Lesson 1 - Building a brain

Building blocks in the brain

Learning Objectives:
● Describe the structure of prototypical neurons
● Describe the function of axons and dendrites
● Identify ways of characterising and naming neurons
● Describe the role and location of the four types of glial cells:
○ Myelinating glia
○ Astrocytes
○ Microglia
○ Ependymal cells

There are two major classes of cells in the nervous system: Neurons & Glia
A. Neurons have specialised structure and function
Neurons
● Neurite = neuronal process = axons and denrites (extensions of neurons)
● In general, electrical signals (information) is transmitted:
○ Away from body via axons
○ Towards the body via dendrites
● Action potentials represent the way information is transmitted.
● Information flow is chemical between neurons.

Neuronal Cytoskeleton
● Forms the scaffolding of the neuron; maintaining neuronal shape & controlling its
movement.
● Neurons have extended neurites
● Neuron shape is dynamic
● Microtubules
○ Rule longitudinal down neurites
○ Mediate intracellular transport
○ Change length to change shape/length of cell
● Neurofilaments
○ Provide structural support
○ Regulate diameter of axons
● Microfilaments
○ Linked to microtubules & membrane
○ Comprised of actin molecule (same protein found in muscles)

Axons
● Its structure reflects function
● Three important parts of axons
○ Axon hillock (beginning) - where action potential is generated
○ Axon proper (middle)
○ Axon terminal (end) - where axons can transfer information to another cell
■ No microtubules
■ Lots of internal vesicles containing chemical messengers (neurotransmitters)
■ Membrane is protein-dense → specialized function
 ■ Lots of mitochondria → energy demanding

Material transport in axon

● What is physically transported?
○ Proteins
○ Neurotransmitters
○ Metabolites
○ (not information/electrical signals)
● Fast axoplasmic transport
○ Proteins synthesized in soma are actively transported toward the axon terminal
(requires ATP/energy)
○ Metabolic waste products from the axon terminal are transported to the cell body
○ Up to 1m/day
● Slow axoplasmic transport
○ Mechanism unclear (stop & go?)
○ 0.1-10mm/day
● Transport direction
○ Anterograde via kinesin (foward/towards axon terminal)
○ Retrograde via dyenin (backward/away from axon terminal)

Synapse
● A special connection between 2 neurons (see Lesson 2) → Connect axon of one neuron to
denrite of a neuron
● Comprise of
○ Pre-synaptic membrane - releases vesicles containing neurotransmitter
○ Synaptic cleft - small gap between membranes of two neurons
○ Post-synaptic membrane - neurotransmitter (chemical signal) binds to specialized
proteins and is converted into electrical signal

Dendritic Spines
● Small extension of cell membrane where axons of another neuron come into close
proximity
● The density & length of dendritic spinse depends on environment and development
● Actin to change shape
● Region through which Ca2+ flows into activated cell

Neuronal structure and function varies

● Structure begets function
● Neurons vary in
○ Number of neurites: unipor, bipolar & multipolar (number of connection into soma)
○ Shape & dendrites
■ Stellate cell (star-shaped): collate information locally within a brain region.
Involved in local processing
■ Pyramidal cell: send information to other brain regions (due to long apical
dendrites)
○ Axon length
○ Connections
○ Neurotransmitter

B. Glia support neuronal function

Glia
● Support neuronal function & maybe involved in information transmission
● Critical role in electrical insulation, structural support, nourishing neurons, removing waste
and protection.
● There are 4 main types:
○ Myelinating glia - increase reliability and velocity of axonal signals
■ Oligodendroglia (CNS)
■ Schwann cells (PNS)
○ Astrocytes - a range of supporting roles
○ Microglia - the brain’s immune system
○ Ependymal cells - produce cerebrospinal fluid to cushion the brain from hard
impacts (physical protection)

Myelinating glia
● Oligodendroglia (CNS) and Schwann cells (PNS) generate myelin
● Myelin - forms a sheath around axons, proving electrical insulation → increase axonal
conduction velocity
● Nodes of Ranvier - regular gaps in myelin, critical for electrical communication, as they
provide a connection between the cytosol in the axon and the extracellular fluid.
● Schwann cell - wrap one segment of one axon in PNS
● Oligodendrocytes - wrap as many as 30 axons

Astrocytes - most numerous glia in the brain, in close proximity to neurons

● Fill spaces between neurons and vessels
● Influence neurite growth
● Regulate chemical content of extracellular space (e.g. K+ buffering)
● Contain glycogen & capable of gluconeogenesis
● Maybe contribute to or impair nervous system repair

● Are intimately related with axons & dendrites

○ Can regulate neurotransmitter in synapse
■ Involve in neural communication
● Ensheath small arterioles and capillaries
○ Help maintain blood-brain barrier (modulate blood flow)
■ Provide metabolic support for neurons
■ Blood-brain barrier is hard to pass for large molecules due to tight
junctions formed by endothelial cells

Microglia - 10-15% of glia in the nervous system

● Macrophages - remove debris associated with dead/degenerating cells
● Fight inflammation within the brain
● From specialized immune system within the brain

Ependymal Cells
● Epithelial-like cells that line fluid filled ventricles
● Produce cerebrospinal fluid (CSF)
● Control fluid release between brain tissue and cerebrospinal fluid

Getting oriented
Learning Objectives:
 ● Familiarise with standard terms for describing relative position within the brain and body

Axes in the body

● Rostral – towards the nose
● Caudal – towards the tail
● Dorsal – towards the back (think of the shark fin)
● Ventral – towards the belly

In humans, these axes are different in the spinal cord and head,
because our head has been tipped forward relative to our spine in
comparison with our four-legged friends.

