summary of hydrocarbons The following table shows the four types of hydrocarbons and their corresponding general structure and functional group. Table 3.1. Hydrocarbons. Class of Compound Alkane
General Structure
Functional group -
Alkene
double bond
Alkyne
triple bond
Aromatic compound
phenyl group/aromatic ring
SAQ-3. Given the following compounds, encircle the functional group and determine what class of hydrocarbons they belong to. STRUCTURE
CLASS OF HYDROCARBON
STRUCTURE
CLASS OF HYDROCARBON
Learning Resource: Generate Molecules Using MolView URL Link: (https://molview.org/) Annotation: Using MolView, you can generate structures of thousands of organic and inorganic compounds simply by searching for the name of your molecule of interest. In this activity, you will search five organic compounds, draw their structures as you see them on the website, encircle the functional groups present, and identify what class of hydrocarbons they belong to. Follow the steps below to successfully accomplish this online activity.
1. Go to the website of MolView (https://molview.org/). Upon seeing what is displayed in the photo below, click on Close.
2. Afterwards, click on the Toggle skeletal formula icon (
), encircled blue below.
3. Then, click on the search bar (encircled green above). Search for the following compounds, draw their structures, encircle the functional groups, then determine the classes of compounds to which the functional groups belong. a) octane b) ectocarpene c) epi-aristolochene d) 1-phenyl-1-propyne e) 1-(pent-3-yn-1-yl)cyclopent-1-ene
3.2.3. Organic Compounds with Heteroatoms Many functional groups in organic chemistry contain heteroatoms or atoms other than carbon and hydrogen. Several atoms can be found bonded to carbons in organic compounds; however, the most common heteroatoms are halogens (F, Cl, Br, I, generally represented as X), oxygen (O), nitrogen (N), sulfur (S), and phosphorus (P). Organic compounds containing heteroatoms undergo many chemical reactions due to their pronounced reactivity as they provide electron-deficient sites in carbon atoms. Functional groups containing these heteroatoms will be briefly discussed in this module.
3.2.3.1. Halogen-containing compounds: Organic Halides Organic halides are organic compounds containing halogens (fluorine, chlorine, bromine, iodine) and are classified according to what carbon-containing group the halogen is bonded to. The simplest organic halides are alkyl halides, wherein the halogen (X) replaces one or more hydrogens in an alkane. Hence, this halogen is bonded to a saturated, sp3hybridized carbon atom. Alkyl halides are also referred to as haloalkanes. Depending on the halogen present, the alkyl halides have general names or classifications. They can be alkyl chlorides (R—Cl), alkyl bromides (R—Br), alkyl iodides (R—I), or alkyl fluorides (R—F). The functional group in alkyl halides is called the halo group (—X).
Alkyl halides have diverse uses and applications. Simplest forms of these compounds, such as chloroform or trichloromethane (CHCl3) and carbon tetrachloride or tetrachloromethane (CCl4) can be utilized as solvents since they are not flammable and they can dissolve a wide variety of organic compounds. The structural formulas and 3D models of these alkyl halides are given as follows. The gray balls represent carbon, the white ball represents hydrogen, while the green balls represent chlorine.
When a halide is directly attached to ana romantic ring, it is referred to as aryl halide. Alkyl halides may also contain unsaturations or double or triple bonds in their structures.
Some alkyl halides also exist as polymers, with uses in the industries of production of insulators, plastic wraps, and coatings. The yellow balls in the 3D model below represent fluorine.
Key Questions: a) What is the functional group present in alkyl halides? b) How are alkyl and aryl halides different from each other? SAQ 3. Encircle the functional group/s present in each compound and identify to what class or classes of organic compound they belong.
a)
b)
3.2.3.2. Oxygen-containing compounds: Alcohols and Phenols Alcohols are a diverse class of organic compounds which have the hydroxyl or hydroxy (-OH) group attached to an sp3-hybridized carbon atom as functional group.
Along with phenols and ethers, alcohols are considered as organic derivatives of water since they can be structurally viewed by replacing one of the hydrogens of water with an alkyl group (R).
The oxygen atom in alcohols are surrounded by two atoms and two nonbonded electron pairs, making the O atom tetrahedral and sp3 hybridized. Because only two of the four groups around O are atoms, the electron pair geometry of alcohols is bent, same as that of water. The bond angle around the O atom in an alcohol has an approximately tetrahedral value (~109.5°). Shown as an example below is the Lewis structure and ball-and-stick representation of the simplest alcohol, methanol (CH3).
Alcohols with two -OH groups are called diols or glycols, those with three -OH groups are termed triols, and so forth. Hydroxyl groups can also be attached to alicyclic ring systems.
Enols have the -OH group linked to one of the carbons in a C-C double bond while phenols have an -OH group attached to a benzene ring.
Phenols are considered as a separate class of compounds from alcohols, but both have the hydroxy group as functional group. Phenols have the same geometry as alcohols in terms of bond angles and hybridization of the O atom. Phenols occur widely in nature and serve as intermediates in the industrial synthesis of pharmaceutical products, adhesives, antiseptics, food preservatives, polymers, and resins. Moreover, phenols are also present in a number of biological systems and natural products such as neurotransmitters, flavoring agents, and vitamins to name a few.
The compound 4-hexylresorcinol is an active ingredient in antiseptic preparations for use on the skin. Dopamine is a biological neurotransmitter that plays a role in locomotion and emotional responses of humans.
Biological alcohols provide the many flavor and scent of some plants. Menthol, found in oil of peppermint, is an alcohol used both for flavoring and for medicinal purposes. Borneol, which can be isolated from artemisia, is a component of many essential oils.
