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BIOCH 320 > membrane proteins > Flashcards

membrane proteins Flashcards

1
Q

are membranes flexible

A

yes

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2
Q

are membranes self sealing

A

yes

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3
Q

when does shape change of membrane occur

A

growth, division, endo/exocytosis

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4
Q

are membranes thick or thin

A

thin - essentially 2D

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5
Q

why is it good that membranes are thin

A

they enhance reaction rates

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6
Q

are membranes permeably

A

selectively permeable

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7
Q

can polar molecules pass through the membrane

A

they have a limited ability to pass through

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8
Q

what drives the formation of the membrane

A

hydrophobic effect

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9
Q

where are a majority of the glycolipids in the membrane

A

extracellular lumen

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10
Q

are glycolipids more on the cytosolic or lumen side

A

lumen

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11
Q

how do individual lipids orient in the bilayer

A

based on distribution of hydrophobic and hydrophilic character

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12
Q

what/were is lateral diffusion

A

within a leaflet

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13
Q

how fast is lateral diffusion + why

A

very rapid because interactions are non covalent and there is little barrier to motion

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14
Q

how fast is transverse diffusino

A

slow

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15
Q

what are the 3 stages of increasing temperatures in bilayers

A

gel phase –> liquid ordered state –> liquid disordered state

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16
Q

what is another name for the liquid ordered state

A

the liquid crystal state

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17
Q

how do they maintain fluidity in membranes

A

by altering membrane lipids (homeoviscous adaptation)

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18
Q

what is the protein-lipid composition myelin sheath and why

A

more fatty and glycolipids (lower polarity) because its an insulator for nerve signals

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19
Q

what is the protein-lipid composition inner mitochondrial membranes and why

A

high in protein cause of energy production OXPHOS, ETC

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20
Q

where are the carbohydrate aspects of glycoproteins/ glycolipids (where in the plasma membrane)

A

facing exterior to cell at the plasma membrane

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21
Q

where does synthesis of lipids carry out in eukaryotes

A

integral membrane proteins in ER in eukaryotes

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22
Q

where does synthesis of lipids carry out in prokaryotes

A

integral membrane proteins in plasma membrane in eukaryotes

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23
Q

what can happen with an appearance of specific lipids in other leaflets trigger
+ example

A

it can trigger other events

appearance of phosphatidylserine in outer leaflets triggers cell for engulfment/degradation

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24
Q

what does appearance of phosphatidylserine in outer leaflets trigger

A

engulfment/degradation

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25
Q

are membranes symetrical

A

no

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26
Q

are lipids distributed symmetrically in the membrane

A

no

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27
Q

how are lipids distributed in the membrane

A

asymmetrically

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28
Q

how are proteins distributed in the membrane

A

they all have the same orientation/directionality in the membrane (like all the same proteins in the same membrane would be pointing in the same direction, not like one is up and another is down)

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29
Q

where are most choline containing lipids in erythrocyte membranes

A

primarily in the outer leaflet

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30
Q

where are most sphingomyelin in erythrocyte membranes

A

primarily in the outer leaflet

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31
Q

where are most phosphatidylcholine lipids in erythrocyte membranes

A

primarily in the outer leaflet

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32
Q

which lipid should only be in the inner leaflet

A

phosphatidylserine primarily in the outer leaflet

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33
Q

what can changes in phospholipid distribution signal

A

signal or target cell for death

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34
Q

how fast is movement of lipids from one from one leaflet to another in bilayers

A

slow

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35
Q

how fast is movement of lipids from one from one leaflet to another in membranes

A

rapid

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36
Q

what do integral membrane proteins do for movement of lipids

A

help reduce the energy barrier for movement of lipids

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37
Q

what kind of proteins help reduce the energy barrier for movement of lipids

A

integral membrane proteins

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38
Q

what does lipid asymmetrical transport require

A

input of energy (active transport process)

