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
• R group


  Side chain - vary 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
• Polar acidic and basic amino acids

  • Aspartic acid (Asp, D)
  • Glutamic acid (Glu, E)
  • Lysine (Lys, K)
  • Arginine (Arg, R)
• Glycine is the only amino acid without a chiral center
• Chirality


  19 of the 20 standard amino acids contain a chiral center and exist in left and right handed forms (L and D isomers)
• The amino acids found in nature and in proteins are L isomers
• 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
• Cysteine is the only standard amino acid with a sulfhydryl (-SH) group
• Cystine


  Two cysteine residues linked via a covalent disulfide bond
• Peptide


  An unbranched chain of covalently-linked amino acids
• Types of peptides based on length

  • Dipeptide (2 amino acids)
  • Oligopeptide (10-20 amino acids)
  • Polypeptide (large number of amino acids)
• Peptide bond


  The covalent bond between amino acids in a peptide
• Peptide nomenclature


  1. terminal amino acid keeps full name, others have -yl suffix, sequence starts from N-terminal
• Peptides with the same amino acids but in different order are constitutional isomers
• Protein


  A peptide in which at least 40 amino acid residues are present
• Protein classification by chemical composition

  • Simple proteins (only amino acids)
  • Conjugated proteins (with non-amino acid prosthetic groups)
• Primary structure of proteins


  The order in which amino acids are linked together
• Every protein has its own unique amino acid sequence
• Proteins of the same organism always have the same sequence
• Proteins from different sources (e.g. insulin from pigs, cows, sheep, humans) can have different sequences
• Prosthetic groups


  Groups that are attached to proteins and are essential for their function
• Glycoproteins


  • Contain carbohydrate groups
• Metalloproteins


  • Contain a specific metal as prosthetic group
• Primary structure of proteins

  The order in which amino acids are linked together in a protein
• Frederick Sanger (1953) sequenced and determined the primary structure for the first protein - Insulin
• Primary structure of a human myoglobin


  • Sequence of amino acids