Key Questions: a) What is the functional group present in alcohols and phenols? How do these two classes of organic compounds differ from each other? b) Why are alcohols considered organic derivatives of water? c) What are some biological sources and uses of alcohols and phenols? 3.2.3.3. Oxygen-containing compounds: Ethers and Epoxides Ethers are organic compounds wherein the oxygen atom is bonded to two organic groups (R groups) that can be alkyl, aryl, or vinylic. Like alcohols, they are also organic derivatives of water since they result when the two hydrogens of water are replaced by the aforementioned organic groups. The functional group of an ether is the characteristic —C—O—C— bond or the alkoxy group. When the ether has similar R-groups attached to the oxygen atom, it is said to be symmetrical. Conversely, if two different organic groups are bonded to the oxygen atom, the ether is unsymmetrical. An example of a symmetrical ether is diethyl ether while that of an unsymmetrical ether is ethyl methyl ether.
Ethers, like alcohols and water, have a tetrahedral molecular geometry and a bent electron pair geometry. The R—O—R bonds have an approximately tetrahedral bond angle (~109.5°) and the O atom is sp3 hybridized. In the case of the dimethyl ether, the simplest ether, the bond angle is 112°. Dimethyl ether is an example of an ether wherein the oxygen atom is in an open chain. The O atom may also be part of a ring, just like in tetrahydrofuran (THF), a cyclic ether. In the ball-and-stick models, the gray balls represent carbon, the white balls represent hydrogen, and the red balls represent oxygen.
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Ethers, with their sweet smell and high volatility when exposed to air, are used as an antiseptic to prevent infection when an injection is administered to the body. Diethyl ether is used as an anesthetic in hospitals to induce sleep or unconsciousness to patients who will undergo surgeries. Ethers are also popular as organic solvents, again due to their volatility. Some examples of ethers used as solvents include diethyl ether, THF, dimethoxyethane (DME), and dioxane. Some ethers are also naturally occurring as components of essential oils. One example is anisole, an aryl ether ether with one or two R groups as phenyl group/s), which is a major constituent of the essential oil of anise seed.
A class of organic compound having an almost similar structural feature as cyclic ethers are epoxides or oxiranes, except that the oxygen atom is part of a three-membered ring. Although considered as an ether, epoxides are singled out because they behave differently from open-chain and cyclic ethers due to the angle strain brought about by its ring. The alkoxy group is also the functional group in epoxides. Deviating from the bond angle in ethers of approximately being similar to that of the tetrahedral geometry, the C—O—C bond angle in epoxides have a bond angle of 60°. Due to this angle strain, epoxides are relatively more reactive than ethers. Interestingly, the ring in epoxides can be opened or cleaved by acids and bases.
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Contrary to the abundance of alcohols and ethers, epoxides occur less widely in natural products. There are pharmaceutical drugs, eplerenone and tiotropium bromide, which contain oxiranes in their structures. Eplerenone is a prescription drug to patients who already had a heart attack in order to reduce cardiovascular risk, while tiotropium bromide is an anticholinergic drug used to prevent bronchospasm or narrowing of the airways in lungs in people with bronchitis and emphysema.
Key Questions: a) What is the functional group present in ethers and epoxides? How do these two classes of organic compounds differ from each other? b) What are some important uses of ethers?
c) Why are epoxides considered as a different class of organic compound from ethers even though they have the same functional group? d) How do ethers and epoxides compare in terms of occurrence in nature? SAQ-3. Encircle the functional group/s present in each organic compound and identify to what class or classes of organic compound they belong.
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3)
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3.2.3.4. Oxygen-containing compounds: Aldehydes and Ketones The next two classes of compounds contain a common functional group in their structure. This is the C—O double bond or the carbonyl group. This group is highly reactive because it is a polar bond, making the carbonyl carbon (carbon directly attached to oxygen in a carbonyl group) electron-deficient and the oxygen electron-rich due to the differences in electronegativity between these two atoms. The electrostatic potential map below shows this polarization in the carbonyl group. The carbonyl group also contain a π bond, which is more easily broken than a C—O σ bond.
Organic compounds with the carbonyl group differ in their classification depending on the atom or group of atoms attached to the carbonyl carbon. Aldehydes have a carbonyl group wherein one of the bonded atoms to the carbonyl carbon is hydrogen, with the exception of formaldehyde, which bears two hydrogen atoms. Ketones, on the other hand, have a carbonyl group wherein the carbonyl carbon is directly bonded to two alkyl or aryl groups. The general formulas for these two classes of carbonyl compounds are given as follows.
Aldehydes and ketones both have a trigonal arrangement of groups around the carbonyl carbon atom, with bond angles of ~120. Shown as an example is the simplest aldehyde, formaldehyde, which has a bond angle of 121° around the H—C—O bond and of 118° around the H—C—H bond. The C atom in the carbonyl groups of aldehydes and ketones is sp2 hybridized. The π bond in their carbonyl groups is formed by the overlap of two p orbitals and extends above and below the plane.
Aldehydes and ketones are among the most widely occurring organic compounds. They are required by many living organisms to support the progress of many biological functions and are also found in many natural sources. For example, the aldehyde pyridoxal phosphate acts as a coenzyme for some metabolic reactions and it is also the active form of vitamin B6. The ketone R-muscone is the primary contributor for the scent of musks. The aldehyde cinnamaldehyde is the provider of the flavor and aroma of cinnamon and is found to display important anti-hyper glycemic properties which cause the decrease in entire cholesterol and triglyceride intensity. The ketone testosterone is the primary male sex hormone which plays a crucial role in the development of male reproductive tissues and in promoting secondary sexual characteristics.
Key Questions: a) Describe the functional group of aldehydes and ketones. b) How are aldehydes and ketones structurally distinct from each other? c) Give some functions of aldehydes and ketones. SAQ 3. Encircle the functional group/s present in each organic compound and identify to what class or classes of organic compound they belong.
