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Introduction to Organic Chemistry BIOB111 CHEMISTRY & BIOCHEMISTRY Session 7 Session Plan Introduction to Organic Compounds Differences between organic and inorganic compounds Functional Groups Nomenclature Structural Isomers Stereo isomers Organic Compounds Organic compounds: • All compounds or molecules containing the elements carbon and hydrogen. – • Organic compounds found in living organisms needed for life’s processes – • Carbohydrates, lipids, proteins, and nucleic acids, fats, plastics, and fuels Many common organic compounds contain: – • A compound that contains carbon is a organic compound Oxygen, nitrogen, or sulphur atoms Hydrocarbons: Organic compounds containing only carbon and hydrogen atoms are called – Sources of organic compounds: • • Nature Laboratory synthesis Organic vs Inorganic Chemistry • Organic Chemistry – Study of the compounds of the element carbon – The study of hydrocarbons & their various derivatives. – Examples: natural gas (methane CH4), petroleum, plastics, rubbers, paper, carbohydrates (sugars, starches), proteins, enzymes, fatty acids, vitamins, drugs, textiles, etc. • Inorganic Chemistry – Study of the compounds of the other 117 elements – The study of all substances other than hydrocarbons & their derivatives. – Examples: water, sulfuric acid, nitric acid, ores & minerals, air, baking powder, caustic soda, table salt, metal alloys (brass, bronze), etc. Stoker 2014, Figure 12-1 p340 Organic vs Inorganic Compounds (Properties) 0 Diversity of Organic Compounds • What is the basis for the huge diversity of organic compounds? – The ability of carbon to from covalent bonds with other elements (e.g. H, O, N and S) and itself – Each carbon has 4 unpaired electrons in it’s valence shell >>> each can be involved in one covalent bond • Total covalent bonds formed by a carbon atom = 4 Bonding of Carbon Atoms • Organic Chemistry is based on Carbon & its ability to form chains. – Carbon belongs to Group IV.A & has 4 valence electrons – Carbon shares these 4 valence e- with other atoms to acquire a noble gas arrangement of 8 valence e- • To form a stable compound: – Carbon always forms 4 covalent bonds (= shares 4 pairs of of e-) Stoker 2014, p119 Basis for Formation of Organic Compounds • What is the basis for the formation of organic compounds? – Ability of constituent atoms (within compound) to achieve a stable configuration (octet rule) – To achieve complete valence shell (satisfy octet rule): • • • • • Carbon forms four covalent bonds Nitrogen forms three covalent bonds Oxygen forms two covalent bonds Hydrogen will form one covalent bond Halogens (F, Cl, Br, I) form one covalent bond Hydrocarbons • Hydrocarbon – Organic compounds that contain only H & C atoms • Saturated Hydrocarbons – Have only single covalent bonds between C atoms – Are saturated with Hydrogen atoms – Include Alkanes (straight chains) & Cycloalkanes (carbon rings) Hydrocarbons • Saturated Hydrocarbons – – – – Have only single covalent bonds between C atoms Alkane: Propane Chemical formula: C3H8 >>> CH3CH2CH3 Ends of the chain have CH3, whereas the middle has CH2 Hydrocarbons • Saturated Hydrocarbons – – – – – Have only single covalent bonds between C atoms. Cycloalkane: cyclohexane Chemical formula: C6H12 >>> CH2CH2CH2CH2CH2CH2 No ends to the chain all connected, all are CH2 Has two less hydrogens than comparable alkane (due to lack of ends) Hydrocarbons Unsaturated Hydrocarbons – – – – Have 1 or more double or triple covalent bonds between C atoms Alkene: Propene Chemical formula: C3H6 >>> CH2CHCH3 Extra carbon-carbon = two less hydrogens in structure Alkene Alkane H H C C H Propene C H H H H H H H C C H Propane C H H H Hydrocarbons Unsaturated Hydrocarbons – – – – Have 1 or more double or triple covalent bonds between C atoms Cycloalkene: cyclohexene Chemical formula: C6H10 >>> CHCHCH2CH2CH2CH2 Extra carbon-carbon = two less hydrogens in structure CH CH2 CH2 CH Alkene CH 2 CH2 Cyclohexene CH2 CH2 CH2 Alkane CH2 CH 2 CH2 Cyclohexane IUPAC Nomenclature common Hydrocarbons Number of