Biochemistry-Lehinger CH4
Home Intersection Biochemistry(4) Protein conf w/ lowest ENG = MAX # weak interactions (4) Stability is not just sum of free energies Net stability contri by weak interaction/ difference in dG maybe close to 0 Solvation shell can form around polar molecules C(alp)-N = phi C(alp)-C = psi Phi psi – any value between 180 and -180 alpH – 5.4 ANG, 3.6 AA, takes advantage of H bonds Charged prevents Pro and Gly prevents Bulk and shape prevents – ASN, SER, THR, CYS Ionic (1-3/4) forms Aromatic simarly spaced forms Dipole (terminal ends 4 not H bonding) – (+) AA at NH3 end destabilizing (-) AA at COO end destabilizing D and L AA will disrupt each other Natural L forms either Rhand/Lhand Rhand alpH betC – betSHEET - GLY and ALA forms Antiparallel – staggared (longer) Parallel – stack (shorter) When 2+ layered, R must be small betT: (4 AA) Gly and Pro – connects two antiparallel Type 1 - Non Gly as 3rd residue Type 2 - Gly is ALWAYS 3rd residue Two levels of organization: class and fold (structural) – below fold is evo rel. Protein family: primary sim, similar struc, similar func, strong evo rel SCOP is a database of protein domain/motif Multimer: mutlisubunit protein Oligomers either have Rotational symmetry: subunits pack about rotational axes to form closed struct Cyclic – around single axis Dihedral – two fold rotational Icosahedral – looks like a virus polygon Helical symmetry: subunits pack open ended spiraling away Virus capsids – circular stairs Size dictated by: Genetic coding Either copies of small or large complexes Accuracy of protein biosynthetic process Error Assisted Folding Not all fold spontaneously Folding can be facilitated by specialized proteins (molecular chaperones) molecular chaperones: interact with partially/improperly folded facilitating correct folding pathways Chap Types Hsp70 (heat shock proteins) - abundant in cells stressed by elevated T Function: bind to regions of unfolded poly peptides rich in hydrPHO preventing inappropriate aggregation Protect proteins denatured by heat and peptides being synthesized Block the folding of certain proteins that must remian unfolded until translocated across membranes Some facilitate QUAT assembly oligomeric protiens Bind and release in a cycle that involves other proteins (Hsp40) and ATP hydrolysis Chaperonins - do not fold spontaneously Proteins became known when they were found necessary for certain phages Folding pathways req two enzymes to catalyze isomerization RXNs Protein disulfide isomerase (PDI): catalyzes interchanging/shuffling of disulfide bonds until native conformation formed Elim folding intermediates with inappropriate disulfide cross links Pepdite prolyl cis-trans ismoerase (PPI): catalyzes the interconversion of the cis and trans isomers of Pro peptide bonds Slow step in the folding that contain Pro in the cis conformation