1)
2)
3.2.3.5. Oxygen-containing compounds: Carboxylic Acids and Derivatives The succeeding functional groups contain a carbonyl group. However, one of the R groups attached to the carbonyl carbon may be an atoms or group of atoms that produce a new functional group, and therefore a unique class of organic compounds. When one of the R groups is replaced by a hydroxy (OH) group, the resulting functional group is called a carboxyl (-COOH) or carboxy (COOH) group, from the fusion of carbonyl and hydroxyl. Organic compounds with this functional group are called carboxylic acids. The structure of carboxylic acids is usually abbreviated as RCOOH or RCO2H. Take note that for this shorthand notation, the central carbon atom of the functional group is doubly bonded to one oxygen atom and singly bonded to another.
There are similarities in the structure of carboxylic acids with that of ketones and alcohols. For instance, carboxylic acids are like ketones in that the carboxyl carbon is sp2 hybridized and trigonal planar, and carboxylic acid groups are therefore planar with C—C=O and O=C— O bond angles of approximately 120°. Moreover, the C=O bond of a carboxylic acid is shorter than its C-O bond. The given example below is acetic acid, the simplest and most known carboxylic acid.
The C—O bond of a carboxylic acid is shorter than the C—O bond of an alcohol. This is because the carbon in an alcohol is sp3 hybridized while the carbon in a carboxylic acid is sp2 hybridized. Shown below are representative examples for each class of compound, acetic acid and methanol.
Carboxylic acids have a variety of uses such as in soap manufacture, food industry, pharmaceutical industry, and dye, perfume, and rayon preparations. Many carboxylic acids are components of the food and drinks we consume. These include malic acid (in apples), tartaric acid (in grape juice), oxalic acid (in spinach), and butyric acid (in rancid butter). A known biological carboxylic acid is lactic acid, which is generated in muscles of the body as cells metabolize sugar and perform their functions. When we suddenly perform activities requiring a lot of muscle effort resulting to overexertion of cellular work, there are times when lactic acid accumulation occurs, causing the feeling of fatigue in the muscles. After some time when we have rested, the lactic acid is gradually converted to water and carbon dioxide, relieving the fatigue that we feel. Salicylic acid is an aromatic benzoic acid which is well-known for being a skin-care product as it aids in removing dead skin cells, which can clog pores and contribute to acne breakouts.
The carboxyl group is not only present in carboxylic acids, but it is also the parent group of a large class of related organic compounds called carboxylic acid derivatives or acyl compounds. They are derivatives of carboxylic acids because they are synthesized by using carboxylic acids as starting materials. Now the term has been mentioned, the R—C=O group
wherein one of the R groups directly attached to carbon is not another carbon nor hydrogen is called an acyl group. The different carboxylic acid derivatives are shown in Table 3.2. Highlighted in orange is the characteristic carbonyl groups and in green are the R’ and R’’ atoms or group of atoms replacing the hydroxyl group in carboxylic acids, while enclosed in a round box are the functional groups of each compound. Acid halides result from replacing the hydroxyl group of carboxylic acids by chlorine or bromine. Acid halides are highly reactive compounds used primarily in the laboratory for reactions requiring the acyl group. Hazards come with acid halides as these substances can irritate the skin, mucous membranes, and the eyes. Some acid halides can react with water at the surface of the eye producing irritative compounds. Examples of acid halides include acetyl chloride, benzoyl bromide, cyclohexanecarbonyl chloride, and adipoyl chloride, which has two acyl halide functional groups. In the given examples, the functional group is enclosed in a box and the carbonyl group is colored orange. These designations will also be applied to future examples of acyl compounds in this section.
Acid anhydrides are acyl compounds wherein two carbonyl groups are joined together in a molecule by a single oxygen atom. They can be symmetrical, mixed, or cyclic. Symmetrical anhydrides have two similar groups bonded to the carbonyl carbons while mixed anhydrides contain two different R groups. An example of a mixed anhydride is ethanoic propanoic anhydride, exhibited in Table 3.2. Examples of symmetrical and cyclic ones are shown as follows.
Acid anhydrides have uses in manufacture of industrial products, pharmaceuticals, explosives, and perfumes. They are also starting materials in the synthesis of esters, of aspirin, and of heroin.
Table 3.2. Carboxylic Acid Derivatives Name of Acyl General Structure Compound
Name
Acyl (or acid) halide
acetyl chloride
Acid anhydride
ethanoic propanoic anhydride
Ester
ethyl acetate or ethyl ethanoate
acetamide
Amide
N-methylmethanamide
N,Ndimethylethanamide
Thioester
Acetyl-CoA
Acyl phosphate
palmitoyl phosphate
Nitrile
acrylonitrile
Example
Structure
Esters are carboxylic acid derivatives whose carbonyl carbon is singly bonded to an oxygen atom, which is in turn singly bonded to another carbon atom. They are polar compounds, but unlike carboxylic acids and alcohols they cannot form strong hydrogen bonds to each other due to the lack of a hydroxyl group. Accordingly, esters have low boiling points relative to organic acids and alcohols of comparable molecular weight. The boiling points of esters are about the same as those of comparable aldehydes and ketones. Esters, such as isoamyl acetate and isopentyl pentanoate, are distinguished for their fruity and pleasant odors and thus, are used in the manufacture of synthetic flavors.
Amides are a class of organic compounds containing a carbonyl group whose carbon atom is linked to a nitrogen atom. They are derived from the reaction between a carboxylic acid and an amine. Amides are renowned for their use in the polymer industry as they link the monomer units in the polymer nylon. Nylon 66 was first synthesized in 1931 through the reaction of adipic acid with hexamethylene diamine, producing a strong, fiber-like material. The 66 part of the name reflects the fact that adipic acid and hexamethylene diamine each contain six carbon atoms in their molecules. Other nylon-like polymers were then discovered and industrially manufactured. In the pharmaceuticals industry, amides are known to be analgesics such as acetaminophen and phenacetin. Other commercially important amides are N,N-dimethyl-m-toluamide (an insect repellant), lidocaine (a local anesthetic), and meprobamate (a tranquilizer).
Key Questions: a) What is the functional group present in carboxylic acids and their derivatives? b) What are some uses of carboxylic acids? c) How are the different carboxylic acid derivatives distinct from each other?