● Anterior – towards the front

● Posterior – towards the back
● Superior – towards the top
● Inferior – towards the bottom

Planes used to slide and visualize the body

● Coronal = frontal (like a crown or tiara)
● Mid-sagittal – a sagittal plane that symmetrically divides body at midline
○ Lateral view = brain viewed from the side.
○ Medial view = view of sagittally sectioned brain

Positions in relations to the middle of the body

General organisation of the nervous system

Learning Objectives:
 ● Describe the structure and function of the major nervous system components:
○ Central vs Peripheral
○ Autonomic nervous system
○ Spinal cord

The scope of nervous system

● ~1.3kg brain + spinal cord + all peripheral nerves (e.g. to skin, internal organs, muscles,...)
● Brain contains ~86 billion neurons & similar glia number
● Brain contains ~100 billion synapse (inter-neuronal connections)
● There are general organising principles
○ Hundres of functionally distinct regions - neurons with similar roles are physically
adjacent
○ Systematic maps within regions - e.g. brain has visual maps of the world &
somatosensory maps of skins surface
○ Connected sub-systems perform specialized functions (e.g. autonomic nervous
system)
○ Canonical circuit microstructure within cortex

A single neuron filled with green fluorescent dye

Central vs Peripheral nervous system (CNS, PNS)

● CNS - structures encased in bone (brain + spinal cord)
● PNS - everything else

● Note the distinction between:

○ Nervous system - everything
○ Brain - neural tissue inside skull cavity (cranium)
○ Spinal cord - neural tissue inside vertebral column
 ○ Cortex - outermost layer or ‘bark’ of brain - most recently evolved part & highly
specialized circuitry; densely filled with neuron cell bodies
● Nerve = a bundle of axons or multiple neurons
● Cervical/thoraic/lumbar/sacral nerves correspond to the nerves entering & exiting different
levels of spinal cord

PNS: Somatic & Autonomic components

● Somatic component (see Sensory & Motor lessons)
○ Afferents (inputs) from sensory receptors in skin, muscles & tendons
○ Efferents (outputs) to skeletal muscles
● Autonomic component (see ANS lessons)
○ Afferents from sensors in internal organ, e.g. heart, gut & blood supply
○ Efferents to smooth muscle, heart & glands

● Motor neurons have cell body in CNS (spinal cord) but their axons target muscles in PNS
● Somatosensory neurons carry information from skin surface to other neurons in spinal
cord; have cell bodies in CNS but synapses are in PNS

Nervous system
● A montoring and control system
● Subdivided into CNS & PNS
● Have sensory receptor that are part of both somatic & autonomic systems - these sense
external & internal world
● Effectors can act both on world (e.g. via skeletal muscles) & on internal state of body (e.g.
cardiac muscle in heart, smooth muscle in intestines)

ANS: parasympathetic & sympathetic divisions

● Controls homeostasis & function beyond voluntary control
● Parasympathetic division - “rest & digest”
○ Generally slower activating
○ Dominate in absence of external stimulation
● Sympathetic division - “fight or flight”
○ Rapidly mobilizing system
 ○ Active in stressful/exciting situation with external stimulation
● Division can be simultaneously active, e.g. during sexual response

● The ANS can receive & process information without conscious control
● Sympathic chain ganglia contain cell bodies of neurons (in PNS) innervating range of
organs

The spinal cord connects brain with PNS

● White matter - there are tracts form brain up and down spinal cord. There are also the
axons of neurons that are exiting protection of vertebral column
● Sensory afferents/inputs are dosal (at back)
● Motor efferents/outputs are ventral (at the front)
● Dorsal root ganglion = collection of cell bodies whose axons form dorsal root of spinal
nerve (unipolar axons)
Key subdivisions of the brain
Learning Objectives:
● Describe the layered structure of the neocortex and how it relates to input-output
processing
● Describe the general function of the major subdivisions of the cortex
● Define and distinguish the brain, cerebrum, cerebral cortex and central nervous system

Key areas of CNS

1. Spinal cord - connects brain with PNS
● Conduit for information – sending out motor information, receiving sensory
information.
N.B the distinction between spinal cord (nerves) & vertebral column (bones protecting spinal cord)
● Spinal cord contains cell bodies at its core & axons heading up/down connecting to
brain
● Spinal nerves, bundles of axons where information enter and exits spinal cord
N.B while there are nerves exiting form spinal cord at all levels, there are many more at neck &
lumbar region. This where nerves enter and exit for arms and legs

2. Brain stem (medulla, pons, & midbrain)

● Continuous with spinal cord
 ● Regulates many autonomic & subconscious functions
● Provides sensory and motor innervation of face/neck
● Midbrain
○ Basic visual and auditory orienting responses
○ Sleep/wake cycles & arousal
○ Temperature regulation
● Pons
○ Relay signals from cerebrum to cerebellum
○ Sleep, respiration, bladder control, balance, posture, some sensation and
eye movements
● Medulla
○ Autonomic functions
○ Cardiac, respiratory, vasomotor, some reflexes

3. Cerebellum
● Cerebellum = Latin for “little brain”
● Clear role in motor control, especially motor learning & co-ordination incorporating
sensory feedback (see Motor Control lesson)
● Implicated in cognitive functions (attention & language)
Note the convoluted structure alternating grey matter (cell bodies) and white matter in the
cross-section below.

1. Midbrain
2. Cerebellum
3. Pons
4. Medulla oblongata
5. Inferior colliculus
6. Superior medullary velum
7. Fourth ventricle

4. Diencephalon
● Thalamus
● Relay station & gateway station controlling sensory flow & motor signals to and from
cerebrum (see Sensory Lessons)
● Regulates consciousness, sleep, alertness

● Sub-structures relate to homeostatic regulation by the autonomic nervous system

○ Hypothalamus – regulates metabolic processes
○ Pituitary gland – endocrine gland critical for homeostasis; reproductive &
stress hormones
○ Pineal gland – endocrine organ modulating sleep
5. Cerebrum (brain)
a. Cerebral cortex
● Outermost sheet of neural tissue
● Widespread functions in sensory perception, motor control, affect, cognition
● Extensive folding (encephalisation) increases surface area, leading to
alternating sulci and gyri (Sulcus = furrows; gyrus = ridge)

● Neural cell bodies are found in the outer “grey matter”

○ Relative positions of grey+white matter are reversed between spinal
cord (cell bodies in grey matter found centrally) & cerebrum (cell
bodies in grey matter found on the outer surface)
○ While the gray matter is dense with cell bodies, it also contained
axons and dendrites of neurons.
○ The white matter almost exclusively contains myelinated axons
projecting from neurons in one brain region to another

Frontal (coronal) slice of brain:

1. Cerebrum
2. Thalamus
3. Mesencephalon - Midbrain
4. Pons
5. Medulla oblongata
6. Medulla spinalis - Spinal cord

● Cerebral cortex is a layered structure

Golgi stain – sparsely labels whole cells (cell bodies +

axons & dendrites). Not all cells are labelled, but those that
uptake the label do so strongly.
Nissl stain – strongly labels rough ER in cell bodies of all
neurons
Weigert stain – labels myelin (so only axons).
Based on anatomy, 6 layers in cortex were originally
defined, but many layers have anatomical/functional
subdivisions.

