NSCS 307 EXAM 2 UPDATED ACTUAL QUESTIONS AND
CORRECT ANSWERS
Question:
What properties are necessary for a protein to act as an ion channel?
Answer:
- opens and closes - transmembrane - forms pore for ions to go through - speed
- friendly for charged particles - able to be regulated - different ways that you
can gate the channel - selective (specificity to ion channel)
Question:
What are the three most important properties of ion channels?
Answer:
Combining speed, ion specificity and being able to regulate whether it is open
or closed
Question:
What does a patch clamp allow you to do?
Answer:
Look at the current through an individual ion channel.
Question:
How does the patch clamp work?
Answer:
A small patch of membrane containing a single voltage gated channel is
electrically isolated from the rest of the cell by the patch electrode. The current
that enters the cell through the channel is recorded by a current monitor
connected to the patch electrode
Question:
voltage clamp vs patch clamp?
Answer:
- patch clamp is a specific type of voltage clamp. - Voltage clamp is when you
clamp the membrane potential of the cell at a desired voltage by adding the
necessary current - patch clamp is when you clamp the potential of an
individual ion channel and see the resulting current through just that channel
Question:
What is a patch clamp record?
Answer:
The aggregate/sum of current through a channel in a patch clamp over several
(hundreds) of trials
Question:
What shape are patch clamp currents? why?
Answer:
- Square - the current goes out/in and back to 0 in a square fashion - because it
is an individual ion channel
,Question:
What would the patch clamp record look like during an action potential if you
recorded from a voltage gated sodium channel in a squid?
Answer:
- inward current - square - turns off on its own (inactivates) before pulse ends
Question:
What would the patch clamp record look like during an action potential if you
recorded from a voltage gated potassium channel in a squid?
Answer:
- outward current - square - relatively late in pulse (takes longer for potassium
channels to open) - never inactivates - stays open until after the voltage pulse
Question:
What is different about voltage gated potassium channels in mice?
Answer:
voltage gated potassium channels in mice inactivate
Question:
What would the patch clamp record look like during an action potential if you
recorded from a voltage gated potassium channel in a mouse neuron?
Answer:
- outward current - square - relatively late in pulse (takes longer for potassium
channels to open) - inactivates - turns off on its own before the pulse ends
Question:
Which interesting protein goes halfway through the membrane on either side?
Answer:
Gramicidin A
Question:
How does gramicidin A look/work?
Answer:
- big, not specific - each individual protein goes through half of the bilayer
- thus the two proteins must be lined up in the membrane to form a functional
channel for ions to go through
Question:
Why do we study gramicidin A for patch clamps?
Answer:
- because this is the definition of a channel that is either open or closed. - if the
two halves are not next to each other, the channel is closed -if the two halves
are together, the channel is open and you get a current - thus you get nice
square currents pulses
Question:
What do the patch clamp records look like for gramicidin A as you
increase/decrease the clamp voltage?
Answer:
- Amplitude of square current pulses increases as you move away from 0 mV
in either direction - current switches from outwards to inwards at 0 mV -
There is no current flow at 0 mV
,Question:
For the patch clamp record of gramicidin A, why is there no current at 0 mV?
Answer:
- Because 0 mV is the reversal potential for gramicidin A - gramicidin A lets a
lot of things though, so the reversal potential of 0mV is a combination of all of
the things that go through it
Question:
For the patch clamp record of gramicidin A, why does current amplitude
increase as voltage gets further from the reversal potential of 0 mV?
Answer:
- Driving force
Question:
Describe physical model for the opening and closing of ion channels:
conformational change in one region.
Answer:
- a localized conformational change occurs in one region of the channel
Question:
Describe physical model for the opening and closing of ion channels: general
structural change
Answer:
- a generalized structural change occurs along the length of the channel
Question:
Describe physical model for the opening and closing of ion channels: blocking
particle
Answer:
a blocking particle swings into and out of the channel mouth
Question:
What are the main two ways to gate channels?