SAQ 3. Encircle the functional group/s present in each organic compound and identify to what class or classes of organic compound they belong.
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3.2.3.6. Nitrogen-containing compounds: Nitriles and Amines Amides are carboxylic acid derivatives containing the nitrogen atom. Aside from these class of compounds, there are also other substances with functional groups containing the N atom. Nitriles are organic compounds containing the cyano group, in which the carbon atom is bonded to an alkyl group or any other R functional group. The cyano group will be colored blue in future examples of nitriles.
In nitriles, both the carbon and nitrogen in nitriles are sp hybridized, resembling the C—C triple bond in alkynes with a linear geometry and a bond angle of 180°. Given as examples below are the structural formula and ball-and-stick model of acetonitrile, wherein the blue ball represents nitrogen.
Acetonitrile is the common name for the two-carbon nitrile ethanenitrile, while acrylonitrile is the common name for the three-carbon nitrile, propenenitrile. Cyclic nitriles have the —CN group attached to a cyclic system and have names with the suffix -carbonitrile. Examples of cyclic nitriles include benzenecarbonitrile or benzonitrile and cyclohexanecarbonitrile.
Nitriles have significant uses in the household. For instance, methyl cyanoacrylate is a component of super glue. This nitrile is sensitive to humidity and thus when exposed to air will polymerize within seconds at room temperature. Nitrile rubber, a copolymer of acrylonitrile and butadiene, is an oil-resistant polymer that is found in latex-free gloves, in hoses that transport oils, in seals, and in various moulded products.
The last class of nitrogen-containing organic compounds are amines. Just as alcohols and ethers are organic derivatives of water, amines are organic derivatives of ammonia (NH3).
Amines result by replacing one or more hydrogens of NH3 with alkyl or aryl groups. In amines, the functional group present is the amino group, boxed in the given examples. The carbon atoms to which the N atom in the amino group is directly attached are colored red while the N atom is colored blue in the structures.
Similar to ammonia, amines have a trigonal pyramidal shape since the N atom is surrounded by three atoms and one nonbonded electron pair. Hence, the nitrogen atom in amines is sp3 hybridized with the unshared electron pair occupying one orbital. The C—N—C bond angles in amines have a value very close to 109.5°, the tetrahedral angle value. For instance, the C—N—C bond angle is 108.7° and the C—N bond length is 147 pm in trimethylamine, whose structural formula and 3D model is shown as follows.
A notable characteristic of low-molecular weight amines is their foul and fishy odor. Aniline, the simplest aromatic amine, is a precursor to the manufacture of polyurethane and other industrial chemicals and has the odor of rotten fish. Putrescine is a primary amine that is partly responsible for the odors of semen, urine, and bad breath.
Amines that are naturally occurring and are derived from plant sources belong to a large class of compounds called alkaloids. Perhaps the most famous alkaloid is caffeine, a natural stimulant most commonly found in tea, coffee, and carbonated drinks. It stimulates the brain and nervous system to keep the mind alert and to prevent the onset of tiredness. Another well-known alkaloid is nicotine, an amine found in the tobacco plant and is an addictive central nervous system (CNS) stimulant. Another notable alkaloid is theobromine, a bitter alkaloid found in cacao plant and in chocolates. This compound can cause poisoning in animals which metabolize it slowly, such as dogs.
Key Questions: a) What is the functional group present in nitriles and in amines? b) What are some important uses of nitriles and amines? c) Aside from its functional group, what are other distinguishable properties of amines? 3.2.3.7. Sulfur-containing compounds: Thiols and Sulfides Previously on the discussion of acyl compounds, thioesters are carboxylic acid derivatives containing a sulfur atom. There are other classes of organic compounds which have sulfurcontaining functional groups. Thiols, sometimes called mercaptans, are sulfur analogs of alcohols in that the oxygen is replaced by the sulfur atom. Hence, the functional group in thiols is the thiol group or mercapto group (S—H). Thiols, just like alcohols, are weakly acidic. However, the sulfur atom in the thiol group is not sufficiently electronegative so it does not typically form hydrogen bonds. They are also named in a similar fashion as alcohols except that the -ol suffix is replaced by -thiol.
Thiols are remarked for their horrendous stench. The vile odor of the gas emitted by skunks is caused primarily by the thiols 3-methyl-1-butanethiol and 2-butene-1-thiol.
Thiols are important compounds in the biochemistry laboratory. The thiols βmercaptoethanol (BME) and dithiothreitol (DTT) are reducing agents used to maintain proteins or peptides in their reduced state.
Just as thiols are the sulfur analogs of alcohols, sulfides are the sulfur analogs of ethers wherein two organic groups are bonded to the sulfur atom. If sulfur is simultaneously connected to different positions of the same carbon chain, a cyclic sulfide results. Sulfides are named the same way as ethers except that the word sulfide is added at the end instead of ether for simple compounds and alkylthio replaces alkoxy for more complex substances. The functional group in sulfides is the sulfide group or alkylthio group (—S—R)
Sulfides, in general, have low water solubility and are soluble in organic solvents. Thiophene, a cyclic sulfide, is a very stable sulfide. Similar to thiols, sulfides are known for their unpleasant odors. An example is allyl methyl sulfide, which is a major contributor to the “garlic breath” of humans.
There are also biological sulfides such as 2-phenylethyl methyl sulfide, which is a trailmarking secretion from the striped hyena; methionine, an essential amino acid involved in biological methyl transfer, and terthiophene, a pigment that is responsible for the insecticidal activity of Tagetes minuta, a marigold plant.
When two thiol groups are coupled, a special functional group results which is the disulfide. The disulfide linkage refers to a functional group wherein there are two bonded S atoms, wherein each atom is linked to other organic groups. It is often referred to as disulfide bridge and is most important in the linkage between two cysteine residues, which are components of the secondary and tertiary structure of proteins. Key Questions: a) How are thiols structurally different from sulfides? b) What are some biological functions of sulfides and thiols? 3.2.3.8. Phosphate-containing compounds: Organic Phosphates Organic compounds which contain a phosphate group in their structures are called organic phosphates or organophosphates. These molecules have the phosphate group attached to the carbon atom through one of its oxygens. In the general structure shown below, take note that R’ and R’’ can also be a hydrogen atom.
