Amino acids

• The functions of all proteins depend on the structures and properties of the twenty common amino acids. This section describes the essential features of these amino acid building blocks.
• The structure of a single typical amino acid is shown in Figure 4.1. Central to this structure is the tetrahedral alpha (a) carbon (Ca), which is covalently linked to both the amino group and the carboxyl group. Also bonded to this a-carbon are a hydrogen and a variable side chain. It is the side chain, the so-called R group, that gives each amino acid its identity. The detailed acid–base properties of amino acids are discussed in the following sections
• In a neutral solution (pH 7), the carboxyl group exists as OCOO2 and the amino group as ONH3 1
• The resulting amino acid contains one positive and one negative charge, it is a neutral molecule called a zwitterion
• Amino acids


  • They are chiral molecules
  • The α-carbon has four different groups attached to it, making it asymmetric
  • The two possible configurations for the α-carbon constitute nonsuperimposable mirror-image isomers or enantiomers
• Amino acids

  • Existence of two identifying chemical groups: amino (ONH3 1) and carboxyl (OCOO2) groups
• Polymerization of amino acids to form peptides and proteins

  1. Amino and carboxyl groups react in a head-to-tail fashion

  2. Eliminate a water molecule

  3. Form a covalent amide linkage (peptide bond)
• Peptide bond formation requires energy input
• Repetition of the reaction produces polypeptides and proteins
• The remarkable properties of proteins depend on the unique properties and chemical diversity of the 20 common amino acids
• There are several ways to classify the common amino acids. The most useful of these classifications is based on the polarity of the side chains
• s. Thus, the structures shown in Figure 4.3 are grouped into the following categories: (1) nonpolar or hydrophobic amino acids, (2) neutral (uncharged) but polar amino acids, (3) acidic amino acids (which have a net negative charge at pH 7.0), and (4) basic amino acids (which have a net positive charge at pH 7.0).
• Nonpolar amino acids


  Amino acids with alkyl chain R groups (alanine, valine, leucine, and isoleucine), as well as proline (with its unusual cyclic structure), methionine (one of the two sulfur-containing amino acids), and two aromatic amino acids, phenylalanine and tryptophan
• Nonpolar amino acids


  • Critically important for the processes that drive protein chains to fold, that is to form their natural (and functional) structures
• Tryptophan


  Borderline member of the nonpolar amino acid group because it can interact favorably with water via the NOH moiety of the indole ring
• Proline


  Not an amino acid but rather an a-imino acid
• Polar, Uncharged Amino Acids

  • Contain R groups that can (1) form hydrogen bonds with water, and (2) play a variety of nucleophilic roles in enzyme reactions
  • Usually more soluble in water than the nonpolar amino acids
• Polar, Uncharged Amino Acids

  • Asparagine
  • Glutamine
  • Tyrosine
  • Threonine
  • Serine
  • Cysteine
  • Glycine
• Amide groups


  Good hydrogen bond–forming moieties
• Hydroxyl groups


  Good hydrogen bond–forming moieties
• Sulfhydryl group


  Good hydrogen bond–forming moiety
• Glycine


  • Simplest amino acid, has only a single hydrogen for an R group, and this hydrogen is not a good hydrogen bond former
  • Solubility properties mainly influenced by its polar amino and carboxyl groups, and thus glycine is best considered a member of the polar, uncharged group
• Tyrosine has significant nonpolar characteristics due to its aromatic ring and could arguably be placed in the nonpolar group
• With a pKa of 10.1, tyrosine's phenolic hydroxyl is a charged, polar entity at high pH
• Acidic amino acids


  Aspartic acid and glutamic acid
• Acidic amino acids


  • Their R groups contain a carboxyl group
  • The side-chain carboxyl groups are weaker acids than the a-COOH group but are sufficiently acidic to exist as OCOO2 at neutral pH
  • Aspartic acid and glutamic acid have a net negative charge at pH 7
• Aspartate and glutamate


  The negatively charged forms of aspartic acid and glutamic acid
• Aspartate and glutamate play several important roles in proteins
• Many proteins that bind metal ions for structural or functional purposes possess metal-binding sites containing one or more aspartate and glutamate side chains
• Basic Amino Acids


  Three of the common amino acids have side chains with net positive charges at neutral pH: histidine, arginine, and lysine
• Histidine


  • Contains an imidazole group
  • Side-chain pKa of 6.0, is only 10% protonated at pH 7
  • With a pKa near neutrality, histidine side chains play important roles as proton donors and acceptors in many enzyme reactions
• Arginine


  • Contains a guanidino group
  • Side chain is fully protonated at pH 7
  • Participates in electrostatic interactions in proteins
• Lysine


  • Contains a protonated alkyl amino group
  • Side chain is fully protonated at pH 7
  • Participates in electrostatic interactions in proteins
• Histidine-containing peptides are important biological buffers, as discussed in Chapter 2
• Hydrophobic: Hydrophilic: Amphipathic: Alanine Proline Arginine Glutamine Lysine Glycine Valine Asparagine Histidine Methionine Isoleucine Aspartic acid Serine Tryptophan Leucine Cysteine Threonine Tyrosine Phenylalanine Glutamic aci
• The common amino acids contain a central a-carbon covalently linked to an amino group, a carboxyl group, a hydrogen, and a side chain, also known as an R group.
• The amino group of one amino acid and the carboxyl group of another amino acid can link together covalently to form an amide bond, also termed a peptide bond.
• Nonpolar amino acids


  • alanine
  • isoleucine
  • leucine
  • methionine
  • phenylalanine
  • proline
  • tryptophan
  • valine
• Polar, uncharged amino acids

  • asparagine
  • cysteine
  • glutamine
  • glycine
  • serine
  • threonine
  • tyrosine
• Acidic amino acids


  • aspartic acid
  • glutamic acid