Communication, Electrical Signalling, Channels and Transporters

Question 1

Direct Signalling

Answer 1

• gap junctions between cells found joining nearly all cells in solid tissues
• -connexon in each cell membrane join together to form channel between the two cells

-cell-cell recognition, receptors on one cell surface bind to specific ligands on nearby cell initiating a cascade of events

Question 2

Non-Direct Signalling

Answer 2

• panacrine signalling - molecules released by endocyotsis and transmitted to other cell by diffusion through extracellular fluid
• synaptic signalling - neurotransmitter released and diffuses across synapse
• long distance (hormonal) signalling - molecule released into blood stream, communication molecule transported in blood to other cells

Question 3

Stages of Cell Signalling

Answer 3

• transmitting cell releases primary messenger molecules
• received by cell membrane receptors triggering transduction
• inside the cell, secondary messenger molecules which trigger cellular responses / change in gene expression

Question 4

Quoram Sensing

Answer 4

• regulation of gene expression in response to changes in cell population density
• cells release a sepcific signalling molecule constantly ase well as detecting it
• so signalling molecules increase in concentration as a function of cell population density
• receptors that recognise the molecules respond when a threshold concentration is reached
• at low cell density cells exhibit individual behaviours
• above the threshold cell density quoram sensing genes are activated enabling group behaviours

Question 5

Molecular Communication Timescales

Answer 5

• it takes ~50s for a drop of blood to circulate the body
• it takes ~7hrs for ions to diffuse the length of an axon by random diffusion
• it takes ~4hrs for a molecular motor to walk the axon length
• these are all very slow compared to the sub-second reactions observed

Question 6

Electrical Signalling (Neurons)

Answer 6

• ions move across the membrane generating a current
• this changes the potential across the membrane
• if conditions are right charge flows and the potential change propagates down the axon in ms
• diffusion wants to make uniform the concetration of ions across the membrane by diffusion but a electric potential could prevent this

Question 7

Nernst Relation

General Case

Answer 7

-consider charge distribution in the presence of a battery
-what will be the voltage for a given charge distribution:
ln[ c(L) / c(0)] = - qΔV/kbT

Question 8

Nernst Relation

Membranes

Answer 8

ΔV = - kbT/q ln[cin/cout]

-for postive ions, for negative ions: cout/cin

Question 9

Establishing Existence of Membrane Potential Experiment

Answer 9

• electrodes inserted into giant squid axons to measure potential across membrane
• found that positive ions were mobile across the membrane whilst negative ions tended not to be

Question 10

What happens when you have a population of mobile and immobile ions?

Answer 10

• the mobile positive ions would like to diffuse away from the cell to make the inside and outside concentrations the same
• but doing this pulls them away from negative ions therefore costing electrostatic energy
• as a result an equilibrium is set up

Question 11

Setting the Membrane Potential

Answer 11

• if some positive ions flow out:
• -the negative charges inside are attracted to the inner membrane due to the cloud of positive charges outside that have just flowed out
• like parallel plate capacitor with +/- q on the surface
• this sets up the voltage difference across membrane, V given by Nernst

Question 12

Donnan Equilibrium

Answer 12

-cells have >2 species of ion and charged proteins (usually negative)
-how do all of these come to equilibrium?
-at equilibrium, by charge neutrality:
cin,tot = cout,tot = 0
-and from the Nernst relation:
ΔV = -kbT/q ln[c1+in/c1+out] = -kbT/q ln[c2+in/c2+out]
= -kbT/q ln[c3-out/c3-in]
-e.g. for three types of ion, 1 & 2 positive and 3 negative
-at equilibrium, these values can be maintained by the cell without using any energy

Question 13

Osmotic Pressure Due to Charge Imbalance

Answer 13

-at Donnan equilibrium there can be a significant concentration difference causing osmotic pressure
Δp = Δc kb T
-where Δc = cin,tot - cout,tot
-to resolve this the cell pumps (mainly Na+) ions out of the cell

Question 14

Sodium Anomaly Experiment

Answer 14

• equilibirum predicts ΔV<0 but sodium is way off, (positive)
• this Na+ being way out of equilibrium is refered to as the ‘sodium anomaly’
• the large Na+ difference between in a out balances the osmotic pressure so the cell is not in equilibrium
• it burns energy to pump Na+ out of the cell to balance osmotic pressure

Question 15

Ionic Current

Answer 15

-can describr flow of ions using Ohm’s Law:
I = V/R OR I=gV
-where g is conductance
-for ion species, i, the current flux is given by:
Ji = Ii/A = gi [ΔV - Vi,nernst]

Question 16

Membrane Conductance

Answer 16

• there are different conductance values, g, for each ion
• generally, Na+ is the least conductive species
• with g(K+) ~ 25 g(Na+)

Question 17

Membrane Flux With Pumps

Answer 17

-even with ΔV=0 and cin=cout there is still current flowing due to ion pumps:
Ji = Ii/A = gi [ΔV - Vi,nernst] + ji,pump
-ji,pump are related to each other by the ratio of ions pumped in/out
-e.g. 2K+ pumped in for every 3Na+ pumped out

Question 18

Membrane Steady State

Answer 18

• with pumps, what is the resting state of the membrane?
• despite being out of equilibrium, the cell is in a steady state so ΔV and the concentrations don’t change in time
• in the steady state, the fluxes of each ion =0
• this allows ΔV to be written in terms of the ion conductance and Nernst potential for each ion
• the rest potential, ΔV, lies nearest the Nernst potential for the most conductive ion

