Unit 4

Question 1

3 types of membrane proteins

Answer 1

1. Integral membrane proteins
2. Lipid anchored proteins (GPI anchored, fatty acid anchored)
3. Peripheral protein

Question 2

Integral proteins _____ & ______ through lipid bilayer (single or multi). They are ______, with _____ domains anchoring them in the bilayer and ________ regions forming functional domains outside bilayer.

Answer 2

Penetrate,
Pass,
amphipathic,
Hydrophobic,
Hydrophilic

Question 3

When Integral proteins only embed into the membrane and do not emerge on both sides, called:

Answer 3

Monotopic

Question 4

With one or odd numbered membrane-spanning domains, proteins assume an _______ orientation, with ends of the protein on either side of the bilayer. With an even number of membrane-spanning domains, proteins assume one of two orientations: _____ or _____, with both ends of the proteins on the same side of the bilayer.

Answer 4

In-out,
In-In,
Out-Out

Question 5

Lipid anchored proteins do not ________ by protein portion, rather, they are linked to the _____ which embeds the membrane.

Answer 5

Embed by protein portion,
Lipid

Question 6

Two main types of Lipid-anchored proteins:

Answer 6

1. GPI-anchored proteins (protein covalently attached to glycosylated phosophtidylinositol)
2. Fatty acid anchored (attached to phosphotidylinositol)

Question 7

Peripheral proteins attach to membrane by ________ bonds that are easily ______. They are located entirely _______ of the bilayer on either _______ or _____ side.

Answer 7

weak electrostatic,
Solubilized,
Outside,
extracellular,
cytoplamsic

Question 8

Marked characteristic of peripheral proteins:

Answer 8

No lipid to anchor them,
Non-covalent interactions involved

Question 9

Proteins cross the membrane as an _______, formed by _____ bonds. ______ residues per turn. One (n) residue is H-bonded to the ______ residue above. AA side chains in lipid bilayer are all ______ .

Answer 9

alpha-helix,
hydrogen bonds,
3.6,
n+4,
Hydrophobic

Question 10

Requires about _____ AA’s in alpha helix to span through lipid bilayer. Do the math:

Answer 10

20: (depends on thickness of bilayer and length of fatty acid tails)
approx 3nm to pass through… 0.54nm / AA 3.6 residues

Question 11

In an alpha-helix that spans the lipid bilayer one time, all amino acid side chains will be ______ since they all interact with a part of the _______.

Answer 11

Hydrophobic,
hydrophobic tail of the surrounding lipids

Question 12

A single, hydrophobic helix is often found on proteins that act as receptors for _______.
The ________ part of these proteins binds the signal molecule (extracellular ligand) while their
_______ signals to the cell interior.

Answer 12

Extracellular signals,
Extracellular,
Cytosolic part

Question 13

Some alpha-helices can fold such that one face contains predominantly
___________, and the opposite face contains _________, forming an amphipathic helix. Such helices are found in ______ (multiple amphipathic helices), allowing the protein to form a
________, which function in the selective transport of large polar molecules (e.g.
______) and small charged molecules (e.g._____) across membranes.

Answer 13

Hydrophobic AA’s,
Hydrophilic AA’s,
Multipass helices,
Hydrophilic pore,
Nucleotides, sugars, amino acids,
Ions

Question 14

Proteins can also cross membrane (other than alpha helices) via:

Answer 14

B-sheets/barrels

Question 15

Two types of Beta sheets:

Answer 15

1. Parallel
2. Antiparallel

Question 16

Beta strand is a _____ protein structure, Beta sheet is a ____ protein structure. Strands bound together to make a sheet stabilized by ______. Several sheets can form a ____(more energetically favourable for more than one sheet to combine) creating an ______.

Answer 16

Secondary,
Tertiary,
H-bonds,
B-Barrel,
Aqueous pore

Question 17

Transmembrane proteins can be ______, but only by treatments that can disrupt the ______ by disrupting the ______

Answer 17

Solubilized,
Lipid bilayer,
Hydrophobic interactions in the lipid tails,

Question 18

Why you can’t just put it into an aqueous solution because of hydrophobic parts?

Answer 18

There needs to be something to shield them. It will start to aggregate with other hydrophobic proteins in that solution and once you have large enough aggregates they just precipitate out of solution.

Question 19

The most commonly used reagents for solubilisation of transmembrane proteins are
________, which are small, _______, lipid-like molecules containing both hydrophobic and hydrophilic groups.

Answer 19

Detergents,
Amphipathic,

Question 20

Two most commonly used detergents:

Answer 20

1. SDS (ionic, strong: can denature proteins)
2. Triton X-100 (non-ionic, mild: Doesn’t denature)

Question 21

Which Detergent leaves structure of protein intact and why?

Answer 21

It leaves the structure of the protein intact because it breaks apart the interactions between the bilayer and the protein.

Question 22

Detergent vs. Bilayer Lipids

Answer 22

Detergents have single tail (lipids have 2 and more cylindrical shape) and detergents have more conic shape and thus form a micelle around it.

Question 23

At low enough concentrations of detergent, it will
want to _______ and thus will______.

Answer 23

Associate with something else amphipathic,
embed in the membrane,

Question 24

As you increase the concentrations of detergent in solution, it forms into _____. The concentration where it goes from going into the membrane to becoming micelles is called the _______. Micelles form with the lipids from the bilayer in it as well as _____. Detergents have to be used ____ in order to solubilize these membrane proteins.

Answer 24

Micelles,
CMC (Critical Mycelle Concentration),
Proteins,
At/above CMC

Question 25

Although membrane proteins can diffuse within the bilayer, sometimes their movement is restricted, forming _____, which rely on ________.

Answer 25

Membrane domains,
Protein-Protein interactions

Question 26

Four types of protein-protein interactions that form membrane domains:

Answer 26

1. B/w similar proteins to cause aggregation
2. B/w membrane protein and an extracellular protein (e.g., ECM)
3. B/w membrane protein and underlying intracellular cytoskeleton
4. B/w membrane proteins on surface of two cells

Question 27

Cellular adhesion molecules (CAMs) function

Answer 27

mediate binding between cells

Question 28

Some CAMs are ______ (bind to same molecule on different cell) and some are _____ (bind to a different molecule on a different cell) and also can ____

Answer 28

Homophilic,
Heterophilic,
Mediate binding between cell and ECM,

Question 29

CAMs membrane proteins include:

Answer 29

Integrins,
Selectins,
Cadherins

Question 30

Immobilization of membrane proteins accounts for their differences in ______ (D) within the _____. The fluidity of the membrane also influences the _____. These can be studied using ______.

Answer 30

Diffusion constants,
Membrane,
Mobility of membrane proteins,
FRAT

Question 31

Other than CAMs, another way of localizing membrane proteins is via ______, which is a membrane domain that has a high concentration of specific ______. At the plasma membrane, rafts are enriched in _____ and ______ with long and _______ tails. This makes lipid raft more _____ and _____ than surrounding membrane.

Answer 31

Lipid rafts,
Lipids,
Cholesterol and glycosphingolipids,
Saturated hydrocarbon tails,
rigid and thicker

Question 32

Lipid rafts are enriched in

Answer 32

GPI-anchored proteins, where proteins going to be tethered to the membrane by this GPI anchor.