As shown in its general structure, organophosphates are hypervalent, for phosphorus can have an expanded octet. They also contain five bonds and they can form salts through ionic bonds between a cation and one of the oxygen anions. Organic phosphates are known to be involved in energy transfer reactions, one example being adenosine triphosphate or ATP, a high-energy organophosphate that is said to be the energy currency of life.
Organic phosphates are widely used in agriculture for fertilizers and for industries as lubricant additives, fire retardants, plasticizers, and chemical intermediates. Organophosphates are also found in rubber, plastics, paper, varnish, and metal industries. They are components of cleaning compounds, pyrotechnics, explosives, and pesticides. For instance, tri-ortho-cresyl phosphate is the most human hazardous isomeric component of TCP or tricresyl phosphate, a substance used as a fire retardant and in manufacturing lacquers and varnishes. Tributylphosphate, on the other hand, is an industrial chemical used as a plasticizer, as a heat exchange agent, and as a solvent and extractant for metal ions.
Key Questions: a) What is the functional group present in phosphates? b) How are phosphates utilized in different industries? c) Aside from the phosphate group, can you point out the other functional groups present in adenosine triphosphate (ATP)? SAQ-3. Encircle the functional group/s present in each organic compound and identify to what class or classes of organic compound they belong.
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3.2.3.8. Summary of Classes of Organic Compounds with Functional Groups containing Heteroatoms From the previous sections, we have discussed the different classes of organic compounds containing heteroatoms and their respective functional groups. If you have not noticed, some compounds having more than one functional groups also exist in nature and, at the same time, can be synthesized in the laboratory. These compounds are called multi-functional organic compounds. If you are given such compounds, you should be able to correctly determine all of the functional groups present in them. Compounds with more functionality can have enhancements in their physical and chemical properties and they can also participate in many more reactions. The following table summarizes all of the classes of organic compounds containing heteroatoms that we have discussed, as well as their functional groups. Table 3.3. Organic compounds containing heteroatoms. Class of Compound General Structure Alkyl Halide
Alcohol Ether
Aldehyde
Functional group
Ketone
Carboxylic Acid
Acid Halide
Acid Anhydride
Ester
Amide
Nitrile
Amine
Thiol
Sulfide
Organophosphate
SAQ-3. Given the following multifunctional organic compound, encircle all of the functional groups and determine their corresponding class of organic compound.
Learning Resource: Gridlocks: Can You Unlock the Grid? (URL Link: http://www.rsc.org/learn-chemistry/resources/gridlocks/puzzles/level3/functional-groups.html) Annotation: This is an online game regarding functional groups that you can play. To access the game, click on the hyperlink or URL link above. In this timed game, you need
to drag blocks containing the structure of a functional group to its respective name and vice versa. Learning Resource: Functional Groups (URL Link: https://www.purposegames.com/game/e88e081913) Annotation: This is a virtual self-assessment online activity where you will be given a single multi-functional organic compound from which you will point out the stated functional groups. To access this activity, click the hyperlink or URL link above.
3.4. Biomolecules Compounds containing multifunctional groups (more than one functional group) in their structures exist in nature. Some are even important in survival and in perpetuating life, as these molecules constitute every single living thing that exists. These compounds are called biomolecules, which are complex which are complex naturally-occurring substances that confer living things their extraordinary attributes and properties such as high degree of chemical complexity and microscopic organization, systems for extracting, transforming, and using energy form the environment, defined functions for each of an organism’s components and reguiated interactions among them, mechanisms for sensing and responding to alterations in their surroundings, capacity for precise self-replication and self-assembly, and capability to change over time by gradual evolution. The in-depth study of biomolecules, including their structures, the reactions they undergo, the reactions that they regulate and maintain in living systems, and their overall role and function in different organisms are the concern of a field of chemistry called biochemistry. In this course, we will only deal with the structural features of biomolecules, integrating the knowledge that we already acquired regarding functional groups, as these groups also constitute the complex organization of such compounds. The four biomolecules that we will discuss are carbohydrates, lipids, proteins, and nucleic acids.
3.4.1. Carbohydrates Carbohydrates are a broad class of polyhydroxylated aldehydes and ketones commonly called sugars. Not only are these molecules found in the food that we consume, but they are also present in every living organism. Carbohydrates are constituents of the coating around living cells, are part of the nucleic acids that carry our genetic information and are used as medicines. Carbohydrates are termed as such because the first simple carbohydrate to be obtained pure, glucose, has the molecular formula C6H12O6 and was originally thought to be a “hydrate of carbon, C6(H2O)6”. Glucose is known in medical work as dextrose. The structure of glucose is illustrated as follows, in which the aldehyde group is boxed while the hydroxide
groups are colored purple. As seen from the illustration, the sugar glucose contains an aldehyde and five hydroxy groups (—OH) in its structure.
A very important role of carbohydrates is that these compounds are storehouses of chemical energy. They are synthesized in green plants and algae through a process called photosynthesis, a complex process that utilizes the energy from the sun to convert, or specifically to reduce of “fix”, carbon dioxide in the presence of water, into glucose and oxygen. This stored energy from glucose will be released when it is metabolized or processed by biological pathways and systems. When glucose is metabolized, it is oxidized through a multistep process that reforms carbon dioxide and water, and at the same time produces a great deal of energy. The overall equation for photosynthesis is shown as follows.
