1.2 Membrane Proteins Flashcards
can proteins and lipids move from one leaflet of the bilayer to another
yes, but very restricted
general structure of amino acid
insert image of amino acid (slide 2)
difference between beta strand and beta sheet
beta sheet is made up of beta strands
2 main types of protein secondary structures
1) alpha helix
2) beta sheet
how are protein secondary folds stabilized
hydrogen bonding between N-H (amide) and C=O (carbonyl) groups in the backbone
alpha helix: how many residues per turn
3.6 (1 and 8 align on top)
alpha helix: describe the directionality of the N-H and C=O groups
- N-H groups point up
- C=O groups point down
where are a-helix abundant?
membrane proteins
how is an alpha helix able to stick in the PM?
perpendicular non-polar side chains protruding to outside of the helix
a-helix: how are amides and carbonyls of the backbone held together
via hydrogen bonds
width of hydrophobic bilayer
30 A
rise of a-helix
1.5 A/aa
a-helix: how many aa necessary to cross lipid bilayer
20 AA (can be more or less)
main structural feature of TMS domains of proteins?
a-helix
a-helix: describe how the AA close to the extracellular space side helps the TMS of the protein
- has some hydrophobic residues that helps to penetrate the outer face of the lipid bilayer
a-helix: describe how the AA close to the cytosolic space side helps the TMS of the protein
- has positively charged side chains to bind the negatively charged phospholipid head groups to help anchor the protein into the membrane
draw an example of a hydropathy plot and label the axis
img slide 18
what does a high peak represent in a hydrophobicity plot represent?
middle of hydrophobic transmembrane domain
b-sheet: hydrogen bonds with what?
forms hydrogen bonds with another adjacent b-strand
b-sheet: orientation of side chains
alternate up and down
bacteria staining colour (+ vs -)
gram+ purple
gram- pink
pros/cons of bacteria having a second, outer membrane
pro: additional protection
con: import is more difficult
how have gram- bacteria gotten around the fact that the presence of an outer membrane makes import more difficult?
have porins: allow passage of certain nutrients
what are the TMS of bacterial outer membrane proteins made of?
membrane-spanning b-strands instead of a-helices
why do hydropathy plots not work for TMS beta sheets?
1) are shorter than a-helices (10 AA instead of 20), so less strong peaks
2) side chains alternate orientation (go between hydrophobic and hydrophilic)
OmpX
first b-barrel crystalized
- might be adhesion protein
- protruding loops provide binding sites for other proteins
are planar b-sheets found in the membrane?
no, they fold to form cylindrical b-barrels
b-barrel structure
- polar amino acids oriented towards interior of barrel
- each b-strand hydrogen-bonded to neighbour in antiparallel arrangement, curls up to form pore
- outside nonpolar
effect of increased porin diameter on hole size
increase porin diameter = increased hole size
small porin: function
water-filled channels selective for small-ish hydrophilic molecules (sugar)
large porin: function
channels for large molecules (ie iron), plugged by a protein, but small ions can still go through
