Unit 10: Organic Chemistry Carbon. Carbon is the chemical basis for life. It is the backbone of nearly all compounds found in biological compounds and is made up of carbon chains. Lipids are long chains of connected carbon atoms with two hydrogens sticking out like thorns and a phosphate or similar group at the top. Proteins are nearly all carbons, connected in chains and rings and branching out in all directions. Carbohydrates are six and five carbon chains and rings with many oxygens added. These three substances make up much of the soft body tissues. A Phospolipid Membrane Protein Lipids http://upload.wikimedia.org/wikipedia/ commons/f/f1/succinate_dehydrogenase _1YQ3_and_Membrane.png Carbon is so versatile because it has four valence electrons each of which can bond with four other atoms or can create double and triple bonds. Carbon also tends to bond with itself and creates a multitude of different structures. The vast number of different structures of carbon and their importance in natural systems lead to the creation of a branch of chemistry called organic chemistry (which itself has divided many times itself into biochemistry, synthetic chemistry, physical organic, organometallic, and others). Organic chemistry is the study of the properties, structure, reactivity, and synthesis of compounds that contain carbon and are part of living organisms or related to those compounds. Much of organic chemistry is focused on organizing and classifying the structures that are to be studied. The simple naming systems of ionic compounds and diatomic molecules was not sufficient for the millions, or billions, of organic compounds that chemists where purifying and identifying in the early history of the science. So a systematic naming scheme was adopted to help scientists communicate their work to ensure that everyone was talking about the same substance.
Naming Hydrocarbons and Organic Compounds Hydrocarbons are covalent compounds containing carbon and hydrogen. The length of the chain of carbons is the basis for naming carbon chains in organic compounds. If the chain has one carbon the prefix is meth-, if the chain has 2 carbons the prefix is eth-, etc. The prefixes are listed here Prefix meth- eth- prop- but- penta- Length of Carbon Chain 1 2 3 4 5 Prefix hex- hept- oct- non- dec- Length of Carbon Chain 6 7 8 9 10 A hydrocarbon consisting only of carbons and hydrogens and having no double or triple bonds is an alkane and is named with the suffix ane. Alkanes and their Names with 1 to 4 Carbons Chemical Formula Model Name of Compound CH 4 methane C 2 H 6 ethane C 3 H 8 propane C 4 H 10 butane Models of Hydrocarbons You can see that there is a pattern to the building of a hydrocarbon chain and to the number of hydrogens present on each carbon. A carbon has four bonding points, so if a carbon is at the end and is bonded to only one carbon, then there will be three hydrogens bonded to the carbon. If the carbon is in the middle and the carbon chain is a unbranched then there are two
carbon bonds and two hydrogen bonds. Because this is an unchanging pattern, the model of a hydrocarbon simply is lines representing the bonds between carbons. The hydrogens, that are so predictable, are dropped altogether. Furthermore, the pattern of the number of carbons and hydrogens is so predictable that there is a formula for alkanes: C n H (n + 2). The plus two is because every carbon has two hydrogens except the carbons on the ends, which have three. Following is the hydrocarbons up to decane. Alkanes and their Names with 5 to 10 Carbons Chemical Formula Model Name of Compound C 5 H 12 pentane C 6 H 14 heptane C 7 H 16 C 8 H 18 C 9 H 20 C 10 H 22 heptane octane nonane decane
Alkenes Carbon must make four bonds to have a stable octet and sometimes this means sharing two pairs of electrons and even three pairs of electrons. When two pairs of electrons are shared between atoms then there is a double bond between the atoms, and when three pairs of electrons are shared then there is a triple bond. If a double bond is formed in a hydrocarbon then the molecule is an alkene. An alkene has a chemical formula that differs from an alkane by two H s so the formula of all alkenes is C n H n. The prefixes for alkenes is the same as for alkanes but the suffix changes to ene. Chemical Formula Model Name of Compound C 2 H 4 ethene (there is no methene) C 3 H 6 propene C 4 H 8 butene C 5 H 10 C 6 H 12 pentene hexene Isomers When an alkene gets to four carbons it is possible to have isomers, which are compounds with the same formula, but they have different geometries. In the case of the alkenes the double bond can be between the 1,2 carbons,, or between the 2,3 carbons,. The formal name for these are 1-butene and 2-butene, where the 1 and 2 refer to the starting carbon. Propene does not have an isomer because moving the double bond to the other side is the same compound but a mirror image, so it is a matter of point of view instead of different pattern of bonding. Likewise 1-butene is the same as 3-butene; they are mirror images of one another. Isomers are very common in organic chemistry. The D-amino acids are isomers of the L-amino acids and though they look nearly identical our proteins are built using the L-amino acids. Most hydrocarbons have isomers too. For alkanes, the carbons can branch off into more and more complex forms. Here are some branched isomers of hexane.,,,, and.