Question 19

Voltage Sensitive Ion Channels

Answer 19

• if we could make Na more conductive thean K+, the potential would switch by more than 50mV
• there are voltage sensitive ion pumps that make the membrane conductance in favour of Na+ so the potential flips which generates a voltage pulse
• under the right conditions this voltage pulse can propagate leading to an action potential or nerve pulse

Question 20

Action Potential

Description

Answer 20

• cell membrane starts at resting potential of -70mV
• if the threshold potential of -55mV is reach actino potential will propagate
• the membrane depolarises to +40mV
• renormalisation to -80mV overshooting the resting potential
• refactory period where the potential returns to the resting state of -70mV

Question 21

Action Potential

Resting Potential and Threshold Potential

Answer 21

• membrane voltage is -70mV
• inside is generally negative and outside is generally positive
• closed voltage gated sodium and potassium channels in the membrane
• threshold potential -55mV triggers sodium ion chanenls to open
• sodium ions move in through channels down a concentration gradient
• flow of positive charge into cell

Question 22

Action Potential

Depolarisation and Repolarisation

Answer 22

• the positive charge that has come in through the sodim channels diffuses inside the cell propagating the action potential and triggering the next sodium channels to open
• this continues to propagate down the cell
• after 1ms, ball and chain inactivation of sodium channels - ball of amino acids attached to the channel blocks the pore
• higher positve voltage across the membrane triggers potassium ion channels to open
• potassium ions diffuse out of cell down their concentration gradient, this begins to equal out the charge of the sodium ions that have entered resetting the membrane potential

Question 23

How are concentration gradients maintained for future action potentials?

Answer 23

• ion exchange pump used energy from ATP hydrolysis to pump 3Na+ out of the cell and 2K+ into the cell at a time
• this is constantly working so that the action potential doesn’t completely deplete Na+ and K+

Question 24

Importance of Channels and Transporters

Answer 24

• channels and transporters allow:
• -electrical signalling
• -chemical sensing
• -vision
• -hearing
• -touch
• -pressure
• -temperature sensing
• -muscle contraction
• -release of neurotransmitters
• -growth
• -energy production

Question 25

Channels vs Transporters

Channels

Answer 25

• allow ions to move across membranes down concentration gradients
• can be opened/closed by pH, temperature, signalling molecules, change in voltage, mechanical stress etc.

Question 26

Channels vs Transporters

Transporters

Answer 26

• physically assist small molecules across the membrane
• ususally via input of energy (ATP) or chemical potential
• act against concentration gradients with multiple steps / conformational changes
• a more complex set of dynamics

Question 27

Discrete State Systems

Answer 27

-for a system at temperature T, the probability of finding the system in state with energy E:
P(Ei) = 1/Z exp(- Ei/kbT)
-where Z is the partition funciton, the sum over all energy states of the system:
Z = Σ exp(- E/kbT)
-sum over all energies

Question 28

Two State Systems

Answer 28

• ion channels are two state systems, either open or closed
• there is a free energy barrier associated with transition between the two states
• the probabiltiy of a given state depends on the free energy difference between them and the temperature
• when the states are in equilibirum flow between them in each direction is equal

Question 29

Gating Mechanisms

Answer 29

-switching between open and closed conformations requires a change in free energy at a rate depending on the free energy barrier:
Po / Pc = exp[- (Go-Gc)/kbT]
-biology tunes these free energy differences and barriers using external forces e.g. voltage, tension, interaction with other molecules, light, temperature

Question 30

Voltage Gated Ion Channels

Answer 30

• open in response to a change in membrane potential
• usually ion specific
• the V_1/2 is the voltage at which the probabiltiy of being open is 0.5

Question 31

Mechanosensitive Ion Channels

Answer 31

-open in response to force e.g. membrane tension
-vital for senses such as touch and hearing
-used by bacteria to regulate turgor pressure in response to changes in external osmotic pressure
-

Question 32

Ligand Gated Ion Channels

Answer 32

• open in response to binding of a chemical messenger e.g. neurotransmitter
• involved in communication between synapses, taste and smell
• probabiltiy of opening depends on the concentration of the ligand

Question 33

Polymodal Ion Channels

Answer 33

-single ion channels modulated by multiple stimuli

Question 34

Selectivity Filters

Answer 34

• narrowest part of the channel is lined with amino acid residues that interact with the passing ions and mimic the arrangement of water molecules for the specific ion
• in order to pass through each ion has to shed its water molecules
• dimensions of the channel minic the shell of water

Question 35

Types of Transporter

Answer 35

• ATP pumps - couple ATP hydrolysis with movement of ions across a membrane against the concentration gradient
• symport - uses energy already stored in ion gradients to move a molecule across the membrane with some ions
• antiport - same as symport but ions move in the opposite direction to the target molecule

Question 36

Molecular Mechanisms of Transporters

Answer 36

• rocker switch - substrate binds between two domains catalysing the rearrangement of the two domains around the central binding site to allow the substrate move into the other side of the membrane
• rocking bundle - one structurally disimilar domain rearranges against a less labile domain
• elevator model - one domain moves against another relatively rigid domain to physically translocate the substrate across the membrane

Question 37

Experimental Techniques to Determine Physical Protein Structure

Answer 37

• x-ray crystallography
• cryo-electron microscopy
• NMR

Question 38

Experimental Techniques for Observing Protein Dynamics

Answer 38

• single ion-chanel recordings
• FRET
• high speed AFM