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39
Q

what do flippases do

A

import lipids from outside the cell to inside the cell

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40
Q

what do floppases do

A

export lipids from interior of the cell to the exterior of the cell

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41
Q

what do scramblases do

A

passive transport to equalize concentrations between leaflets

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42
Q

is flippase active or passive (What kind)

A

primary active

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43
Q

is floppase active or passive (What kind)

A

primary active

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44
Q

is scramblases active or passive

A

passive transport

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45
Q

which flip or flop would deal with phosphatidylserine

A

flippase

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46
Q

which flip or flop would deal with phosphatidylethanolamine

A

flippase

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47
Q

which flip or flop would deal with phosphatidylcholine

A

floppase

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48
Q

which flip or flop would deal with phosphatidylsphingolipids

A

floppase

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49
Q

can proteins associated with the cytoskeleton diffuse laterally

A

maybe not

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50
Q

why can some proteins not be able to diffuse laterally

A

if theyre anchored/associated with the cytoskeleton

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51
Q

what are the 3 main types of membrane proteins

A

peripheral
lipid linked
integral

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52
Q

what are the integral membrane proteins

A
  • lipid linked

- integral

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53
Q

are peripheral membrane proteins integral

A

no

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54
Q

are lipid linked membrane proteins integral

A

yes

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55
Q

how can you isolate/remove peripheral proteins

A

through moderate changes like pH and salt

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56
Q

how can glycosylated phosphoinositol linked proteins be removed from the membrane

A

through the action fo phospholipases (C or D)

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57
Q

are proteins or lipids more free to move in the membrane

A

lipids usually i think

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58
Q

how can you isolate/remove integral membrane proteins

A

using detergents or organic solvents to mimic the hydrophobic environment of the membrane

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59
Q

are integral or peripheral membrane proteins easier to isolate from the membrane

A

peripheral

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60
Q

how can you classify integral membrane proteins (2)

A

based on structural composition of transmembrane region

or

topology

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61
Q

what are 3 classifications on integral membrane proteins

A

whether the transmembrane region is

  • single helices
  • helical bundles
  • beta barrels
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62
Q

what are 2 classifications for classifying membrane proteins based on topology

A
  • how many times they pass the membrane

- where the N terminal is located

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63
Q

what is bitopic

A

when the proteins passes 1 time through the membrane

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64
Q

what is polytopic

A

when the protein passes multiple times through the membrane

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65
Q

what is monotopic + 2 examples

A

when the membrane proteins are found only associated with one side of the membrane
ex: peripheral and lipid anchored proteins

66
Q

what do you call it when the N terminal is on the inside of the cell

A

cytosolic

67
Q

what do you call it when the N terminal is on the outside of the cell

A

lumen or extracellular

68
Q

what is a type 1 integral membrane protein

A

single transmembrane domain with C on interior (cytosolic) and N on exterior (lumen or extracellular)

69
Q

what kind of transmembrane regions can be described as polytopic

A

helical bundles and beta barrels

70
Q

what is a type 2 integral membrane protein

A

single transmembrane domain with N on interior (cytosolic) and C on exterior (lumen or extracellular)

71
Q

how many amino acid residues per turn

A

3.6

72
Q

how many angstroms per residue

A

5.4

73
Q

what is glycoPhorin (where found)

A

eryhtyocyte protein

74
Q

what is special about glycophorin

A

it is heavily modified with sialic acid derivativs

75
Q

what does glycophorin associate as

A

a dimer in the membrane

76
Q

where is the N terminal in glycophorin

A

extracellular

77
Q

what type of integral membrane protein is glycophorin

A

type 1 bitopic membrane protein

78
Q

what happens to the N terminal in glycophorin

A

it is glycosylated

79
Q

what happens to the C terminal in glycophorin

A

nothing

80
Q

which terminal of glycophorin is modified and how

A

N terminus is glycosylated

81
Q

where is the C terminal in glycophorin

A

intracellular

82
Q

what kind of transmembrane region crosses the membrane in glycophorin

A

a single alpha helix

83
Q

what kind of residues are seen in the alpha helix in the membrane of glycophorin

A

hydrophobic

84
Q

how does the asymmetry of glycophorin compare to other integral membrane proteins

