Protein

Asp, Glu, Lys, Arg, and His

*these are the main determinants of the overall charge of a protein, which strongly affects the protein shape and its function

Ser, Thr, Gln, Asn

Ala, Val, Leu, Ile, Met, Phe, Trp, Gly, Pro, Cys and Tyr

• 1. Hydrophobic AAs occupy the folded interior of the protein to minimize contact with water
• 2. Folded surface of protein contains mostly charged and polar AAs
• 3. Secondary struc, which forms early in the folding process, enable the polar polypeptide bckbone to pernetrate the hydrophobic core of the protein
• 4. Loops that lack secondary structure are generally located on the surface of the protein.

The linear sequence of amino acids composing the protein

Simple, frequently-used patterns (recognizable shapes) into which parts of a polypeptide are folded

• -result fromH bond between NH and CO in backbone without involving Rgroups
• -twist around itself to form a rigid cylinder (one spiral = 3.6aa)
• -R groups project radially (not || to xis); H bonds are || to axis
• -can exist by itself
• can be on the outside

• -result from a H bond b/w NH and CO in the backbone without involving R groups
• -2 types: paralles and antiparallel
• -has to have @ least two strands b/c H bond goes b/w sheets & || to axis
• -tail points to N terminus; arrow points to C terminus
• -R groups project above and below sheets alternatively

• *chain of residues of variable length and shape that connect adjacent secondary structure
• -Hairpin loops-connects two adjacent antiparallel beta strands
• -Beta-turns- very short hairpin loops (e.g. 4 AAs)
• -Omega loops- compact loops that connect adjacent secondary structure (e.g. antibodies)

• the absence of recognizable secondary structure
• -found on the surface because the backbone is not bonded to itself, therefore, it is able to bond to liquid medium