Membranes Flashcards
1
Q
A
2
Q
What are the three main functions of the membrane?
A
- Nerve transmission (action potentials). 2. Membrane trafficking. 3. Signalling.
3
Q
What can biochemical systems be described as?
A
Modular.
4
Q
Why is it thought at biochemical systems are modular?
A
As this would have been the simplest way for it to evolve.
5
Q
Why would membranes first have arose?
A
As a barrier.
6
Q
What was suspected to be in the membranes of early organisms?
A
Channels.
7
Q
What evolved in membranes after channels?
A
Pumps (the ability to move things with a concentration gradient.)
8
Q
What is an example of something regulated via pumps in membranes?
A
Glucose intake.
9
Q
What can membranes convert a membrane potential gradient into?
A
Energy- such as with the ATP pumps.
10
Q
Cell recognition is different in prokaryotes and eukaryotes. Why is thought to be the case?
A
The last universal common ancestor didn’t do this- thought to have evolved later as a late evolutionary adaptation.
11
Q
Is signalling universal?
A
No, only similar.
12
Q
What type of cell does compartmentalisation occur in?
A
Eukaryotes.
13
Q
What is the average dimensions of E.coli?
A
1um by 2um.
14
Q
How much bigger is a mammalian eukaryotic cell compared to a E.coli cell?
A
1000x bigger (10X bigger along each dimension).
15
Q
Fibroblasts in the skin layer are not as thick as the epithelial cells. How much times wider are they?
A
4.
16
Q
How much longer is a nerve axon compared to an epithelial cell?
A
500,000 times longer.
17
Q
Why is compartmentalisation vital in eukaryotes?
A
As the cell is much bigger and diffusion will not be fats enough.
18
Q
How much plasma membrane is in in a eukaryotic cell?
A
700 um2.
19
Q
How much internal membranes are in the prokaryotic cell?
A
7000 um2.
20
Q
What can you make membranes spontaneously aggregate into in a lab?
A
Lipid bilayer, liposome, vesicle.
21
Q
Are vesicles or liposomes spherical?
A
Liposomes.
22
Q
Are vesicles or liposomes made of layers?
A
Vesicles.
23
Q
What direction of movement is fast in a membrane?
A
Lateral.
24
Q
In cells what will membranes spontaneously aggregate into?
A
Just bilayers.
25
Lipid anchor proteins are solvable proteins with what added to them?
Hydrophobic tail.
26
Lipid anchor proteins are often involved in directing cells. Can the cells move these?
Yes.
27
What process is being described here? Proteins are made fluoresce. A certain region has this removed via bleaching. Monitored how long it takes for the fluoresce to come back. Some will not.
FRAP.
28
Why will some of the fluorescence not return in FRAP?
As the proteins are fixed.
29
What did Atomic Force Microscopy show in regards to the membrane surface?
Showed that the membrane was pretty flat with membrane proteins sticking up out of it.
30
What is an example of an organelle with lots of membrane proteins?
Mitochondria.
31
Why is it a disadvantage for an organelle to have lots of surface proteins?
Barrier to movement.
32
What is the issue with he fluid mosaic model?
It concentrates on proteins and not lipids.
33
What two other things can a phospholipid be called?
A phosphoglycerides or glycerolipids.
34
What type of double bonds are often found in phospholipids?
Cis.
35
What type of bonds are often found in sphingolipids?
Trans.
36
What is present instead of O in sphingolipids?
NH.
37
Name one example of a sterol.
Cholesterol.
38
Sterols can be described as what compared to other membrane proteins?
Shorter and fatter.
39
What type of double bonds do membranes prefer due to their lower energy?
Trans.
40
How high can the molar % of cholesterol be in some membranes?
Up to 50%.
41
What shape is cholesterol?
Fairly flat.
42
Is cholesterol polar?
Yes but it does not contain a polar head group, it only contains one polar OH.
43
Archae membranes are similar to those found in prokaryotes and eukaryotes?
False they are completely different.
44
What bonds are found in the fluid phase of the membrane?
Cis bonds as they are more flexible.
45
What bonds are found in the gel phase of the membrane?
Trans bonds.
46
What stage does the cell want the membrane to be?
Fluid.
47
How can you change from the gel phase to fluid phase?
Heat. The change is sudden.
48
Apart from regulating the fluidity what else does changing the phase of the membrane from gel to fluid do?
Makes the membrane thinner.
49
50
What does patch clamping measure?
Change of current in a membrane due to the flow of ions.
51
52
Describe the basic process of patch clamping.
