Chapter 4A Proteins

• Protein


  A naturally-occurring, unbranched polymer in which the monomer units are amino acids

  
• Proteins are the most abundant molecules in cells after water - account for about 15% of a cell's overall mass
• Elements present in proteins

  • Carbon (C)
  • Hydrogen (H)
  • Nitrogen (N)
  • Oxygen (O)
  • Sulfur (S)
  • Iron (Fe)
  • Phosphorus (P)
  • Other metals
• The average nitrogen content of proteins is 15.4% by mass
• Amino acid


  An organic compound that contains both an amino (-NH2) and carboxyl (-COOH) groups attached to the same carbon atom

  
• Amino acids


  • Position of carbon atom is Alpha (a)
  • -NH2 group is attached at alpha (a) carbon atom
  • -COOH group is attached at alpha (a) carbon atom

  
• Side chain (R)


  Varies in size, shape, charge, acidity, functional groups present, hydrogen-bonding ability, and chemical reactivity
• More than 700 amino acids are known
• Standard amino acids


  • 20 based on common "R" groups

  
• Groups of standard amino acids based on R-group properties

  • Non-polar
  • Polar neutral
  • Polar acidic
  • Polar basic

  
• Non-polar amino acids


  1. groups are non-polar, hydrophobic (insoluble in water), located in the interior of proteins

  
• Polar neutral amino acids

  1. groups are polar but neutral

  
• Polar acidic amino acids

  1. groups contain carboxyl group

  
• Polar basic amino acids

  1. groups contain amino group

  
• Amino acid nomenclature


  Common names, three letter abbreviations, one letter symbols

  
• 19 of the 20 standard amino acids contain a chiral center and exist in left and right handed forms

  
• The amino acids found in nature and in proteins are L isomers</b>

  
• Zwitterion


  An ion with positive and negative charges on the same molecule with a net zero charge
• Isoelectric point (pI)


  pH at which the concentration of zwitterion is maximum and net charge is zero
• Calculating pI of amino acids

  Using pK values
• Cysteine


  The only standard amino acid with a sulfhydryl (-SH) group, can form cystine via disulfide bond

  
• Peptide


  An unbranched chain of covalently-linked amino acids

  
• Types of peptides


  • Dipeptide
  • Oligopeptide
  • Polypeptide

  
• Peptide nomenclature


  1. terminal amino acid keeps full name, other amino acids have -yl suffix, sequence starts from N-terminal

  
• Peptides with same amino acids but different order are constitutional isomers

  
• Polypeptide vs Protein


  Polypeptide has at least 40 amino acid residues, several proteins have >10,000 residues, common proteins have 400-500 residues, small proteins have 40-100 residues

  
• Glutathione


  An antioxidant that protects cellular contents from oxidizing agents such as peroxides and superoxides
• Glutathione has an unusual structural feature - Glu is bonded to Cys through the side-chain carboxyl group

  
• Polypeptide


  A protein in which at least 40 amino acid residues are present

  
• Several proteins with >10,000 amino acid residues are known

  
• Common proteins contain 400–500 amino acid residues

  
• Small proteins contain 40–100 amino acid residues
• Monomeric protein


  A protein that contains one peptide chain

  
• Multimeric protein


  A protein that contains more than one peptide chain

  
• Simple protein


  A protein in which only amino acid residues are present
• Conjugated protein


  A protein that has one or more non-amino acid entities (prosthetic groups) present in its structure

  
• Lipoprotein


  A conjugated protein that contains lipid prosthetic groups

  
• Glycoprotein


  A conjugated protein that contains carbohydrate groups
• Metalloprotein


  A conjugated protein that contains a specific metal as prosthetic group
• Primary structure


  The order in which amino acids are linked together in a protein