Forces And Structures Flashcards
Hydrophobic effect
Tendency of nonpolar molecules to interact with each other rather than with water
Nonpolar: no charges, dipoles, H bond groups
Polar goes to exterior, nonpolar goes to interior
Water forms H bonded clathrates around nonpolar solutes
Van der waals
Mutually induced dipole when two atoms are brought near each other at any given instant
Gecko’s toes
Proteins fold to maximize van der waals energy, tightly packed
Alpha helix
3.6 residues, every 4th amino acid is close enough to H bond
Backbone-backbone interactions and side chain-side chain interactions
most frequently observed secondary structure
Alanine is helix former due to lack of side chain, proline (imine) and glycine (flexible) are strong helix breakers
Beta sheet
Straight and nearly completely extended rather than coiled
H bonds between peptide groups
Can be anti parallel or parallel (less common)
Frequently amphipathic, alternating patter of hydrophilic/hydrophobic residues
Interactions between adjacent beta strands form amyloids
Reverse beta turn
Glycine and proline present to reverse directions
Irregular structure
Random coil
Loops lack regular H bonded conformation
Help give proteins their individuality, frequently form the binding site
Motifs
Small functional units that are part of larger structures, for molecular recognition
Helix-turn-helix motif: most common elements by which proteins recognize specific sequences of DNA, minimally consists of a recognition alpha-helix and a support alpha-helix
Zinc finger motif: bind DNA weakly, 2 his, 2 cys side chains and Zn2+ ion
Domains
Stable, semi-independent units of structure
Interact more with each other than with residues outside of it->stability
Coiled coil domains: extremely stable, heptad repeat
Ex) GCN4 transcription factor: parallel, coiled coil homodimer DNA binding domain
Other purposes: protein-protein recognition, mechanical force transduction (myosin), viral penetration (stalk structure in haemagglutinin)