The glass electrode is pulled to a very small point on the membrane and tiny currents are measured between the two electrodes. The pipette pushing on the cell is called the on cell positioning. A very tight seal is formed between the tip and the membrane so nothing leaks.
53
What does 'Inside out' geometry refer to?
What was inside the cell corresponds to whats outside the tip.
54
Why is it good that patch clamping involves a very small surface area of the membrane?
As only a very small number of channels will be present. Allows you to study the channels individually.
55
What does 'outside out' geometry used for?
To study external ligands linked with channels.
56
What do voltage gates across a membrane cause?
Channels to open.
57
How much current is present across the membrane when the channel is closed?
0.
58
What charge value corresponds to a channel being open?
5pa.
59
Do all channels have the same current when open?
Yes.
60
What two types of channels are present only axons of nerve cells?
Na+ specific and k+ specific.
61
What is the resting voltage of an axon membrane?
-70mv.
62
What happens when the axons membrane potential reaches 0?
Maximum ion flow.
63
When does the plug attach to the voltage gated Na+ channel ?
1ms. It will detach a few sections after the membrane potential has returned to normal.
64
What does 'whole cell geometry' in patch clamping allow?
Allow the cells total response to be monitored.
65
What is the voltage gated Na+ plug made from?
4 identical a helices with positive residues.
66
Why can the plus on the Na+ voltage pump close after depolarisation has occurred?
The plug is made of positive helices. When the cell depolarises and becomes more positive the plug will move to the positive side of the membrane.
67
What way does Na+ flow through the axons Na+ voltage gated channel?
Either way.
68
When is the axon said to be refracting?
When the plug is in the whole.
69
What is the main difference between the Na+ voltage gated channel and the K+ voltage gated channel in the axon?
The K+ channel opens and closes slower.
70
What is the K+ voltage channel of the axon also called?
The delayed K+ channel.
71
When the current is bigger why is it easier to driveK+ through the voltage gated axon channel?
The difference in charge is greater meaning it is easier to drive the positive ion through. THE CHANNEL DOES NOT OPEN MORE.
72
What two pumps are present in the membrane of all cells?
1. Na+/K+ pump. 2. Resting K+ channel (K+ lack channel.)
73
What does the Na+/ K+ pump require?
ATP.
74
What way do the Na+ and K+ ions flow in the Na+/K+ channel?
Na+ out K+ in.
75
What is the concentration of Na+ on either side of the Na+/K+ pump?
150mM exterior and 12mM cytosol.
76
What is the concentration of K+ on either side of the Na+/K+ pump?
4mM exterior, 140mM cytosol.
77
When is the resting K+ channel open?
All the time.
78
What channel is responsible for the cells negative potential?
Resting K channel.
79
The resting K+ channel does not transport much K+ so it is not energetically costly. True or false?
False.
80
The K+ leak is the only channel in the axon open at rest. Why?
It tries to neutralise the K+ concentration, causing a negative charge inside the axon. (The cell does not have enough energy to completely neutralise this charge.)
81
What is the difference between the motor neurone and the sensory neurone?
The motor neurone brings nerve signals from the brain to the muscle and the sensory neurone does the reverse.
82
Nerve impulses make an all or nothing response. How is a stronger signal obtained?
More frequent action potentials.
83
Is there attenuation of the nerve signal as you travel down the axon?
No.
84
How frequent are nerve impulses at their maximum?
4 m/s.
85
Are resting K+ channels voltage gated?
No.
86
How much ATP does the Na+/K+ pump use?
25%.
87
The resting K+ channel causes the membrane to slowly depolarise. At what voltage does the Na+ gated channel open?
-40mv.
88
The Na+ voltage gated channel opens at -40mv. What way do the Na+ ions move?
In due to the concentration gradient. This causes the axon to depolarise more.
89
The opening of the Na+ channel causes the voltage of the membrane to go up to what?
+35mv.
90
What type of feedback is found in the axon?
Postive.
91
When does the Na+ voltage gate get plugged in the transmission of a nerve impulse?
When the membrane potential reaches +35mv.
92
When does the delayed K+ channel open in the transmission of an action potential?
Once the membrane potential has reached +35mv and the Na channel has closed. This brings the membrane potential back to normal.
93
Why does the membrane slightly hyperpolarise in neurotransmission?
As there is a delay in shutting the K+ voltage gated channel.
94
Why is there a refractory period in neurotransmission?
As the Na+ plug stops the Na+ channel opening immediately.
95
Why can the action potential only go one way along the axon?
