PRELIMS 5

• Amino acid


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

  • The position of carbon atom is Alpha (a)
  • -NH2 [AMINO] group is attached at alpha (a) carbon atom
  • -COOH [CARBOXYL] group is attached at alpha (a) carbon atom
• R group


  Side chain that varies in size, shape, charge, acidity, functional groups present, hydrogen-bonding ability, and chemical reactivity. Distinguishes or differentiates the amino acid from one another
• Over 700 amino acids are known
• Standard amino acids


  • 20 standard amino acids that are usually and regularly present in the protein chain
• The amino and carboxyl group are found in the horizontal line. The side-chain or the radical group and the H atom are found vertically
• Amphoteric


  The structure of amino acid is said to be amphoteric, meaning they contain 2 ionizable sites [1 proton accepting group and 1 Proton donating group]
• Zwitterion


  When both sides are ionized, the amino acids are called ampholyte or zwitterion [dipolar ion]
• The charge of the amino acids affect how each protein moves in an electric field that allows us to separate them using specialized techniques
• Non-polar amino acids


  • Hydrophobic
  • Water-fearing
  • Alkyl
  • Aromatic
• Polar amino acids


  • Neutral
  • Acidic
  • Basic
• Non-polar amino acids


  Located into the interior portion of the protein where there is no polarity
• 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 of amino acid name is compulsory and capitalized followed by next two letters not capitalized except in the case of Asparagine (Asn), Glutamine (Gln) and tryptophan (Trp)
• One-letter symbols


  Commonly used for comparing amino acid sequences of proteins: Usually the first letter of the name, when more than one amino acid has the same letter the most abundant amino acid gets the 1st letter
• Neutral non-polar amino acids


  Do not interact or poorly interact with the water, may have hydrocarbon chains, do not carry any charges
• Polar neutral amino acids


  Have a functional group capable of forming hydrogen bonds that interact with water, do not carry any charges
• Polar acidic amino acids


  Have carboxyl group like aspartic acid and glutamic acid
• Polar basic amino acids


  Have amino groups forming ionic groups like histidine, lysine, and arginine
• Classification of amino acids

  • Aliphatic side chain
  • Hydroxyl groups
  • Sulfur atoms
  • Acidic groups or their amides
  • Basic groups
  • Aromatic rings (Aromatic Amino Acids)
  • Imino acids
• Classification of amino acids by reaction in solution or charge

  • Acidic
  • Basic
  • Neutral
• Classification of amino acids by number of amino and carboxyl groups

  • Mono-amino mono-carboxylic acid (Glycine)
  • Mono-amino dicarboxylic acid (Glutamate)
• Classification of amino acids by nutritional importance

  • Essential amino acids
  • Non-essential amino acids
• Optical isomerism


  Four different groups are attached to the a-carbon atom in all of the standard amino acids except glycine, therefore 19 of the 20 standard amino acids contain a chiral center
• Chirality


  Amino acids found in nature as well as in proteins are L isomers, while carbohydrates have both L and D isomers
• Acid-base properties of amino acids

  Amino acids in solution exist in three different species (zwitterions, positive ion, and negative ion) - Equilibrium shifts with change in pH
• Isoelectric point (pI)


  pH at which the concentration of Zwitterion is maximum -- net charge is zero, different amino acids have different isoelectric points
• Cysteine


  The only standard amino acid with a sulfhydryl group (-SH group), can dimerize to form cystine
• Peptide


  Bond between amino acids, can be dipeptide, oligopeptide, or polypeptide, has an N-terminal end and a C-terminal end
• Peptide nomenclature

  Rule 1: C-terminal amino acid residue keeps its full name, Rule 2: All other amino acid residues have names ending in -yl, Rule 3: Amino acid naming sequence begins at the N-terminal
• Isomeric peptides


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

  • Hormones
  • Neurotransmitters
  • Antioxidants
• Small peptide hormones

  Best-known are oxytocin and vasopressin, produced by the hypothalamus and stored in the posterior pituitary gland, nonapeptides with a disulfide bond
• Small peptide neurotransmitters


  Enkephalins are pentapeptide neurotransmitters produced by the brain that bind to receptors and help reduce pain, best-known are Met-enkephalin and Leu-enkephalin