Neuroscience Review: Neurons, Glia, Signals, Synapses, and Sensory Systems

Foundations of Neurobiology: The Neuron Doctrine and Cellular Organization

All organs and tissues in the body consist of cells. The specialized functions of cells and their interactions determine organ functions. The brain operates under the same biological principles as organs like the pancreas or lung. Fully understanding the individual and concerted actions of brain cells provides the basis for understanding mental abilities.

The adult human brain contains approximately equal numbers of neurons and glia: roughly $85 \times 10^9$ neurons and $85 \times 10^9$ glial cells. Neurons are responsible for most unique brain functions, including sensing environmental changes, communicating these changes to other neurons, and commanding body responses. Glial cells contribute primarily by insulating, supporting, and nourishing neighboring neurons.

The History of Neurohistology

Progress in studying brain cells required overcoming several technical obstacles:

• Small Cell Size: Neurons range from $0.01\text{--}0.05\text{ mm}$ ($10\text{--}50\text{ }\frac{1}{1000}\text{ mm}$ or $\text{μm}$) in diameter. For scale, an unsharpened pencil lead tip is approximately $2\text{ mm}$ across, making neurons 40 to 200 times smaller. Cellular neuroscience could not advance until the compound microscope was developed in the late seventeenth century.

• Tissue Consistency: Fresh brain tissue has a consistency similar to Jell-O, making it too soft to slice thin enough for microscopic observation. In the early nineteenth century, scientists discovered how to fix tissues by immersing them in formaldehyde, and developed the microtome to make ultra-thin slices.

• Uniform Pigmentation: Freshly prepared brain tissue exhibits a uniform, cream-colored appearance under a light microscope. Histology (the microscopic study of tissue structure) required selective stains to color parts of cells.

The Nissl Stain

Introduced by German neurologist Franz Nissl in the late nineteenth century, the Nissl stain uses basic dyes (such as cresyl violet) to color the cell nuclei of all cells, as well as dense clumps of material surrounding the nuclei of neurons. These clumps are called Nissl bodies (now known to be rough endoplasmic reticulum).

The Nissl stain performs two crucial functions:

1. It distinguishes neurons from glial cells.

2. It enables histologists to study the cytoarchitecture (arrangement of cells) in different brain regions, revealing that the brain consists of specialized functional areas.

The Golgi Stain

In 1873, Italian histologist Camillo Golgi discovered that soaking brain tissue in a silver chromate solution selectively stains a small percentage (~1%) of neurons in their entirety. This revealed that the cell body (soma, perikaryon) contains the nucleus but represents only a small fraction of the total neuronal structure.

The Golgi stain demonstrated two main structural components of neurons:

• Soma (Perikaryon): The central swollen region containing the nucleus.

• Neurites: Thin tubes radiating from the soma, categorized into two types:

  • Axons: Usually single, uniform in diameter throughout their length, with right-angle branches (axon collaterals). Axons act as wires carrying output signals and can extend over great distances ($1\text{ m}$ or more).

  • Dendrites: Rarely longer than $2\text{ mm}$, multiple dendrites extend from the soma, tapering to fine points. They contact numerous axons and act as antennae receiving input signals.

Cajal and the Neuron Doctrine

Santiago Ramón y Cajal used Golgi's silver chromate stain starting in 1888 to map the neural circuitry of brain regions, including the motor cortex. Golgi and Cajal reached opposing conclusions:

• Reticular Theory (Golgi): Neurites of different cells are fused together into a continuous network or reticulum, making the brain an exception to Schwann's cell theory.

• Neuron Doctrine (Cajal): Neurites of different neurons are not continuous; they communicate by contact, not continuity. Cell theory applies fully to neurons.

Golgi and Cajal shared the Nobel Prize in 1906. Proof of the Neuron Doctrine was achieved in the 1950s using the electron microscope, which demonstrated that neurites are separated by a physical gap ($20\text{ nm}$ synaptic cleft).

Microscopy Resolution Limits

• Unaided Human Eye: Limit of resolution is approximately $0.1\text{ mm}$ ($100\text{ }μm$).

• Standard Light Microscope: Theoretical limit of resolution is approximately $0.1\text{ }μm$ ($100\text{ nm}$).

• Electron Microscope: Uses an electron beam instead of light; limit of resolution is approximately $0.1\text{ nm}$ (1 million times better than the human eye, 1,000 times better than light microscopy).

• Laser / Fluorescence / Super-Resolution Microscopy: Uses laser beams to excite fluorescent molecules in living tissue, achieving resolutions down to $20\text{ nm}$.

The Prototypical Neuron

The neuronal soma is roughly spherical, measuring approximately $20\text{ }μm$ in diameter. The watery fluid inside is the cytosol (a salty, potassium-rich solution). The cytosol and organelles (excluding the nucleus) are collectively termed the cytoplasm.

The Nucleus

Centrally located and spherical, the nucleus measures $5\text{--}10\text{ }μm$ across. It is enclosed by a double membrane called the nuclear envelope, perforated by pores $0.1\text{ }μm$ in diameter.

Inside the nucleus are 46 human chromosomes containing deoxyribonucleic acid (DNA). DNA forms a double-stranded braid $2\text{ nm}$ wide. Uncoiled, the total DNA across 46 chromosomes measures $>2\text{ m}$ in length. Genes are specific segments of DNA ($0.1$ to several $\text{μm}$ long) used to code for proteins.

• Transcription: The synthesis of messenger RNA (mRNA) from DNA by RNA polymerase. Transcription initiates when RNA polymerase binds to a promoter region (regulated by transcription factors) and stops at a terminator sequence.

• RNA Splicing: Non-coding regions within genes (introns) are removed from the initial RNA transcript, and coding regions (exons) are fused together. Alternative splicing can yield distinct mRNAs encoding different protein isoforms from a single gene.

