1.2 Membrane Proteins

Question 1

can proteins and lipids move from one leaflet of the bilayer to another

Answer 1

yes, but very restricted

Question 2

general structure of amino acid

Answer 2

insert image of amino acid (slide 2)

Question 3

difference between beta strand and beta sheet

Answer 3

beta sheet is made up of beta strands

Question 4

2 main types of protein secondary structures

Answer 4

1) alpha helix

2) beta sheet

Question 5

how are protein secondary folds stabilized

Answer 5

hydrogen bonding between N-H (amide) and C=O (carbonyl) groups in the backbone

Question 6

alpha helix: how many residues per turn

Answer 6

3.6 (1 and 8 align on top)

Question 7

alpha helix: describe the directionality of the N-H and C=O groups

Answer 7

• N-H groups point up

- C=O groups point down

Question 8

where are a-helix abundant?

Answer 8

membrane proteins

Question 9

how is an alpha helix able to stick in the PM?

Answer 9

perpendicular non-polar side chains protruding to outside of the helix

Question 10

a-helix: how are amides and carbonyls of the backbone held together

Answer 10

via hydrogen bonds

Question 11

width of hydrophobic bilayer

Answer 11

30 A

Question 12

rise of a-helix

Answer 12

1.5 A/aa

Question 13

a-helix: how many aa necessary to cross lipid bilayer

Answer 13

20 AA (can be more or less)

Question 14

main structural feature of TMS domains of proteins?

Answer 14

a-helix

Question 15

a-helix: describe how the AA close to the extracellular space side helps the TMS of the protein

Answer 15

• has some hydrophobic residues that helps to penetrate the outer face of the lipid bilayer

Question 16

a-helix: describe how the AA close to the cytosolic space side helps the TMS of the protein

Answer 16

• has positively charged side chains to bind the negatively charged phospholipid head groups to help anchor the protein into the membrane

Question 17

draw an example of a hydropathy plot and label the axis

Answer 17

img slide 18

Question 18

what does a high peak represent in a hydrophobicity plot represent?

Answer 18

middle of hydrophobic transmembrane domain

Question 19

b-sheet: hydrogen bonds with what?

Answer 19

forms hydrogen bonds with another adjacent b-strand

Question 20

b-sheet: orientation of side chains

Answer 20

alternate up and down

Question 21

bacteria staining colour (+ vs -)

Answer 21

gram+ purple

gram- pink

Question 22

pros/cons of bacteria having a second, outer membrane

Answer 22

pro: additional protection
con: import is more difficult

Question 23

how have gram- bacteria gotten around the fact that the presence of an outer membrane makes import more difficult?

Answer 23

have porins: allow passage of certain nutrients

Question 24

what are the TMS of bacterial outer membrane proteins made of?

Answer 24

membrane-spanning b-strands instead of a-helices

Question 25

why do hydropathy plots not work for TMS beta sheets?

Answer 25

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)

Question 26

OmpX

Answer 26

first b-barrel crystalized

• might be adhesion protein
• protruding loops provide binding sites for other proteins

Question 27

are planar b-sheets found in the membrane?

Answer 27

no, they fold to form cylindrical b-barrels

Question 28

b-barrel structure

Answer 28

• 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

Question 29

effect of increased porin diameter on hole size

Answer 29

increase porin diameter = increased hole size

Question 30

small porin: function

Answer 30

water-filled channels selective for small-ish hydrophilic molecules (sugar)

Question 31

large porin: function

Answer 31

channels for large molecules (ie iron), plugged by a protein, but small ions can still go through