Microbial Physiology notes lec17 11-3-10

The aldehyde on the end of the retinal is the

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the aldehyde on the end of the retinal is the reactive component of the molecule ii. the schiff’s base (lysine216) is attached to the plasma membrane of the rhodopsin iii. the Nitrogen on the schiffs base attacks the aldehyde on the retinal forming a covalent bond this process requires no enzyme to catalyze the rxn because it happens spontaneously all the time so the bacterio-rhodopsin: K216(lysine216) is covalently linked to the retinal via a schiff’s base( lys216) c. The internal cavity is divided into 2 half channels it has a cytoplasmic and external side this is the Proton Pathway d. The Internal half channel is hydrophobic cytoplasmic side e. The External half channel is hydrophilic periplasmic side f. The N terminus of Rhodopsin protein is on the outside(external), and the C terminus of rhodopsin is on the inside (cytoplasmic) g. i. energy cycling: 1. hv (photon) hits the retinal and the hv is absorbed by the retinal this causes photoisomerization of the retinal from all trans to 13-cis configuration a. one of the retinal’s double bond is isomerized from a trans cis conformation therefore changing the conformation of the retinal molecule b. the change in conformation of the retinal causes conformational changes in the surrounding proteins (changes conformation of the rhodopsin protein) c. the light induced conformational change in the retinal is the key event in the H+ pumping ii. the photoisomerization of the retinal causes pKa changes in the schiff’s base and the amino acid residues around it
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1. this then results in sequential conformational changes which is differential access to the 2 half channels iii. The pKa changes and conformational changes allow access of the schiff’s base to protionation from the cytoplasmic side, or deprotonation to the external medium at any point in time 1. Cytoplasmic side of the rhodopsin protein is hydrophobic a. Therefore the  pKa weakly acidic therefore has the tendency to bind H+ i. pKA  H+ binding b. so the D96 has a high pKa that is facing on the cytoplasmic side of the rhodopsin is going to want to bind H+ 2. the external—periplasmic side of the rhodopsin protein is hydrophilic a.
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