Refractory period is present.
96
At neuronal junctions, such as in the brain a logic gate is present. What is a logic gate?
A signal can produce either a positive or negative response which can add up. An action potential in the scone neurone will only be started once the net voltage at the axon hillock reaches a certain level.
97
How much Na+ moves into the cell/ how much K+ moves out of the cell with each action potential per um2 of the membrane?
10^5.
98
What percentage of Na+ and K+ in the cell is involved in the Na+/K+ pump?
1%. Neurones can transmit multiple signals without effect on the Na+ and K+ concentrations of the cell.
99
How fast does an action potential travel without a myelin sheath?
1m/s.
100
How may times faster does the myelin sheath make action potentials?
1000X.
101
How large are the gaps on the nodes and how regular are they?
1um and every 100um.
102
At the nodes what does the membrane contact?
Extracellular fluid.
103
What is caused by loss of myelin in some areas of the brain and spinal cord?
MS.
104
Can real and artificial membranes be altered by heat?
Yes.
105
What three things does lipid composition influence in a membrane?
1. Fluidity. 2. Shape. 3. Thickness.
106
When cholesterol is at a high concentration in the membrane what does it do?
Make the membrane flatter.
107
What bond causes disorder resulting in shorter membranes?
Cis.
108
What does cholesterol do to SM trans bonds?
Makes them longer and with it thicker. .
109
Do membranes have different types of local thickness?
Yes.
110
What does the head shape of PC cause?
The membrane to all line up as the cross sectional area of the tail and the head group are the same.
111
Why does PE have a much smaller head?
It only has a H in place of a methyl group.
112
What does PE's head shape result in?
The membrane folds up so the heads are closer together. This prevents holes.
113
What is special about the head group of PI?
It is much bigger.
114
What does the large head group of the PI cause?
The membrane to curve.
115
What 5 things can the membrane control to alter the curvature?
1. Location of lipids. 2. Helix insertion into one side. 3. Membrane proteins. 4. Cytoskeleton. 5. Scaffolding of proteins.
116
Where are direct proteins scaffolds found?
Inside and out.
117
Where are indirect protein scaffolds found?
Inside.
118
Where is positive direct scaffolding found?
Outside.
119
Where is negative direct scaffolding found?
Inside.
120
In what membrane is there more SM and cholesterol?
Outer membrane.
121
All GPI anchored proteins are found on the outside. True or false?
True.
122
All lipid anchored proteins are found on the outside. True or false?
False.
123
Why can lipids not flip themselves in a membrane?
It requires too much energy.
124
What ATP dependant enzyme is needed to flip a membrane lipid?
Flipase.
125
Describe phase separation.
Different lipids components separate within a membrane due to their different compositions of lipids and because of the fact that each component likes to associate with itself. The membrane will want to do this spontaneously but can also encourage this.
126
Why does the fluid mosaic model not describe the membrane properly?
Phase separation
127
A lipid raft is a thicker region of the membrane. What is it made of?
Cholesterol and sphingolipids.
128
Where do proteins with longer transmembrane helices go?
Lipid rafts.
129
Where do proteins with GPI anchors go?
Lipid rafts.
130
Where do proteins with palmitoyl anchors go?
Lipid rafts.
131
What sort of proteins prefer not to be in lipid rafts?
Proteins with prenyl anchors.
132
Does phase separation happen to lipid rafts?
Yes.
133
Is the formation of lipid rafts spontaneous?
No.
134
The formation of lipid rafts is controlled by the cell. Why is this beneficial for the altering the location of membrane proteins (3 reasons.)
1. Bringing signal systems together. 2. Organising the start of endocytosis. 3. T cell activation.
135
What did AFM show in regards to lipid rafts?
They were much thicker than other parts of the membrane.
136
What can sometimes form when a cell is stimulated?
A large, stable lipid raft.
137
Why can a lipid anchor be moved?
It is just an ester bond that can be moved with covalent modification.
138
Proteins are tagged allowing localisation in a cell. Is the membrane vesicles also tagged?
Yes.
139
Can lipid components of the membrane regulate targeting?
Yes.
140
What brings about ligand-mediated endocytosis?
Lipid rafts.
141
What protein binds to the lipid raft formed for ligand-mediated endocytosis allowing it to bend?
Caveloin.
142
What two proteins can caveloin recruit?
Cavin and clathrin.
143
When will a lipid raft be small and short lived?
When it is unstimulated.
144
What two functions do lipid rafts have?
1. Signalling. 2. Endocytic pits.
145
What are the three main functions of ion pumps and channels?