Carbohydrates can be structurally categorized in several ways. Generally, carbohydrates are identified as simple sugars or complex carbohydrates, depending on the number of unique sugar units in their structures. Simple sugars are most commonly known as monosaccharides, which have three to seven carbon atoms in a chain. They are characterized by the presence of a carbonyl group and one or more hydroxy groups. Monosaccharides can be further classified as aldoses and ketoses. Aldoses are those sugars with an aldehyde carbonyl group while ketoses are those monosaccharides with a ketone carbonyl group at carbon. The general structure of a monosaccharide is shown as follows.
Monosaccharides have a general formula of (CH2O)n, where n=3 is the simplest. In fact, according to the value of n or the number of carbons, monosaccharides can be classified as triose (n=3), tetrose (n=4), pentose (n=5), hexose (n=6), and heptose (n=7). Monosaccharides can then generally be categorized or named depending on both the number of carbons and the classification as an aldose or a ketose. For instance, glyceraldehyde has three carbon atoms and has an aldehyde group. Hence, glyceraldehyde is an aldotriose sugar. Fructose, on the other hand, is a ketotriose because it has five carbons and has a ketone group.
When monosaccharides are linked to each other, what results are complex carbohydrates. Complex carbohydrates are classified according to the number of monosaccharide units combined in order to form them. One of them are disaccharides, which contain two monosaccharide units joined together by a glycosidic linkage. The four most abundant disaccharides are maltose, lactose, sucrose, and cellobiose, whose structures are shown as follows
Oligosaccharides are complex carbohydrates containing 3 to 10 sugar units. However, the use of oligosaccharides have been extended by some scientific authors to include carbohydrates with up to 20 residues or even disaccharides. They occur naturally in many plants such as onions, leeks, garlic, legumes, wheat, asparagus, and Japanese artichoke, among others. An example of an oligosaccharide is raffinose, which is made up of one unit each of galactose, glucose, and fructose
Polysaccharides, also known as glycans, are complex carbohydrates which can contain tens, hundreds, or even thousands of monosaccharide units linked together through glycoside bonds. The three most important polysaccharides, all of which are homopolysaccharides, are cellulose, starch, and glycogen. Cellulose is an unbranched polymer composed of repeating glucose Due to the many hydroxy groups in its structure, several cellulose units can interact with each other to create a large aggregate structure. Cellulose is used by nature primarily as a structural material and to
impart strength and rigidity to wood and plant stems. Cotton, leaves, and grasses for instance, are essentially pure cellulose.
Starch is a polymer of glucose. Plants have starch as their primary storage form of carbohydrates and have them found in their roots, tubers, and seeds. Corn, potatoes, rice, and wheat are some foods containing remarkable amount of starch. This complex carbohydrate have two common forms – amylose and amylopectin. The counterpart of starch in animals is glycogen, a polymer of glucose which has branching as often as every 6 units and has a very high molecular weight as it can contain up to 100,000 glucose molecules. As an energy storage form of sugars in animals, it is principally stored in the liver and muscle in humans. When there is not enough glucose, glycogen is broken down in order to generate the monomer units and to provide energy in the cell. Because glycogen has a highly branched structure, there are many glucose units at the ends of the branches that can be cleaved whenever the body needs them.
Key Questions: a) What functional groups are common to all carbohydrates? b) What is the basis for the classification of carbohydrates? c) How are monosaccharides classified? d) What are some important disaccharides and how are they distinguished from each other? e) What are the three most important biological polysaccharides? f) What are some biological functions of carbohydrates?
SAQ-3. For the monosaccharides, encircle the functional groups present and identify to what class of organic compounds they belong to.
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SAQ-3. Encircle the functional groups in the given disaccharide and identity to what classes of organic compounds they belong.
3.4.2. Lipids Lipids are diverse biomolecules with the distinct characteristic of being insoluble in water unlike the other macromolecules. The name lipid comes from the word lipos which means fat. They are also unique relative to the other biomolecules in such a way that their identity is defined based on a physical property and not by the presence of a particular functional group. Hence, lipids have variable structures and can contain a wide array of functional groups. Lipids are soluble in organic solvents due to the presence of a large number of carbon-carbon and carbon-hydrogen σ-bonds in their structures. Consequently, lipids have coinciding properties with hydrocarbons. Lipids can be classified as either saponifiable or non-saponifiable. Saponifiable lipids, also called hydrolysable lipids, are those that can be cleaved into smaller molecules through hydrolysis with water. Most of these lipids contain an ester unit. On the other hand, nonsaponifiable lipids or nonhydrolyzable lipids are those that cannot be hydrolyzed by water
into their smaller molecular components. They have more varying structures compared to hydrolysable lipids.
The first hydrolysable lipids, which are also the most abundant, are triacylglycerols or triglycerides. These lipids contain glycerol and three fatty acid molecules in their structures. Fatty acids are long-chain carboxylic acids, most having unbranched chains and an even number of carbon atoms, and are synthesized from two-carbon units. Treatment of a triacylglycerol with a strong base in the presence of water and heat, followed by a reaction with an acid, will yield its component glycerol and fatty acids. This reaction is specifically called aqueous hydrolysis. In the cell, the main function of triacylglycerols is energy storage.
Triglycerides are classified in a variety of ways. First, those triacylglycerols existing as liquids in room temperature are called oils while those existing as solids are called fats. Oils have lower melting points than fats. Some examples of oils include vegetable oils (corn oil, peanut oil, soybean oil, etc.), palm oil, and coconut oil and fish oils (cod liver and herring oils, etc.) while fats include butter, lard, and tallow. An example of a triglyceride is shown as follows.
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Following triacylglycerols are phospholipids, a large class of saponifiable lipids that are organic derivatives of phosphoric acid, formed by replacing two of the H atoms by R groups. Phospholipids can also be viewed as being structurally derived from a glycerol derivative called phosphatidic acid. In a phosphatidic acid, two hydroxyl groups of glycerol are joined in ester linkages to fatty acids and one terminal hydroxyl group is joined in an ester linkage to phosphoric acid.