• Translation: Assembly of protein molecules from 20 distinct amino acids directed by mRNA transcripts on ribosomes in the cytoplasm. Central dogma of molecular biology: $\text{DNA} → \text{Transcription} → \text{mRNA} → \text{Translation} → \text{Protein}$.

Genetic Variation and Engineering

• Gene Copy Number Variations: Duplications or deletions of gene segments during conception, implicated in psychiatric conditions such as autism and schizophrenia.

• Single Nucleotide Polymorphisms (SNPs): Minor single-base misspellings in coding or regulatory DNA sequences that alter protein structure or function.

• Fragile X Syndrome: Intellectual disability and autism caused by the disruption of a single gene.

• Transgenic/Knockout Models: Techniques developed by Martin Evans, Oliver Smithies, and Mario Capecchi (2007 Nobel Prize). Knockout mice have a gene deleted; transgenic mice overexpress an introduced transgene; knock-in mice have a native gene replaced by a mutated transgene. Homologous recombination inserts exogenous DNA targeting specific loci in embryonic stem (EK) cells.

• Microglia & Hoxb8: Capecchi demonstrated that mutating the Hoxb8 gene in mouse microglia causes obsessive hair-pulling (trichotillomania), which can be cured by transplanting wild-type bone marrow stem cells.

Cytoplasmic Organelles

• Rough Endoplasmic Reticulum (Rough ER): Stacks of membrane studded with ribosomes (Nissl bodies). Major site of protein synthesis for membrane-bound proteins or proteins destined for organelle enclosure. Transcripts encoding cytosolic proteins utilize free ribosomes or polyribosomes (mRNA strands bound by multiple ribosomes).

• Smooth Endoplasmic Reticulum (Smooth ER): Heterogeneous membranous stacks lacking ribosomes. Functions in folding membrane proteins and regulating internal calcium ($Ca^{2+}$) concentrations (prominent in muscle as sarcoplasmic reticulum).

• Golgi Apparatus: Membrane-enclosed disks farthest from the nucleus. Functions in post-translational chemical sorting and delivery of proteins to neuronal destinations (axons vs. dendrites).

• Mitochondrion: Sausage-shaped organelles $∼1\text{ }μm$ long. Possesses an outer membrane and folded inner membrane (cristae) surrounding a central matrix. Site of cellular respiration:

  • Inhales pyruvic acid (from sugars, digested proteins, fats) and $O_2$.

  • Pyruvic acid undergoes the Krebs cycle (Hans Krebs, 1937).

  • Biochemical products feed into the electron-transport chain on cristae, phosphorylating adenosine diphosphate (ADP) into adenosine triphosphate (ATP).

  • Exhales 17 ATP molecules per pyruvic acid molecule taken in.

The Neuronal Membrane and Cytoskeleton

The membrane is a $5\text{ nm}$ thick phospholipid bilayer studded with proteins. Protein composition varies depending on whether it is soma, dendritic, or axonal membrane.

The cytoskeleton is a dynamic scaffolding comprising three structural elements:

1. Microtubules: $20\text{ nm}$ diameter hollow pipes running longitudinally down neurites. Composed of tubulin strands (polymers of globular tubulin pearls). Regulated by microtubule-associated proteins (MAPs).

   • Alzheimer's Pathology: The MAP called tau detaches from axonal microtubules and accumulates in the soma as paired helical filaments (phf), forming neurofibrillary tangles. This causes axonal microtubule breakdown, leading to neuronal death. Abnormal amyloid secretion is believed to trigger tau pathology.

2. Microfilaments: $5\text{ nm}$ diameter braids of two actin polymer strands. Anchored to the membrane via a fibrous protein web.

3. Neurofilaments: $10\text{ nm}$ diameter intermediate filaments. Ropelike structure consisting of long protein strands wound together, conferring mechanical strength.

The Axon

Uniquely specialized for long-distance information transfer. Originates at the axon hillock (tapering from the soma) and initial segment.

Structural distinctions from the soma:

1. No rough ER extends into the axon, and few to no free ribosomes exist in mature axons (no axonal protein synthesis; all axonal proteins are supplied by the soma).

2. Membrane protein composition is distinct, enabling long-distance electrical impulse propagation.

Axon structures include axon collaterals and recurrent collaterals (branches returning to synapse on the same cell or neighboring dendrites). Diameter ranges from $<1\text{ }μm$ to $25\text{ }μm$ in humans (and up to $1\text{ mm}$ in squid). Conduction speed increases with axonal diameter.

Axon terminal (terminal bouton) features:

• Microtubules do not extend into the terminal.

• Contains synaptic vesicles ($∼50\text{ nm}$ diameter).

• High concentration of membrane proteins facing the synaptic cleft.

• Dense abundance of mitochondria reflecting high metabolic energy demand.

Synaptic transmission involves the transfer of information from the presynaptic side (axon terminal) across the synaptic cleft to the postsynaptic side (dendrite or soma) via chemical signals called neurotransmitters.

Axoplasmic Transport

Interruption of axoplasmic transport causes Wallerian degeneration. Transport mechanisms include:

• Slow Axoplasmic Transport: Paul Weiss demonstrated material moving down axons at $1\text{--}10\text{ mm/day}$ by tying a thread around an axon.

• Fast Axoplasmic Transport: Radioactive amino acid tracing revealed rates up to $1000\text{ mm/day}$. Material enclosed in vesicles is carried along microtubules by kinesin ("walking legs") powered by ATP. This direction is anterograde transport (soma to terminal).

• Retrograde Transport: Movement from terminal to soma carried out by dynein. Functions to provide feedback to the soma regarding terminal metabolic needs. Exploited experimentally by horseradish peroxidase (HRP) tracing, and by viruses including oral herpes and rabies.

Dendrites

Dendrites form the dendritic tree of a neuron. Covered in thousands of synapses studded with neurotransmitter receptors.

