Biochem ppt

• Protein


  A naturally occurring, unbranched polymer in which the monomer units are amino acids
• Proteins are the most abundant molecules in the cells after water – accounting for about 15% of a cell's overall mass
• Elements found in proteins

  • Carbon (C)
  • Hydrogen (H)
  • Nitrogen (N)
  • Oxygen (O)
  • Sulfur (S)
  • Iron (Fe)
  • Phosphorus (P)
• 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 same carbon atom
• Amino acids

  • The position of carbon atom is Alpha (a)
  • −𝑁𝐻2 group is attached to alpha (a) carbon atom
  • - COOH group is attached to alpha (a) carbon atom
• R group


  Side chain that 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
• Types of 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 (water fearing, insoluble in water), located in the interior of proteins
• Polar neutral amino acids


  Contain polar but neutral side chains
• Polar acidic amino acids


  Contain carboxyl group as part of the side chains
• Polar basic amino acids


  Contain amino group as part of the side chain
• Common names


  Currently used for naming amino acids
• Three letter abbreviations


  Widely used for naming amino acids, first letter capitalized followed by next two lowercase except for Asn, Gln, Trp
• One-letter symbols


  Commonly used for comparing amino acid sequences, usually the first letter of the name, most abundant amino acid gets the 1st letter
• 19 of the 20 standard amino acids contain a chiral center

  
• Chiral center

  Amino acids exhibit enantiomerism (left- and right-handed forms)

  
• The amino acids found in nature as well as in proteins are L isomers

  
• Bacteria do have some D-amino acids
• Nature favors D-isomers with monosaccharides
• Fischer projection formula for amino acids


  • COOH group at the top, R group at the bottom, -NH2 group in a horizontal position, -NH2 on the left is L isomer, -NH2 on the right is D isomer

  
• Zwitterion


  An ion with + (positive) and – (Negative) charges on the same molecule with a net zero charge, formed by carboxyl groups giving up a proton and amino groups accepting a proton
• Isoelectric point (pI)


  pH at which the concentration of Zwitterion is maximum, net charge is zero, amino acids are not attracted towards an applied electric field
• Cysteine


  The only standard amino acid with a sulfhydryl group (-SH), can form covalent disulfide bonds with other cysteine residues to form cystine

  
• 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 bonds between amino acids in a peptide
• Peptide nomenclature


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

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

  • Hormones
  • Neurotransmitters
  • Antioxidants
• Oxytocin and vasopressin


  Best-known peptide hormones, produced by the pituitary gland, nonapeptides with a disulfide bond
• Enkephalins


  Pentapeptide neurotransmitters produced by the brain, help reduce pain
• Glutathione


  A tripeptide antioxidant that regulates oxidation–reduction reactions and protects cells from oxidizing agents
• Protein


  A peptide in which at least 40 amino acid residues are present, the terms polypeptide and protein are often used interchangeably

  
• Some proteins have >10,000 amino acid residues, common proteins have 400–500 residues, small proteins have 40–100 residues
• Protein classification based on chemical composition

  • Simple proteins (only amino acids)
  • Conjugated proteins (have non-amino acid prosthetic groups)
• Types of conjugated proteins

  • Lipoproteins (contain lipid prosthetic groups)
  • Glycoproteins (contain carbohydrate groups)
  • Metalloproteins (contain a specific metal as prosthetic group)
• Protein structures

  • Primary
  • Secondary
  • Tertiary
  • Quaternary