Chapter 24 The Chemistry of Life: Organic and Biological Chemistry Lecture Presentation Chapter 24 The Chemistry of Life: Organic and Biological Chemistry James F. Kirby Quinnipiac University Hamden, CT

Organic Chemistry and Biochemistry Chapter focus on the molecules that bridge chemistry and biology. Most common elements: C, H, O, N Organic chemistry: Study of compounds containing carbon. Biochemistry: study of chemistry of living systems.

24.1 General Characteristics of Organic Molecules Carbon can have a maximum of 4 bonds. 4 single bonds: tetrahedral, sp3 hybridized. 1 double bond: trigonal planar, sp2 hybridized. 1 triple bond: linear, sp hybridized. C—H are most common in organic molecules. C forms stable (strong) bonds with many elements, including C, H, O, N, and the halogens. Groups of atoms that determine how an organic molecule reacts are called functional groups.

Remember: Carbon can have a maximum of 4 bonds. 24.2-24.3 Hydrocarbons Alkanes (CnH2n+2) – only C−C single bonds CH3–CH2–CH2–CH3 Alkenes (CnH2n) – one or more C−C double bonds CH3–CH2–CH=CH2 Alkynes (CnH2n-2) – one or more C−C triple bonds CH3–CH2–CΞCH Remember: Carbon can have a maximum of 4 bonds.

24.2-24.3 Hydrocarbons C3H6 C4H8 C6H12 Cyclic Alkanes (CnH2n) – ring, only C−C single bonds cyclopropane cyclobutane cyclohexane Isomerism: Same formula but different bonds C4H10 C4H10 n-butane 2-methylpropane isobutane

24.2-24.3 Hydrocarbons Aromatic hydrocarbons – ring, alternating double/triple and single bonds The simplest aromatic hydrocarbon is benzene (C6H6).

24.2-24.3 Hydrocarbon Nomenclature IUPAC Rules of Naming Alkanes 1. For alkanes, add –ane to the Greek root for the number of carbons. CH3–CH2–CH2–CH2–CH2–CH3 hexane 2. Alkyl substituents: drop the –ane and add –yl. C2H6 ethane C2H5 ethyl

24.2-24.3 Hydrocarbons increasing molar mass increasing mp increasing bp

24.2-24.3 Hydrocarbons: Nomenclature Alkyl Substituents Used when the alkyl part is not in the longest hydrocarbon chain.

24.2-24.3 Hydrocarbons: Nomenclature IUPAC Rules of Naming Alkanes Prefix−Parent−Suffix What substituents? How many carbons? What family? 1. Find the parent (longest) hydrocarbon. 2. Number the atoms in the chain sequentially as such substituents are at lowest possible number along the chain. 3. Substituents are named in alphabetical order and use di–, tri–, etc. CH3–CH2–CH–CH2–CH2–CH3 CH3 3-methyl hex ane 1 2 3 4 5 6 CH3–CH2–CH–CH2–CH2–CH3 CH3 3,4-dimethyl hex ane 1 2 3 4 5 6

Name the following compounds: EXERCISE #1 Name the following compounds: a) b) 1 2 3 4 5 6 2,2,4,5-tetramethyl hex ane 3 4 5 6 7 8 2 1 3,6-diethyl-3-methyl oct ane

24.2-24.3 Hydrocarbons: Nomenclature Prefix−Parent−Suffix IUPAC Rules of Naming Alkenes 1. For alkenes, add –ene to the Greek root for the number of carbons. C2H4 ethene 2. With more than 3 carbons, double bond is indicated by the lowest–numbered carbon atom in the bond. CH3–CH=CH–CH2–CH3 2–pentene 1 2 3 4 5

24.2-24.3 Hydrocarbons: Nomenclature Prefix−Parent−Suffix IUPAC Rules of Naming Alkynes Same as for alkenes except use –yne as suffix. C2H2 ethyne CH3–CH2–CΞC–CH2–CH2–CH2–CH3 3–octyne 1 2 3 4 5 6 7 8

Name the following compounds: EXERCISE #2 Name the following compounds: a) b) 6 5 4 3 2 1 2,3,5-trimethyl-2-hexene 2 1 3 4 5 6 7 8 6-ethyl-3-methyl-3-octene

24.4 Organic Functional Groups An atom or a group of atoms attached to a hydrocarbon.

EXERCISE #3 Identify the functional group in the following hydrocarbon. a) b) c) alcohol, ROH ether, ROR’ ester, RCOOR’

24.6 Introduction to Biochemistry Biomolecules Biopolymers (large biological molecules built from small molecules. Proteins Polysaccharides (carbohydrates) Nucleic acids Lipids are large molecules, but are not polymers.

24.7 Proteins Proteins (polypeptides) H C R COOH H2N C = α-carbon R = side chains Biopolymers made up of monomers called amino acids. Biomolecules with molar masses ~ 6000 to > 1,000,000 g/mol. There are 20 amino acids commonly found in proteins. Peptide bond

20 natural a-amino acids that make up proteins

24.7 Proteins Protein structure Primary structure: the sequence of amino acids in a polypeptide strand. Secondary structure: a-helix formed from C＝O and N—H interactions between side-chains in a strand. b-sheets formed from interactions between amide H of one strand and carbonyl O of another strand.

24.7 Proteins Protein structure Tertiary structure: gives the 3D structure of proteins. Tertiary structure is formed from interactions between side-chains of multiple strands. Quaternary structure: arrangement of multiple tertiary structures and/or incorporation of non-amino acid portions of proteins.

Starch (energy source) 24.8 Carbohydrates Carbohydrates glucose Sucrose (table sugar) Biopolymers made up of monomers e.g. glucose, fructose, and/or galactose. The name comes from an empirical formula for sugars: Cx(H2O)y—for the simplest sugars, x = y. Glycoside bond Cellulose (cell wall) Starch (energy source)

24.9 Lipids Lipids Nonpolar, water insoluble biomolecules. Our energy storage (fats, oils) and building blocks in biological structures (phospholipids in cell membranes). Fats and oils are made from glycerol and long-chain carboxylic acids. Fats have only saturated carboxylic acids. Oils have at least one unsaturated carboxylic acid. Phospholipids are made from glycerol with ester linkage to two fatty acids, and phosphate ester linkage to one polar or charged group, such as choline.

24.9 Lipids Comparing Fats to Phospholipids

24.10 Nucleic Acids Nucleic acids Biopolymers made up of monomers nucleotides. DNA (deoxyribonucleic acid) stores and transmits genetic information, responsible for protein synthesis. Molar masses of several billion g/mol. deoxyribose RNA (ribonucleic acid) helps in protein synthesis. OH Molar masses 20,000 – 40,000 g/mol. ribose

22.6 – Natural Polymers Organic bases in DNA and RNA DNA OH RNA

End of Chapter 24