Chapter 4 for printing - Page 1 of 34 Chapter 4 Amino Acids...

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Page 1 of 34 Chapter 4: Amino Acids and Peptides In this chapter, we learn about amino acids and peptides, the third major class of biomolecules vital for life. We start with the description of the properties of -amino acids and their chemical and biological synthesis. We then move on to a detailed discussion of poly(amino acids), or peptides, that encompass proteins and enzymes vital for living cells. 4.1 WHAT ARE AMINO ACIDS AND PEPTIDES? Amino acids are compounds that contain both an amine and a carboxylic acid. Often, they contain other functionalities as well, but the core feature is the amine (usually primary) and the terminal carboxylic acid. There are many different possibilities, depending on the location of the amino group on the carbon chain. -Amino acids have the amino group at carbon 2 (or ) of the chain, adjacent to the carboxylic acid. -Amino acids have the amino group at carbon 3 (or ), -amino acids have it at carbon 4 (or ), etc. Each of these amino acid types represent core structures found in a wide variety of naturally- occurring compounds. -Amino acids condense to make peptides, -, - and -amino acids cyclocondense to -, - and -lactams, respectively.
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Page 2 of 34 Practice problem 1: Identify the -amino acid substructure within the following compounds. Peptides are long chain molecules comprised of different -amino acid units, all joined to one another via amide bonds. The amino group of one amino acid is attached to the carboxylic acid of a different amino acid, in repetitive fashion, to create stable poly(amino acid)s that we call peptides. Oligopeptides are short chain peptides of up to a dozen or so amino acid residues, while longer chain peptides are often referred to as polypeptides . Proteins are polypeptides made in the cell for various biological functions, such as biological catalysts known as enzymes. 4.2 -AMINO ACIDS -Amino acids are by far the most common types of amino acids found in nature. Although in this discussion we draw the chemical structures of the amino acids as containing both an amino (NH 2 ) substituent and a carboxylic acid (CO 2 H), neither is ever present at the same time. This is due to the amine being more basic, and thus more easily protonated, than the carboxylate, and thus the proton would be attached to the amine nitrogen rather than to the carboxylate oxygen. As a neutral species, the amino acid would be an ammonium carboxylate. Dropping the pH would enable the carboxylate to protonate to afford a cationically-charged species, while raising the pH would lead to deprotonation of the ammonium cation. These acid-base dynamics are illustrated below. Since there are two acidic sites in the molecule, the ammonium and carboxylic acid moieties, each could undergo sequential deprotonation through the addition of a base. First, the carboxylic acid proton is removed, upon addition of one equivalent of hydroxide to the fully-protonated
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Page 3 of 34 compound. Then the ammonium substituent is deprotonated with the addition of a second
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