Mem. proteins structure + function (B1,2)

Question 1

How can membrane proteins be classified?

Answer 1

By how easily they dissociate from the lipid bilayer
Peripheral = easy
Integral = hard

Question 2

How can integral and peripheral proteins be removed from the lipid bilayer?

Answer 2

Integral = interacts extensively with fatty acid tails of phospholipids, can be released by introducing detergents which compete with non-polar reactions, integral proteins form micelles with the detergents

Peripheral= mainly bound by electrostatic + H-bonds, changing pH or adding a salt can release protein (adding NaCl)

Question 3

Name three types of lipid anchor

Answer 3

Acylation, prenylation and GPI anchor

Question 4

Describe acylation anchor

Answer 4

• Covalent amide bond formed at N-terminus glycine (simplest AA) with C12 or C16 carboxylic acid
• Normally co-translational - remove methionine to expose glycine residue
• Inner leaflet
• Distorts membrane as only single HC chain

Question 5

Describe prenylation anchor

Answer 5

• Thioether link with C-terminal cysteine residue (has CH2-SH group)
• Post translational (c-terminal = need whole peptide formed first)
• Signature motif Cys- a - a - X (a-a-X removed after attachment)
• Single HC chain so distorts membrane
• Example = Ras family of small GTPases
• Inner leaflet

Question 6

Describe GPI anchor

Answer 6

• Glycosyl phosphatidyl inositol anchor
• Modified C-terminus (post-translational)
• Peptide linked to ethanolamine phosphate, oligosaccharides, glucosamine and inositol phosphate with double fatty acid tails
• Doesn’t distort membrane as has double tail
• Outer leaflet (signalling)

Question 7

What residues would you expect lining the hydrophilic core of a channel protein?

Answer 7

Charged/polar AAs
Lysine, arginine, aspartic acid…

Question 8

What residues would you expect on the hydrophobic lipid facing side of a channel protein?

Answer 8

Non-polar/uncharged AAs
Leucine, glycine, tyrosine

Question 9

Describe a beta channel with an example

Answer 9

Porins in bacteria
Antiparallel strands forming a beta sheet which curves to form channel
Alternating hydrophobic and hydrophilic residues- hydrophobic facing lipid
Ring structures at top and bottom to act as dampers at the interphase- stops channel from going to far into mem. and too far out into extracellular

Question 10

Advantage of having anti parallel structure

Answer 10

Maximises interaction between residues to allow many H-bonds
H-bonds protect residues from hydrophobic environments (lipid bilayer)

Question 11

Why aren’t porins good for eukaryotic cells?

Answer 11

let anything in and out
Electrochemical gradient disrupted and membrane polarity changed
Can’t send nerve signals, photosynthesis or respiration

Question 12

Describe an alpha helical integral protein with an example

Answer 12

Span the membrane, alpha helical portion = exact length of membrane
H-bonds protect from hydrophobic environment
Bacteriorhodopsin
Hydrophobic regions = transmembrane domain
Conserved charged residues have functional properties

Question 13

What is hydropathy free energy?

Answer 13

Free energy of transfer of residue in alpha helix from membrane interior to water
Positive free energy = hydrophobic (phenylalanine)
Negative free energy = hydrophilic (Arginine)

Question 14

How can a hydropathy plot predict protein structure? Why doesn’t this work for beta barrels?

Answer 14

Window of around 19 residues spans the membrane exactly
If that window above +84 free energy then region predicted to cross the membrane (hydrophobic region)
Beta barrels have alternating hydrophobic and hydrophilic residues that never go above the +84 threshold so can’t predict which part= transmembrane

Question 15

Describe passive transport

Answer 15

Movement down electrochemical gradient with channels
Channels can’t directly control movement so rely on gradients

Question 16

Describe the generic structure of a channel

Answer 16

Hydrophobic interface protecting pore from hydrophobic mem.
Narrow pore with selectivity filter
Some have gates in pore which allow switching on (open) or off (closed)

Question 17

Why are aquaporins important? Describe features, example of where found

Answer 17

Normal water osmosis fairly slow- aquaporins increase rate at which H2O flows through mem.
Typically bidirectional, very fast, very selective as blocks ions and protons
In kidneys- rapid water reabsorption into bloodstream after filtration

Question 18

Describe hour glass structure of aquaporins

Answer 18

4 peptide chains (4 subunits = tetramer)
Helices tilted 30 degrees
Each individual sub unit has own pore (no evidence of cooperativity)
Pseudo-twofold symmetry- each subunit = 6 helices
Inverted topology repeat

Question 19

Describe key residues on aquaporin channels and what they do

Answer 19

Histidine- very large AA, allows size restriction, only water can fit through
Arginine- Electrostatic regulation, has positive charge so repels positive molecules
Conserved Asparagine, proline, alanine- Asparagine interacts with H2O to break water column preventing proton entry
Water dipole reorientation

Question 20

Why are protons not co-transported ?

Answer 20

If water channel was uninterupted chain of H2O protons could be co-transported via “proton conducting wire”
Prevented by asparagine residues forming H-bonds with water- breaking the “wire”

Question 21

How is leakage of molecules and ions prevented with GLUT1 carrier protein?

Answer 21

Closure on protein that allows glucose into cytosol and prevents other molecules from extracellular environment into cell