Carbon Atoms Prefix Alkanes Alkenes Alkynes CnH2n+2 CnH2n CnH2n-2 (Single bonds) (Double bonds) (Triple bonds) 1 Meth- Methane - - 2 Eth- Ethane Ethene Ethyne 3 Prop- Propane Propene Propyne 4 But- Butane Butene Butyne 5 Pent- Pentane Pentene Pentyne 6 Hex- Hexane Hexene Hexyne 7 Hept- Heptane Heptene Heptyne 8 Oct- Octane Octene Octyne 9 Non- Nonane Nonene Nonyne 10 Dec- Decane Decene Decyne Important rules for distinguishing between alkanes, alkenes and alkynes Nomenclature and Structure of First 10 Alkanes (Saturated Hydrocarbons) • Biob Stoker 2014, Table 12-2 p350 Summary of Organic Compounds • Biob Stoker 2014, Figure 12-2 p342 Key concept: valence shell, octet rule, atom/compound stability When an atom adopts it’s most stable state, how full is it’s valence (outer) shell? What is the octet rule? What does the octet rule say about the electron arrangement within an atom’s valance shell? Are each of the atoms that make up an organic compound more stable within the compound or as individual atoms? G Multiple atoms come together to form compounds, where the multiple atoms are attached to one another via chemical bonds. For example, to form a H2O molecule, an oxygen atom forms a covalent bonds to two separate hydrogen atoms. Are the oxygen and hydrogen atoms more stable within the H2O compound or as separate atoms and why? a) The atoms are more stable as individual atoms, as all of their electrons are paired, whereas as within compounds the atom are more reactive as some of the electrons are unpaired b) The atoms are equally stable when in the compounds and as individual atoms c) The atoms are more stable within the compound, as all of their electrons are paired, whereas as within the individual atoms some of the electrons are unpaired and reactive d) The atoms are more stable as individual atoms as they can move about more freely than when they are a part of a compound The outer shell of a carbon atom contains four unpaired valence electrons. The number of unpaired valence electrons an atom contains is equal to the number of covalent bonds the atom is capable of forming. Which of the following accurately describes the covalent bonding of a carbon atom? a) Each of the four unpaired valence electrons must form a covalent bond with another carbon atom to become more stable b) Each of the four valence electrons within the carbon atom can covalent bond to each other to become more stable c) Each of the four valence electrons of a carbon atom can form a covalent bond via electron sharing with other atoms such as hydrogen and carbon d) Each of the four valence electrons of a carbon atom can covalent bond to more than one different atom simultaneously Key concept: Saturated and unsaturated hydrocarbons What is the functional group of a saturated/unsaturated hydrocarbon? How is a unsaturated hydrocarbon different from a saturated hydrocarbon? For two compounds with an equal number of carbons, does a saturated or unsaturated hydrocarbon contain more atoms in total? Why? Compounds composed of carbon and hydrogen are referred to as hydrocarbons. Hydrocarbon derivatives can also have additional atoms such as nitrogen and oxygen. Hydrocarbons are grouped into those that are saturated and those that are unsaturated. Which of the following best describes the difference between a saturated and an unsaturated hydrocarbon? d a) The carbons within saturated hydrocarbons are connected to other carbons by single bonds, whereas at least one carbon in an unsaturated hydrocarbon connects to another carbon atom through a double or triple bond b) Saturated hydrocarbons contain only single carbon-carbon bonds, whereas unsaturated hydrocarbons contain only double or triple carbon-carbon bonds c) The carbons within unsaturated hydrocarbons are connected to other carbons by single bonds, whereas at least one carbon in an saturated hydrocarbon connects to another carbon atom through a double or triple bond d) Unsaturated hydrocarbons contain only single carbon-carbon bonds, whereas saturated hydrocarbons contain only double or triple carbon-carbon bonds Even