in this lecture we'll review the concepts from organic in general chemistry that you should know in order to proceed in this course the periodic table is shown with the major components of by organic compounds highlighted in red these elements are carbon C hydrogen H oxygen O nitrogen n phosphorus P and sulfur s they constitute more than 99 percent of the mass of the organic components of living cells listed here are all the elements that are necessary for cellular function the table includes the components of organic compounds and also various inorganic ions that participate in enzyme reactions nerve impulse transmission cellular signaling in other physiological functions all of these elements must be obtained in the diet because their elements they cannot be assembled from simpler building blocks or synthesized from any other materials the four elements shown here are the major constituents of bio organic compounds the hydrogen atom each has one proton and one electron it can form one single covalent bond to fill its outer electron shell with two electrons the oxygen atom o has eight protons in its nucleus and six electrons in its outer shell it can form two single bonds or one double bond to fill its outer electron shell with eight electrons the nitrogen atom n has seven protons in its nucleus and five electrons in its outer shell it can form three single bonds or one double bond and a single bond or one triple bond to fill its outer electron shell with eight electrons the carbon atom C forms the core framework of organic compounds it has six protons in its nucleus and four electrons in its outer shell it can form four single bonds or one double bond in two single bonds or one triple bond in one single bond to fill its outer electron shell with eight electrons what's so special about the carbon atom the carbon atom has four outer shell electrons and can readily accept four more electrons to fill its outer shell it can form single double or triple bonds it forms very stable linear or branched chain polymers these carbon polymers constitute the backbone of biomolecules this table compares the bond strength of a variety of covalent bonds the point here is that the carbon-carbon single bond is very strong compared to other bonds that carbon could form for example the combined strength of two carbon-carbon single bonds is greater than of one carbon-carbon double bond what this means is that a compound with many carbon-carbon single bonds will be at a relatively low energy state and thus will be quite stable the result of the strong carbon-carbon single bond strength is that carbon polymers with a high content of carbon-carbon single bonds will tend to persist in the biosphere carbon-carbon bonds are stronger than carbon oxygen bonds therefore carbon-carbon single bonds can form in the presence of oxygen in contrast silicon silicon bonds are weaker than silicon oxygen bonds for this reason silicon oxygen bonds tend to predominate under the conditions that prevail on the earth most silicon exists as some oxidation product such as sio2 and does not form chains with itself two carbon-carbon single bonds are stronger than one carbon-carbon double bond and so carbon tends to form single bonds in contrast with oxygen and nitrogen double and triple bonds tend to have more bond strength than exhibited by multiple single bonds as a consequence oxygen and nitrogen atoms tend to form double and triple bonds the carbon atom is quite versatile with respect to the types of structures that it can form shown here are a few examples of hydrocarbon molecules containing four carbon atoms carbon compounds can be linear or branched they can contain all single bonds or single and double bonds triple bonds between carbon atoms are relatively rare in biomolecules methane is the simplest hydrocarbon molecule it contains one carbon and four hydrogen atoms in this structure each hydrogen atom has two electrons in its outer shell and the carbon atom has eight electrons in its outer shell sharing electrons makes all the atoms happy although we often depict the carbon-carbon single bonds in organic compounds as planar those bonds are in fact tetrahedral in nature for example in methane if the two hydrogen atoms linked to the carbon by the bold triangles were in the plane of the screen the other two hydrogen atoms connected by the stippled triangles would radiate back away from the screen in this tetrahedral structure the four hydrogen atoms are equidistant from each other when two carbon atoms are linked by a single bond the atoms are free to rotate through 360 degrees in this example the hydrogen atoms of ethane can assume any orientation with respect to each other this freedom of rotation is generally true of carbon-carbon single bonds however because of steric interactions certain positions in which the hydrogen atoms are offset from each other tend to be favored the hydrogen atoms tend to dwell in these offset orientations longer than in positions in which they are lined up exactly this phenomenon is more pronounced in compounds which have very bulky groups attached to single bonded carbons in the case of extremely bulky groups certain orientations may be totally excluded because of steric hindrance there's one more thing that we can add to the list of unusual features of carbon compounds that is the carbon atom can exist in a variety of oxidation states in fact it's the ability of reduced carbon atoms to react with and be oxidized by molecular oxygen which makes it possible for most living organisms to obtain energy in the context of bio organic chemistry the most reduced carbon compounds are defined as having the highest percentage of hydrogen and or the lowest percentage of oxygen conversely the most oxidized carbon