Chapter 20 - Biochemistry

20.1 Composition, Structure and Function of Amino Acids

Proteins

Proteins are the most abundant class of biomolecules in all animals; major component for various tissues, enzymes, molecules and hormones that contribute to biological function

Amino Acids: building blocks of proteins; named because they each contain at least one amine (-NH2) group and carboxylic acid (-COOH) group.

• amino acids in proteins are called α-amino acids because they’re directly attached to the carbonyl group of the carboxylic acid group and to the nitrogen atom of the amine group; is the structure directly attached to the functional group
• R Group: generally highlighted in pink, often called side-chain groups
  • first category, which contains nine amino acids, contains mostly carbon and hydrogen atoms and are nonpolar
  • second category, which contains eleven amino acids contain at least one heteroatom (O, N, S) and are polar.
  • Aspartic acid and glutamic acid have R groups with carboxylic acid functional groups
  • Histidine, lysine and arginine contain groups with nitrogen atoms and are weakly basic
• Essential Amino Acids: 10 amino acids that must be present in what we eat, marked with subscript b
• α-carbon groups are chiral centers because the generic structure of an amino acid is bonded to four different groups
  • amino acid enantiomers are disignated by prefixes (D-dextro, right and l-levo, left), pertains to how the chiral atom is oriented in space
  • dextrorotary and levorotary enantiomers are designated with (+) and (-) signs according to optical properties
• Zwitterions: describes molecules that contain positive and negatively charged functional groups even when its a neutral molecule
• Deprotonates: alanine loses a hydrogen from its -NH3+ group to form an -NH2 group
• Peptides: shortest chains, only a few amino acids long
  • dipeptides: two amino acid residues
  • tripeptides: three amino acid residues
  • oligopeptides: up to twenty amino acid residues
  • polypeptides: more than twenty amino acid residues
• peptide bond: bond linking the amino acids in peptides and proteins, forms when the α-carboxylic group of one amino acid reacts with the α-amine group of another

Drawing peptide structures

1. place amino acid with free α-amine group at left end of peptide chain and the amino acid with a free α-carboxylic acid at the right end

   1. amine (N-) terminus: left end
   2. carboxylic acid (C-) terminus: right end

2. peptide name is formed from the name of its amino acids starting at the N-terminus and changing the ending of the following amino acid names to by -yl for all but the C-terminal amino acid

20.2 Protein Structure and Function

Primary (first degree) structure: sequence of amino acids starting with the N-terminus

Secondary (secondary degree) structure: first stage of folding process, pattern of arrangement of segments in a protein chain; reflects hydrophobic interactions and intermolecular forces

• α helix: coiled arrangement with R groups pointing outwards
• β- pleated sheet: puckered two-dimensional array of protein strands held together by hydrogen bonds, R groups extend above and below the pleats

Tertiary (third degree) structure: three-dimensional biologically active structure of protein that arises because of interactions between R groups on amino acids

• formed by intermolecular forces and covalent bonds - specifically disulfide bonds

Quaternary (fourth degree) structure: larger structure functioning as a single unit that results when two or more proteins associate

• strands held together by many of the same intermolecular forces and covalent bonds that determine tertiary structures
  • intermolecular forces create flexible and elastic substances
  • covalent bonds produce tissues that are hard and less flexible

Enzymes: proteins that are biological catalysts

• catabolism: breakdown of molecules
• anabolism: synthesis of complex materials from simple feedstocks
• catalysts (enzymes) speeds up reversible reaction in both directions
• higher turnover number results in a faster enzyme-catalyzed reaction
• biocatalysis: use of enzymes to catalyze chemical reactions run in industrial-sized reactors
  • run best in dilute solutions which limits production
• active sites: bind reactant molecules, called substrates, held in site by intermolecular interactions
• inhibitors: compounds that diminish or destroy effectiveness of enzymes

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