Membrane Proteins

Question 1

describe the primary protein structure

Answer 1

a chain of amino acids with a free amino group at the N-terminus and a free carboxyl group and the C-terminus. amino acids are joined by covalent peptide bonds which are polar.

Question 2

describe secondary protein structure

Answer 2

this is the bending and folding of the peptide chain. Mainly includes alpha helices and beta pleated sheets

Question 3

alpha helix

Answer 3

maximizes hydrogen bonding as peptide bonds within a bilayer form hydrogen bonds with other peptide bonds located 4 amino acids away. Most transmembrane proteins use an Alpha helix to traverse the bilayer.

Question 4

what is necessary for an alpha helix to completely traverse the bilayer?

Answer 4

in order to completely traverse the bilayer, the transmembrane segment must be 20-30 amino acids and contain primarily non-polar or hydrophobic amino acid side chains

Question 5

integral membrane proteins (3 types)

Answer 5

1. single-pass transmembrane protein: one alpha helix in protein
2. multi-pass transmembrane protein: more than one Alph helix in protein
3. beta-barrel transmembrane protein: a rolled up beta sheet structure

Question 6

integral monotopic membrane protein

Answer 6

a hydrophobic face of an alpha helix inserts into one monolayer, but no transmembrane domain is present

Question 7

anchored proteins

Answer 7

lipid anchored protein with myristyl, palmitoyl, or farnesyl groups or
Glycosylphosphatidylinositol (GPI)-anchored proteins.

Question 8

peripheral proteins

Answer 8

associate with membranes through non-covalent interactions with integral membrane proteins

Question 9

lipid anchored proteins

Answer 9

covalently attached lipid moieties allow cytosolic proteins to associate either permanently or transiently with the cytoplasmic monolayer of the bilayer. includes Myristylated protein (myristyl group attached), palmitoylated protein (palmitoyl group attached), and prenylated protein (farnesyl group attached).

Question 10

GPI anchors

Answer 10

covalent attachment of a glycosylphosphatidylinositol (GPI) anchor to a protein. this occurs within the lumen of the ER. proteins attached to the lumenal monolayer of the ER will be exposed on the extracellular surface of the PM following vesicle transport (topological equivalence)

Question 11

topologically equivalent means

Answer 11

the environments of the area are equivalent. for example, the lumenal monolayers of the ER, Golgi, and secretory vesicles are topologically equivalent to the extracellular monolayer of the PM so the transmembrane proteins remain in the cytoplasm through transport.

Question 12

Hydropathy index plot

Answer 12

a measure of the predicted energy needed to transfer a 10-20 amino acid long segment of a protein from the bilayer into water. helps to predict transmembrane regions of proteins and thus the transmembrane topology of proteins.

Question 13

based on hydropathy index plot analysis, how many proteins are likely to have transmembrane domains and thus be membrane proteins?

Answer 13

about 30%

Question 14

how does the tertiary structure of transmembrane alpha helices come about?

Answer 14

the alpha helices are first sequentially inserted into the bilayer during cotranslational translocation of the protein in the ER. the translated protein will then fold/slide to assume tertiary structure. this sliding ability is important for the function of ion channels and enzymes because they require considerable flexibility.

Question 15

How do beta-strands of beta-barrel proteins differ from alpha helix? where are beta-barrels found?

Answer 15

beta-strands are much more rigid and beta-barrel proteins are not very flexible. they are abundant in outer membranes of bacteria, mitochondria and chloroplasts. rare in eukaryotic cells

Question 16

where are oligosaccharide attachments and disulfide bonds found and why?

Answer 16

exclusively within the extracellular domains of membrane proteins because the more acidic environment of the cytoplasm prevents formation of disulfide bonds within the intracellular domains of proteins.

Question 17

what is the glycocalyx?

Answer 17

the cell coat, composed of carbohydrates (oligosaccharide chains bound to glycoproteins, glycolipids, and proteoglycans. it is involved in cell-cell recognition processes.

Question 18

SDS

Answer 18

stron anionic detergent. it completely unfolds (denatures) proteins. proteins lose tertiary structure and their biological activity.

Question 19

Triton X-100 and betaoctylglucoside

Answer 19

mild, nonionic detergents. removes proteins from bilayers without denaturing the proteins, allowing them to be purified in biologically active states.

Question 20

describe the experiment that shows lateral diffusion of membrane proteins

Answer 20

a heterokaryon is formed with human and mouse proteins labeled with different dyes. after some time the previously separated colors are now evenly spread throughout the cell.

Question 21

describe FRAP

Answer 21

FRAP shows the lateral diffusion of membrane proteins by zapping an area with fluorescence and watching as the fluorescence becomes diffused through the cell

Question 22

what is a molecular fence?

Answer 22

structures of tight suctions that prevent lateral diffusion of some membrane proteins. restricted localization is critical for function in some cells (example sperm cells)

Question 23

4 known mechanisms for preventing lateral mobility of membrane proteins

Answer 23

1. proteins form crystalline aggregates or rafts
2. proteins bind to and be tethered by an extracellular substrate
3. proteins bind to and be tethered by an intracellular substrate
4. proteins bind to proteins expressed on the surface of other cells

Question 24

corrals

Answer 24

membrane proteins can diffuse freely within corrals but escaping from a corral is difficult.

Question 25

Bending phospholipid bilayers

Answer 25

a hydrophobic region of a protein can insert as a wedge into only one monolayer, inducing bilayer curvature.
curved surface of a protein can bind to phospholipid head groups, inducing curve
protein can bind to and cluster lipids that have large head groups, inducing curve

Question 26

How is using HDL to isolate a protein different from a detergent?

Answer 26

high-density lipoprotein renders a patch of isolated bilayer water-soluble, isolating a protein along with its native bilayer. this allows for more accurate study of the protein and its function with the bilayer intact.