compounds have the lowest percentage of hydrogen and or the highest percentage of oxygen the most reduced form of carbon occurs in alkanes which contain only carbon and hydrogen atoms in alkanes the carbon atoms are either bonded to other carbon atoms or to hydrogen atoms beginning with alkanes the oxidation states of carbon increase from alcohols to el de Hyde's or ketones to carboxylic acids and finally to carbon dioxide which is the most oxidized carbon compound in nature in alkanes there are no bonds between carbon and oxygen in alcohol there is a carbon atom that has one bond to oxygen in aldehydes or ketones there's a carbon atom that has two bonds to oxygen in carboxylic acids there's a carbon atom with three bonds to oxygen and finally in carbon dioxide a carbon atom has four bonds to oxygen reactions which add bonds between oxygen and carbon atoms are referred to as oxidations reactions which remove bonds between oxygen and carbon atoms are referred to as reductions there are a number of reasons to focus on oxidation reduction reactions in our introductory consideration of bio organic chemistry oxidation reactions often release energy these oxidation reactions are the fundamental means by which biological organisms capture energy from food in most organisms energy is stored in food as reduced carbon compounds the rich pool of oxygen and the atmosphere is used by living organisms as an oxidizing agent to oxidize reduced organic compounds catabolism releases energy by oxidizing reduced carbon atoms converting them to a higher oxidation state anabolism uses stored energy to reduce carbon atoms converting them to a lower oxidation state a highly reduced carbon atom contains energy that the cell can capture for example methane is fully reduced an energy can be harvested by oxidizing methane using oxygen as the oxidizing agent highly oxidized carbon atoms have no energy that the cell can capture for example carbon dioxide is fully oxidized and we cannot extract any energy from it when we study the TCA cycle we will see that succinate is oxidized to fumarate coupled to the reduction of FA D to fadh2 in a further step in the cycle Mele is oxidized to oxaloacetate coupled to the reduction of nad plus to NADH the to reduced cofactors fadh2 and NADH are converted back to their oxidized form when they donate their electrons into the electron transport chain those electrons ultimately react with molecular oxygen to produce water overall succinate in Mele are being oxidized with molecular oxygen serving as the ultimate oxidizing agent there's one more important feature of the carbon atom that we should consider carbon can form covalent bonds with a variety of other atoms including oxygen nitrogen phosphorus and sulfur this versatility allows for the rich variety of compounds that we find in living organisms in biological compounds certain bonds with carbon tend to predominate the carbon atom forms single and double bonds with itself single bonds with hydrogen single bonds and double bonds with nitrogen single and double bonds with oxygen and single bonds with sulfur there are six types of functional groups that are found most frequently in biomolecules those are alcohol aldehyde ketone carboxylic acid phosphate and amine groups to proceed successfully in this course you must be able to recognize and understand all of these functional groups here is a more extensive list of the functional groups that appear in biochemical compounds I urge you to commit them all to memory as they form the basis for all the structural chemistry and metabolic pathways that we will be discussing failure to learn these groups as the equivalent of trying to learn a language without learning the key words now we'll start a systematic survey of bio organic compounds an alkene compound has the general formula CH 2 taken n times plus 2h a two alkane compound consists of only carbon and hydrogen and has no oxygen and no double bonds although complete alkanes do not commonly occur in most living organisms alkane like structures form the backbone of many organic compounds for example the linear hydro carbon backbone structures of fatty acids have alkane like character alkanes are nonpolar and relatively insoluble in water the addition of any functional group containing a double bond or oxygen nitrogen or sulfur places a compound in some non L Kane family the IUPAC names for alkanes end in a and E the name of an alkane compound identifies the number of carbon atoms in that compound the common chain length for alkanes vary from 1 in methane to 12 in dodecane it would be in your best interest to commit these names into your memory bank when groups containing only carbon and hydrogen are connected to other parts of an organic molecule they're referred to as alkyl groups the alkyl groups retain the same root name as the corresponding alkanes but they add the suffix yl so methane becomes methyl in ethane becomes ethyl the alkene compounds are similar to alkanes except that they have at least one carbon-carbon double bond they have the general formula cnh2n times and contain only carbon and hydrogen atoms no true alkenes are found in biological systems but alkene like structures occur in the side chains of unsaturated fatty acids the alkenes have a carbon-carbon double bond which makes that area of the compound of planar structure when double bonds are present in a compound it creates two possible isomeric forms sister trans isomers occur at the double bond in sis compounds the bulkier groups attached to the two carbons connected by the double bond are on the same side of the double bond entrace compounds the bulkier groups attached to the two carbons connected by the double bond are across from each other the addition of a double bond to