In both plants and animals, phospholipids make up approximately 50% to 60% of cell membranes, the component which regulates the entry and exit of substances into and out of the cell. These compounds have long non-polar hydrocarbon tails, which are the fatty acid chains, and a polar ionic head, which is the charged phosphate group and R’’ groups. Due to this feature, glycerophospholipids can arrange themselves into a lipid bilayer, which is essentially the structural organization of cell membranes. Shown in the illustration below is a cephalin molecule and its conformation into a lipid bilayer. In green are the polar heads while in brown are the nonpolar hydrocarbon tails.
The simplest hydroyzable lipids are waxes, which are mixtures of esters formed from a high molecular weight alcohol and a fatty acid. Waxes are highly hydrophobic lipids due to their long hydrocarbon chains. The fatty acid component usually contains even number of carbons from 16 through 36, while the alcohol component also has even number of carbons from 24 through 36. Waxes are usually found as protective coatings on the skin, fur, and feathers of animals on the leaves of fruits of plants. Some examples of esters that are components of waxes include, triacontyl hexadecanoate from beeswax, and the ester of carnauba wax, and cetyl palmitate (3D model shown as follows) from spermaceti wax in sperm whales.
The next set of lipids are under nonhydrolyzable lipids. These are steroids, eicosanoids, terpenes, and fat-soluble vitamins. Steroids are lipids that contain the perhydropercyclopentanophenanthrene ring system, where each ring is labelled from A to D. The different types of steroids vary according to the types of atoms and functional groups bonded to the cyclic rings.
The subclasses of steroids include steroid hormones such as sex hormones (e.g. estrogen, testosterone, and progesterone) and anabolic steroids (e.g. cortisol, stanozolol, nandolone); bile salts (e.g. sodium glycocholate); and cholesterol. Cholesterol is essential to life because it forms an important component of cell membranes and is the starting material for the synthesis of all other steroids. Cholesterols are not needed in our diet because they are synthesized in the liver and then transported to other tissues through the blood stream. Structurally, cholesterols contain only one polar OH group and many nonpolar C—C and C— H bonds; thus, they are water-insoluble. Contrary to popular belief, not all cholesterols are tied to heart diseases. There are good cholesterols called HDLs or high-density lipoproteins, which carry lipids from the tissues to the liver for degradation and excretion. The bad cholesterols are the LDLs or low-density lipoproteins. Examples of the different subtypes of steroids are shown as follows, where the different functional groups are colored accordingly.
cholesterol
Eicosanoids are a group of nonhyrolyzable lipid molecules that are biologically active and are composed of 20 carbon atoms. They are local mediators or molecules which perform their function in the environment in which they are synthesized. The three types of eicosanoids are prostaglandins, which have a cyclopentane ring with two long side chains function in the regulation of contraction and relaxation of smooth muscle tissues; thromboxanes, which have a six-membered oxygen-containing ring and promote formation of blood clots; and leukotrienes, which are acyclic and function as signaling lipids for inflammatory and hypersensitivity/allergic responses.
Terpenes are nonhydrolyzable units structurally distinguished for the presence of repeating five-carbon units or C5 units called isoprene units.
They have a variety of structures, from being acylic or cyclic and to having solely C and H atoms or having heteroatoms. Terpenes are usual components of mixtures of odoriferous compounds called essential oils, which are isolated from plant sources by distillation and are known to have uses in medicine and in perfume concoctions. Some examples of terpenes are shown as follows.
Fat-soluble vitamins are non-saponifiable lipids that are water-insoluble, distinguished from the other class of vitamins which are the water-soluble vitamins. They are required in small quantities for normal metabolism and they cannot be synthesized by cells so they must be obtained in the diet. The four fat-soluble vitamins—A, D, E, and K—can be acquired from fruits, vegetable, fish, liver, and daily products.
Key Questions: a) What are the two classifications of lipids? How are they different from each other? What subclasses are under each type? b) What makes up a triglyceride? What are the functional groups present in each component of triglycerides? c) From the given examples in this section, what functional groups can be found on phospholipids and on waxes? d) What is the characteristic feature present in all steroids? How are they differentiated from each other? d) What functional groups are present in the structures of eicosanoids? e) What is the characteristic feature of terpenes? f) What are the fat-soluble vitamins? How do they differ in terms of function?
SAQ-3. Encircle the functional groups present in each lipid and identify to what class of organic compounds they belong.
3.4.3. Amino Acids and Proteins Proteins, among the biomolecules, have the most diverse functions including providing strength and support to tissues as structural proteins (e.g. keratin and collagen), catalyzing and regulating reactions in the body as enzymes and hormones, providing means for movement as muscles and tendons, transferring oxygen in different organs as hemoglobin molecules, and protecting organisms from diseases as antibodies. They are varying in terms of sizes and shapes are and remarkable in terms of molecular weights. Structurally, proteins are polyamides, meaning they are comprised of several amide functional groups. Moreover, the monomeric or repeating units or the building blocks of proteins are called amino acids. Amino acids, as the name implies, contain both a basic amino group and an acidic carboxyl group. These amino acids are linked together into long chains by forming amide or peptide bonds between the —NH2 of one amino acid and the —COOH of another. The term peptides is used to classify amino acid chains with fewer than 50 amino acids while the term proteins is generally used for longer chains. Shown as follows are general structural formulas for an amino acid and a portion of a protein molecule.
Proteins are not occurring as a straight chain of amino acids. Rather, the proteins are folded or coiled into intricate 3D structures. The primary structure of a protein refers to the exact amino acid sequence making up the protein. It is very crucial that the amino sequence is correct since the primary function of a protein depends on its primary structure. Folding of the amino acid chains gives rise to higher levels of complexity called the secondary and tertiary structures of the protein. The quaternary structure results when a protein contains an aggregate of more than one polyamide chain. Shown as an example is the 3D structure of hemoglobin, which is a component of redblood cells responsible for circulating oxygen throughout the body.