Answer:
1. voltage-gated
2. ligand-gated
Question:
Describe voltage-gated channels
Answer:
- has a voltage sensor that allows them to open or close - can be very specific
for whichever ions go through them
Question:
What determines whether a channel is specific or it is general about which
ions go through?
Answer:
- the spacing of the inside of the channel allows ion specificity
Question:
Describe ligand gated channels
, Answer:
- opens if the ligand binds
Question:
When we see the long string of letters for a channel, what are we looking at?
Answer:
- amino acid sequence for the gene that codes for a particular ion channel
Question:
What can we tell by looking at an ion channel's amino acid sequence? Why is
this importnt?
Answer:
- each amino acid is either hydrophobic or hydrophilic - if the channel is
forming a pore through the membrane there needs to be particular areas in
the sequence that are hydrophobic and will be stable in the membrane - we
can also put the sequence into a protein database and see if it matches the
sequence of
proteins whose function we already know - certain sequences match certain
functions
Question:
Describe the makeup of an ion channel
Answer:
- multiple transmembrane domains (made from multiple alpha helices)
needed to form an ion channel/pore (minimum of 3-4) - usually an alpha helix
- usually between 21-23 amino acids long
Question:
What plots measures hydrophobic score?
Answer:
Hydrophobicity plot
Question:
Describe the purpose and x/y axis of a hydrophobicity plot?
Answer:
- gets an average hydrophobic score by looking at the number of hydrophobic
(nonpolar) amino acids - x axis: number of amino acids (location you are at in
the sequence of the protein) - y axis: hydrophobicity score (average of how
hydrophobic it is)
Question:
How does hydrophobicity change on a hydrophobicity plot?
Answer:
- increasing from 0: increasingly nonpolar/hydrophobic - decrease from 0:
increasingly polar/ hydrophilic - at 0: equally hydrophobic and hydrophilic
Question:
What are you looking for in a hydrophobicity plot?
Answer:
- particularly hydrophobic regions that could potentially be transmembrane
domains - 1 spike would be 1 domain
CORRECT ANSWERS
Question:
What properties are necessary for a protein to act as an ion channel?
Answer:
- opens and closes - transmembrane - forms pore for ions to go through - speed
- friendly for charged particles - able to be regulated - different ways that you
can gate the channel - selective (specificity to ion channel)
Question:
What are the three most important properties of ion channels?
Answer:
Combining speed, ion specificity and being able to regulate whether it is open
or closed
Question:
What does a patch clamp allow you to do?
Answer:
Look at the current through an individual ion channel.
Question:
How does the patch clamp work?
Answer:
A small patch of membrane containing a single voltage gated channel is
electrically isolated from the rest of the cell by the patch electrode. The current
that enters the cell through the channel is recorded by a current monitor
connected to the patch electrode
Question:
voltage clamp vs patch clamp?
Answer:
- patch clamp is a specific type of voltage clamp. - Voltage clamp is when you
clamp the membrane potential of the cell at a desired voltage by adding the
necessary current - patch clamp is when you clamp the potential of an
individual ion channel and see the resulting current through just that channel
Question:
What is a patch clamp record?
Answer:
The aggregate/sum of current through a channel in a patch clamp over several
(hundreds) of trials
Question:
What shape are patch clamp currents? why?
Answer:
- Square - the current goes out/in and back to 0 in a square fashion - because it
is an individual ion channel
,Question:
What would the patch clamp record look like during an action potential if you
recorded from a voltage gated sodium channel in a squid?
Answer:
- inward current - square - turns off on its own (inactivates) before pulse ends
Question:
What would the patch clamp record look like during an action potential if you
recorded from a voltage gated potassium channel in a squid?
Answer:
- outward current - square - relatively late in pulse (takes longer for potassium
channels to open) - never inactivates - stays open until after the voltage pulse
Question:
What is different about voltage gated potassium channels in mice?