a compound also makes it an unsaturated compound which means that the compound has less than the maximum possible content of hydrogen atoms two hydrogen atoms are lost when a carbon-carbon single bond is converted into a double bond the IUPAC formal names for alkenes end with E and E here are some examples of alkenes note that the two lower compounds highlighted in yellow illustrate the difference between a sis and trans isomer alcohol's have an O H group that's attached to a saturated carbon atom that is the carbon bearing the O H group is bonded to either hydrogen or carbon atoms but not to oxygen or nitrogen the addition of the O H group raises the oxidation state of the carbon atom by one unit the presence of the O h group also increases the solubility of a compound in water compared to the corresponding alkane the solubility of alcohols and water decreases with the length of the carbon chain methyl alcohol with one carbon and ethyl alcohol with two carbons are infinitely soluble in water whereas alcohols with 10 or more carbons are relatively insoluble alcohols are more reactive than alkanes they can be oxidized under relatively mild conditions and they will react with aldehydes ketones or carboxylic acids to form condensation products the IUPAC names for alcohols end in Oh L here are some examples of common alcohol derivatives you will meet up with each of these compounds or a close relative at some time in this course this would be a good time to start adding them to your memory bank in particular we'll learn about ethanol when we studied glucose fermentation glycerol is a component of triacylglycerols and fossil glycerols which are important lipid compounds the phenol group is a component of the amino acid tyrosine amines of the basic form are NH 2 in order to qualify as an amine the nitrogen atom must be connected to a saturated carbon atom an example of an an amine would be a compound with a nitrogen atom attached to a carbon atom which also has a double bond to an oxygen that compound would be an amide not an amine the presence of that carbonyl oxygen and the carbon dramatically changes the behavior the nitrogen atom amines can be thought of as analogues of ammonia nh3 as with alcohols amines are more soluble in water than the corresponding alkanes their water solubility decreases with the length of the attached carbon chain amines are relatively reactive with aldehydes ketones carboxylic acids in acid derivatives such as acyl halides or in hydrides compounds containing an amine group are referred to using the prefix amino or the suffix amine the amino acids have an amino group and a carboxylic acid group attached to the same carbon atom these amino acids also have an R group which varies for each type of amino acid there are twenty different amino acids found in polymeric form in protein molecules we will deal with amino acids when we consider protein structure the other heads have a central carbonyl carbon a carbon atom with a double bond to an oxygen atom in aldehyde must also have at least one bond from the carbonyl carbon to a hydrogen atom and will usually have one bond from the carbonyl carbon to another carbon atom the cell dahye groups are found at the end of a hydrocarbon chain not in the middle a carbonyl group which is sandwiched between two carbons is referred to as a ketone see the next slide aldehyde compounds of the general formula are CH oh this is a shorthand way of writing the compound do not be fooled into thinking that the oxygen atom is connected to the hydrogen atom the oxygen is connected by a double bond to the carbonyl carbon and the hydrogen is connected by a single bond to the carbonyl carbon aldehydes can be oxidized to carboxylic acids under relatively mild conditions and are also reactive with alcohols the IUPAC names for aldehyde in in al ketones are like aldehydes and that they have a central carbonyl carbon a carbon atom with a double bond to an oxygen atom the ketone must also have two bonds from the central carbonyl carbon to two other carbon atoms thus ketone groups are found at the middle of hydrocarbon chains not at the end ketone compounds have the general formula RC o R as with aldehydes this is a shorthand way of writing the compound the oxygen atom is not connected to the R group the oxygen is connected by a double bond to the carbonyl carbon and the our groups are connected by single bonds to the carbonyl carbon ketones are somewhat resistant to mild oxidizing conditions but they are reactive with alcohols the IUPAC names for ketones and in O n E acids are like aldehydes and ketones and that they have a central carbonyl carbon in order to qualify as a carboxylic acid the compound must have an O H group connected to the carbonyl carbon we sometimes represent carboxylic acids as RC o o H but it's important to recognize that this again is organic chemists shorthand in that one of the oxygen atoms is connected to the carbonyl carbon by a double bond and the other Oh H oxygen is connected to that same carbonyl carbon by a single bond there is no oxygen oxygen bond carboxylic acids are called acids because of the O H part of the carboxylic acid which can dissociate to form RC o oh minus plus a proton the RC o o minus is the conjugate base of the acid the RF COOH or acid form of the molecule is designated with the ending IC acid for example acetic acid the irco - form of the molecule is designated with the ending a te for example acetate carboxylic acids can react with the means to form an amide or with alcohols to form an ester carboxyl groups are very polar in the short chain carboxylic acids dissolve readily in water isomers are differing forms of a molecule that have the same empirical formula there are carbon chain isomers sis trans isomers