A

similar, applicable to other ones

85
Q

how many amino acids typically cross the membrane with integral membrane proteins

A

20

86
Q

what kind of amino acids typically cross the membrane with integral membrane proteins

A

hydrophobic

87
Q

which terminal of many intergral membrane proteins is modified and how

A

N terminus domain is glycosylated

88
Q

which terminus of glycophorin is heavily modified with sialic acid derivatives

A

N terminus domain

89
Q

why is it good for glycophorin to be heavily modified with sialic acid derivatives in erythrocytes

A

So with 2 erythrocytes close together will repel electrostatically, so this way they can flow easily in the blood stream

90
Q

how many transmembrane helices in bacteriorhodopsin

A

7

91
Q

how long are each helix in bacteriorhodopsin

A

around 20 aa long

92
Q

what kind of structure is in bacteriorhodopsin

A

polytopic alpha-helical bundle

93
Q

what are exposed protein domains similar to

A

structures resembling soluble globular proteins

94
Q

what is the exterior like in transmembrane domains

A

hydrophobic (transmembrane so still in the membrane, not like exterior of the protein)

95
Q

what is the interior like in transmembrane domains

A

hydrophilic residues clustered in the interior ion channel

96
Q

what will the amino acids be like that are exposed to the exterior aqueous environment

A

polar

97
Q

what can helical transmembrane domain be like

A

single pass or multi pass

98
Q

how many amino acids are in transmembrane structures

A

usually 20

99
Q

what kind of amino acids are in transmembrane structures

A

hydrophobic

100
Q

how can you determine helical transmembrane structures

A

using a hydropathy plot

101
Q

are helical transmembrane structures single pass or multo pass

A

either or

102
Q

what can hydropathy plots be used for

A

detecting/predicting helical transmembrane structures

103
Q

whats the positive inside rule

A

interior cytoplasmic loops are often enriched with arginine and lysine (cytoplasmic edge of transmembrane helices)

104
Q

is it easy to determine the structure for integral membrane proteins

A

its challenging

105
Q

what kind of environments are required for purification and correct folding (topology prediction)

A

hydrophobic

106
Q

what is the hydropathy index

A

a scale that measures the relative hydrophobic and hydrophilic tendencies of a chemical group

107
Q

what score would a region with lots of hydrophobic residues get

A

relatively high

108
Q

what would a high hydropathy index score mean

A

there are lots of hydrophobic residues

109
Q

what would a low hydropathy index score mean

A

not lots of hydrophobic residues

110
Q

what score would a region with very few of hydrophobic residues get

A

relatively low

111
Q

how thick is the membrane (angstroms)

A

around 30

112
Q

what happens if theres multiple peaks in the hydropathy index

A

likely a polytopic strucutre

113
Q

what are beta barrel transmembrane proteins (what type of topic)

A

multipass (polytopic)

114
Q

how are beta barrel strands oriented

A

at angle relative to membrane (45 degrees)

115
Q

what are the interiors of beta barrels like

A

polar

116
Q

what # of antiparallel strands are in beta barrels + why

A

an even number so that like 1 and the last can pair, etc

117
Q

what are amino acids that are exposed to aqueous environments like

A

polar

118
Q

what are amino acids that are exposed to interior environments like

A

non polar

119
Q

what is the amino acid pattern like with beta-barrel transmembrane proteins

A

alternating polar non-polar (some exposed to polar exterior and some exposed to hydrophobic lipid bilayer cause they go up and down in the strand)

120
Q

do hydropathy plots detect transmembrane domains

why

A

no, because the strands are too short and they may not be exclusively hydrophobic (alternating)

121
Q

which amino acids are near the interface in integral membrane proteins

A

Trp Tyr

122
Q

which amino acid types are near the interior exposed loops in integral membrane proteins

