Ion Channels and Transporters Flashcards
Central dogma of biology: 3 processes
- DNA synthesis through replication
- RNA synthesis through transcription
- Protein synthesis through translation
Difference between DNA and RNA in terms of number of strands
DNA: double-stranded
RNA: single stranded
Type of RNA used to make protein
mRNA
Building blocks of DNA and RNA are called ____.
Nucleotides
Building blocks of proteins are called ____.
Amino acids
A small protein is called a ____.
Peptide
What is the same for all amino acids?
Backbone
How are amino acids linked in a protein?
Covalent bonds
3 basic types of amino acid side chains
Neutral (non-polar), charged, polar
Interactions among amino acid ____ ____ drives folding of protein.
Side chains
How does the aqueous environment of the cell drive the folding of proteins?
Proteins will fold such that their polar side chains are on the outside and non-polar side chains are on the inside
Secondary structure of amino acid involves ____ driven entirely by ___ ____ sequence
Folding
Amino acid
How tertiary structure differs from secondary structure
Folding is more complicated
What type of secondary structure makes good transmembrane proteins?
Alpha helices
Domain definition
Functional unit of protein
Domains are from the same _____, so they are from the same ____.
Protein
Gene
If domains were separated, would each one retain its function?
Yes
In an alpha helix, the ____ side chains are on one side and the ____ side chains are on the other
Polar
Charged
Primary structure of a protein is determined by what?
Sequence of amino acids
What causes the alpha helix shape?
Interaction of side chains
How many alpha helices combine to form a pore? What does the pore allow?
5
Ions to pass through
Can a protein subunit fold on its own? Does it have full function on its own? Why or why not?
Yes
No- needs to associate with other protein(s)
When subunits interacting are the same, it is called ____.
Oligomerization
Quaternary structure is due to what?
Multiple subunits associating with each other to form functional protein
When a subunit associates with the same type of protein, it forms a _____.
Homopolymer
When a subunit associates with different type of protein, it forms a _____.
Heteropolymer
Two main differences between subunit and domain: level of structure, which is part of the other
Subunit is part of quaternary structure
Domain is part of subunit
4 ways that proteins can associate with a membrane
Transmembrane
Monolayer-associated
Lipid-linked
Protein-attached
Most ion channels are ____ proteins.
Transmembrane
In a lipid-linked protein, does lipid linkage cause the protein to be on one or both sides of the membrane?
One side of membrane
Trimeric G proteins are what type of membrane-associated proteins?
Protein-attached (attached to transmembrane protein)
What type of method is a more “subtle” version of voltage clamp? How is it more “subtle”?
Patch clamp
Suitable for the smaller neurons of most animals
Patch clamp can be used to record whole ____ as well as single ____.
Cells
Channels
Patch clamp studies of ion channels can be completed in genetically modified ____ ____ that express foreign ____ ____.
Frog eggs
Ion channels
When patch clamping Na channels for analysis, what must be done with K channels and how?
K channels must be blocked with TEA
In a patch clamp experiment with Na, when does inward current start and when does it go away, relatively speaking?
As soon as patch clamp starts
Goes away quickly
Patch clamp experiments tell us the _____ that a given channel will open.
Probability
When running a patch clamp experiment on a whole cell or a single Na channel, is the duration the same or different for the whole cell and the single channel?
Same
In a patch clamp experiment, at what point is the first time that there is a reasonable probability of Na or K channels opening?
Threshold
At ____ mV, there is maximum conductance for Na because there is a maximum ____ of opening.
20
Probability
At 20 mV, there is a(n) _____% chance that all Na channels will be open.
80
When patch clamping K channels for analysis, what must be done with Na channels and how?
Na channels must be blocked with tetrodotoxin
In patch clamp experiments with K channels, there is a ___ in opening, but they ___ ____ the entire time thereafter.
Delay
Stay open
When comparing a whole cell vs a single channel in a patch clamp experiment, the ____ of current changes but the ____ stay the same.
Magnitude
Kinetics
Like with Na channels, at ___ mV there is a maximum probability of K channels being ____.
20
Open
At 20 mV, there is a(n) _____% chance that all K channels will be open.
60
Plotting probability of channel opening and whole cell conductance for K and Na reveal similar or dissimilar graphs? Why? What is different between the 2 ions in regards to channel opening?
Similar- same properties
Kinetics of opening and closing channels are different for each ion
Sodium current is ___ (timing), ____ (length), and ____ (direction).
Early
Transient
Inward
Potassium current is ___ (timing), ____ (length), and ____ (direction).