Many dendrites are covered with dendritic spines—specialized postsynaptic structures that isolate specific chemical reactions triggered by synaptic activity. Spine structure is dynamically regulated by experience. In individuals with intellectual disability (e.g., phenylketonuria [PKU], Down syndrome, fetal alcohol syndrome, environmental impoverishment), dendritic spine density is markedly reduced, and remaining spines are abnormally long and thin, resembling fetal spines. Polyribosomes reside directly beneath spines to conduct local activity-dependent protein synthesis.

Classifying Neurons

1. Based on Number of Neurites:

   • Unipolar: Single neurite.

   • Bipolar: Two neurites.

   • Multipolar: Three or more neurites (majority of CNS neurons).

2. Based on Dendritic Architecture:

   • Cerebral cortex classes: Stellate cells (star-shaped, spiny or aspinous) and Pyramidal cells (pyramid-shaped, all spiny).

3. Based on Connections:

   • Primary Sensory Neurons: Neurites in sensory body surfaces.

   • Motor Neurons: Axons form synapses with muscles.

   • Interneurons: Form connections only with other neurons (majority).

4. Based on Axon Length:

   • Golgi Type I (Projection Neurons): Long axons extending to distant brain regions (e.g., cortical pyramidal cells).

   • Golgi Type II (Local Circuit Neurons): Short axons confined to local neighborhood (e.g., cortical stellate cells).

5. Based on Gene Expression / Neurotransmitters:

   • Classified by neurotransmitter expression (e.g., motor neurons expressing choline acetyltransferase are cholinergic). Green fluorescent protein (GFP) or Cre-loxP technology (using Cre recombinase driven by cell-specific promoters like ChAT to excise loxP-flanked/floxed genes) allows selective cell identification and manipulation.

Glia

Astrocytes

Most numerous glial cells in the brain. They fill the space between neurons (leaving an extracellular gap of only $∼20\text{ nm}$). Functions include:

• Regulating extracellular chemical content.

• Enveloping synaptic junctions to restrict neurotransmitter diffusion.

• Actively clearing neurotransmitters via membrane transporters.

• Possessing neurotransmitter receptors that trigger internal events.

• Buffering extracellular potassium ion ($K^+$) concentrations.

Myelinating Glia

Provide lipid layers of membrane (myelin sheath) wrapped spirally around axons to insulate and speed nerve impulse conduction. The sheath is interrupted at nodes of Ranvier, exposing the axonal membrane.

• Oligodendroglia: Found only in the Central Nervous System (CNS); one cell myelinates segments of multiple axons.

• Schwann Cells: Found only in the Peripheral Nervous System (PNS); each cell myelinates a single axon segment.

Other Non-Neuronal Cells

• Ependymal Cells: Line fluid-filled ventricles, directing cell migration during development.

• Microglia: Phagocytes derived from bone marrow that clean up debris from dead/degenerating cells and prune synapses.

• Vasculature: Arteries, capillaries, and veins supplying oxygen and nutrients via blood.

Biophysics of the Resting Neuronal Membrane

Electrical signals in axons travel down the cytosol, which is far less conductive than copper wire and surrounded by salty, conductive extracellular fluid. To send signals over distances without decay, excitable membranes generate action potentials (nerve impulses). At rest, the cytosol along the inner surface of the neuronal membrane maintains a negative electrical charge relative to the outside. This potential difference is the resting membrane potential ($V_m = -65\text{ mV}$).

Chemical Components

Water

Water ($H_2O$) is the main constituent of cytosol and extracellular fluid. Oxygen has a greater electronegativity than hydrogen, creating polar covalent bonds. Oxygen acquires a net negative charge ($δ^-$) and hydrogen atoms acquire a net positive charge ($δ^+$), making water an effective polar solvent for charged or polar molecules.

Ions

Atoms or molecules with a net electrical charge held together in crystals by ionic bonds (e.g., $Na^+Cl^-$). Water forms spheres of hydration around ions, insulating them:

• Cations: Net positive charge ($Na^+$, $K^+$, $Ca^{2+}$).

• Anions: Net negative charge ($Cl^-$).

• Monovalent: Charge difference of 1 ($Na^+$, $K^+$, $Cl^-$).

• Divalent: Charge difference of 2 ($Ca^{2+}$).

The Phospholipid Bilayer

Hydrophilic ("water-loving") substances dissolve in water due to polarity. Hydrophobic ("water-fearing") nonpolar compounds (like lipids) do not dissolve. Phospholipids contain a polar hydrophilic phosphate "head" and a nonpolar hydrophobic hydrocarbon "tail". Membrane phospholipids assemble into a bilayer $5\text{ nm}$ thick, isolating cytosol from extracellular fluid.

Membrane Proteins

Proteins span the membrane to provide ion pathways. Protein structure levels:

1. Primary: Amino acid chain linked by peptide bonds (joining the carboxyl group of one amino acid to the amino group of another).

2. Secondary: Coiling into an alpha helix.

3. Tertiary: Three-dimensional folding driven by R-group interactions.

4. Quaternary: Bonding of separate polypeptide subunits into a multi-subunit complex.

Ion channels are formed by 4 to 6 protein subunits creating a central pore. Channel properties include:

• Ion Selectivity: Dependent on pore diameter and charge of R-groups lining the pore (e.g., potassium channels are selectively permeable to $K^+$).

• Gating: Opening or closing of channels driven by local microenvironmental changes (voltage, chemical ligands).

Ion pumps are membrane-spanning enzymes that consume ATP to transport ions ($Na^+$, $Ca^{2+}$) against concentration gradients.

Movement of Ions

Diffusion

Random thermal movement causes net ion migration from regions of high concentration to regions of low concentration down a concentration gradient. Diffusion requires:

1. Open channels permeable to the specific ion.

2. A concentration gradient across the membrane.

Concentrations are measured in moles per liter ($M$). One mole is $6.02 \times 10^{23}$ molecules. A $1\text{ mM}$ solution equals $0.001\text{ moles/L}$.

Electricity

Using an electrical field induces ion movement because opposite charges attract and like charges repel.

