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MSF1- Em > Membrane Proteins 1/2 > Flashcards

Membrane Proteins 1/2 Flashcards

1
Q

How can membrane proteins act as a means by which information can enter a cell?

A

Change conformation upon ligand binding and transmit a signal across the membrane.

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2
Q

How are high levels of complexity achieved in membrane proteins?

A

Via association with different proteins and other molecules.

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3
Q

Give some molecules that associate with photosystem II?

A

Carotenoids, quinones, chlorophyll etc.

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4
Q

Describe the composition of a membrane.

A

Made of a phospholipid bilayer, complex mix of lipids and membrane proteins.

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5
Q

How are lipids within the membrane affected by hydrophobicity?

A

Hydrophobicity often dictates lipid position and function.

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6
Q

What regions of a membrane protein are associated with function?

A

Soluble regions

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7
Q

What are multipass proteins?

A

Made of several integral membrane proteins that pack together to allow the overall function of the protein.

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8
Q

How can a peripheral membrane protein be anchored to a membrane?

A

By an amphipathic helix or a lipid

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9
Q

What is an amphipathic helix?

A

One side of the helix is hydrophobic and the other is hydrophilic, allowing insertion into the membrane.

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10
Q

Which lipid modifications of membrane proteins occur on the intracellular side of the membrane?

A

Palmitoyl, N-myristoyl and Farnesyl additions.

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11
Q

Where are GPI anchors found and what do they consist of?

A

Only added on the extracellular side of the membrane. GPI anchors consist of phosphate, sugar and lipid groups.

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12
Q

What is a monotopic membrane protein?

A

A small region of the protein inserts into the membrane but does not pass all the way through.

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13
Q

Give an example of a monotopic membrane protein.

A

Electron transfer flavoprotein-ubiquinone oxidoreductase which must associate with the membrane in order to access ubiquinone which is lipid soluble.

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14
Q

Describe a beta barrel membrane protein.

A

Beta strands making up a barrel where hydrophobic residues face the lipid environment and hydrophilic residues face the hydrophilic core and interact with charged substrates. Allows formation of an aqueous pore through the membrane.

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15
Q

Give examples of beta barrel membrane proteins.

A

FepA/OmpLA- iron transport
Maltoporin- maltose transport
TolC- drug export from bacteria

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16
Q

Describe the features of an alpha helix.

A

3.6 residues per turn, stabilised by intrahelical hydrogen bonding between n and n+4 residues. All hydrogen bond donors and acceptors are used- very stable.

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17
Q

How else can alpha helices be stabilised in a membrane protein?

A

Stabilised by hydrophobic interactions between side chains that project out from the helix.

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18
Q

What is helix length partially dependent on?

A

The lipid composition of the membrane- areas including lipid rafts will be thicker and require a longer helix to cross the membrane.

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19
Q

What is given in a hydrophobicity scale?

A

The free energy required to transfer each amino acid from a lipid to an aqueous environment. If less energy is required, the amino acid is more likely to exist in an aqueous environment.

20
Q

Which amino acids are more likely to exist in an aqueous environment?

A

Charged amino acids that can form polar/hydrophobic interactions with other molecules in the aqueous environment.

21
Q

Which amino acids are more likely to exist in the membrane environment?

A

Amino acids which require a lot of energy to be transferred to an aqueous environment, e.g. Phe/Met

22
Q

Why do TM domains carry some hydrophilic and charged residues? Give an example.

A

To allow the formation of pores, necessary for transport. An example is the K+ channel formed from helices creating a helix bundle.

23
Q

What is hydrophobicity analysis?

A

Prediction of the number and location of TM domains from the primary sequence of a protein.

24
Q

Why is topology important for membrane proteins?

A

Membrane proteins are asymmetrical and must be guided into the membrane in the correct orientation in order to function properly.

25
Q

Give some functions of membrane proteins.

A

Produce oxygen, use oxygen to produce energy, ion and nutrient transport, removal of waste products/toxins from cells.

26
Q

How was it originally suggested that proteins could exist in both orientations?

A

Originally thought that there were two genes coding for the protein with different topology and charge distribution.

27
Q

What was proven to be the way proteins can exist in both orientations?

A

One gene coding for one protein, with little charge difference between inside and outside regions so can exist in either orientation.

28
Q

What is meant by the positive inside rule?

A

Membrane proteins tend to have more positively charged residues in regions on the intracellular side of the membrane- this maintains asymmetry.

29
Q

Give programs that can predict the orientation of alpha helices.

A

TMHMM and Prodiv-TMHMM

30
Q

How does TMHMM predict the orientation of alpha helices?

A

TMHMM searches for continuous stretches of hydrophobic residues and looks at the distribution of positively charged residues in flanking regions.

31
Q

What are the limitations of TMHMM?

A

Cannot predict localisation of soluble proteins or the topology of beta barrel proteins.

32
Q

Why can’t TMHMM predict the topology of beta barrels?

A

A beta barrel has a completely different distribution of charged amino acids to an alpha helix.

33
Q

How can topology be determined experimentally?

A

Generation of fusion proteins, using a marker that only folds or gives a signal in a specific part of the cell. Generate fusion proteins with the markers in different places in order to determine the location of the termini and loop regions- allows determination of the orientation of the protein in the membrane.

34
Q

How can GFP and PhoA be used to experimentally determine topology?

A

GFP- only folds and fluoresces in the cytosol
PhoA- only folds in the periplasm between the membrane
Regions that show PhoA activity shouldn’t give GFP signal.

35
Q

Describe a 3(10) helix?

A

Hydrogen bonds between n and n+3 residues. Forms a longer and thinner helix. Less stable than standard alpha helix due to hydrogen bond donors/acceptors not all being used.

36
Q

Describe a pi helix.

A

Hydrogen bonds between n and n+5 residues. Forms a shorter and fatter helix. Less stable than standard alpha helix due to hydrogen bond donors/acceptors not all being used. Can have a region of pi helix within a standard alpha helix- called a pi bulge.

37
Q

What do helix variations cause?

A

Regions of local instability which is often important for conformational change. Allows for similarly structured proteins with different functions.

38
Q

What is the role of proline residues within a membrane protein?

A

Acts as a helix breaker, forces polypeptide chain into a conformation that isn’t ideal for helix formation, causing a random coil region to form.

39
Q

What is the role of glycine residues within a membrane protein?

A

Allows tight packing of the helix and provides a flat surface for helix packing. When found either side of a TM domain, it allows the next TM domain to pack closely to the first. Can also induce local flexibility.

40
Q

What is the aromatic belt in membrane proteins?

A

Collection of Trp/Tyr residues at the transition point between the non-membrane and membrane environment as these residues can exist in both environments.

41
Q

Which lipid is essential for the folding of lactose permease?

A

Phosphatidylehthanolamine (PE)

42
Q

What is the role of cholesterol in the membrane?

A

Reduces permeability and increases the rigidity of the membrane. Involved in post-Golgi protein sorting. Necessary for lipid raft assembly.

43
Q

How can cholesterol affect membrane proteins?

A

Can stabilise certain conformations. Increases thermostability of MPs. Can affect ligand binding affinity of MPs.

44
Q

How does cholesterol bind to membrane proteins?

A

Via a groove on the surface of the protein.

45
Q

For what family of proteins is cholesterol essential for function?

A

GPCRs

46
Q

Why is cholesterol essential in macrophage membranes?

A

Allows macrophages to squeeze through layers of epithelial cells without bursting.

MSF1- Em (7 decks)

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