There are almost no cell bodies in the white matter – it’s all
myelinated axons.
 b. Basal ganglia
● 4 internal nuclei, which form feedback circuits with cerebral cortex.
● Critical in motor control, behaviour switching, learning, reward

c. Limbic system (not shown)

● Disparate collection of nuclei, grouped more for their location than a
coherent function
● Hippocampus - memory & spatial navigation
● Amygdala - emotional valence & importance of stimuli (e.g. reward / fear)

Brodmann’s cytoarchitectonic maps

● Identified different regions based on differences in the size & density of neurons across
layers.
● Highlighted that cerebral cortex contains anatomically distinct areas

Primary sensory areas

 ● Brodmann areas were defined anatomically, but many have clearly distinct functions:
○ Area 17 - Primary visual cortex (V1)
■ Contains a retinotopic “map” of the world.
○ Areas 1-3 - Primary somatosensory cortex (S1)
■ Contains a somatotopic “map” of the body surface
○ Areas 41-42 - Primary auditory cortex (A1)
■ Contains a tonotopic map of frequencies
● Secondary sensory areas elaborate on earlier processing (e.g. areas 18,19 are visual
areas)

Motor areas

● Area 4 - Primary motor cortex (M1)

○ Controls movements (but does not directly target muscles)
○ contains a somatotopic map of muscle groups in the body
● Area 6 - Premotor and supplementary motor areas
○ Involved in planning of complex movements

Coarse somatotopic map: the motor homunculus (homunculus = little man)

 Coronal section of the brain, through M1 – the primary motor cortex

(Distorted) topographic organisation in primary somatosensory and motor cortex

Lesson 2 - Communication with action potentials

Calculating the membrane potential
Learning Objectives
● Identify the factors that affect ion movement across a membrane
○ Concentration gradient
○ Electric field
 ● Distinguish the factors affecting an ionic equilibrium potential and a cell’s membrane
potential
○ Ionic equilibrium potential - concentration ratio, electric charge, but not
membrane permeability
○ Resting membrane potential - concentration ratio, electric charge & permeability
of all ions
● Apply the Nernst equation and Goldman equation

Biological “wires” - the role of leaky membranes and ion flow in electrical signalling
● Axons and dendrites are not wires (but they share some properties with wires)
○ Electrical wiring
■ Substrate - metal
■ Charge is carried by free electrons
■ Usually very well insulated
➢ Only charge flow along the length of the wire matters
○ Biological systems
■ Substrate - intracellular fluid / cytosol
■ Charge is carried by ions (Na+; K+; Ca2+; Cl-)
■ Poor insulation between intra- and extracellular space
➢ Charge flow along the neurite and across the membrane matters
○ Common properties
■ Insulation is important (what insulates axons?)
■ Diameter - thicker wires/axons conduct faster
■ Temperature affects conduction in different ways
➢ Warmer axons conduct faster
■ Length - does not affect conduction velocity
➢ Length between nodes of ranvier matter more than length of
neurons as it affect conduction velocity
■ Kv density - action potential to polarized faster but not affect conduction
velocity
■ Myelination - increase axon conduction velocity

● Intracellular and extracellular spaces are separated by the phospholipid membrane

○ Diffusion of water and ions across the membrane is difficult and slow
○ Ion channels and pumps links the intra- and extracellular fluid

○ Membrane is a Phospholipid bilayer – hydrophilic head with a phosphate group; two

hydrophobic carbon chains.
■ The combined hydrophilic exterior & hydrophobic interior of the membrane
→ difficult for both charged & uncharged particles to cross the membrane.
■ If the membrane only contained the phospholipid bilayer, ions would not be
able to cross → to transfer materials between intra/extra, there are
specialised proteins.
➢ Extracellular fluid – mainly water, dissolved ions (water is a polar
molecule)
➢ Intracellular fluid – mainly water, same dissolved ions, but in different
concentrations

● Ions can only (easily) cross the phospholipid membrane via specialised proteins that
form ion channels and pumps
 ○ Amino acids (then will form a protein) are linked by peptide bonds (C-N) to form
polypeptide chains
○ Multiple polypetide chains can associate to form subunits

○ Subunits have hydrophobic and hydrophilic regions that allow them to sit stably
within the membrane.
○ Multiple subunits form ion channels that selectively allow ions to cross the
membrane

● Membrane-bound ion channels act like gatekeepers

○ Channels are selectively permeable. This selectivity arises due to:
■ Physical shape
■ Chemical properties (amino acid residues)

○ There are many types of channel, e.g.

■ Chloride channels
■ Potassium channels
■ Non-selective cation channels
○ Some channels can be gated – they may be open or closed depending on:
■ The membrane potential
■ The binding of a ligand to the channel

● Water crosses the membrane through specialised channels - aquaporins

○ Water diffusion through the membrane is very slow
○ Aquaporins allow the relatively free flow of water between intra- and extracellular
space
■ Aquaporins are blocked → diseases, e.g. brain edema or swelling of cells

How does ionic concentration affect ion movement across a membrane

● Ions cannot move freely across the membrane:
1. Ions diffuse “down” their concentration gradient
2. Ions move towards opposite charges
■ Assume water moves freely
■ Ion movement requires open channels.
■ Ion movement across a membrane depends on
○ Concentration gradient1 across the membrane
 ○ Electrical field across2 the membrane

■ At equilibrium there is no net ion flow (although ion movement still occurs)

Nernst Equation - the (hypothetical) equilibrium potential

● Membrane is permeable to a single ion

● Need to know:
○ Ionic concentrations (insided & outside of cell)
○ Ionic charge

Goldman Equation - the (measurable) membrane potential

● Use out/in for cations

● Use in/out for anions
● Need to know:
○ Internal and external concentration of each ion
○ Membrane permeability for each ion