functional group isomers position of functional group isomers geometrical isomers and stereo isomers and then of course there are those why so many isomers just kidding about those last ones isomers differ from each other in chemical and physical properties hydrocarbons with four or more carbon atoms can exist either as linear compounds or as branched isomers here are three examples of five carbon alkane compounds and they're common and IUPAC names such isomers all have the same empirical formula but they will have different chemical and physical properties and they will be discriminated from one another by enzymes many organic compounds have a carbon-carbon double bond which makes that area of the compound a planar structure double bonds lack freedom of rotation when double bonds are present in a compound it creates two possible isomeric forms Scizor trans isomers occur at the double bond in Syst compounds the bulkier groups attached to the two carbons connected by the double bond are on the same side of the double bond in trans compounds the bulkier groups attached to the two carbons connected by the double bond are across from each other there are atoms other than carbon and hydrogen and a molecule for example oxygen nitrogen or sulfur the position of these atoms in the way that they are arranged can define what type of functional group is produced dimethyl ether and ethyl alcohol have the same empirical formula but the oxygen atoms are arranged in a different manner the two compounds differ markedly in physical and chemical properties compounds differ in the position of functional groups along a carbon chain the position of a functional group usually alters the reactivity and the physical properties of a compound stereoisomers differ in the way various functional groups are oriented in space in order to exhibit this type of isomerism a compound must have a carbon atom that is attached to four different functional groups in the examples shown the amino acid alanine has four different functional groups in amino group a carboxyl group a hydrogen atom and a methyl group alanine exists as two different stereoisomers adi isomers shown on the left and an l isomer shown on the right inorganic chemistry sis trans isomerism or geometric isomerism is a form of stereoisomerism describing the orientation of functional groups within a molecule in general such isomers contain double bonds which cannot rotate we've talked about this already but these isomers can also arise from ring structures wherein the rotation of bonds is greatly restricted Ella cyclic compounds can also display systrace isomerism a biological example would include sterile derivatives in which functional groups on the non aromatic ring systems can assume different orientations if you're disinclined to look at photos you can stop right here this photo illustrates why we moved out to the Olympic Peninsula the photograph was taken from my living room window on February 22 it was in the high 40s and everything was green then on February 24 the shoe dropped we got 8 inches of snow in about three hours just like Minnesota dang we moved out here to get away from that it's nice to look at snow on the mountains but not on my driveway we live on one horse lane actually right now there are about four horses on the lane the lane isn't paved and it's one car wide when it snows I sometimes wish I had a four-wheel drive behemoth to get us out on the highway the rest of the time our compact car does just fine we live off from Blue Mountain Road it's called that because it runs right up to our Blue Mountain the higher up the road you go the colder the climate sometimes it rains on us and snows on people one mile up the road this time it snowed on everybody a friend of ours keeps a herd of llamas in my backyard these animals might be fine in the Andes but they're essentially worthless in Washington they look at you with great disdain and then spit llamas used to be a trendy diversion for gentlemen farmers they sold for thousands of dollars now you can buy one for 50 bucks in fact you can get a rescue llama for free if you really want something like this get yourself an alpaca they're smaller and marginally nicer animals also you can sell therefore nobody wants llama fur I owned this little beauty for a while it's a 1949 Ford f1 it was just six years younger that's right younger than me it really looks cool but it was very hard to drive I never did figure out how to shift it very well its gears weren't synchronized so you had to double clutch or sometimes just get the RPMs just right when you shifted I did a lot of grinding I could have made a lot of hamburger with all that grinding I wish someone would make this same truck now because it's a really beautiful design this truck with a nice Japanese engine now that would be something beautiful design and smooth shifting it looks really nice out here when it snows those are my footprints from walking out to the mailbox no mail that day I thought that neither rain nor sleet nor snow but I guess not well you have to get your exercise some way might as well shovel a little snow to build up those biceps and get some aerobic exercise at the same time see those llamas over by the shed they seem to like snow maybe they could learn to pull a snow plow if you look hard you can see the streets of Juan de Fuca off to the right if you look even harder you might see a bit of Canada or you can just enjoy the beautiful clouds here's a weeping willow by one of our ponds my dad always told me that one should never plant a weeping willow near to water her sewer pipes they're beautiful trees but their roots love to invade and clog pipes this willow will have to send out roots about a hundred feet in order to get into my pipes