• Electrical Current ($I$): Movement of electrical charge, measured in amperes (amps, $\text{A}$). Current flows in the direction of positive charge movement.

• Electrical Potential / Voltage ($V$): Force exerted on a charged particle, reflecting the charge difference between anode (+) and cathode (-), measured in volts ($ ext{V}$).

• Electrical Conductance ($g$): Relative ability of a charge to migrate, measured in siemens ($ ext{S}$).

• Electrical Resistance ($R$): Relative inability of a charge to migrate, measured in ohms ($Ω$). $R = \frac{1}{g}$.

Ohm's Law relates these parameters: I = gV &quad \text{or} &quad I = \frac{V}{R} If conductance ($g$) is zero, no current flows regardless of voltage magnitude.

The Ionic Basis of the Resting Membrane Potential

Measuring $V_m$ requires inserting a microelectrode ($0.5\text{ }μm$ glass tip filled with salt solution) into the cytosol, connected to a voltmeter relative to an extracellular reference ground wire. In neurons at rest, $V_m = -65\text{ mV}$.

Equilibrium Potentials ($E_{\text{ion}}$)

Consider an artificial cell separated by a phospholipid bilayer:

• Inside: High concentration of potassium salt ($K^+$ and $A^-$ anions).

• Outside: Diluted potassium salt (20-fold lower concentration).

If $K^+$ selective channels are inserted:

1. $K^+$ flows down its concentration gradient out of the cell.

2. Impermeable $A^-$ anions remain inside, creating a net negative interior charge.

3. The expanding interior negative charge electrostatically pulls positive $K^+$ ions back into the cell.

4. An equilibrium state is established where the outward diffusional force equals the inward electrical force. No net $K^+$ movement occurs.

The electrical potential difference that counterbalances an ionic concentration gradient is the ionic equilibrium potential ($E_{\text{ion}}$).

Four Critical Equilibrium Principles:

1. Minuscule Concentration Changes Cause Large $V_m$ Shifts: In a $50\text{ }μm$ diameter cell with $100\text{ mM } K^+$, shifting $V_m$ from $0\text{ mV}$ to $-80\text{ mV}$ requires a net concentration change of only $0.00001\text{ mM}$ (internal $K^+$ drops insignificantly to $99.99999\text{ mM}$).

2. Net Charge Separation Occurs at the Membrane Surface: Electrostatic attraction across the thin ($<5\text{ nm}$) membrane causes net charges to line up along the inner and outer surfaces. The bulk cytosol and extracellular fluid remain electrically neutral. This ability to store charge is capacitance.

3. Ionic Driving Force: Ions are driven across the membrane at a rate proportional to the difference between the membrane potential and the equilibrium potential: $\text{Driving Force} = V_m - E_{\text{ion}}$.

4. Nernst Equation: Used to calculate the exact equilibrium potential ($E_{\text{ion}}$) for any ion: $E_{\text{ion}} = \frac{2.303 R T}{z F} \text{log} \frac{[\text{ion}]_o}{[\text{ion}]_i}$ Where:

• $R$ = Gas constant

• $T$ = Absolute temperature (Kelvin)

• $z$ = Charge valence of the ion

• $F$ = Faraday's constant

• $[\text{ion}]_o$ = Extracellular ion concentration

• $[\text{ion}]_i$ = Intracellular ion concentration

Simplified Nernst equations at body temperature ($37^\text{o}\text{C}$): $E_K = 61.54\text{ mV} \text{log} \frac{[K^+]_o}{[K^+]_i}$ $E_{\text{Na}} = 61.54\text{ mV} \text{log} \frac{[\text{Na}^+]_o}{[\text{Na}^+]_i}$ $E_{\text{Cl}} = -61.54\text{ mV} \text{log} \frac{[\text{Cl}^-]_o}{[\text{Cl}^-]_i} = 61.54\text{ mV} \text{log} \frac{[\text{Cl}^-]_i}{[\text{Cl}^-]_o}$ $E_{\text{Ca}} = 30.77\text{ mV} \text{log} \frac{[\text{Ca}^{2+}]_o}{[\text{Ca}^{2+}]_i}$

Distribution of Ions Across the Neuronal Membrane

• Potassium ($K^+$): Intracellular $150\text{ mM}$, Extracellular $5\text{ mM}$, Ratio Out:In $1:20$, $E_K = -80\text{ mV}$.

• Sodium ($Na^+$): Intracellular $15\text{ mM}$, Extracellular $150\text{ mM}$, Ratio Out:In $10:1$, $E_{\text{Na}} = 62\text{ mV}$.

• Calcium ($Ca^{2+}$): Intracellular $0.0002\text{ mM}$, Extracellular $2\text{ mM}$, Ratio Out:In $10,000:1$, $E_{\text{Ca}} = 123\text{ mV}$.

• Chloride ($Cl^-$): Intracellular $13\text{ mM}$, Extracellular $150\text{ mM}$, Ratio Out:In $11.5:1$, $E_{\text{Cl}} = -65\text{ mV}$.

Ion Pumps

Concentration gradients are maintained by active transport pumps:

• Sodium-Potassium Pump ($Na^+/K^+$ ATPase): Enzyme breaking down ATP in the presence of internal $Na^+$. Pumps $3\text{ Na}^+$ out and $2\text{ K}^+$ in against concentration gradients. Consumes up to 70% of total ATP used by the brain.

• Calcium Pump: Enzyme actively pumping $Ca^{2+}$ out of the cytosol. Intracellular $Ca^{2+}$ is kept low ($0.0002\text{ mM}$) by calcium-binding proteins, mitochondria, and endoplasmic reticulum.

Relative Permeability & The Goldman Equation

If a membrane were permeable only to $K^+$, $V_m = E_K = -80\text{ mV}$. If permeable only to $Na^+$, $V_m = E_{\text{Na}} = 62\text{ mV}$. Real resting neurons are predominantly permeable to $K^+$ but have a small leak of $Na^+$. Resting permeability to $K^+$ is approximately 40 times greater than to $Na^+$.

