Protein Structure and Function: From Amino Acids to Polypeptides

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∑ - Amino acids are linked together by condensation to form polypeptides.

  • Amino acids are then combined to create large polypeptides through condensation reactions which produce many molecules of water (i.e. polypeptides - Hemoglobin and Insulin).

B  Skill: Drawing molecular diagrams to show the formation of a peptide bond.

  • Basic dipeptide shown to the right. Students should practice drawing  with a variety of different amino acids (different “R” groups)
  • Every peptide bond should be between the NH2 (amine group) and the COOH (carboxyl group). One H comes from the NH2 and an –OH group comes from the –COOH group to produce H2O
  • Condensation reaction

∑ - There are 20 different amino acids in polypeptides synthesized on ribosomes.

  • Twenty different amino acids are used by the ribosomes to create polypeptides in our body
  • They all contain an amine (NH2) group, a carboxyl (-COOH) group which combine to form the peptide bond and a “R” group
  • The different “R” groups are what makes the amino acids different and allow the proteins to form a wide array of structures and functions
  • Some are charged or polar, hence they are hydrophilic
  • Some are not charged and are non-polar, hence they are hydrophobic

∑ - Amino acids can be linked together in any sequence giving a huge range of possible polypeptides.

  • Ribosomes link amino acids together forming a peptide bond according the mRNA sequence copied from the gene or genes (DNA) for a particular polypeptide
  • Since there are 20 amino acids, an enormous variety of polypeptides can be produced
  • Basically the number of different polypeptides that can be produced is 20^n, where 20 represents the number of amino acids that can be used and n represents the number of AA’s in a particular polypeptide.
  • So if a protein has 200 AA’s, the number of different combinations would be 20^200, which is an astronomically large number. Some proteins can be in the thousands or tens of thousand

∑ - The amino acid sequence of polypeptides is coded for by genes.

  • The sequence of amino acid in polypeptides is coded by the base sequence in an organism’s genes
  • Each 3 bases codes for 1 amino acid in a polypeptide
  • So if a polypeptide is 300 amino acids in length, 900 bases actually code for that polypeptide (not including the 3 base pairs that code for the stop codon). Also, the genes are actually longer as they contain non-coding regions that don't code for the polypeptide.
  • The actual coding region is called the reading frame

∑ - A protein may consist of a single polypeptide or more than one polypeptide linked together.

  • Some proteins consist of a single polypeptide, while some contain more than one polypeptide
  • Hemoglobin for example has 4 linked polypeptides, which are folded into a globular protein to carry oxygen in the blood
  • Collagen consists of 3 polypeptides wound together like a rope (structural protein in tendons)
  • Keratin consists of 2 polypeptides twisted into a double helix (structural protein in hair and fingernails). Insulin also has two polypeptides
  • Glucagon consists of only 1 alpha helix polypeptide. Glucagon breaks down glycogen into glucose when the body needs sugar for energy

∑ - The amino acid sequence determines the three-dimensional conformation of a protein.

  • There are 4 levels of proteins, primary, secondary, tertiary and quaternary
  • How a protein twists and folds to form secondary and tertiary structures is determined by the primary sequence of amino acids
  • Secondary structures for fibrous proteins such as collagen and keratin are determined by repeating sequences in the amino acid sequence. They are formed by the interactions between the amine and carboxyl groups
  • Tertiary structures which form globular proteins are still determined by the original amino acid sequence. They form from interactions between the different “R” groups causing them to fold to create an active protein

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