Proteins contain several amino acids of different identities in their primary structures. There are 20 amino acids that occur naturally in proteins, and they are distinguished depending on the R group or side chain bonded to the α-carbon. Glycine, the simplest amino acid, has an H atom as the R group. The R groups extend the number of functional groups that amino acids may contain. The following table shows the 20 common amino acids as well as their classification – alkyl/aliphatic, sulfur-containing, alcohols, aromatics, acidic, basic, and amides. Try to identify the functional group present in the R chains of these amino acids.
Table 3.4. List of the 20 common amino acids Structure
Alkyl/Aliphatic
Name
Structure
Aromatics
Name
Glycine (Gly, G)
Phenylalanine (Phe, F)
Alanine (Ala, A)
Tyrosine (Tyr, T)
Tryptophan (Try, W)
Proline (Pro, P)
Acidic
Leucine (Leu, L)
Aspartic Acid (Asp, D)
Glutamic Acid (Glu, E)
Isoleucine (Ile, I)
Basic
Valine (Val, V)
Histidine (His, H)
Sulfur-containing Cysteine (Cys, C)
Methionine (Met, M)
Lysine (Lys, K)
Arginine (Arg, R)
Alcohols
Amides
Threonine (Thr, T)
Asparagine (Asn, N)
Serine (Ser, S)
Glutamine (Gln, Q)
Key Questions: a) What are some of the biological functions of proteins? b) How will you structurally describe proteins? What are their building blocks? What are the functional groups present in peptides and proteins? c) What do you call the bonds that link amino acids together in a peptide chain? d) How do the twenty common amino acids differ in terms of their side chains?
SAQ-3. Encircle the functional groups and box the peptide bonds in the given peptide chain. Moreover, identify to what class of organic compounds each functional group falls under.
3.4.4. Nucleic Acids Nucleic acids are the last of the four major classes of biomolecules that we will discuss. Nucleic acids are chemical carriers of genetic information in cells. There are two known nucleic acids – deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA is the library of the cell, responsible for storing and transferring genetic information which determines the nature of the cell, controls cell growth and division, and directs biosynthesis of the enzymes and other proteins required for cellular functions. On the other hand, RNA directly codes for amino acids and acts as a messenger between DNA and ribosomes to make proteins. Structurally, nucleic acids are composed of carbon, hydrogen, nitrogen, and phosphorus atoms. They are biological polymers of subunits called nucleotides, joined together to form a long chain. Nucleotides are then composed of nucleosides—a combination of (1) pentose sugar, a five-carbon monosaccharide, and (2) a heterocyclic base from either the purine or pyrimidine family—and a (3) phosphate group. The general structure of a nucleoside and a nucleotide is shown as follows.
In distinguishing DNA from RNA, we need to look into the differences in the pentose sugar and nitrogenous base in their nucleotide structures, as well as their overall conformation. In an RNA, the sugar present is ribose, while in DNA the monosaccharide present is 2’deoxyribose. The major difference is that at the 2’ carbon of DNA, no hydroxy group (OH) is attached unlike that in an RNA.
Furthermore, the nitrogenous or amine bases in DNA can be any of the two substituted purines (adenine and guanine) or two substituted pyrimidines (cytosine and thymine). The same bases can also be found in RNA except that thymine is replaced by a closely related pyrmidine
base called uracil. The structures of purine and pyrimidine, as well as the five nitrogenous bases, are displayed accordingly.
Combining the corresponding nitrogenous base and pentose sugar, as well as a phosphate group, will give us a deoxyribonucleotide unit for DNA and a ribonucleotide unit for an RNA. A representative example for each nucleotide is shown as follows.
When several nucleotides bond with each other, DNA and RNA molecules are formed. Nucleotides in nucleic acids are linked together by phosphodiester bonds between phosphate, the 5’-hydroxyl group on one nucleoside, and the 3’-hydroxyl group on another nucleoside. As shown in the following illustrations, one end of the nucleic acid polymer has a free OH at C3’ (the 3’ end) and the other end has a phosphate at C5’ or the 5’ end. The sequence of nucleotides in nucleic acids is read from the 5’ to the 3’ end, and the identities of the bases are determined chronologically as the chain extends using the capital letter designations for the nitrogenous bases (A, T, C, G, or U).
DNA is singled out from RNA in terms of size in that molecules of DNA can contain as many as 245 million nucleotides and having molecular weights as high as 75 billion. On the other hand, molecules of RNA are much smaller, containing as few as 21 nucleotides and having molecular weights as low as 7000. Moreover, DNA is stable under alkaline conditions, while RNA is not stable. A key difference between the two nucleic acids is that DNA coils into a double helix or is a double-stranded molecule while RNA is only a single-stranded molecule. The DNA is able to achieve its double helix conformation due to the capability of their nitrogenous bases to hydrogen bond with each other at some selective extent due to specific base pairing. In DNA, adenine always pair or hydrogen bond with thymine while cytosine pairs with guanine. The same is true for RNA except that adenine associates with uracil rather than thymine. This discovery of the base-pairing in DNA is attributed to James Watson and Francis Crick. The following figure shows the secondary structures of RNA and DNA, as well as the base-pairing for the latter.
Key Questions: a) What are the two nucleic acids and how do they differ in terms of their functions? b) What are the three structural components of nucleotides? c) How do RNA and DNA differ in terms of their nucleotide structure? d) What are the nitrogenous bases that can make up nucleic acids? How do they differ in terms of structure? e) What do you call the bonds that link nucleotides in a nucleic acid? f) How can you differentiate the specific base pairing in DNA and RNA?
SAQ-3. Given the following nucleotide, encircle the functional groups and determine what class of functional groups they belong to. Is the given nucleotide a portion of a DNA or RNA? Why?
Learning Resource: Quiz on Functional Groups (URL Link: https://cloud.scorm.com/sc/InvitationConfirmEmail?publicInvitationId=a6e08727-b619438e-a1f8-d146021bee7e) Annotation: This is an online multiple-choice quiz regarding identification of functional groups given the structure of an organic compound. Click on the hyperlink or URL link below to be redirected to the quiz.