The resting potential is calculated using the Goldman Equation (taking relative permeabilities $P_K$ and $P_{\text{Na}}$ into account): $V_m = 61.54\text{ mV} \text{log} \frac{P_K [K^+]_o + P_{\text{Na}} [\text{Na}^+]_o}{P_K [K^+]_i + P_{\text{Na}} [\text{Na}^+]_i}$ Assuming $P_K : P_{\text{Na}} = 40 : 1$: $V_m = 61.54\text{ mV} \text{log} \frac{40(5) + 1(150)}{40(100) + 1(15)} = 61.54\text{ mV} \text{log} \frac{350}{4015} = -65\text{ mV}$

Potassium Channel Structure and Function

Potassium channels consist of 4 subunits forming a pore. Subunits contain a pore loop region that forms the selectivity filter, allowing $K^+$ to pass while excluding $Na^+$.

• Shaker Mutant: Discovered in Drosophila melanogaster (ether causes leg shaking due to defective potassium channels).

• Scorpion Toxin: Chris Miller and Roderick MacKinnon showed scorpion toxin plugs potassium channel pores by binding amino acids in the pore loop. MacKinnon solved the 3D atomic X-ray crystal structure of K+ channels (2003 Nobel Prize in Chemistry).

• Weaver Mutation: Single amino acid mutation in the pore loop of cerebellar potassium channels allows $Na^+$ to pass alongside $K^+$, depolarizing membrane potential and causing motor incoordination and premature cell death.

Regulation of Extracellular Potassium

Because resting $V_m$ is near $E_K$, $V_m$ is sensitive to changes in $[K^+]_o$. Increasing $[K^+]_o$ from $5\text{ mM}$ to $50\text{ mM}$ depolarizes $V_m$ from $-65\text{ mV}$ to $-17\text{ mV}$.

• Blood-Brain Barrier: Specialized brain capillary walls that limit $K^+$ entry into brain extracellular fluid.

• Potassium Spatial Buffering: Astrocytes take up excess extracellular $K^+$ via membrane potassium channels and pumps; the $K^+$ depolarizes the astrocyte and is dissipated over distance through the astrocytic gap-junction network.

• Lethal Injection Mechanism: Intravenous $KCl$ elevates systemic $[K^+]_o$, abolishing the resting potential of cardiac muscle cells, preventing heart contraction (Jack Kevorkian, Janet Adkins).

Mechanics and Propagation of the Action Potential

The action potential is a rapid reversal of membrane potential where the interior becomes briefly positive relative to the exterior ($V_m$ spikes from $-65\text{ mV}$ to $+40\text{ mV}$). Terms: spike, nerve impulse, discharge. Duration: $∼2\text{ ms}$.

Properties of the Action Potential

Phases

1. Rising Phase: Rapid membrane depolarization up to peak voltage ($∼40\text{ mV}$).

2. Overshoot: The portion of the action potential where $V_m > 0\text{ mV}$.

3. Falling Phase: Rapid repolarization toward resting potential.

4. Undershoot (After-Hyperpolarization): $V_m$ becomes more negative than normal resting potential before returning to $-65\text{ mV}$.

Action Potential Generation

• Threshold: Critical level of depolarization required to trigger an action potential (typically $∼-40\text{ mV}$). Action potentials are all-or-none.

• Generator Potential: Initial depolarization caused by sensory stimulation (e.g., stretching nerve endings in skin opening $Na^+$ channels) or synaptic inputs.

• Firing Frequency: Encodes stimulus intensity. Increased depolarizing current increases firing frequency up to a maximum rate of $∼1000\text{ Hz}$.

• Absolute Refractory Period: Time window of $∼1\text{ ms}$ after an action potential initiation during which it is impossible to initiate another spike (due to sodium channel inactivation).

• Relative Refractory Period: Several milliseconds following the absolute refractory period where threshold remains elevated, requiring higher depolarizing current to fire a spike.

Optogenetics

Technique using foreign light-sensitive ion channels introduced into neurons:

• Channelrhodopsin-2 (ChR2): Discovered by Georg Nagel in Chlamydomonas reinhardtii. Encodes a light-sensitive cation channel permeable to $Na^+$ and $Ca^{2+}$. Opens in response to blue light ($460\text{ nm}$), triggering inward current and action potential firing.

• Halorhodopsin: Microbial protein from Natronomonas pharaonis. Imports $Cl^-$ in response to yellow light ($580\text{ nm}$), hyperpolarizing neurons and inhibiting spikes.

Theoretical Framework

Ionic current flow equation: $I_{\text{ion}} = g_{\text{ion}} (V_m - E_{\text{ion}})$.

• Resting state: $g_K >> g_{\text{Na}}$; $V_m ≈ E_K = -80\text{ mV}$.

• Rising phase: Opening of sodium channels increases $g_{\text{Na}}$. $g_{\text{Na}} >> g_K$. Large driving force on $Na^+$ ($V_m - E_{\text{Na}} = -65\text{ mV} - 62\text{ mV} = -127\text{ mV}$) causes massive inward $Na^+$ current ($I_{\text{Na}}$), driving $V_m$ toward $E_{\text{Na}} = +62\text{ mV}$.

• Falling phase: Sodium channels rapidly close ($g_{\text{Na}} → 0$) and potassium channels open ($g_K >> g_{\text{Na}}$). Large driving force on $K^+$ drives outward $K^+$ current ($I_K$), repolarizing $V_m$ toward $E_K = -80\text{ mV}$.

Biophysical Mechanics in Real Neurons

Voltage Clamp and Channel Dynamics

In the 1950s, Kenneth Cole invented the voltage clamp, used by Alan Hodgkin and Andrew Huxley on the squid giant axon (1963 Nobel Prize). The voltage clamp allowed holding $V_m$ at set values to measure membrane conductances. They demonstrated that the rising phase is caused by a transient increase in $g_{\text{Na}}$ and $Na^+$ influx, and the falling phase by an increase in $g_K$ and $K^+$ efflux. They postulated voltage-sensitive membrane "gates".