Answer:
voltage gated potassium channels in mice inactivate
Question:
What would the patch clamp record look like during an action potential if you
recorded from a voltage gated potassium channel in a mouse neuron?
Answer:
- outward current - square - relatively late in pulse (takes longer for potassium
channels to open) - inactivates - turns off on its own before the pulse ends
Question:
Which interesting protein goes halfway through the membrane on either side?
Answer:
Gramicidin A
Question:
How does gramicidin A look/work?
Answer:
- big, not specific - each individual protein goes through half of the bilayer
- thus the two proteins must be lined up in the membrane to form a functional
channel for ions to go through
Question:
Why do we study gramicidin A for patch clamps?
Answer:
- because this is the definition of a channel that is either open or closed. - if the
two halves are not next to each other, the channel is closed -if the two halves
are together, the channel is open and you get a current - thus you get nice
square currents pulses
Question:
What do the patch clamp records look like for gramicidin A as you
increase/decrease the clamp voltage?
Answer:
- Amplitude of square current pulses increases as you move away from 0 mV
in either direction - current switches from outwards to inwards at 0 mV -
There is no current flow at 0 mV
,Question:
For the patch clamp record of gramicidin A, why is there no current at 0 mV?
Answer:
- Because 0 mV is the reversal potential for gramicidin A - gramicidin A lets a
lot of things though, so the reversal potential of 0mV is a combination of all of
the things that go through it
Question:
For the patch clamp record of gramicidin A, why does current amplitude
increase as voltage gets further from the reversal potential of 0 mV?
Answer:
- Driving force
Question:
Describe physical model for the opening and closing of ion channels:
conformational change in one region.
Answer:
- a localized conformational change occurs in one region of the channel
Question:
Describe physical model for the opening and closing of ion channels: general
structural change
Answer:
- a generalized structural change occurs along the length of the channel
Question:
Describe physical model for the opening and closing of ion channels: blocking
particle
Answer:
a blocking particle swings into and out of the channel mouth
Question:
What are the main two ways to gate channels?
Answer:
1. voltage-gated
2. ligand-gated
Question:
Describe voltage-gated channels
Answer:
- has a voltage sensor that allows them to open or close - can be very specific
for whichever ions go through them
Question:
What determines whether a channel is specific or it is general about which
ions go through?
Answer:
- the spacing of the inside of the channel allows ion specificity
Question:
Describe ligand gated channels
, Answer:
- opens if the ligand binds
Question:
When we see the long string of letters for a channel, what are we looking at?
Answer:
- amino acid sequence for the gene that codes for a particular ion channel
Question:
What can we tell by looking at an ion channel's amino acid sequence? Why is
this importnt?
Answer:
- each amino acid is either hydrophobic or hydrophilic - if the channel is
forming a pore through the membrane there needs to be particular areas in
the sequence that are hydrophobic and will be stable in the membrane - we
can also put the sequence into a protein database and see if it matches the
sequence of
proteins whose function we already know - certain sequences match certain
functions
Question:
Describe the makeup of an ion channel
Answer:
- multiple transmembrane domains (made from multiple alpha helices)
needed to form an ion channel/pore (minimum of 3-4) - usually an alpha helix
- usually between 21-23 amino acids long
Question:
What plots measures hydrophobic score?
Answer:
Hydrophobicity plot
Question:
Describe the purpose and x/y axis of a hydrophobicity plot?
Answer:
- gets an average hydrophobic score by looking at the number of hydrophobic
(nonpolar) amino acids - x axis: number of amino acids (location you are at in
the sequence of the protein) - y axis: hydrophobicity score (average of how
hydrophobic it is)
Question:
How does hydrophobicity change on a hydrophobicity plot?
Answer:
- increasing from 0: increasingly nonpolar/hydrophobic - decrease from 0:
increasingly polar/ hydrophilic - at 0: equally hydrophobic and hydrophilic
Question:
What are you looking for in a hydrophobicity plot?
Answer:
- particularly hydrophobic regions that could potentially be transmembrane
domains - 1 spike would be 1 domain