Naming Branched Isomers Rule 1: The naming of branched isomers starts by finding the longest chain. For,, the longest chain of carbons is 5 and for, the longest chain is 4 carbons. This will be the name of the hydrocarbon, pentane and butane respectively. Rule 2: The name must tell what is attached to the longest chain and where on the chain it is located. For example, in there is a one carbon functional group replacing the normal H in the middle of pentane so the name for a one carbon group is methyl and the name for the molecule is 3 methylpentane. If there are 2 methyl groups like in this molecule, the name is 2,2-dimethylbutane., then Rule 3: The numbering of the longest chain can start at either end, but it must start at the end nearest the double bond or at the end with the closest functional group. That is, if the last molecule was flipped so that it looked like this,, then it would be tempting to use the name 3,3-dimethylbutane. However, the numbering must start closest to the functional groups, which is why the molecule is named 2,2-dimethylbutane. Rule 4: Names of functional groups appear in alphabetic order not numeric order. Example 1., longest chain is in black, a methyl group is shown in green and an ethyl group in blue. So the name is 3-ethyl-3-methylpentane. (groups in alphabetical order) Example 2., the longest chain is in black, there are two methyl groups in green and 1 propyl group in blue. If the carbons are numbered 1, 2, etc. from left to right the numbers are smallest so the name is 3, 5-dimethyl-4-propyloctane. Example 3., longest chain is in black (this time it isn t a straight line). The numbering of carbons must start at the top, since this will give the smallest sum of numbers. The name is 4-ethyl-3, 5-dimethyloctane
Example 4., the longest chain includes a double bond and the double bond should have the smallest number, so the name is 4-methyl-2-pentene. Dienes It is possible to have more than one double bond in a hydrocarbon. These molecules are called dienes. There is a rich variety of organic compounds so that trienes, rings, and other structures are possible; however, it is beyond the scope of this unit to cover all the possibilities. Alkynes When three pairs of electrons are shared and there is a triple bond in a hydrocarbon then the molecule is an alkyne. The prefixes for alkynes is the same as for alkanes but the suffix changes to yne. Alkynes follow the formula C n H (n 2) Chemical Formula Model Name of Compound C 2 H 2 ethyne (there is no methyne) C 3 H 4 C 4 H 6 C 5 H 8 propyne butyne pentyne C 6 H 10 hexyne
Functional Groups Hydrocarbons is just the tip of the iceberg for the compounds that are included in organic chemistry. While carbon is the backbone to organic molecules, oxygens, sulfurs, nitrogens, and other atoms are added to the carbon chain to make an unimaginable number of compounds. Groups of atoms that are part of an organic molecule and give the molecule a certain set of properties are called functional groups. Functional groups also have a systematic naming, or nomenclature, that chemists use to communicate the type of substance they are studying or describing. Here is a list of the most common functional groups and the suffix that is used to identify the functional group. The R is a carbon group with or without any additional functional groups attached, R (called R prime) is a second carbon group that may or may not be the same, and R (called R double prime). Functional Group Model Suffix alcohol, R-OH ether, R O R -ol ex. propanol ether ex. diethyl ether O ketone, R C R O ester, R C OR -one ex. propanone -oate ex. methyl ethanoate and ethyl propanoate First name is the group on O Second is C chain up to O O carboxylic. acid R C OH aldehydes, R C H O -oic acid ex. ethanoic acid or acetic acid -al ex. butanal
Functional Group Model Suffix amine, R NH 2 R NH ; R N R. R R. aminoex. 1-aminopropane 1-methylaminoethane 1-dimethylaminomethane (Longest carbon chain is the ending name, the number is where the N is attached starts the name, and the other groups attached to the N are named after the number of carbons.) Benzene Benzene has played an important role in chemistry. Its chemical formula of C 6 H 6, was difficult to explain, until August Kekulé developed a ring of carbons to explain the unusual formula, (As Kekulé tells it after much work and puzzling over the possible structures a dream of six dancing imps forming a whirling circle provided his inspiration for the structure). Note the six hydrogens are not shown in the models. I II III Benzene and other aromatic compounds cannot be represented by a single drawing, but must be shown as a combination of two drawings. The double bonds can be shifted to make a resonance structure. Resonance structures have the same arrangement of atoms, but new placement of bonds that are equally likely to occur (because the energy of the different arrangements are the same or nearly so). Clearly, the two benzene arrangements I and II are the same except for the placement of double bonds. But resonance structures are not true structures. They are approximations of still pictures of the molecule in which the electrons are in constant motion changing from one resonance structure to another. So the true structure of benzene is a combination, or melding, of the structures I and II. Structure III tries to show this constant movement of electrons with a ring, but this structure isn t possible using the Lewis electron dot model we learned earlier. Have you seen the trick where you draw a bird on one side of a piece of paper and a bird cage on the other. Then the paper is attached to the top of a pencil. If you spin the pencil between your palms so the paper is spinning like a top, the bird appears in the bird cage. Like the benzene model, the two pictures, the bird and the bird cage, meld as it spins to show the real picture, the bird in the bird cage.
