Organic Chemistry 2: Important Reactions In the biological world, organisms are capable of synthesizing or degrading nearly any molecule For the remainder of this class, we are going to look at the chemistry of basic biological molecules and the reaction mechanisms these molecules are involved in

Reaction Types We are going to focus on 3 basic reaction types: Nucleophilic Substitution Reactions: An electron rich atom (nucleophile) attacks a electron deficient atom Acid-Base Catalysis: Certain amino acid side chains of enzymes can accept or donate protons, making them act like acids (donate protons) or bases (accept protons) Condensation Reactions: The involve the combining of two molecules to form a larger molecule and a smaller one The reverse reaction is called a Hydrolytic Reaction. We’ll look at those as well.

Nucleophilic Substitution Reactions Terminology: Nucleophile: An electron rich atom. May be negatively charged or have an available lone pair Electrophile: An electron poor atom. May or may not have a positive charge

Nucleophilic Substitution Reactions Two types of Sn Reactions Exist They are classified and named based upon the slowest (rate limiting) step: Sn1 and Sn2 The General form of these reactions is: R:X + :Z --> R:Z + X :Z is the nucleophile X is the leaving group In a condensation reaction for the formation of a lipid from a glycerol and a fatty acid, a glycerol hydroxyl is the nucleophile attacking the carbonyl carbon of the carboxylic acid Remember: The nucleophile attacks atoms of partial positive charge

Types of Nucleophilic Substitution Reactions Sn1: The rate is dependent on the leaving group leaving Stands for: Substitution Nucleophilic Unimolecular Note: The first step is the dissociation of the chlorine

Types of Nucleophilic Substitution Reactions Sn2: The rate is dependent on the nucleophile and the substrate forming a bond at the SAME TIME the leaving group dissociates Stands for: Substitution Nucleophilic Bimolecular Steric hindrances may prevent Sn2 reactions The concentration of both reactants affects the rate

Nucleophilic Substitution Reactions Actually, many reactions are mixtures of Sn1 and Sn2 mechanisms Many factors affect whether a reaction proceeds via the Sn1 or Sn2 route, including: Nucleophilicity Bond polarizability Leaving group stability Solvent composition Think about these factors, you will see them again in Organic Chemistry

General Acid-Base Catalysis In these reactions, groups accept or donate protons, thereby acting as acids or bases In proteins, acid-base catalysis is mediated by side chains containing: Imidazole, hydroxyl, carboxyl, sulfhydryl, amino and phenol groups For an enzyme catalyzed reaction in which the enzyme abstracts a proton from a substrate, the protein is acting like a base R-H+ + R-O- --> R + R-OH

General Acid-Base Catalysis For an enzyme catalyzed reaction in which the enzyme donates a proton to a substrate, the protein is acting like an acid R-H+ + R-O- --> R + R-OH We would call this General Acid Catalysis For an enzyme catalyzed reaction in which the enzyme abstracts a proton from a substrate, the protein is acting like a base R-H+ + R-OH --> R + R-O- We would call this General Base Catalysis

General Acid-Base Catalysis: An Example Keto-Enol Tautomerization Uncatalyzed General acid catalysis: Partial proton transfer from an acid lowers the free energy of the high-free energy carbanionlike transition state of the keto-enol tautomerization General base catalysis: The rate can be increased by partial proton abstraction by a base. Concerted acid-base catalyzed reactions involve both processes occurring simultaneously. Adapted from Voet, Voet and Pratt. Fundamentals of Biochemistry, 3rd Ed. 2008.

General Acid-Base Catalysis: An Example Enzymatic Degradation of 4-Nitrophenylacetate proceeds via a General Acid-Base mechanism Imidazole nitrogen extracts proton from water initiating the reaction

Condensation Reactions Two molecules combine with the generation of a smaller molecule

Condensation Reactions Reaction of Acetic Acid and Ethanol

Looking at the Reaction Mechanism The carbonyl carbon is: Electron deficient In a trigonal planar geometry 120º between substituents The carbonyl oxygen is pulling electrons towards it Resonance stabilization The Lone Pair of the alcohol oxygen can react with the carbonyl carbon to set the whole thing in motion Remember your VSEPR Geometry

Condensation Reactions: Making Lipids from Sugars and Fatty Acids Your cells can synthesize lipids from glycerol and fatty acids in a condensation reaction 

Condensation Reactions: Polymerizing Carbohydrate Monomers

Condensation Reactions: Forming a Peptide Bond What are the amino acids in the figure? What function group is formed? Its not really this simple, but it illustrates a point!