Specialized membrane proteins

Learning Objectives:
● Describe the function of the Na/K-ATPase (Na-K pump)
○ Electrogenic pump - 3 Na+ out, 2 K+ in, uses 1 ATP
○ Maintains intracellular ionic concentrations and accounts for resting membrane
potential
● Describe how selectivity and gating occur in Na+ and K+ channels
 ○ Pore loops act as a physical filter (due to their close proximity)
○ Charged domains on amino acid residues act as a chemical filter
○ Channels can be voltage-gated with delayed opening or delayed closing

The Na/K-ATPase
● Maintaining resting membrane potential & concentration gradient
○ The sodium-potassium pump actively transports Na+ & K+ across the membrane
■ Powered by ATP (~70% of energy used by brain)
■ Pushes Na+ out of the cell (against its concentration gradient)
➢ High [Na+]in
■ Pushes K+ into the cell (against its concentration gradient)
➢ High [K+]out

● Has 2 ‘conformations’ or physical shapes

1. While open intracellularly, the pump binds ATP & 3 intracellular Na+ ions
2. The ATP is hydrolyzed, leading to phosphorylation of the pump & release of ADP
3. The pump change conformation, releasing Na+ ions to the extracellular space
4. The pump binds 2 extracellular K+ ions, causing dephosphorylation & a 2nd
confirmation change
5. ATP binds & K+ ions are released

Types of Potassium channel

● All K channels have 4 protein subunits with pore loops that regulate permeability

1. Two-pore-domain potassium channels (K2p)

■ Contain 2 pore loop domains, which are generally open
■ Contribute to ongoing K+ leak (i.e. high K+ permeability at rest)
■ Help set the resting membrane potential
■ 15 known types
2. Voltage-gated potassium channels (KV)
 ■ Open-state depends on the membrane potential
■ Normally closed at resting membrane potential
■ Also called ‘delayed-rectifier’ channels
○ “delayed” → take some time to open;
○ “rectifier” → return membrane potential to its resting level
■ 40 known types
3. Calcium-activated potassium channels
■ Presence of calcium will trigger channel opening
4. Inward-rectifying potassium channels
■ Passes positive charge more easily into than out of cell

Voltage-gated Sodium channels

Open when the membrane potential depolarises
○ Resting membrane potential is around -65 mV (polarised)
○ The channel conformation (protein shape) depends on the membrane potential.
○ Thus, membrane permeability for Na+ depends on membrane potential, but the
permeability also affects the membrane potential!

● Have three states: closed, open, or inactive

1. At rest (-65 mV), the channel is closed
2. At approximately -40 mV, the channels open for ~ 1 ms, allowing sodium influx
3. After ~1 ms, channels inactivate – the pore is occluded by a globular portion of the
protein
4. Channels reactivate (remaining closed) when the membrane potential reaches -65
mV

N.B. channel opening is stochastic – higher voltages increase the probability that a channel will
open, but we can’t predict exactly when a channel will open or exactly what the membrane
potential will be

● Tetrodotoxin (TTX) - sodium channel blocker

○ Blocks one class of voltage-gated sodium channel
○ Does not cross the blood-brain barrier
 ○ Remain conscious, but lose ability to generate action potentials (electrical
communication) in peripheral nerves

Phases of an action potential

Learning Objectives
● Describe the phases of an action potential, including what channels are involved, and
when.
● Explain the action potential in terms of changes in the membrane permeability and ionic
concentrations.

Slight depolarisation of the membrane potential leads to an action potential

● Action potentials
○ Can be explained completely by ionic concentrations and changes in channel
permeability over time
○ Are “all-or-none”
○ Have a stereotypical shape
○ Travel predominantly along an axon from the cell body to axon terminals
○ Convey information in their timing and their rate

1. Depolarization to threshold
 ○ An action potential begins when the membrane is depolarised past a threshold that
triggers opening of voltage-gated sodium channels. Action potentials are
“all-or-none”. If threshold is crossed, an AP does not occur

○ Na channel opening => membrane is more permeable to Na than K => membrane

potential rapidly approaches Na equilibrium potential (ENa). Assume the K and Na
concentrations do not change during the AP.

○ What causes the initial membrane depolarisation?

■ Physically-gated Na channels may open (e.g. stretch sensitive Na channels
in the skin)
■ The depolarisation may be “inherited” from elsewhere in the neuron

2. Voltage-gated Na channels open – rapid depolarisation

○ When voltage-gated Na channels open PNa >> PK. Therefore, Vm → ENa

○ As the membrane continues to depolarise, more and more voltage-gated Na

channels open → This is like a positive-feedback loop

3. Voltage-gated Na channels close – repolarisation

 ○ The voltage-gated Na channels only open for ~1 ms, and then they close and
inactivate. Therefore, Vm does not reach ENa!

○ Instead, as the Na channels close, we return to having PNa < PK. Therefore, Vm →
EK

4. KV delayed rectifier K channels open – hyperpolarisation

○ A second class of voltage gated channels now open - the “delayed rectifier” voltage
gated K channels. N.B. the K2p leak channels stay open throughout the entire AP!
○ Like NaV channels, KV channels are triggered to open when the membrane potential
reaches ~ -45 mV. However, their opening is delayed.
○ Now, PNa << PK, and the membrane potential hyperpolarises, below the normal
resting membrane potential (i.e. the membrane potential approaches EK)

5. Sodium channels inactivate – absolute refractory period

 ○ Sodium channels remain inactive until the membrane potential is repolarised
(deinactivation = the channel goes from being inactive to deactive and closed)
○ Thus we cannot get a second AP for at least 1 ms.
○ This prevents subsequent action potentials, limiting the theoretical maximum AP
rate to <1000 spikes/s. In practice, AP rates rarely exceed 100 spikes/s.

6. Potassium channels close – relative refractory period

○ The delayed rectifier, voltage-gated potassium channels also take some time to
close.
○ This prolongs the period of hyperpolarisation while PNa <<PK
○ During this period it is more difficult (but not impossible) to initiate further AP. This
could be because:
■ Membrane potential is lower than the resting level, so it must depolarise
further to reach the NaV threshold
■ Other types of channels (not discussed here) are open, which make it harder
to depolarise the membrane

Why are action potentials useful?

● Within a neuron, a “signal” is a change in voltage – i.e. deviations from the resting
membrane potential
 ● Diffusion requires passive movement of ions – this is ineffective over long distances, as the
concentration gradients become smaller and therefore weaker.
● N.B. Active transmission is not instantaneous; note that there is a pattern of 3 AP in
yellow – this is repeated at later time points, further along the axon.