Naming benzene compounds is similar to names for hydrocarbons. Each carbon is numbered to be able to say where the different functional groups are located. The numbering must give the lowest sum of numbers. Benzene, ; chlorobenzene, ; methylbenzene or toluene, ; 1,2-dimethylbenzene, ; 1,3-dimethylbenzene, ; 1,4-dimethylbenzene, ; nitrobenzene, ; 2,4,6-trinitro-1-methylbenzene or trinitrotoluene (TNT); Biological Macromolecules Biology is arguably the hottest science in the late 20th century. Chemists were able to develop an understanding of the structure and properties of organic molecules, and then they developed methods for looking at larger and more complex molecules (like NMR). From these discoveries, our understanding of the chemical processes in cells and all living organisms lead to, and continue to lead to, deeper, more fundamental understandings of what is happening in the cell and other biological systems.
This section introduces the structure of some common biological macromolecules, extremely large molecules: DNA, carbohydrates, lipids, and proteins. All these molecules have repetitive structures. For example proteins are formed by combining amino acids. A molecule, manmade or natural, composed of a large number of repetitive units with a large molecular mass is called a polymer. Most plastics are polymers as are natural fibers like silk, cotton, and wool as well as synthetic fabrics like nylon, rayon, acetate, and polyester. The individual units that make up a polymer are monomers. For example, the polymer polypropylene, which is used in plastic bags, bottle caps, toys, cars, and much more is made up of 1000 s of linked monomer (the grey highlighted unit). Single Polymer Chains using an atomic force microscope http://commons.wikimedia.org/wiki/file:single_po lymer_chains_afm.jpg taken from Y. Roiter and S. Minko, AFM Single Molecule Experiments at the Solid-Liquid Interface: In Situ Conformation of Adsorbed Flexible Polyelectrolyte Chains, Journal of the American Chemical Society, vol. 127, iss. 45, pp. 15688-15689 (2005). DNA DNA is the code of life but it is not very complex chemically. DNA is made up a repeating chain of sugars (the pentagon in the diagram at the right) and phosphorous atoms (the circle) and four different types of molecules called nitrogen bases, or just bases (the colored molecules A, T, C, G). The three structures phosphorous plus sugar plus the base is called a nucleotide, which is a repeating structure in DNA. DNA is a long, an incredibly long, set of two chains of nucleotides with randomly sequenced bases. The bases pair up on the two chains so that A pairs with T & C pairs with G. In the cell DNA is wrapped up tight by proteins.
G, guanine: http://commons.wikimedia.org/wiki/file:nucleotides.gif http://commons.wikimedia.org/wiki/file:dna_sketch.png RNA has a similar structure, but it is in a single strand, a second OH is added to the sugar (next to the other OH), and the thymine base is replaced by a uracil base. Carbonhydrates Carbonhydrates are long chains of sugar molecules. A sugar molecule is usually a five or six membered carbon chain with OH s and H s bound to most carbons. Usually, the sugar molecule is found wrapped into a hexagon ring with five carbons and an oxygen. Glucose Glucose Fructose Ribose http://commons.wikimedia.org/wiki/file:alpha-d-glucopyranose.svg, http://commons.wikimedia.org/wiki/file:dglucose_fischer.svg, http://commons.wikimedia.org/wiki/file:beta-d- Fructose-structure.png, http://commons.wikimedia.org/wiki/file:d-ribose.png When the monosaccharides glucose, fructose, ribose, et. al. combine in pairs the sugars are called dissaccharides lactose, maltose, and many other, including table sugar, glucose.