The Voltage-Gated Sodium Channel

• Structure: Single long polypeptide with 4 domains (I–IV). Each domain has 6 transmembrane alpha helices (S1–S6). S4 is the voltage sensor containing positively charged amino acid residues that shift upon depolarization, twisting the pore open. Pore loops form a selectivity filter 12 times more permeable to $Na^+$ than $K^+$ (stripping water down to a hydrated $Na^+$ complex that fits the filter dimensions; hydrated $K^+$ is too large).

• Functional Properties (Patch-Clamp Technique - Erwin Neher & Bert Sakmann, 1991 Nobel Prize):

  1. Channels open with minimal delay upon reaching threshold ($∼-40\text{ mV}$).

  2. Stay open for $∼1\text{ ms}$ and then undergo inactivation (a globular protein domain swings up to block the pore).

  3. Cannot be reopened by depolarization until $V_m$ returns to negative resting potential near threshold (deinactivation).

Channelopathies and Toxins

• Generalized Epilepsy with Febrile Seizures: Single amino acid mutations slowing sodium channel inactivation, prolonging action potentials.

• Tetrodotoxin (TTX): Isolated from puffer fish ovaries; clogs the $Na^+$ pore from the outside, blocking action potentials.

• Saxitoxin: Produced by Gonyaulax dinoflagellates ("red tide"); accumulates in shellfish, blocks $Na^+$ channels.

• Batrachotoxin: Isolated from Colombian frog skin; causes $Na^+$ channels to open at more negative potentials and stay open longer.

• Veratridine (lilies) & Aconitine (buttercups): Force $Na^+$ channels to remain open.

• Scorpion and Sea Anemone Toxins: Disrupt $Na^+$ channel inactivation.

• Lidocaine (Local Anesthetic): Binds to the S6 alpha helix of domain IV inside the $Na^+$ channel pore from the cytosol. Small, active axons are blocked fastest.

Voltage-Gated Potassium Channels

Consist of 4 separate polypeptide subunits forming a pore. Channels open $∼1\text{ ms}$ after depolarization ("delayed rectifiers"), serving to reset (rectify) $V_m$.

Action Potential Conduction

Propagation occurs orthodromically (soma to terminal). Experimental backward propagation is antidromic. Refractory inactivation of sodium channels behind the wave prevents back-propagation.

Factors Influencing Conduction Velocity

Typical velocity: $10\text{ m/s}$ (engaging $∼2\text{ cm}$ of axonal length at any instant).

• Axonal Diameter: Wider axons lower internal resistance ($r_i$) relative to membrane resistance ($r_m$), pushing current further down the cytosol and increasing conduction velocity (e.g., Squid giant axon, up to $1\text{ mm}$ diameter, studied by J. Z. Young in 1939).

• Myelination and Saltatory Conduction: Insulation provided by oligodendroglia (CNS) or Schwann cells (PNS) increases $r_m$. Voltage-gated sodium channels are clustered at nodes of Ranvier ($0.2\text{--}2.0\text{ mm}$ spacing). Action potentials skip from node to node (saltatory conduction).

• Demyelinating Diseases: Multiple Sclerosis (MS; attacks CNS myelin, causing slowed optic nerve conduction) and Guillain-Barré syndrome (attacks PNS myelin).

Spike-Initiation Zone

In typical CNS neurons, spikes initiate at the axon hillock due to a high density of voltage-gated sodium channels. In sensory neurons, the spike-initiation zone is at the sensory nerve endings.

Electrical firing patterns vary by cell type:

• Aspinous Stellate Cells: Steady firing rate throughout a stimulus.

• Pyramidal Cells: Show adaptation (firing slows over time).

• Bursting Cells: Fire rhythmic clusters of action potentials.

Principles of Chemical and Electrical Synaptic Transmission

Synaptic transmission is the process of information transfer across specialized contacts called synapses (named by Charles Sherrington, 1897).

Types of Synapses

Electrical Synapses

Occur at gap junctions ($3\text{ nm}$ intercellular gap). Six connexin subunits assemble into a connexon; two connexons (one from each cell) line up to form a gap junction channel (pore diameter $1\text{--}2\text{ nm}$). Transmission is bidirectional, extremely fast, and fail-safe.

• Electrically coupled cells show postsynaptic potentials (PSPs) of $≤1\text{ mV}$.

• Function: Synchronize activity of neighboring neurons (e.g., inferior olive neurons via Connexin36 / Cx36, studied by Michael Long and Barry Connors). Common in embryonic development.

Chemical Synapses

Presynaptic and postsynaptic membranes are separated by a synaptic cleft $20\text{--}50\text{ nm}$ wide, filled with an extracellular matrix web. Fast chemical transmission demonstrated by Otto Loewi (1921, vagusstoff / acetylcholine in frog heart - Box 5.1) and Bernard Katz (neuromuscular junction).

Structures:

• Presynaptic Element: Contains synaptic vesicles ($50\text{ nm}$ diameter, storing amino acid or amine transmitters) and/or secretory granules / large dense-core vesicles ($100\text{ nm}$ diameter, storing peptide transmitters). Active zones are dense protein pyramids on the presynaptic membrane where vesicles fuse.

• Postsynaptic Element: Contains the postsynaptic density packed with neurotransmitter receptors.

CNS Chemical Arrangements:

• Axodendritic: Axon to dendrite.

• Axosomatic: Axon to cell body.

• Axoaxonic: Axon to axon.

• Axospinous: Axon to dendritic spine.

• Dendrodendritic: Dendrite to dendrite.

Morphological Categories (Gray's classification):

• Gray's Type I: Asymmetrical differentiations (postsynaptic membrane thicker); usually excitatory.

