Lecture 02 Review of Bioorganic Chemistry PDF

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Lecture 2: Review of Bioorganic Chemistry Slide 1: Review of Bioorganic Chemistry In this lecture, we will review the concepts from organic and general chemistry that you should know in order to proceed in this course. Slide 2: Periodic Table with Central Elements of Bioorganic Compounds The periodic table is shown with the major components of bioorganic compounds highlighted in red. These elements, Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), Phosphorus (P), and Sulfur (S) constitute more than 99% of the mass of the organic components of living cells. Slide 3: Periodic Table with Elements Found in Living Organisms Listed here are all of 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, and other physiological functions. All of these elements must be obtained in the diet. Because they are elements, they cannot be assembled from simpler building blocks or synthesized from any other materials. Slide 4: Bond Characteristics of the Major Elements The four elements shown here are the major constituents of bioorganic compounds. The Hydrogen atom (H) has one proton and one electron, and 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 1

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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 one 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 and two single bonds, or one triple bond and one single bond to fill its outer electron shell with eight electrons. Slide 5: Special Features of Carbon What is so special about the carbon atom? The carbon atom has 4 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. Slide 6: Bond Strength of Various Covalent Bonds 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 that 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.

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Slide 7: Comparison of Carbon-Oxygen and Carbon-Silicone Bonds Carbon-carbon bonds are stronger that carbon-oxygen bonds. Therefore, carbon-carbon single bonds can form in the presence of oxygen. In contrast, silicone-silicone bonds are weaker than silicone-oxygen bonds. For this reason, silicone-oxygen bonds tend to predominate. Under the conditions that prevail on the earth, most silicone exists as some oxidation product such as SiO2 and does not form chains with itself due to the weaker nature of silicone-silicone bonds. Slide 8. Comparison of Bond Strength of Carbon, Oxygen and Nitrogen Two carbon-carbon single bonds are stronger than one carboncarbon 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 that exhibited by multiple single bonds. As a consequence, oxygen and nitrogen atoms tend to form double and triple bonds. Slide 9. Carbon Atoms Form Chains 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. Slide 10. The Methane Molecule 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 very happy.

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Slide 11. Perspective Formula for Methane Although we often depict the carbon-carbon single bonds in organic compounds as planar, they are, in fact, tetrahedral in nature. For example, in methane, if the two hydrogen atoms linked to carbon by the bold triangles were in the plane of the screen, the other two hydrogen atoms connected by the stippled triangles would radiate into the back of the screen. In this tetrahedral structure, the four hydrogen atoms are equidistant from each other. Slide 12. Rotation About Carbon-Carbon Single Bonds When two carbon atoms are linked by a single bond, the atoms are free to rotate 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. Slide 13. Another Special Feature of Carbon Compounds There is one more thing that we can add to the list of unusual features of the carbon compounds. That is, the carbon atom can exist in a variety of oxidation states. In fact, it is the ability of reduced carbon atoms to react with and be oxidized by molecular oxygen that makes it possible for most living organisms to obtain energy. Slide 14. Oxidation Levels of Carbon (In the context of bioorganic chemistry, the most reduced carbon compounds are defined as having the highest percentage of hydrogen and/or the lowest percentage of oxygen. Conversely, the 4

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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 that contain only carbon and hydrogen atoms. In alkenes, 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 aldehydes (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 alcohols, there is a carbon atom that has one bond to oxygen. -In aldehydes or ketones, there is a carbon atom that has two bonds to oxygen. -In carboxylic acids, there is a carbon atom with three bonds to oxygen. -In carbon dioxide, a carbon atom has four bonds to oxygen. Reactions that add bonds between oxygen and carbon atoms are referred to as oxidations. Reactions that remove bonds between oxygen and carbon atoms are referred to as reductions. Slide 15. Biological Importance of Oxidation-Reduction reactions There are a number of reasons to focus on oxidation-reduction reactions in our introductory consideration of bioorganic 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 from food as reduced carbon compounds. 5

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-The rich pool of oxygen in 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 Slide 16. Energy Stored in Reduced Carbon Compounds A highly reduced carbon atom contains energy that the cell can capture. For example, methane is fully reduced, and energy can be harvested by oxidizing methane using oxygen as the oxidizing agent. A highly oxidized carbon atom has no energy that the cell can capture. For example, carbon dioxide is fully oxidized, and we cannot extract any energy from it. Slide 17. Oxidation of Succinate to Oxaloacetate When we study the TCA cycle, we will see that succinate is oxidized to fumarate coupled to the reduction of FAD to FADH2. In a further step in the cycle, malate is oxidized to oxaloacetate coupled to the reduction of NAD+ to NADH. The two reduced cofactors, FADH2 and NADH, are converted back to their oxidized forms when they donate their electrons into the electron transport chain. Those electrons ultimately react with molecular oxygen to produce water. Overall, fumarate and malate are being oxidized, with molecular oxygen serving as the ultimate oxidizing agent.