Lactose Maltose Complex Carbohydrates Complex carbohydrates are three or more sugars, often in very long chains like polymers. Starch; cellulose, which is the fibrous material of plants; and chitin, which is the main component of insect exoskeletons, are examples of complex carbohydrates. Carbohydrates are the body s energy resource. But complex carbohydrates are recommended by nutrition experts because they come from sources that include minerals, vitamins, and other beneficial molecules and they are harder to break down so the body cannot absorb all the calories contained in these longer molecules. Amylose, a major component of starch: http://en.wikipedia.org/wiki/file:amylose_3dprojection.corrected.png Cellulose: http://en.wikipedia.org/wiki/file:cellulose_sessel.svg
Chitin: http://en.wikibooks.org/wiki/file:chitin_fixed.png
Lipids Lipids are large, naturally occurring molecules that are not water soluble. Lipids are the phospholipids of cell membranes, steroids and cholesterol, fats, oils, waxes, triglycerides, and more. The long carbon chain of hydrocarbons or multiple carbon rings without the O s and OH s of sugars makes this class of chemicals non-polar and insoluble in water. Fatty acid, trans-oleic acid: http://en.wikipedia.org/wiki/file:isomers_of_oleic_acid.png Cholesterol: http://en.wikipedia.org/wiki/file:cholesterol.svg and the main component of cell membranes, phospholipids http://commons.wikimedia.org/wiki/file:phospholipid_model.jpg Proteins Proteins are arguably the most important molecule in the body. While other molecules provide structure, instruction, and nutrition, it is the proteins that are responsible for initiating and monitoring most of the functions of living organisms. Some common proteins are: enzymes, muscles molecules, antibodies, hormones, hairs and feathers, food proteins, and those molecules involved in transporting material into the cell.
All proteins of made of amino acids. There are twenty amino acids that are responsible for nearly all proteins. Amino acids have an amine group, NH 2, that is basic, and a carboxylic acid, COOH that is acidic. Because of their basic and acidic character, amino acids are often shown with a protonated amine, NH 3 +, and the conjugate base of the acid, COO. In between the amine and acid are different numbers of carbons and in different arrangements. The difference in the carbon chain changes the properties of the amino acid and consequently the function and reactivity of the protein. 20 Amino Acids alanine arginine asparagine aspartic acid cysteine glutamic acid glutamine glycine histidine isoleucine leucine lysine methionine phenylalanine proline serine threonine tryptophan tyrosine valine http://en.wikipedia.org/wiki/list_of_standard_amino_acids
Summary Organic chemistry is the study of carbon compounds that are part of living systems or are closely related to these compounds. There are a wide variety of carbon compounds found in nature and made by man. The four valence electrons of carbon create four bonding locations on any carbon (the most of any second period atom); thus, the number of straight chains, branched chains, and rings that can be created by carbon grows quickly as the number of carbons increases. The simplest carbon compounds are hydrocarbons, which are chains of carbon with hydrogens bonded to carbons where they are not bonded to other carbons. Carbon chains can contain double and triple bonds, form rings, and can form a six membered ring with three double bonds that are known as benzene. Functional groups are atoms or combination of atoms that are connected to one or more of the carbon chains. Functional groups include -OH, for alcohols, C=O for ketones, C=O for aldehydes, C=O for carboxylic acids, H OH C=O for esters, C O C for ethers, C N for amines and additional hydrocarbon chains. There is a systematic naming system for carbon compounds that is based on the longest chain of carbon. For example a chain with 1 carbon is meth=, a chain of 2 carbons is eth-, etc. (see tables above). If a 2 carbon chain contains only single bonds the name is ethane. If there is a double bond the name becomes ethene, and if there is a triple bond the name becomes ethyne The addition of functional groups requires additional information about where and what is attached to the carbon chain and there are naming conventions that are used to name these more complex compounds too. When any large molecule is created from repetitive units the molecule is called a polymer. Each of the units that is repeated is called a monomer. While plastics are man-made polymers, usually of simple hydrocarbons with limited functional groups, nature has a number of polymeric macromolecules (macromolecules are compounds of very large molecular weight. Proteins are long biological molecules composed of amino acids (20 amino acids make up most of the proteins in our bodies), carbohydrates are large molecules composed of sugars, lipids have long hydrocarbon chains, and nucleic acids, DNA and RNA s, are made up of four different nucleotides which are nitrogen base pair attached to the same phosphorous-sugar monomer that is repeated in the long molecule.
Organic Chemistry and Biochemistry 10. The bonding characteristics of carbon allow the formation of many different organic molecules of varied sizes, shapes, and chemical properties and provide the biochemical basis of life. As a basis for understanding this concept: a. Students know large molecules (polymers), such as proteins, nucleic acids, and starch, are formed by repetitive combinations of simple subunits. b. Students know the bonding characteristics of carbon that result in the formation of a large variety of structures ranging from simple hydrocarbons to complex polymers and biological molecules. c. Students know amino acids are the building blocks of proteins. d.*students know the system for naming the ten simplest linear hydrocarbons and isomers that contain single bonds, simple hydrocarbons with double and triple bonds, and simple molecules that contain a benzene ring. e.*students know how to identify the functional groups that form the basis of alcohols, ketones, ethers, amines, esters, aldehydes, and organic acids. f. *Students know the R-group structure of amino acids and know how they combine to form the polypeptide backbone structure of proteins. Starred standards are non-tested standards on the California Standards Test Contributed by Kenneth Pringle Edited by Kathleen Duhl Formatted and Wiki Contribution by Christine Mytko