A

positive

123
Q

whats the positive inside rule (specific aa)

A

interior exposed loops of helical bundles are often enriched for arg lys his (cytoplasmic edge of transmembrane helices)

124
Q

what kind of philicity for solvent exposed (non buried) surfaces in integral membrane proteins

A

hydrophilic

125
Q

what kind of philicity for amino acids exposed to bilayer core in integral membrane proteins

A

hydrophobes

126
Q

why are tyr and trp often found in the surface area of the integral membrane protein

A

theyre amphipathic, so their polar parts interact with the polar head groups (hydrogen bonding) of the lipid, and the hydrophobic portions of the amino acid are

127
Q

where are most charged residues in integral membrane proteins

A

almost exclusively on the surface/solvent exposed portions

128
Q

what do lipid anchors do (2 things)

A

anchor proteins to membranes

may also target proteins to specific membrane locations

129
Q

what are the types of lipid anchors

A

fatty acid, prenyl group or GPI linkage

130
Q

what are prenyl anchors

A

isoprene based structures

131
Q

what are 2 types of prenyl anchor residues

A

farnesyl residues and geranylgeranyl residues

132
Q

what is the sequence that prenyl anchors are most commonly added to

A

C-X-X-Y
X=aliphatic aa
Y=specificity

133
Q

how does prenyl anchor adding work

A

sequence C-terminal to Cys removed (irreversible), then a thioether to C-terminal Cys

134
Q

which amino acid determines specificity of prenyl anchors

A

the Y in the sequence C-X-X-Y (terminal amino acid)

135
Q

is prenyl anchor reversible

A

no

136
Q

what is removed when prenyl anchors are added

A

sequence C-terminal to cys

137
Q

which terminal is modified with prenyl anchors

A

C

138
Q

when does prenylation occur and why

A

post translational because you need the C terminal to be made

139
Q

which direction are proteins synthesized

A

N to C

140
Q

what are 2 types of lipid-linked proteins

A

palmitoylation

myristoylation

141
Q

what is palmitoylation (what becomes attached)

A

16:0 fatty acid

142
Q

what is myristoylation (what becomes attached)

A

14:0 fatty acid

143
Q

what kind of linkage happens with palmitoylation

A

thioester linkage to cys or ester linkage to ser to the fatty acid

144
Q

what kind of linkage happens with myristoylation

A

amide linkage (from fatty acid and N terminus)

145
Q

is myristoylation reversible

A

no

146
Q

is palmitoylation reversible

A

yes

147
Q

is palmitoylation or myristoylation reversible

A

palmitoylation

148
Q

is palmitoylation or myristoylation irreversible

A

myristoylation

149
Q

when does myristoylation occur (translation)

why

A

co or post

its a mod on the N terminal end

150
Q

when does palmitoylation occur (translation)

why

A

post because its an internal polypeptide modification

151
Q

where does palmitoylation and myristoylation occur (where in membrane)

A

on the inside/ inner face of plasma membrane

152
Q

which lipid linked membrane protein happens in the middle

A

palmitoylation

153
Q

which lipid linked membrane protein happens on the N terminus

A

myristoylation

154
Q

which lipid linked membrane protein happens on the C terminus

A

prenylation

155
Q

which lipid linked membrane protein has 16 fatty acid

A

palmitoylation

156
Q

which lipid linked membrane protein has 14 fatty acid

A

myristoylation

157
Q

what are GPI anchors (what do they stand for)

A

glycosylated derivative of phosphatidyl inositol

158
Q

where do GPI anchors do

A

on outer face of plasma membrane

159
Q

what kind of modification happens with GPI anchors + why

A

post translational modification

bc as C terimus

160
Q

where in the peptide chain do GPI anchors occur

A

C terminus

161
Q

what can happen to GPI anchors and why

A

they can be cleaved by phospholipases as part of regulation

BIOCH 320 (16 decks)

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