Week 4 - lipids and cell membranes part 2 Flashcards
What is the structure of bacteriorhodopsin?
- 7 TM helices
- protein uses light energy to transport protons form inside to outside, generating a proton gradient to used to form ATP
Describe the amino acid sequence of bacteriorhodopsin
- seven alpha-helical regions (mostly hydrophobic)
- charged residues in red in between
Whats the structure of porin?
- channel forming b-strands off porin
- sugars and amino acids can passively diffuse through the hydrophilic pore
- amino acid primary structure arranged alternating - hydrophobic parts in contact with membrane, hydrophilic parts lie inside of barrel
How is prostaglandin H2 synthasase 1
Describe the structure of membrane proteins
- parts of the protein that interact with the hydrophobic parts of the membrane have non-polar side-chains
- structures within the membrane are regular so that all hydrogen bonds are established
name the bond energy of covalent bonds
Ca. 100 kcal/mol
Name the bond energy of electrostatic bonds
Ca. 10-40 kcal/mol
Name the bond energy of hydrogen bonds
Ca. 1-10 kcal/mol
Name the bond energy of hydrophobic (van der waals) bonds
Ca. 0.1-2 kcal/mol
How to predict transmembrane helices accurately form the aa sequence?
Hydrocarbon core of membrane is typically 30 A wide, length that can be traversed by 20 residue aloha helix
- hydropathy plot - calc of hydrophobicity index
What is the most hydrophobic amino acid in nature?
Phenolalanine
What is the most hydrophilic amino acid found in nature?
Argenine
Was the hydropathy plot valid for detecting beta strands?
No, beta strand structure you have alternating hydrophilic/ hydrophobic energy - fluctuations in energy, not high enough
What can be used to observe the rapid lateral diffusion of lipids and many membrane proteins?
Fluorescence recovery after photobleaching (FRAP)
Explain the experiment for FRAP
What does the rate of recovery of fluoresence depend on?
Lateral mobility of the fluoresence-labelled componenet, diffusion constant D
Name the formula used to calculate rate of diffusion
S= (4Dt)1/2
S - average distance traversed in time t
D- diffusion constant
What is the average time of diffusion in phospholipid molecules?
2 mm in 1 sec (D= 1mm^2 1s-1)
Protein rhodopsin
Fibronectin
How much slower is transverse diffusion for a lipid?
About 109 times
Is transverse diffusion ever observed for a protein? Whats the result?
NO, membrane asymmetry can be perserved for long periods
What factors affect membrane fluidity?
- transition form solid-like to fluid-like depends on the length of fatty acid chains and their degree of unsaturation
- saturated are more rigid
- a cis-bond lowers Tm
Stearate
