They are the most structurally sophisticated molecules known; however, all are polymers of the same 20 amino acid monomers.  Polymers of amino acids are "polypeptide chains."  A protein is one or more polypeptide chains folded and coiled into a specific conformation (or 3D shape). They can be globules (spherical) or fibrous.  Amino acids differ in only what is attached via the 4th bond to the asymmetric carbon ("R-groups"=side chains). Side chains range from (in size) 1 hydrogen atom to a complete C skeleton with various functional groups branching off of that C skeleton.

Side Chains

nonpolar = hydrophobic
polar = hydrophilic
electrically charged = acidic (-) or basic (+) = hydrophilic because they are ionic

A peptide bond is a linkage of amino end of one amino acid to the carboxylic end of another amino acid via condensation. A polypeptide is a polymer of amino acids linked by peptide bonds.

Polypeptide backbone = ...-N-C-C-N-C-C-...
Thus the polypeptide has polarity because it has a C-terminus (H donor) and a N-terminus (H acceptor).

A protein is not just a polypeptide chain but 1 or more chains folded, coiled, twisted, and folded into a unique shape.

There are 4 levels to a protein's structure:

1. Primary is the unique sequence of amino acids.
   1. e.g. lysozyme is a antibacterial enzyme that is a simple, single chain of 129 amino acids.
   2. Fred Sanger at Cambridge University was a primary structure pioneer, demonstrating the "definition" of a protein.
2. Secondary is the coils and folds of a protein and occurs because of hydrogen bonds at regular intervals along the polypeptide backbone.  O and N have weak electronegative charges; the weak positive H is attracted to the O and N of a nearby amino acid.
   1. types include the pleated sheet ( I.) and the alpha helix ( II.)

      I.  /\/\/\/\/\/\/\/\/\/    |  |  |  |  |  |  |      /\/\/\/\/\/\/\/\/\/ | = bonds /\/ = polypeptide

      II.

      A pleated sheet is where 2 regions of a chain run parallel to each other making up dense globular cores of many proteins.  Pleated sheets dominate fibrous proteins like spider silk (silk has strength because of the many pleated sheets).  An alpha helix has hydrogen bonds every 4th peptide bond and is the reason for a protein's twists.

3. Tertiary consists of irregular contortions between the side chains of each amino acid.
   1. Hydrophobic interaction
      • as the protein folds, the hydrophobic R groups congregate to the core of the protein out of contact with the solvent.
      • mutual exclusion keeps the hydrophobes in clusters
      • actually caused by water's behavior:  excluding the nonpolar stuff.
   2. H bonds between side chains
   3. Ionic bonds between basic and acidic R groups
      • helps cumulatively stabilize the protein
   4. Disulfide bridges are strong covalent bonds
      • form where 2 cysteine (amino acid with SH) monomers are brough close together by primary and secondary levels of structure
      • thus the sulfurs bond to each other very tightly forming a "hairpin turn" in the protein
4. Quarterny is the overall protein structure, intertwining tertiary structures.

The Roles of Proteins in the Human Body:

Type	Function	Example
Enzymatic	catalysis	sucrase
Structural	infrastructure/extrastructure	silk / collagen
Transport	transport other molecules	lipoprotein (moves fat)
Receptor	transfer electrical impulses	neuron mitochondrial membrane
Storage	store material for embryonic development	egg whites
Hormonal	send messages	insulin
Contractile	movement	actin/myosin
Defensive	protection against foreign invasion	leukocytes (White Blood Cells)

Impacting the Rate of Enzyme Activity:

A Change In...	Details
pH Temperature concentration solvent/environment	ideal= 6-8; preferably 7-7.5 hot denatures; cold inhibits higher % = faster rxn not all solvents are equal (chemically)