Action potential summary

1. The membrane depolarises past a threshold at which voltage-gated Na channels open
2. Na+ ions enter the cell, further depolarising the membrane and opening more NaV channels
3. NaV channels close; the higher K permeability due to K2p channels causes repolarisation
4. Voltage gated KV channels open, hyperpolarising the membrane below the resting
membrane potential
5. NaV channels are inactivated until the membrane is hyperpolarised, preventing further
generation of AP during this absolute refractory period.
6. KV channels are briefly held open, keeping the membrane hyperpolarised. This makes it
harder to generate AP during the relative refractory period.
N.B For a given neuron, it’s convenient to assume that throughout an action potential the
intracellular and extracellular concentrations DO NOT CHANGE. While the permeability of the
membrane to these ions changes, a relatively small number of ions actually moves across the
membrane, so the concentration does not change.
● Threshold
○ Subthreshold stimuli that causes depolarization but not to the threshold
○ Threshold enough to create an action potential
● Refractory periods
○ Absolute refractory period for some time after one AP, a second AP cannot be
produce - infinite threshold (1-2ms)
○ Relative refractory period different voltage gated Na+ channels recover at different
rate (6-7 ms)
● Spread of current

Action potential propagation

Learning Objectives
● Account for the stochastic nature of action potentials
● Describe factors affecting the speed and nature of action potential conduction.

Channel openings are stochastic

Channel Patterns
● The relationship between the opening and closing of the channels involved in the
generation AP is described as stochastic
● This means that the channels are not all opening and closing at the same time but rather at
different times throughout the AP
● They are also opening for different period of time, some less than 1msec and some at
exactly 1msec
● They each also have a different influx of Na+, some allowing more sodium to enter the cell
while others allow less (i.e. different permeability)

● The same occurs for K+ channels. Often what we are seeing is the summation of individual
ion channels as a collective function of Na/K influx/efflux

Getting to threshold - the spike initiation zone

● What causes the initial membrane depolarisation?

1. “Inherited” from adjacent axonal region
2. “Inherited” from dendritic depolarizations (due to inputs from other neurons).
Remember, inputs are received on dendrites; axon hillock is spike initiation zone
 3. Physically-gated Na channels may open (e.g. stretch sensitive Na channels in skin’s
sensory neurons

Gaps between nodes of Ranvier must be appropriately spaced

● Nodes spaced by 0.2-2 mm.

● AP jump from node to node: diffusion actsquickly over short distances within the axon.
● Separation of nodes is limited by diffusion distance. If they were separated by too much,
then axon membrane potential won’t get past NaV threshold.
● Saltatory (Latin - to leap) conduction is faster – jumps.
● Multiple sclerosis – demyelinating disease. Early symptoms – problems with vision and
peripheral control – dependent on precisely timed signals in sensory and motor nerves.

Myelination and saltatory conduction increases velocity

● Oligodendrocytes & Schwann cells wrap axons in myelin.

● The fatty myelin sheathes are insulating - they prevent ions crossing the membrane.
● Ion channels are concentrated in the Nodes of Ranvier → high permeability when open.

Propagation the action potential

● The AP is described as an “all or nothing” mechanism in which if the membrane potential
reaches the threshold, it will fire. The initial magnitude to reach threshold does not matter
either, a faster depolarization to the threshold will produce the same depolarization that
only reached threshold
● Often, a single ion channel cannot produce enough of a sodium influx to reach the
threshold. Instead, it is the summation of a group of local Na+ channels that allow AP to
commence
● The speed through which an AP travels down an axon depends on how far depolarization
ahead of AP spreads
● This depends on certain physical characteristics of the axon
○ Axon diameter: Na+ can take 2 paths in the axon; it can cross the membrane or it
can move down axon.
■ Axon is narrow & there is high permeability to Na+ as there normally is
during AP initiation, Na+ will mostly move out of cell
■ Axon has wide diameter & very few open pores, majority of Na+ will move
down axon (the further ahead of AP, membrane will be depolarized)
○ Myelination: Myelin sheath consists of many layers of membrane provided by glial
cells. The myelin promotes current flow down the axon by insulating the leakage of
Na+ across the membrane. This insulation increase velocity of AP
○ Saltatory conduction:
■ There are breaks in myelin where ions can cross membrane to generated
APs. These gaps are known as Nodes of Ranvier and are rich in NaV
channels (0.2-2mm - larger gaps in larger axons)
■ Saltatory conduction refers to the way that AP skip from node to node to
speed up the conduction of AP by avoiding the need to generate an AP
along the entire length of axon

● The AP has been found to only propagate in one direction down the axon due to
inactivation of Na+ prior to the current location of depolarization (it cannot move backwards)
● Normally, the propagation direction is from soma to axon terminal. However, it is not
impossible for direction to be moving towards soma due to axons synapsing with other
axons
What affects conduction velocity?
● Myelination - more myelin = faster conduction
● Thickness - thicker = conduct faster signal than thinner ones
● Temperature - colder = slow down conduction

KCl – a lethal injection – does it affect the brain?

● Intravenous injection of KCl leads to a large increase in extracellular K+ ions. (i.e. the K+
ions leave the blood and enter the extracellular space around the body)
● This depolarises the resting membrane potential of excitable cells like neurons and cardiac
cells (which are also electrically active). This quickly prevents the heart from beating.

