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Which amino acids are the polar charged?
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
Which amino acids are polar uncharged?
Ser, Thr, Gln, Asn
Which amino acids are nonpolar?
Ala, Val, Leu, Ile, Met, Phe, Trp, Gly, Pro, Cys and Tyr
What are the guidelines to protein folding?
- 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.
What is the primary shape of a protein?
The linear sequence of amino acids composing the protein
What is the secondary structure of a protein?
Simple, frequently-used patterns (recognizable shapes) into which parts of a polypeptide are folded
What is an alpha-helix?
- -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
What is a beta-sheet?
- -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
What are a loops?
- *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)
What is a random coil?
- 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