though hydrocarbons only contain carbon and hydrogen they belong to one of three functional groups, either the alkanes, alkenes or alkynes. One of the major differences between these functional groups is the ratio between the carbon and hydrogen atoms, as more double and triple carbon-carbon bonds within a compound reduces it’s number of hydrogens. Which of the following best describes the differences between the hydrocarbon functional groups? d d a) Both alkanes and alkenes contain the same number of hydrogen atoms, but alkynes contain less hydrogen atoms due to the presence of one or more triple carbon-carbon bonds b) Alkanes contain the most hydrogen atoms attached to the carbon atoms, as there as only single carbon-carbon bonds, whereas alkenes and alkynes contain less hydrogen atoms due to the presence of double or triple carbon-carbon bonds c) Alkanes contain the most hydrogen atoms as they contain only single carbon-carbon bonds, whereas alkynes do not contain any hydrogen atoms, only carbon atoms d) Alkyne compounds contain the most hydrogen atoms due to their triple carbon-carbon bonds, alkenes have the next most hydrogen atoms and alkanes have the least hydrogen atoms, due to the presence of only single carbon-carbon bonds Common Functional Groups in Organic Chemistry • What are functional groups? – Carbon combines with other elements to form functional groups. • Sites of chemical reactions/key structural components that define how organic molecules react – – Particular functional groups undergo similar chemical reactions E.g. Alcohols (contain OH functional group) have certain chemical properties Alcohol • Functional groups are used to classify and name organic compounds. Functional groups in macromolecules Carbohydrate Glucose Alcohol Lipid Triacylglycerol (TAG) Ether Ester Carboxylic acid Alcohol Protein Amino Acid Carboxylic acid Nucleic acids: DNA/RNA Stoker 2014, p695 Nucleotide Amide Amine Amine Ether Stoker 2014, p650 Alcohol Common Functional Groups #More detail in coming slides# Common Functional Groups #More detail in coming slides# Alkane & Alkyl Groups • Alkanes are saturated hydrocarbons: Alkanes: Propane is used as a fuel for cars (LPG gas) Contain single Carbon-Carbon bonds (CH4) • Alkyl groups: • Carbon branches that has one H less than the parent • • Replace the -ane ending of the corresponding alkane name with yl. Can form a covalent bond with another atom e.g. C or N methane = methyl —CH3 ethane = ethyl —CH2—CH3 propane = propyl —CH2—CH2—CH3 Alkyl Groups • Biob Stoker 2014, Table 12-3 p351 Alkenes and Alkynes • Alkenes contain a double bond between adjacent carbon atoms. C Alkenes: Many, many units of ethene combine to make polyethylene (most common plastic) C • Alkynes contain a triple bond. C C Alkynes: Ethyne is used to generate temps of 3000 degrees used to weld metal • Aromatic compounds contain a benzene ring. Aromatic compounds: Benzene found in crude oil is used to make many industrial products (e.g. synthetic rubber) Alcohols, Thiols and Ethers • An alcohol contains the hydroxyl (–OH) functional group. Thiol Alcohols: Ethanol is present in alcoholic beverages • Thiols contain a thiol (–SH) functional group. • In an ether, a central oxygen atom is bonded to two carbon atoms (–C–O–C–). Thiols: Butenethiol is one of the compounds responsible for the smell of a skunk Ethers: Diethyl ether was used as an aesthetic in the past Aldehydes and Ketones • • Carbonyl group: A carbon atom with a double bond to an oxygen atom An aldehyde contains a carbonyl group (C=O), attached to at least one hydrogen atom Aldehydes: O H3C Formaldehyde (Methanal) is used to preserve biological specimens (e.g. cadavers) • In a ketone, the carbon of the carbonyl group is attached to two other carbon atoms Ketones: Acetone (propanone) used in paint and nail polish removers C H O H 3C C CH3 Stoker 2013, p356 Carboxylic Acids and Esters O • Carboxylic acids contain the carboxyl group – A carbonyl group attached to a hydroxyl group. Carboxylic acids: Acetic acid (ethanoic acid) is found in vinegar • An ester contains the carboxyl