Biochem- 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

  
• Nomenclature - Common names


  Currently used
• Nomenclature - Three letter abbreviations


  First letter capitalized, next two not capitalized except for Asn, Gln, Trp
• Nomenclature - One-letter symbols


  Usually the first letter of the name, most abundant amino acid gets the 1st letter if more than one has the same letter
• 19 of the 20 standard amino acids contain a chiral center

  
• Chirality


  Amino acids 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 the zwitterion is maximum and the 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 nomenclature


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

  
• Peptides with the same amino acids but in different order are different molecules (constitutional isomers)

  
• Biochemically important small peptides

  • Hormones
  • Neurotransmitters
  • Antioxidants
• 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