Membrane Proteins Flashcards
How are bilayers different to micelles?
What do bilayers allow the free flow of?
What property does the membrane have?
What are lipid rafts?
Bilayers have 2 lipid tails but micelles have 1
Large polar molecules/ions
Fluid & mosaic
Lateral separation of lipids to produce organised bilayer - high in cholesterol & are resistant to detergents
What are the 2 features of water soluble globular proteins?
What are the 2 features of globular membrane proteins?
What are peripheral membrane proteins bound to?
What are they soluble in? How would you elute them?
How do lipid-linked membrane proteins bind to the bilayer?
- Diffuses in 3D space in water
- Core buried hydrophobic residues
- Most freely diffuse in 2D space in membrane (but not across it)
- Areas of surface hydrophobic residues & have hydrophilic core
Phospholipid head by electrostatic/hydrogen bonds
Water - salt, pH, chelators
Through tails: GPI anchor, prenylated tails or fatty acid acylated tails
How do integral membrane proteins bind to the bilayer?
What are the properties of integral membrane proteins?
How can you make integral membrane proteins soluble?
How would you elute them?
What is the critical micelle concentration?
Why is SDS-page not used against integral membrane proteins?
Why are detergents favoured in micelle formation?
Hydrophobic interactions
Surface hydrophilic so coexists with water - surface inside bilayer is hydrophobic (no H bonding)
Non-ionic detergents
Chromatography - detergent (micelles) breaks bilayer (by lipid-lipid tail interactions) & use phospholipids to reconstitute into vesicles
Concentration above the detergent can form micelles
Ionic detergent - doesn’t break lipid-lipid interactions
Only have 1 hydrocarbon tail
What secondary structures can be inbedded in the membrane?
What is crucial about these and why?
What is hydrogen bonded in the alpha helix?
What is hydrogen bonded in the beta sheet?
In what form will a beta sheet motif be satisfied?
Which beta motifs are not observed?
What else cannot exist in the hydrophobic core of the bilayer?
Alpha helices & beta strands
Span the bilayer - no free hydrogen bonds permitted
Between C=O and N-H
C=O and N-H at centre of the sheet - but hydrogen bonds between sheets are not ok
Beta barrel
Single beta strand or beta sheet
Free N or C-terminal ends, loops & turns - all must SPAN bilayer
What do hydrophobicity plots measure?
What are the hydrophobicities of amino acids based on?
How do you create a hydrophobicity profile? 4 steps
What does a positive peak/negative valley indicate?
What does this method assume?
What are its limitations?
How do you predict the “inside-outside” topology after the helices are identified?
Predict whether protein is water-soluble or membrane-bound from the sequence
Free energy of transfer of sidechain from water -> hydrophobic phase, observed distribution of side chain between surface & interior proteins
- Assign score to each AA in sequence
- Slide 21-residue window along sequence
- calculate average hydrophobicity inside window
- plot calculated average vs position of window in sequence
+ = membrane-spanning helices
- = hydrophilic region
Membrane-spanning a-helices are hydrophobic
Only picks up a-helix
inter-helix loop is short then “positive-inside” - whichever side has most +ve is the inner side of membrane protein
What is the 3 step mechanism of GPCRs?
What are the properties of the 4 different subunits C L M and H of the photosynthetic reaction centre?
How was this structure crystallised?
In what subunits are the prosthetic groups?
What type of protein is this?
What forms the chlorophyll?
What does this do?
- Hormone/ligand binds
- Receptor changes shape on interior side cell - G-protein binds & activated
- G-protein breaks apart & alpha subunit triggers downstream events
C = peripheral (outside), L & M = 5 membrane helices (inside bilayer), H = 1 membrane helix (cytoplasm)
Detergent & small amphiphiles (to replace large detergent molecules which disturb crystal)
M & L (inside bilayer)
Helices D & E form 4 a-helix bundle in L&M subunits
a-helical membrane protein
Photons absorbed produce energy to transmit electrons from chlorophyl to quinones which are released for reaction
What is the crystal structure of a porin?
What are its features?
What are porins found in & what do they do?
What cannot enter through?
How are ionic molecules affected on how they pass through?
16-stranded beta barrel - antiparallel strands - trimeric
Hydrophobic outer surface & hydrophilic core surrounding aqueous pore
Chloroplasts & outer mitochondrial membranes - uptake & disposal of nutrients/waste
Large molecules (red loop size) & hydrophilic molecules
Channel side lined with +ve charge & other side with -ve charges
What are the 3 types of membrane transporters?
What is the structure of a human Na+-K+ ion channel?
How can the bacterial K+ ion not select for other cations?
Why can Na+ not come through?
Active pumps (ATP)
Channel proteins (rapid ion movements)
Transporters (coupled or down conc gradient)
Four subunits (tetramer) with 6 helices, H5 loop between S5 & S6 & N-terminus that (in)activates open channel
Has 3 helices subunits so pore only permits K+ to pass through pore with oxygens lining it
Smaller, higher solvation energy