group between carbon atoms. Esters: Triacylglycerol (single unit of a fat and oil) contains three esters C H3 C OH O H3C C CH3 O Amines and Amides • In an amine, the functional group is a nitrogen atom with one or more carbon atoms. H3C N H H3C N CH3 H H H3C N H3C C NH2 CH3 CH3 • In an amide, the hydroxyl group of a carboxylic acid is replaced by a nitrogen group. O Amines: Butandiamine responsible for the smell of decaying fish Amides: Methanamide used to make paper Functional groups in macromolecules Carbohydrate Glucose Alcohol Lipid Triacylglycerol (TAG) Ether Ester Carboxylic acid Alcohol Protein Amino Acid Carboxylic acid Nucleic acids: DNA/RNA Stoker 2014, p695 Nucleotide Amide Amine Amine Ether Stoker 2014, p650 Alcohol IUPAC Nomenclature vs. Common Names • IUPAC (International Union of Pure and Applied Chemistry) has developed a system of nomenclature which allow each organic compound to be assign a unique name. – Prefixes are used to name hydrocarbon molecules according to the number of carbons present in the longest continuous chain of carbon bonds. Structural Representation of Organic Compounds • How are the structures of organic compounds represented? – The structure of organic compounds can be represented by: • Molecular Formula C3H8 – Indicate the number and types of atoms present in a molecule but contain no information about their arrangement. • Structural Formula – Complete – Condensed CH3CH2CH3 – Line Bond Formula Stoker 2014, pp.358 Isomers • What are structural isomers? – Molecules that have the same molecular formula, but different bonding arrangements/ structural formulas. – e.g. ethanol vs dimethyl ether propanal vs propanone – Isomers do not necessarily share similar properties. – There are two main forms: • Structural isomerism • Stereoisomerism (spatial isomerism) Conformational and Stereo Isomers • The C-C single bonds enable free rotation of the alkane chain – • Different conformational structures result from C-C single bond rotation but no bonds are broken The groups attached to a C-C single bond can: – Rotate around the bond, giving different relative arrangements called conformational isomers – In the stereoisomers the two methyl group are positioned differently: • • cis isomer = the methyl groups are on the same side of the c-c bond trans isomer = methyl groups on opposite sides of the c-c bond Stereoisomers cis trans Structural (Constitutional) Isomers • Structural isomers are compounds that have the same molecular formula but different structural formulas – Different arrangement of atoms in space • Different structural isomers result from different connectivity of atoms, which requires breaking & re-formation of bonds in the same molecule • Continuous-chain alkane – – • C atoms are connected in a continuous non-branching chain. E.g. Butane: CH3 – CH2 – CH2 – CH3 Branched-chain alkane – – 1 or more branches are attached to a continuous chain. E.g. 2-methylpropane 2-methylpropane CH3 I CH3 – CH – CH3 Methyl group Three carbon chain Structural Isomers of C5H12 • Pentane CH3 – CH2 – CH2 – CH2 – CH3 • 2-methylbutane CH3 I CH3 – CH – CH2 – CH3 • 2,2-dimethylpropane CH3 I CH3 – C – CH3 I CH3 Stoker 2014, Table 12-1 p348 Readings & Resources • • • • • • • • Stoker, HS 2014, General, Organic and Biological Chemistry, 7th edn, Brooks/Cole, Cengage Learning, Belmont, CA. Stoker, HS 2004, General, Organic and Biological Chemistry, 3rd edn, Houghton Mifflin, Boston, MA. Timberlake, KC 2014, General, organic, and biological chemistry: structures of life, 4th edn, Pearson, Boston, MA. Alberts, B, Johnson, A, Lewis, J, Raff, M, Roberts, K & Walter P 2008, Molecular biology of the cell, 5th edn, Garland Science, New York. Berg, JM, Tymoczko, JL & Stryer, L 2012, Biochemistry, 7th edn, W.H. Freeman, New York. Dominiczak, MH 2007, Flesh and bones of metabolism, Elsevier Mosby, Edinburgh. Tortora, GJ & Derrickson, B 2014, Principles of Anatomy and Physiology, 14th edn, John Wiley & Sons, Hoboken, NJ. Tortora, GJ & Grabowski, SR 2003, Principles of Anatomy and Physiology, 10th edn, John Wiley & Sons, New York, NY.