1. Biological energy conversions. 2. Signal transmission in the NS. 3. Muscle activity.
146
Membranes can be c\_\_\_\_\_, c\_\_\_\_\_\_ and m\_\_\_\_\_\_.
Carriers, converters, markers.
147
What are the three types of membrane proteins?
1. Integral. 2. Peripheral. 3. Lipid anchored.
148
How many anchors can a lipid anchor protein have?
Multiple.
149
How many leaflets of the membrane are lipid anchor proteins attached to?
One.
150
How do peripheral anchor proteins attach to the membrane?
Non covalently. This can either be through VDV/ hydrophobic interactions or through non covent interactions with other membrane proteins.
151
What do membrane spanning regions of membrane proteins require?
All main chain hydrogen bonds to be made as the inside of the membrane is hydrophobic.
152
Even when all the H bonds have formed the transmembrane helix can still be described as polar. True or false?
False.
153
What is hydropathy?
Free energy for the transfer of an amino acid residue in an alpha helix from the membrane interior to the water.
154
What does a higher hydropathy value mean?
A more hydrophobic residue.
155
What amino acid is at -4.5 on the Kyte and Doolittle scale?
Arg.
156
What amino acid is at 4.5 on the Kyte and Doolittle scale?
Ile (isoleucine.)
157
The membrane is 3.5nm. How many amino acids need to be in the transmembrane helix to span the whole membrane vertically?
20.
158
A window of how many residues is used to calculate hydropathy?
19 residues.
159
What is sometimes added to the transmembrane helix?
Hydrophilic residues to give extra function to the helix.
160
If a helix is diagonal in the membrane how many residues could it require?
36.
161
Beta barrels can fit into the membrane but beta sheets can not. Why?
Because not all man chain hydrogen bonds are made.
162
What is an omp?
An outer membrane protein.
163
What is the sequence pattern in beta barrels?
Alternating hydrophobic and hydrophilic.
164
Why can you not use the Kyte and Doolittle scale with beta barrels?
As the sequence alternates between hydrophobic and hydrophilic residues.
165
What value does an amino acid need to have on the Kyte and Doolittle scale for it to be part of a transmembrane helix?
1.6.
166
What four linkages can be made by a lipid anchor protein?
1. Acetlylaiton. 2. Prenylation. 3. Thioester. 4. GPI anchor.
167
What is myristoylation?
An amide bond made to the N terminal glycine.
168
Myristoylation is an example of acetylation. When does it occur?
Co transitionally after the N terminal met has been removed.
169
Is acetylation reversible?
No.
170
What is prenylation?
When a thioETHER linkage is formed with a C terminal cysteine.
171
What is the difference between a thioether and a thioester linkage?
A thioether linkage contains a S instead of an O.
172
Does prenylation involve a terminal cysteine?
No it doesn't have to. Cys-a-a-x can be bound too. The a-a-x is cleaved (a represents a aliphatic amino acid.)
173
Where do thioester bonds form in regards to lipid anchors?
With any cysteine in the chain.
174
There are no nonsense sequences involved with thirster sequences in lipid anchors, however they have a higher tendency to be found where?
Close to prenylation and acylation sites.
175
What enzyme makes thioester bond formation reversible?
Thioesterases.
176
What 5 things is signalling a response for?
1. Hormones. 2. Growth Factors. 3. Infections. 4. Neural synapses. 5. Bacterial response to the environment.
177
What are two examples of short term signalling?
Vison and pain.
178
What are two examples of long term signalling?
Cell differentiation/ sex hormones.
179
What two things do external signals normal effect inside the cell?
1. Enzymes. 2. Gene transcription.
180
What four ways can an external signal alter inside the cell?
1. Hydrophobic molecule to an intracellular receptor e.g. NO.
2. Ion through an ion channel e.g. post synaptic receptors.
3. Ligand to an enzyme (normally a kinase.)
4. Ligand to a G protein coupled receptor.
181
Signalling can involve a kinase enzyme. These can only ever be on or off. True or false?
True.
182
When is a G protein on?
When it is bound to GTP.
183
When is a G protein off?
When it is bound to GDP.
184
What is RAS an example of?
A G protein.
185
What residue is found in switch one of Ras?
Thr35.
186
What residue is found in switch two of Ras?
Gly60.
187
How much more GTP is in a cell compared to GDP?
10 times.
188
What does Guanine exchange factor do?
Allow GDP out of RAS and GTP in.
189
What protein helps RAS hydrolyse GTP?