• Gray's Type II: Symmetrical differentiations; usually inhibitory.

Neuromuscular Junction (NMJ)

Synapse between motor neuron axons of the spinal cord and skeletal muscle. The postsynaptic membrane (motor end-plate) contains junctional folds packed with acetylcholine (ACh) receptors, aligned directly opposite presynaptic active zones. NMJ transmission is fast and fail-safe.

Principles of Chemical Transmission

Neurotransmitter Categories

1. Amino Acids: Glutamate (Glu), Gamma-aminobutyric acid (GABA), Glycine (Gly). Medium to fast transmission.

2. Amines: Acetylcholine (ACh), Dopamine (DA), Norepinephrine (NE), Epinephrine, Serotonin (5-HT), Histamine.

3. Peptides: Chains of amino acids stored in secretory granules (e.g., Substance P, Enkephalins, Endorphins, Dynorphin, Neuropeptide Y, Somatostatin, CCK).

Synthesis and Storage

• Amino Acids and Amines: Synthesized locally in the axon terminal cytosol by specific enzymes. Transporters pack them into synaptic vesicles.

• Peptides: Precursor peptides synthesized in the rough ER of the soma, cleaved into active peptides in the Golgi apparatus, packaged into secretory granules, and transported to the terminal via fast axoplasmic transport.

Release Mechanics (Exocytosis)

Action potentials depolarize the terminal, opening voltage-gated calcium channels in active zones. Internal $Ca^{2+}$ rises from $0.0002\text{ mM}$ to $>0.01\text{ mM}$. Fast exocytosis occurs within $0.2\text{ ms}$.

SNARE Proteins (Box 5.3):

• v-SNAREs: Embedded in vesicle membranes.

• t-SNAREs: Embedded in target presynaptic membranes. Cytosolic tails bind tightly, docking vesicles at active zones.

• Synaptotagmin: Vesicle membrane protein acting as the $Ca^{2+}$ sensor that triggers rapid lipid bilayer fusion.

• Recycled via endocytosis. Peptides are released outside active zones via high-frequency trains of spikes, taking $≥50\text{ ms}$.

Receptors and Effectors

1. Transmitter-Gated Ion Channels: Pentameric or tetrameric membrane-spanning channels. Opening within microseconds of ligand binding.

   • Excitatory Postsynaptic Potential (EPSP): Transient membrane depolarization caused by transmitter opening $Na^+$/$K^+$ permeable channels (e.g., ACh-gated or Glu-gated channels).

   • Inhibitory Postsynaptic Potential (IPSP): Transient membrane hyperpolarization caused by transmitter opening $Cl^-$ permeable channels (e.g., GABA-gated or Glycine-gated channels).

2. G-Protein-Coupled Receptors (Metabotropic):

   • Neurotransmitter binds receptor.

   • Receptor activates G-proteins.

   • G-proteins activate effector proteins (ion channels or second messenger enzymes).

3. Autoreceptors: Presynaptic G-protein-coupled receptors sensitive to the released transmitter, typically acting as a brake/safety valve to inhibit further release or synthesis.

Recovery and Degradation

Transmitters are removed from the cleft via diffusion, reuptake by presynaptic membrane or glial transporters (driven by $Na^+$ co-transport), or enzymatic cleavage (e.g., Acetylcholinesterase [AChE] cleaves ACh into choline and acetic acid in the cleft). Failure of removal leads to desensitization.

Toxins and Pharmacology

• Inhibitors / Antagonists: Block receptor action (e.g., curare blocks nicotinic AChR; atropine blocks muscarinic AChR).

• Agonists: Mimic transmitter action (e.g., nicotine, muscarine).

• Botulinum Toxin: Bacterial enzyme destroying SNARE proteins, blocking ACh release.

• Black Widow Latrotoxin: Triggers massive, total $Ca^{2+}$-independent ACh vesicle depletion.

• Cobra $α$-bungarotoxin: Binds tightly to postsynaptic nicotinic ACh receptors, blocking neuromuscular transmission.

• Organophosphates: Irreversible AChE inhibitors causing desensitization paralysis.

Principles of Synaptic Integration

Quantal Analysis

Synaptic vesicles each contain a fixed quantum of neurotransmitter (several thousand molecules). Spontaneous release yields a miniature postsynaptic potential ("mini"). Evoked EPSPs are integer multiples of minis. NMJ releases $∼200$ quanta per AP ($≥40\text{ mV}$ EPSP); CNS synapses often release a single quantum per AP ($0.1\text{--}0.5\text{ mV}$ EPSP).

EPSP Summation

• Spatial Summation: Adding together EPSPs generated simultaneously at many different synapses on a dendrite.

• Temporal Summation: Adding together EPSPs generated at the same synapse occurring in rapid succession (1–15 ms window).

Dendritic Cable Properties

EPSP amplitude decreases exponentially along an unbranched passive dendritic cable: $V_x = V_0 e^{-x/\text{λ}}$ Where $λ$ is the dendritic length constant (distance where depolarization drops to $37\text{\%}$ of origin value): λ = &sqrt;{\frac{r_m}{r_i}}

• $r_m$ = Membrane resistance (depends on open ion channels).

• $r_i$ = Internal resistance (depends on dendritic diameter).

Excitable Dendrites

Many dendrites possess voltage-gated $Na^+$, $Ca^{2+}$, or $K^+$ channels that act as amplifiers of small distant EPSPs.

Inhibition and Shunting Inhibition

Inhibitory synapses using GABA or Glycine open $Cl^-$ channels ($E_{\text{Cl}} = -65\text{ mV}$).

• Shunting Inhibition: Active inhibitory synapse located between an excitatory synapse and the soma creates an electrical shunt, allowing positive current to flow outward across $Cl^-$ channels, preventing EPSPs from reaching the axon hillock.

• Inhibitory synapses are typically Gray's type II and clustered on the soma and axon hillock.