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Slide 18. One More Important Feature of the Carbon Atom Carbon can form covalent bonds to a variety of other atoms including hydrogen, oxygen, nitrogen and sulfur. This versatility allows for the rich variety of compounds that we find in living organisms. Slide 19. Bonds formed by the Carbon Atom In biological compounds, certain types of bonds with the carbon atom tend to predominate. Carbon 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. Slide 20. Most Common Functional Groups in Biomolecules 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 these functional groups. Slide 21. Extended List of Bioorganic 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 is the equivalent to trying to learn a language without learning the key words. Slide 22. Alkanes An alkane compound has the general formula (CH2)n+2H. A true alkane compound consists of only carbon and hydrogen and has no oxygen and no double bonds. Although true alkanes do not occur in most living organisms, alkane like structures form the backbone of many organic compounds. For example, the linear hydrocarbon backbone structures of fatty acids have alkane like character. 7

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Alkanes are non-polar 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-alkane family. The IUPAC names of alkanes end with -ane. Slide 23. Names of Alkane Chains The name of an alkane compound identifies the number of carbon atoms in the compound. The common chain lengths for common alkanes vary from one in methane to twelve in dodecane. It would be in your best interest to (re)commit these names into your memory bank. Slide 24. Alkyl Groups When groups containing only carbon and hydrogen are connected to other parts of an organic molecule they are 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 and ethane becomes ethyl, etc.etc. Slide 25. Alkenes The alkene compounds are similar to alkanes except that they have at least one carbon-carbon double bond. They have the general formula Cn(H2)n 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 C=C double bond which makes that area of the compound a planar structure. When double bonds are present in a compound, it creates two possible isomeric forms—cis or trans isomers at the double bond. In cis 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. The addition of a double bond to a compound also makes it an 8

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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 of alkenes end with –ene. Slide 26. Alkene Compounds. Here are some examples of alkenes. Note that the two lower examples, highlighted in yellow, illustrate the difference between a cis and trans isomer. Slide 27. Alcohols Alcohols have an –OH group that is attached to a saturated carbon atom—that is, the carbon bearing the –OH group is bonded to either hydrogen or carbon atoms but not to oxygen or nitrogen. The addition of the –OH group raises the oxidation state of the carbon atom by one unit. The presence of the –OH group also increases the solubility of a compound in water compared to the corresponding alkane. The solubility of alcohols in 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 ten 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 of alcohols end in –ol. Slide 28. Alcohol Compounds 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 will learn about ethanol when we study glucose fermentation. Glycerol is a component of triacylglycerols and phosphoglycerols, which are important lipid compounds. The phenol group is a component of 9

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the amino acid, tyrosine.

Slide 29. Amines Amines have the basic form RNH2. In order to qualify as an amine, the nitrogen atom must be connected to a saturated carbon atom. For example, a non-amine would be a compound with a nitrogen atom attached to a carbon atom that also has a double bond to an oxygen atom. That compound would be an amide, not an amine. The presence of that carbonyl oxygen on the carbon dramatically changes the behavior of 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 reactive with aldehydes, ketones, carboxylic acids and acid derivatives such as acyl halides or anhydrides. Compounds containing an amine group are referred to using the prefix amino- or the suffix –amine. Slide 30. Amino Acids The amino acids have an amine group and a carboxylic acid group attached to the same carbon atom. These amino acids also have an R-group that varies for each type of amino acid. There are 20 different amino acids found in polymeric form in protein molecules. We will deal with the amino acids when we consider protein structure. Slide 31. Aldehydes Aldehydes have a central carbonyl carbon (a carbon atom with a double bond to an oxygen atom). An 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. Thus, aldehyde groups are found at the end of a hydrocarbon chain, not in the middle. A carbonyl group that is sandwiched between two carbons is referred to as a ketone (see the 10

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next slide). Aldehyde compounds have the general formula RCHO. This is a short hand 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 end in –al. Slide 32. Ketones Ketones are like aldehydes in that they have a central carbonyl carbon (a carbon atom with a double bond to an oxygen atom). A 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 RCOR. As with aldehydes, this is a short hand 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 R 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 end in –one. Slide 33. Carboxylic Acids Carboxylic Acids are like aldehydes and ketones in that they have a central carbonyl carbon. In order to qualify as a carboxylic acid, a compound must also have an –OH group connected to the carbonyl carbon. We sometimes represent carboxylic acids as RCOOH, but it important to recognize that this again is organic chemist shorthand, that one of the oxygen atoms is connected to the carbonyl carbon by a double bond and the other (-OH) oxygen is connected to that same carbonyl carbon by a single bond. There is no O-O bond.

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Carboxylic acids are called acids because the –OH part of the carboxylic acid can dissociate to form RCOO- plus a proton. The RCOO- is the conjugate base of the acid. The RCOOH, or acid form of the molecule, is designated with the ending –ic acid, for example acetic acid. The RCOO- form of the molecule is designated with the ending –ate, for example acetate. Carboxylic acids can react with amines to form an amide or with alcohols to form an ester. Carboxyl groups are very polar, and thus, short chain carboxylic acids readily dissolve in water. Slide 34. Isomers Isomers are differing forms of a molecule with the same empirical formula. There are carbon chain isomers, cis-trans isomers, functional group isomers, position of functional group isomers, geometrical isomers, and stereoisomers. Isomers differ from each other in chemical and physical properties. Slide 35. Carbon Chain Isomers Compounds 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 their common and IUPAC names. Such isomers all ha...