● In practice, the brain is protected from such rises in K+ because of:

○ Blood-brain barrier
○ Astrocytic buffering

Experimental manipulation of neurons

● Greater injection of current will lead to greater depolarisation.
 ● Once injected current leads to crossing past threshold, spikes are evoked.
● Rate of spikes is proportional to current, because the depolarisation (after absolute
refractory period) is faster when there is higher current.
Method 1: inject charge (current) into single neurons to depolarise the membrane

Method 2: biphasic current pulses in the extracellular space can depolarise adjacent
neurons

Lesson 3 - Neural Computation

Synapses - Basic structure and function
Learning Objectives
● Describe the structure and function of electrical synapses
● Describe the structure, function and classification of chemical synapse

Electrical Synapses (gap junction)

● Electrical synapses are relatively simple in structure & function, they allow direct ion
transfer between cells
● This ion transfer occurs at gap junctions in which the gap between 2 cells is 3nm apart.
○ The gap is spanned by clusters of proteins known as connexions.
 ○ Six connexions subunits combine to form a channel called connexon
○ Two of connexon combine to from a gap junction
● The diameter of connexon is approximately 1-2nm, which is big enough for all major
cellular ions & small organic molecules to pass through.
○ This makes gap junctions non-selective

● Most gap junctions allow the movement of ions very well in either direction → bidirectional
● Gap junctions electrically couple neurons but are computationally inflexible
○ Cells connected by gap junctions are referred to as electrically coupled
○ Transmission at electrical synapse is very fast & fail-safe (if the synapses is large
enough)
○ An AP in the pre-synaptic neuron can produce an AP in post-synaptic neuron
● The post-synaptic neuron has small reflection of the original AP seen in pre-synaptic
neuron.
○ Most of it leaks into the extracellular matrix due to a limited amount of charge can
cross into the next neuron
○ One neuron usually makes several synaptic connections so the post-synaptic
potentials summed up maybe enough to trigger an AP

Chemical Synapses (neurotransmitter release at synapse)

● Slow but computationally powerful connections
● Basic properties
○ Pre-synaptic & post-synaptic membranes at chemical synapses are separated by a
cleft 20-50 nm wide
■ Cleft is filled with a protein-rich matrix that functions to bind two membranes
tgt
○ Pre-synaptic membrane is often an axon terminal contains neurotransmitter-filled
vesicles (50 nm diameter)
○ Many pre-synaptic membrane also have large vesicles called secretory granules
(100 nm) containing soluble protein (dense-core vesicles)
 ○ Pre-synaptic “active zones” - location of specialised proteins that bind
vesicles, releasing neurotransmitter
■ The presynaptic membrane consists of proteins jutting pout into the
cytoplasm of terminal along intracellular face of membrane - these resemble
pyramids. The combination of pyramids & membrane to which they are
associated is known as active zone. Synaptic vesicles are clustered in the
cytoplasm adjacent to the active zone
■ The protein thickly accumulated in and just under the post-synpatic
membrane is called post-synaptic density containing neurotransmitter
receptor that convert the intracellular chemical signal into an intracellular
signal in the post-synaptic membrane

Classifying of chemical synapses

1. Axon location: Chemical synapses can be differentiated bases on the connections they
have between pre and post-synaptic membrane
○ Axo-denritic synapses: axon = pre-synaptic membrane & dendrite = post-synaptic
membrane
○ Axo-somatoc synapses: axon = pre-synaptic membrane & soma = post-synaptic
membrane
○ Axo-axonic synapses: axon = pre-synaptic & post-synaptic membrane
○ Dendro-dendritic synapses: dendrites form connection with each other (rare
scenario)

2. Effector: Most axons target other neurons. A special synapse in the periphery is the
“neuromuscular junction” (NMJ), connecting motorneurons to muscle fibers
 ○ Neuromuscular junction is a synapse form between motor neuron and muscle
fibre
○ Neuromuscular junction synaptic transmission is fast & reliable. An AP in motor
axon always causes an AP in muscle cells that it innervates
○ Pre-synaptic membrane contains many active zones aligned with junctional folds
○ Post-synaptic membrane (aka motor end plate) contains series of shallow folds
packed with neurotransmitter receptor

3. Size: Number and size of synapses connecting two neurons indicates the strength and
importance of the signalling.
○ The more connections that a pre-synaptic membrane forms with a post-synaptic
membrane, the stronger the connection will be

4. Microscopic structure
○ Gray’s Type 1
1. Asymmetrical: thicker post-synaptic side than pre-synaptic side.
2. Usually excitatory (lead to depolarization of AP in next neuron)
3. Contain round vesicles
4. Contact dendritic spines
5. Electron dense
➢ E.g. Glutamatergic synapses (neurotransmitter glutamate)
○ Gray’s Type 2
1. Symmetrical: similar thickness on pre-synaptic & post-synaptic sides
2. Usually inhibitory (lead to hyperpolarization of AP in next neuron)
3. Contain oval vesicles
4. Contact dendritic shaft / cell body
5. Less electron dense
➢ E.g. GABAergic synapses (neurotransmitter GABA)
N.B. Individual neurons don’t normally release both excitatory and inhibitory neurotransmitters

5. Neurotransmitter
○ Chemical signals that cross synapse & trigger an AP in post-synaptic membrane
○ Four criteria
1. Synthesized in the presynaptic neuron
2. Defined action on the postsynaptic neuron / effector after release from
presynaptic neuron
3. Exogenous administration mimics actions of endogenous transmitter
4. Specific mechanism exists for removing the substance from the synaptic
cleft
○ Three types
1. Amino acids: Small organic molecules
➢ E.g., Glutamate (usually opens cation channels), GABA (usually
opens Chloride channels), Glycine
2. Amines: Small organic molecules
➢ E.g., Dopamine, Acetylcholine, Histamine
3. Peptides: Short amino acid chains stored in & released from secretory
granules.
➢ E.g., Dynorphin, Enkephalins
○ Synaptic vesicles & synaptic granules are frequently observed in same axon
terminals
○ Different neurons in brain release different neurotransmitters. The speed of synaptic
transmission differ widely, with fasst forms of synaptic transmission taking
10-100msec. Slower forms of synaptic transmission take hundreds of msec
Synapses - Factors affecting synaptic strength
Learning Objectives
● Communication via chemical synapse:
○ Describe factors affecting neurotransmitter release from a pre-synaptic neuron
○ Describe factors affecting changes in the membrane potential of a post-synaptic
neuron

Factors affecting neurotransmitter release from the pre-synaptic neuron

1. Neurotransmitter synthesis
○ Chemical synaptic transmission requires neurotransmitters be synthesized & ready
for release
○ Different neurotransmitters are synthesized in different ways
■ Amino acids (glutamate, glycine) are available within all cells – just need to
be packaged in terminal as they are used to synthesis proteins
■ Amines & GABA require special enzymes for synthesis – the
neurotransmitter precursor and enzymes are actively transported to the axon
terminal, where the neurotransmitter is synthesised and packaged.
■ Peptides are synthesised in Rough ER & packaged into secretory granules
in the nucleus then transported to terminal.