Late
Sustained
Outward
Scorpion alpha- and beta- toxins affect which ion channels?
Na
Scorpion alpha-toxin affects Na current and action potential duration how? What is the mechanism by which is does this?
Increased length of current and action potential
Blocks inactivation of Na channels
Scorpion beta-toxin affects Na channels how? What is the mechanism by which is does this?
Channel opens sooner (at rest) because its threshold is decreased
Voltage sensing properties of Na channel are changed
Channels can be ___- or ____- gated.
Voltage
Ligand
For a ligand-gated channel, what makes it open and what is a ligand?
Binding makes channels open
Ligand: thing that binds
To form a functional channel, is one or many proteins necessary?
Either- depends on channel
What is the function of a pore-loop in a channel and how does it work?
Amino acids of pore-loop line channel pore, determining which ions can pass through the channel
What does voltage-dependence mean for a channel?
Has a threshold and will only open at a certain voltage
Can channels move ions against their driving force?
No
A regulatory subunit comes from the (same/different) protein that comprises the ion channel. It ____ function of the channel but (is/isn’t) required for channel to pass ions.
Different
Modifies
Isn’t
Every protein has ____ carboxy terminal(s) and ___ amino terminal(s).
1
1
How many alpha subunits are needed for a functional voltage-gated K+ channel?
4
What subunits of the “typical” voltage-gated K+ channel aren’t required to make the channel functional?
Beta
The voltage sensing region of the voltage-gated K+ channel is a ___ of the alpha subunit.
Domain
At rest, the voltage sensor of the voltage-gated K+ channel is ____.
Closed
Upon depolarization, what happens to the voltage sensor of the voltage-gated K+ channel?
Undergoes conformational change that allows ions to pass through
What are the 3 types of voltage gated K+ channels talked about in class, and which one is the most typical?
Kv2.1 (most typical)
Kv4.1
HERG
All voltage-gated channels have a voltage ____.
Sensor
Kv2.1, Kv4.1, and HERG channels have how many alpha subunits? How many membrane spanning helices per subunit? How many transmembrane domains per functional channel?
4
6
24
All the K+, Na+, and Ca+ channels talked about in class have _____ ____ attached to their alpha subunits.
Pore loops
Kv2.1, Kv4.1, and HERG channels all have how many beta subunits? The beta subunits function as _____ subunits.
4
Regulatory
What about the kinetics of the Kv2.1 channel and subsequent K+ current make it the “typical” voltage-gated K+ channel?
Slow to open and close
Sustained current above threshold
For a given Kv2.1 channel, are the alpha subunits all the same type (from the same gene) or different (from different genes)?
Could be either
Are the alpha and beta subunits of the voltage-gated K+ channel encoded by same or different gene(s)?
Different
How is the Kv4.1 channel different from the Kv2.1 channel in terms of opening/closing and K+ current that makes it similar to the Na channel?
Kv4.1 channel inactivates shortly after opening
Transient K+ current above threshold
What happens to the HERG (K+ voltage-gated channel) immediately after opening? What does this mean for K+ current with these channels in a voltage clamp experiment?
It inactivates
Don’t see any K+ current during voltage clamp experiment
When does the HERG (K+ voltage-gated channel) de-inactivate? Is it slow or quick to close?
When Vrest is reached again
Slow
Do HERG channels (K+ voltage-gated channel) show transient or sustained K+ current? Between what 2 points does it last?
Transient
Between returning to Vrest and channel closing
K+ inward rectifying (KIR) channels: how many alpha subunits for a functional channel? How many membrane spanning helices/subunit? How many transmembrane domains per functional channel?
4
2
8
Are K+ inward rectifying (KIR) channels voltage-sensitive?
No
Do the K+ inward rectifying (KIR) channels have regulatory subunits?
No
K+ inward rectifying (KIR) channels passes K+ current in what direction only?
Inward
Because the K+ inward rectifying (KIR) channels only pass K+ current in the inward direction, conductance for K+ in these channels only occurs when membrane voltage is ____ than equilibrium potential for K. Why is it that these channels can be open at such a low voltage?
Less
The channels aren’t voltage dependent, so they don’t have a threshold
The K+ inward rectifying (KIR) channels play a role in restoring the membrane potential to _____.
Vrest
The Ca+2 gated K+ channels have how many alpha subunits? How many membrane-spanning helices? How many transmembrane domains per functional channel?
4
7
28
How many types of Ca+2 gated K+ channels are voltage-sensitive? What is/are the name(s) of the type(s) that are?
