Membrane Proteins

Question 1

Describe the beta-pleated sheet structure in proteins

Answer 1

Hydrogen bonds from between each sequential C=O and N-H groups of different parts of the strand

Question 2

Describe the structure of alpha helices

Answer 2

Every C=O links up with every N-H group every 3.6 amino acid residues

Question 3

Involvement of R groups in stabilizing alpha helices

Answer 3

None

Question 4

Name the peptide chains that link the alpha helices and beta pleated sheets

Answer 4

Loop regions

Question 5

What loop regions come in contact with

Answer 5

The solvent environment

Question 6

Number of amino acids usually found in the sharp 180 degree turns connecting anti-parallel beta pleated sheets

Answer 6

Usually four

Question 7

Kinds of tertiary protein structures formed by b-Domain structures

Answer 7

Barrels and saddles

Question 8

How a barrel structure is formed

Answer 8

Flat staggered sheet (H-bonds higher up on one chain associate with parts lower down on another chain)

Question 9

How a saddle structure is formed

Answer 9

Flat rectangular (H-bonds line up on the same spots on the chains)

Question 10

Main domains in NADH:ubiquinone oxidoreductase and each of their functions

Answer 10

1. Reaction centre: taking electrons from NADH
2. Ubiquinone binding domain: binding ubiquinone, reducing it, then releasing it
3. H+ channel: moving protons across the membrane into the intermembrane space

Question 11

Size, composition and weight of NADH:ubiquinone oxidoreductase

Answer 11

Very large, 536kDa, 16 different protein subunits, 64 membrane helices, 9 Fe-S sulphur clusters, quaternary protein arrangement, UQ binding domain, H+ channel

Question 12

Equation of NADH oxidation

Answer 12

NAD+ +2H+ + 2e- -> NADH + H+

Question 13

Equation of ubiquinone reduction

Answer 13

CoQH + H+ + e- -> CoQH2

Question 14

How electrons are transferred in the NADH reaction centre

Answer 14

Iron ions are used (Fe3+ / Fe2+) in haemoglobin molecules to transfer electrons to molecules with higher electron affinities

Question 15

How the H+ channel works

Answer 15

There are four subunits, conformational changes generate conditions for movement, as well as a series of ionisation / de-ionisation reactions. Flipping between glutamate and lysine residues.

Question 16

How ATP-ADP translocase works

Answer 16

It is an inner mitochondrial membrane carrier protein, exchanging 1:1 stoicheometric ADP and ATP. ADP goes in, ATP goes out.

Question 17

Abundance of ATP-ADP translocase

Answer 17

The most abundant in the mitochondrial membrane, 10%

Question 18

Purpose of ATP-ADP translocase

Answer 18

Provides cells with energy in the form of ATP generated inside the mitochondria

Question 19

General structure of ATP-ADP translocase

Answer 19

6 membrane helices. Appears to act as a dimer. Helices form a conical barrel. Cavity lining is hydrophobic. Lipid lining residues are hydrophobic. Size of cavity: max diameter of 20 angstrom, depth of 30 angstrom. 6xTM helices. Short alpha helical connections between odd-even TM helices

Question 20

How one side faces the periplasmic space of ATP-ADP translocase

Answer 20

Atractylosides

Question 21

How one side faces the matrix of ATP-ADP translocase

Answer 21

Bongkreic acid

Question 22

What is in the centre of the cavity in ATP-ADP translocase, and why

Answer 22

Tyrosine residues. They intercalate with adenosine moiety

Question 23

What can bind to ATP-ADP translocase

Answer 23

Only adenosine nucleotides not complexed with Mg2+

Question 24

What cationic groups interact with in ATP-ADP translocase

Answer 24

The phosphate moieties in ATP / ADP