Hydrolysis: The Opposite of Condensation In a hydrolytic reaction, we add the elements of water (H+ and OH-) across a bond Many enzymes use this kind of reaction to degrade polymers Lipases: Hydrolyze lipid esters Glycosidases: Hydrolyze carbohydrate polymers Peptidases: Hydrolyze peptide bonds Compound Name + ase : Usually indicates a hydrolase (but not always!) If it isn’t a compound name and ase, then it usually does something else: Lyase Reductase Kinase Transferase

Hydrolysis of Sugar Polymers We add water across the Glycosidic Bond of Maltose to break it and generate 2 monomers Catalyzed by a glycosidase (Maltase perhaps?)

Hydrolysis of Peptides Dipeptide (What are the amino acids) is hydrolyzed to ??? Catalyzed by a peptidase or a protease

Amino Acids Amino acids are the building blocks of proteins They consist of an amino group bonded to an -carbon, a hydrogen bonded to the -carbon and a carboxylic acid

Amino Acids and Stereochemistry The -carbon is all amino acids except for glycine is chiral Stereoisomers exist that is non-superimposable Any carbon with 4 different substituents can be chiral We describe the chirality of the -carbon as being Levorotary or Dextrorotary L- or D- Refers to how the molecule rotates polarized light

Amino Acids and Stereochemistry

Amino Acid Side Chains: Where the Action is! The amino acids are classified according to the chemical character of the R-grop attached to the -carbon Important Criteria: Polar or Nonpolar side chains Acidic or Basic Charged or uncharged Polar residues

Side Chain Classification Nonpolar (hydrophobic) Amino Acids G, A, V, L, I, P, F, W, M These amino acids have aliphatic side chains Phenylalanine and Tryptophan are aromatic Proline is cyclic Induces turns in proteins

Side Chain Classification Polar, Uncharged Amino Acids S, T, Y, C, N, Q S, T, Y have hydroxyl groups (-OH) C has a sulfhydryl (-SH) N and Q have amide side chains Uncharged at neutral pH

Side Chain Classification Acidic Amino Acids D and E have carboxylic acids on their side chains The side chains are negatively charged at neutral pH This means the pKa’s of the side chains are less than 7

Side Chain Classification Basic Amino Acids H, K and R have side chains that are positively charged at neutral pH Because these side chains have basic groups, they accept protons at pH values lower than the pKa of the side chain

Titrating Amino Acids Free amino acids can have up to 3 pKa values associated with them Carboxylic acid Amino group R-group The carboxylic acid group has the lowest pKa (~2.0) The pKa of the -amino is around 9-10 D, E, H, C, Y, K and R have R-groups that can ionize and their pKa’s range from ~4 to 12

Titrating and Amino Acid: Alanine We’ll start at a pH of 1 The carboxylic acid and the amino group are protonated As we start adding base, more and more of the carboxylic acids start losing protons until we reach pH 2.34 (the pKa of COOH) At this concentration, [NH3+CHCH3COOH]=[NH3+CHCH3COO-] (same as we learned with regular titrations) As we add more base, we deprotonate all the carboxylic acids Midway up the sharp slope increase For alanine, this is the isoelectric point As we add more base, we’ll start deprotonating the -amino group until we reach pH=9.69 (the pKa of the group) [NH3+CHCH3COO-]=[NH2CHCH3COO-] Finally we can keep adding base until the only species is: NH2CHCH3COO-

Titrating and Amino Acid: Histidine We’ll start at a pH of 1, the only species is the fully protonated form. pK1 (COOH) = 1.82 pK2 (Imidazole nitrogen) = 6.0 pK3 (Amino) = 9.17 As we start adding base, the pH increases as the carboxylic acid converts to carboxylate At pK1, the concentration of the carboxylate specie equals the concentration of the carboxylic acid species As we add more base, we start deprotonating the imidazole nitrogen At pK2, the conc. of the deprotonated imidazole group equals that of the protonated state The pI is reached then the imidazole group is completely deprotonated As we add more base, we’ll start deprotonating the -amino group until we reach pH=9.17 (the pKa of the group)

Amino Acid Titrations At the isoelectric point, the molecule has zero net charge The pH where this occurs is called the pI We can calculate the pI of an amino acid using the following equation: We average the pK values from the higher pKa that lost a hydrogen and the lowest pKa that is still protonated For example: Histidine pK1 = 1.82 pK2 = 6.0 pK3 = 9.17 We’d use the last two values Usually it will be the alpha amino and the R group pK’s that are used But we must take care to use the correct pK values!

The Peptide Bond Amino acids are joined together in a condensation reaction that forms an amide known as a peptide bond

The Peptide Bond A peptide bond has planar character due to resonance hybridization of the amide This planarity is key to the three dimensional structure of proteins