GTPase activating protein.
190
When is a kinase activated?
When it is phosphorylated.
191
What mechanism gets a signal across a membrane with receptor- linked kinases?
Dimerisation.
192
What does dimerisation of a receptor linked kinase cause?
2 domains next to each other in the cell to autophosphorylate.
193
What does a phosphorylated receptor act as?
A binding site for modular adaptor proteins including Grb2 and Sos.
194
One kinase domain will be phopsohorylated by the other. What does this do?
Fixes the position of the activation loop allowing the substrate to bind correctly.
195
What are two examples of modular adaptor proteins?
Grb2 and SOS.
196
What two regions is the Grb2 modular adaptor protein made of and how many of each region does it contain?
1 SH2 region and 2 SH3 regions.
197
What do the SH3 domains of Grb2 recognise?
Polyproline helices.
198
What does the SH2 domain of Grb2 recognise?
Phosphotyrosines.
199
Is there a specific SH2 or SH3 for each receptor?
SH3.
200
What part of the SOS modular adaptor protein binds to SH3?
Proline rich arm.
201
What two things come together to activate G protein RAS?
SOS and Grb modular adaptor proteins.
202
What is the main function of the G protein Ras?
To activate Raf.
203
Was does Raf activate?
A chain of kinases.
204
What is an example of a Ras activated signal pathway?
Rad-Raf-Mek-Erk.
205
What is Erk and what does it do?
It is activated by a cascade activated by Ras which phosphorylates several transcription factors. This moves into the nucleus and alters the serum response element which is responsible in controlling early response genes.
206
Using the G protein Ras pathway is a complicated way to get a signal to the nucleus. What are its benefits?
It allows the signal to be amplified at each step and for modification of the signal.
207
What do GPCRs do?
Link the signal more directly with the G protein.
208
What percentage of drugs in clinical use are targeted to GPCRs?
50%.
209
What are GPCRs made from?
7 transmembrane helices.
210
GPCRs are made of 7 transmembrane helices. Between which of these helices is the intracellular loop found?
Between 5 and 6.
211
What does the intercellular loop of GPCRs bind to?
A hetereotomic G protein.
212
What three units are found in a heterotromic G protein?
Alpha Gbeta Ggamma.
213
What two units of the heterotromic G protein are always bound?
Beta and gamma.
214
Where does the ligand bind to in GPCRs?
Well within the membrane.
215
What is an example of a GPCR?
Rhodopsin.
216
What does rhodopsin respond to?
Light.
217
What amino acid is the toggle switch in rhodopsin made from?
Tryptophan.
218
Describe the process used in rhodopsin.
Binding of a ligand moves the tryptophan causing the bent helix in the rhodopsin to rotate. This changes the conformation of loop 3 which opens up a groove allows Ga to bind. A helix from Ga fits into the groove, opening up the binding site in Ga allow GDP to leave.
219
What part of the SOS modular protein activates RAS?
The GEF domain.
220
What can a receptor bound GPCR act as?
A GEF turning on the signal.
221
What is a common target for Ga-GTP?
Adenyl cyclase.
222
What does Adenyl cyclase do?
Coverts ATP to cAMP when it is bound to Ga-GTP.
223
What is Ga its own?
GAP meaning that it can hydrolyse the GTP to turn off the signal.
224
What are ion channels really responsive to?
Ligand concentration.
225
Ion channels are made of multiple subunits. How many are there normally?
5
226
What do the subunits of the ion channel do?
Simultaneously rotate, work like an 'iris of a camera.'
227
One type of lipid anchor is the GPI anchor. What does GPI mean?
Glycosyl phosphatdylinositol anchor.
228
What does the GPI linkage contain?
Modify C-terminus with ethanolamine linked to oligosaccharide linked to inositol of phosphaldyl inosito.l
229
What two linkages are found in bacterial lipid anchors?
Thioether and amide linkages.
230
In what lipid anchor is the lipobox sequence found?
Bacterial.
231
What is the lipobox sequence?
[Lvi]-[AStvi]-[Gas]-C.
232
The lipoprotein signal sequence in bacteria is made up of a general region an a tripartite region. What is the tripartite region made off?
Postive N region, Hydrophobic region, Lipobox with invariant cysteine.
233
How many amino acids is the n region of the tripartite region made of and how many of these are positive?
5-7 residues. 2 positive (R or K).
234
How long is the hydrophobic region of the tripartite sequence?
7-22 residues.
235
What amino acid is found at the N terminal of bacterial lipid anchors?
Met.