1 (Type 1 only; the rest are not)
The (intra-/extra-)cellular domain of Ca+2 gated K+ channels binds what ion? This domain functions as a ____ domain.
Intracellular
Ca+2
Regulatory
For a Ca+2 gated K+ channel, the more (intra-/extra-)cellular ____ present, the more ____ current and conductance is seen.
Intracellular
Ca+2
K+
The Ca+2 binding domain of the Ca+2 gated K+ channel is all part of ___ alpha subunit(s).
1
High intracellular Ca+2 will let the Ca+2 gated K+ channel open when membrane potential is ___ than threshold for Kv2.1. Thus, it can cause _____ K+ current without an action potential.
Less
Outward
The 2P K+ leak channels have how many alpha subunits required for a functional channel? How many membrane spanning helices per subunit? How many transmembrane domains per functional channel?
2
4
8
Are 2P K+ leak channels voltage-sensitive?
No
What 2 things are 2P K+ leak channels sensitive to?
pH
Mechanical stretch
Do 2P K+ leak channels have regulatory subunits?
No
For the 2P K+ leak channels, at what pH is the maximum conductance? Does it also open at biological pH?
8.0
Yes
At Vm less than Ek, 2P K+ leak channels “leak” ____ current and at Vm greater than Ek, 2P K+ leak channels “leak” ___ current.
Inward
Outward
Do the 2P K+ leak channels require an action potential to “leak” K+ current?
No
The voltage-gated Na+ and Ca+2 channels have how many alpha subunits from how many proteins? How many domains, and what are they similar in structure to? How many total membrane spanning helices?
1 subunit from 1 protein
4 domains
Similar to single alpha subunit of voltage-gated K+ channel
24 membrane spanning helices
For the voltage-gated Na+ and Ca+2 channels, how many voltage sensor(s) per domain?
1
The voltage-gated Na+ and Ca+2 channels have a ___ subunit that functions as a ___ subunit. This subunit is encoded by the same/different gene that encodes the alpha subunit.
Beta
Regulatory
Different
The voltage-gated Na+ channel has an (intra-/extra-)cellular ____ loop that functions as a ___ subunit.
Intracellular
Inactivation
Regulatory
What is the only K+ channel that doesn’t have 4 alpha subunits?
2P K+ leak channels
Toxins bind on the (inside/outside) of the Na channel.
Outside
The inactivation domain of the Na channel is located on the (extracellular/cytoplasmic) side of the molecule.
Cytoplasmic
What 2 properties are dependent upon channel being open? (Think I = g x DF)
Current
Conductance
If a voltage-gated Na channel doesn’t completely inactivate, how does that affect Vm and future action potentials after an action potential is completed?
Vm stays close to threshold
Likely to fire more action potentials
Thermosensitive channels: what causes what conformational change?
Warming of membrane causes opening of channel
Thermosensitive and mechanosensitive channels generally pass one or both of what 2 ions?
Na
Ca
Mechanosensitive channels: what causes what conformational change?
Stretching of membrane causes opening of channel
When referring to active transport of ions, a pump uses ____ as energy, whereas a transporter uses ____ as energy.
ATP
Electrochemical gradient
For an ATP pump, ATP _____ causes a conformational change that enables movement of ions ____ their concentration gradients. Are ions moved in the same or opposite directions? Is more than one ion required for the ATP pump to work?
Hydrolysis
Against
Opposite
No- can move one without the other, but still requires ATP
For an anti-porter, energy provided by the driving force of moving ____ ion(s) ____ the gradient enables moving another ion _____ the gradient.
1
With
Against
In an anti-porter, are the ions moving in the same or opposite directions?
Opposite
For a co-transporter, energy provided by the driving force of moving ___-___ ions ____ the gradient enables moving another ion _____ the gradient.
1-2
With
Against
In a co-transporter, are the ions moving in the same or opposite directions?
Same
For the Na/K pump, how many Na and how many K are moved per 1 ATP?
3 Na
2 K
The Na/K pump undergoes conformational change, allowing __ Na to enter on the _____ side of the membrane and ___ K to be released. What causes conformational change that enables Na to be released on the other side and K to bind? What causes the pump to switch back to its other side?
3 Cytoplasmic 2 Phosphorylation Dephosphorylation
What do ouabain and digoxin do to the Na/K pump? How does prolonged exposure to these drugs affect the concentration gradient and membrane potential of a cell?
Inhibit Na/K pump
Depletes concentration gradient for K and Na, bringing Vm close to 0