2. Neurotransmitters loading into vesicles

○ The vesicle membrane is later recovered by the process of endocytosis & the
recycles vesicle is refilled with neurotransmitters
○ During periods of prolonged stimulation, vesicles are mobilized from a reversed pool
that bound to the cytoskeleton of the axon terminal
 ○ Vesicles are made from the same phospholipid bilayer as the cell membrane
○ Vesicles are all approximately the same size (~50 nm) and contain a similar amount
of neurotransmitter → each vesicle has the same effect post-synaptically.
○ Secretory granules (containing special peptides) are larger (~100 nm).

3. Vesicle fusion and neurotransmitter release

i. Neurotransmitter release is triggered by the arrival of an AP in the axon terminal for
rapid signalling → Some vesicles are already partially fused to the membrane

ii. Depolarization of axon terminal causes voltage-gated calcium channels in active

zone to open → Create a large driving force of Ca2+ levels acts as a signal that
causes neurotransmitter to be released from synaptic vesicles

iii. Intracellular Ca2+ triggers binding of the synaptic vesicle and fusion of synaptic
vesicles membrane with pre-synaptic membrane (exocytosis) → Directly releases
neurotransmitter into the cleft in as little as 0.2 ms.

iv. The vesicle disconnects from the release site (endocytosis), so it can later be
refilled. A range of specialised proteins hold vesicles docked in terminal, and
choreograph exocytosis and endocytosis.
➢ The speed of neurotransmission is due to vesicles involved in
neurotransmission being ‘docked’, where special proteins hold them in a
partially fused phase with the pre-synaptic membrane forming a pore,
allowing neurotransmitters to be quickly released.
➢ Secretory granules are also released in this manner. However, a single AP is
rarely enough to release them (Normally, it is a period of high-frequency
trains of AP → Ca2+ that can build up to trigger the release from the active
zone)
Factors affecting changes in the membrane potential of a post-synaptic neuron
4. Neurotransmitters binding to post-synaptic receptors
○ Two mechanisms of neurotransmitter action at the post-synaptic membrane (i.e.
ways in which neurotransmitter binding affects membrane potential)
1. Ionotropic
■ Ion channel is gated by a ligand (the neurotransmitter)
■ Fast, but brief.
■ Typically less selective than voltage-gated channels (e.g. permeable
to multiple cations)

2. Metabotropic
■ Receptor indirectly linked with ion channel
■ Require signalling cascade e.g. receptor activates a G-protein
■ Slower, longer acting, but can have broader, more distributed effects
■ Two modes of action are shown below - a channel & an enzyme
5. Post-synaptic response to neurotransmitter
○ Post-synaptic potential (PSP) – transient change in membrane potential due
to neurotransmitter-mediated channel opening
■ Receptors known as transmitter-gated ion channels are
membrane-spanning proteins consisting of 4 or 5 subunits that come
together to form a pore between them.
■ When neurotransmitters bind to specific site on the extracellular region of
them, it induces a conformational change that causes the pore to open. The
functional outcomes of this conformational change depends on what ion can
pass through the pore
■ Transmitted-gated ion channels do not generally show the same degree of
selectivity that voltage-gated ion channels do

○ Excitatory PSP – EPSP – transient depolarisation (e.g. Na+ channels opened)

■ If the open channels (cation channels) are permeable to Na+, the net effect
is depolarization of post-synaptic membrane from resting potential.
■ As this brings membrane potential closer to the threshold for an AP to be
generated, the process is called excitatory.
■ The effect is called Excitatory Post-Synaptic Potential (ESPS).
■ These can be caused by Acetylcholine and Glutamate

○ Inhibitory PSP – IPSP – transient hyperpolarisation (e.g. Cl- channels opened)

■ If the open channels are permeable to Cl-, the net effect is
hyperpolarization of post-synaptic membrane from resting potential.
■ As this brings membrane potential further from the threshold for an AP to
be generated, the process is called inhibitory.
■ The effect is called Inhibitory Post-Synaptic Potential (IPSP).
■ These can be caused by Glycine and GABA
 ○ Some metabotropic neurotransmitters are not directly linked with ion channels →
They act as neuromodulators & indirectly modify the size of EPSPs associated
with other synapses

○ How does closing some K+ channels affect Vrest? (Assume the leak channels
remain open)
■ Closing a few K+ channels will not greatly affect the membrane potential
(because PK >> Pna). However, decreasing K+ leakage increases membrane
resistance. This makes the neuron more excitable, or more responsive to
other neurotransmitters.

6. Neurotransmitter removal
○ Once the released neurotransmitter has interacted with the postsynaptic receptors,
it must be cleared from the synaptic cleft to allow another round of neural
transmission. Computation requires precise timing – i.e. both turning on and off
neurons. This requires two actions:
1. Removal of Ca2+ from inside the axon terminal
➢ a Na+/Ca2+ exchanger (NCX) performs this role
➢ 3 Na+ move into the cell down their concentration gradient, moving 1
Ca2+ out of the cell.
2. Removal of neurotransmitters. This is achieved through either:
➢ Diffusion of neurotransmitter - away from synapse
➢ Reuptake - neurotransmitter re-enters presynaptic axon terminal
➢ Enzymatic destruction (e.g. acetylcholinesterase breaks down Ach)
N.B. Glial cells, particularly astrocytes, play a role in taking up excess neurotransmitters and
helping with their recycling or degradation.
○ If neurotransmitters were not removed from the synaptic cleft or the receptors,
neurons would undergo desensitisation, in which, despite the continuous presence
of the neurotransmitter, the channels are closed. This state can occur for many
seconds following the removal of the neurotransmitter, which prevents the
propagation of an additional action potential.

Dendrites - Postsynaptic potentials

Learning Objectives
● Describe what determines the size of EPSPs, and their effect at the soma
● Describe the factors affecting spatial and temporal summation of PSPs in dendrites

Dendritic Integration
● A single AP is not usually sufficient enough to trigger an AP in post-synaptic membrane.
The addition of multiple pre-synaptic membranes to a single post-synaptic membrane (i.e.
multiple axons on to a single dendrite or multiple active zones from a single axon) will
improve the chances of the propagation of an AP.
 ● Dendrites integrate information spatially & temporally. This means that if multiple APs occur
at the same time, the summation of these will likely produce an AP. The same occurs for
temporality, where if multiple APs occur within a short succession, the likelihood of an AP
will be produces is increased.

