Proteins

Proteins are polymers of Amino Acids

AminoAcidballProteins provide much of the structural and functional capacity of cells. Proteins are composed of monomers called amino acids. Amino Acids are hydrocarbons that have an amino group (-NH2) and an acidic carboxyl group (-COOH).The R group represents a hydrocarbon chain with a modification that alters the properties of the amino acid. 20 universal amino acids are used to construct proteins. The variation in functional groups along the amino acid chain gives rise to the functional diversity of proteins.

Amino Acids
20 amino acids and their properties. A 21st amino acid on this table represents the non-universally found selenocysteine.
Monomers bond together through a dehydration synthesis reaction between adjacent amino and carboxyl groups to yield a peptide bond.

peptides
Three amino acids bound into a tripeptide.

How amino acids interact with each other and the environment

Use the following simulation to test how a polypeptide chain with fold based on the type of solution it is in and the composition of the amino acids.

Levels of structure

Main protein structure levels en

  • Primary Structure (1┬░): The sequence of amino acids read from the Amino or N-terminal end of the molecule to the Carboxyl or C-terminal end
    • Tyr-Cys-Arg-Phe-Leu-Val-….
  • Secondary Structure (2┬░): local three-dimensional structures that form from interactions of amino acids, like hydrogen bonding
    • Alpha Helix – coils ┬áoccurring from the H-bonds between N-H and C=O groups along the backbone of the protein
      • Alpha helix neg60 neg45 sideview
        Side view of ╬▒-helix illustrating H-bonds in magenta between carboxyl oxygen (red) and amine nitrogen (blue)
        Alpha helix neg60 neg45 topview
        Top-down view of an ╬▒-helix
      • 1gzm opm
        Side view of ribbon diagram of ╬▒-helices traversing a membrane.
    • Beta Sheets – laterally connected strands or sheets of amino acids┬áoccurring from the H-bonds between N-H and C=O groups along the backbone of the protein
      • Beta sheet bonding antiparallel-colorBeta sheet bonding parallel-color
      • Beta-meander1
        Ribbon diagram of ╬▓-sheets
  • Tertiary structure (3┬░): overall 3-D structure of the peptide chain
  • Quaternary structure(4┬░): multimeric protein structure from assembling multiple peptide subunits

 

Disruption to Structure

The weak interactions that govern the secondary and tertiary structure of proteins can be disrupted through the application of energy, removal of the water environment, alteration of salt content or changes in the pH. The unfolding or misfolding of proteins from these disruptions is called denaturation. Changes in salt and pH will disrupt the charges on amino acids to disrupt structure. Since eggs are mostly protein and water, it is understood how frying an egg can push the water out (as steam) to leave behind a a congealed gelatinous solid. Similarly, cooking generally works to denature proteins. As such, there are methods of cooking that rely , not only on heat, but on dehydration or curing (using salts) and changes in pH (using acids or bases).

Diversity of Proteins

Interactive Animation @ PDB :https://cdn.rcsb.org/pdb101/molecular-machinery/

Protein structure examples

Learn more about complexity of protein structures at the Protein Data Bank