● Dendrites integrate information spatially and temporally - the basis of neural computation
○ Left - a single presynaptic action-potential produces a single, small EPSP
■ This is usually insufficient to produce an action potential in the post-synaptic
neuron
○ Middle - EPSPs associated with simultaneous inputs from multiple neurons sum
○ Right - EPSPs associated with sequential inputs from a single neuron can sum over
time

Quantal Analysis of EPSPs

● The elementary unit of neurotransmitter release is the contents of a single synaptic vesicle.
● Vesicles contain about the same number of transmitter molecules; the total amount of
neurotransmitter release in some multiple of the number of neurotransmitters in each
vesicles (a quantum)
● The amplitude of the post-synaptic EPSP is some multiple of the response to the contents
of a single vesicle, making them quantized
● The size of post-synaptic response to the spontaneous release neurotransmitter can be
measured electrophysiologically
● The tiny response is a miniature post-synaptic potential, often called minis.
● Each mini is generated by the transmitter contents of one vesicle
● Quantal analysis is a method that compares the minis and an evoked post-synaptic
potential to establish the amount of vesicles that were released across the synapse

Passive Diffusion in Dendrites

● Passive conduction depends purely on channels.

● The EPSP moves passively in a dendrite due to its membrane's absence of

voltage-gated ion channels.
● Due to this passive diffusion, the EPSP decays as it moves through the dendrites as
charge leaks across the membrane (e.g. K2P channels)
 ● Ions choose to leak across the membrane as they follow the path of least resistance, which
in this case occurs across the membrane
● 𝛌 is the dendritic length constant and represents the length over which
depolarization decays to 1/e of its original value
● The value of 𝛌 depends on two factors:
○ Internal resistance: The resistance to the current flowing longitudinally down the
dendrite (proportional to diameter of dendrite moving towards the soma)
○ Membrane resistance: The resistancte to current flowing across the membrane
(proportional to number of open channels in membrane)

● Signals propagate bi-directionally in dendrites, moving both to and from the soma.
Synapses closer to the soma have a greater influence on spiking probability. Those further
from the somas have more neurotransmitter receptors to allow them to generate a larger
PSP

● The EPSP/IPSP need to reach the spike initiation zone to affect the spiking probability
● The ‘trigger zone’ is a position on axon hillock that has the highest density of voltage-gated
sodium channels, and therefore, the lowest spiking threshold (i.e. it is the easiest point from
which an action potential can propagate)

Active Conduction in Dendrites

● Active conduction (like action potentials), depends on voltage-gated channels, which give
a boost to any membrane depolarisation.

● Although most dendrites relies on passive transport, some can also actively conduct a PSP
○ The ability for active conduction in some dendrites is reliant on the
voltage-gated channels to replenish the decaying depolarizations
 ○ The active conduction improves the probability that an EPSP will reach the soma
and generate an AP
○ The active conduction does not function as it does in axon though, it is often not as
reliable because they do not cause large depolarisation but rather maintain the PSP
as it moves down the dendrites

Spatial and temporal summation are limited by a dendrite’s space and time constants,
which are determined by the dendrite’s diameter and density of open channels
● Temporal Summation: efficacy depends on the membrane time constant (i.e. how quickly
it leaks charge)
○ What affects time constant?
■ Membrane resistance = density of open channels
■ Membrane capacitance, primarily determined by surface area.
■ Long time constants are associated with a less leaky membrane (i.e. fewer
open channels).

● Spatial Summation: efficacy depends on the membrane length constant (i.e. how far
charge can propagate)
○ What affects length constants?
■ Membrane resistance = density of open channels. More channels open →
shorter length constant because charge leaks across membrane
■ Axon diameter = wider → higher length constant because there is less
resistance to charge flow down the axon
■ Long length constants are associated with wider dendrites and less leaky
membranes.

Dendrites - Factors affecting computation using PSPs

Learning Objectives
● Describe the mechanisms by which Cl- channels mediates inhibition
● Identify ways in which the probability of vesicle release can be modified

Shunting Inhibition: Opening chloride ion channels can inhibit current flow travelling from
dendrite to axon hillock
● The post-synaptic receptors under most inhibitory synapses are very similar to those in
excitatory synapses, the only difference being to types of neurotransmitters that bind to
them
● The binding of different neurotransmitters trigger the opening of different ion channels that
will cause the resting membrane potential to hyperpolarize to prevent an AP from
propagating
● These transmitted-gated channels of most inhibitory synapases are permeable Cl- ions,
triggering the influx of negative charge to hyperpolarize the membrane potential ↔
membrane potential less negative than -65mV
● These synapse act as electrical shunts, preventing the current from flowing through
the soma to the axon hillock
● This type of inhibition is known as shunting inhibition and functions in a way that
promotes the leaking of positive charge across the membrane to diminish the PSP
● The action of inhibitory synapses also contributes to synaptic integration. The ISPSs
reduce the size of EPSPs, making the post-synaptic neuron less likely to fire.
Vesicle Release Probability
● An arrival of an AP at axon terminal does not guarantee that a vesicle will be released (i.e.
release probability Pr < 1)
● Thus, modulating the probability of vesicle release is another way that strength of a
synapse can be controlled
● Pr varies in different areas in body:
○ Spinal cord motor neurons: 0-1
○ Cerebellar climbing fire: ~0.9
○ Cortical pyramidal cells: 0.1-0.9
○ Motor neurons: 1

● Action potentials lead to the opening of voltage-gated Ca2+ channels in the axon terminal
● Axo-axonal synapses regulated Ca2+ entry into the axon terminal. This can involve both
ionotropic (fast) and metabotropic (slow) mechanisms
● If a second AP arrives before the Ca2+ has been cleared from the axon terminal, two
distinct spikes will be seen. The second spike is associated with higher intracellular calcium
and a larger excitatory post-synaptic current

● As the separation of the two stimuli increases, the amount of facilitation decreases.
○ If Pr is low = facilitation.
○ If the Pr is high = depression
● Autoreceptors are presynaptic metabotropic receptors that monitor their levels of
neurotransmitters release. They allow high levels of neurotransmitters in the cleft to
regulate further release. They can inhibit both neurotransmitter releases and synthesis.
These operate in a negative feedback mechanism