Modulation

Activating G-protein-coupled receptors alters EPSP efficiency:

• Norepinephrine (NE) binds to $β$ receptor &rightarrow activates $G_s$ &rightarrow activates adenylyl cyclase &rightarrow converts ATP to cyclic AMP (cAMP) &rightarrow activates protein kinase A (PKA) &rightarrow phosphorylates potassium channels, closing them &rightarrow increases $r_m$ and $λ$ &rightarrow increases dendritic excitability.

Specific Neurotransmitter Systems and Intracellular Cascades

Identifying Neurotransmitters

Dale's Principle: A neuron releases only one neurotransmitter (peptide co-transmitters are an exception).

Criteria for a Neurotransmitter:

1. The molecule must be synthesized and stored in the presynaptic neuron.

2. The molecule must be released by the presynaptic axon terminal upon stimulation.

3. The molecule, when experimentally applied, must produce a response in the postsynaptic cell that mimics the natural response.

Experimental Localization Techniques

• Immunocytochemistry (Immunohistochemistry): Inject transmitter candidate into an animal to elicit specific antibodies. Isolate antibodies, tag with a visible/fluorescent marker, and apply to brain slices.

• In Situ Hybridization: Constructs radioactively or fluorescents (FISH) labeled synthetic single-stranded nucleic acid probes complementary to specific mRNA transcripts. Hybridized probes are detected using autoradiography.

• Microiontophoresis: Applies ionized candidate transmitter molecules from a fine glass micropipette via electrical current onto postsynaptic membranes while recording $V_m$ to test for mimicry.

Neurotransmitter Chemistry

Cholinergic Neurons

Synthesize Acetylcholine (ACh) at the NMJ, basal forebrain, and brain stem.

• Synthesis: Choline acetyltransferase (ChAT) transfers an acetyl group from acetyl-CoA to choline in the cytosol. Choline transport into the terminal via $Na^+$ cotransporters is the rate-limiting step.

• Vesicular Loading: Concentrated into vesicles up to $1000\text{ mM}$ ($1\text{ M}$) by vesicular ACh transporters using $H^+$ countertransport (powered by a proton-ATPase pump).

• Degradation: Acetylcholinesterase (AChE) in the synaptic cleft rapidly cleaves ACh into choline and acetic acid.

Catecholaminergic Neurons

All contain tyrosine hydroxylase (TH), converting tyrosine to L-dopa (rate-limiting step regulated by end-product inhibition and $Ca^{2+}$).

1. Dopamine (DA): L-dopa converted to DA by dopa decarboxylase. Degenerates in Parkinson's disease (treated with L-dopa).

2. Norepinephrine (NE): DA transported into vesicles where dopamine $β$-hydroxylase (DBH) converts DA to NE.

3. Epinephrine (Adrenaline): NE exits vesicles to cytosol where phentolamine N-methyltransferase (PNMT) converts NE to epinephrine, which is then re-transported into vesicles.

Terminated by $Na^+$ co-transporters (blocked by cocaine and amphetamine) and degraded by Monoamine Oxidase (MAO) on outer mitochondrial membranes.

Serotonergic Neurons

Synthesize Serotonin (5-hydroxytryptamine, 5-HT) from tryptophan: $\text{Tryptophan} → \text{Tryptophan hydroxylase} → \text{5-HTP} → \text{5-HTP decarboxylase} → \text{5-HT}$ Reuptake via 5-HT transporters (blocked by fluoxetine/Prozac); degraded by MAO.

Amino Acidergic Neurons

• Glutamate (Glu) & Glycine (Gly): Synthesized from glucose/precursors. Concentrated into vesicles by specific vesicular glutamate transporters (VGluT) up to $50\text{ mM}$.

• GABA: Synthesized exclusively by GABAergic neurons from glutamate by Glutamic Acid Decarboxylase (GAD). Reuptake via $Na^+$ transporters; metabolized by GABA transaminase.

Other Messengers

• ATP: Co-stored in vesicles, gates purinergic channels (P2X) or metabotropic receptors (P2Y), degraded to adenosine.

• Endocannabinoids (Anandamide, 2-AG): Retrograde messengers. High $Ca^{2+}$ in active postsynaptic cells stimulates synthesis from membrane lipids on demand (not packaged in vesicles). Small, membrane-permeable molecules that diffuse to presynaptic CB1 receptors (G-protein-coupled), decreasing presynaptic $Ca^{2+}$ channel opening and inhibiting transmitter release.

• Nitric Oxide (NO): Gasotransmitter synthesized from arginine. Membrane-permeable, diffuses freely as a retrograde messenger, evanescent.

Transmitter-Gated Channels

Basic Structure

• Pentameric Channels (Nicotinic AChR, $GABA_A$, Glycine): 5 subunits. Each subunit has 4 hydrophobic alpha-helical transmembrane segments (M1–M4).

• Tetrameric Channels (Glutamate receptors: AMPA, NMDA, Kainate): 4 subunits. The M2 segment forms a hairpin loop entering and exiting the inner membrane without spanning it.

• Trimeric Channels (Purinergic ATP receptors): 3 subunits, each with 2 transmembrane segments.

Glutamate-Gated Subtypes

• AMPA Receptors: Permeable to $Na^+$ and $K^+$, impermeable to $Ca^{2+}$. Inward $Na^+$ current drives rapid depolarization.

• NMDA Receptors: Permeable to $Na^+$, $K^+$, and $Ca^{2+}$. Voltage-dependent $Mg^{2+}$ block at resting potential ($-65 ext{ mV}$) prevents ion flow. Depolarization relieves the $Mg^{2+}$ block. Requires both glutamate binding and postsynaptic depolarization to pass inward $Ca^{2+}$ and $Na^+$ currents.

• Excitotoxicity: Excessive glutamate release triggers persistent NMDA activation, leading to massive $Ca^{2+}$ influx, activating autolytic enzymes and digesting the cell (implicated in ALS, stroke, Alzheimer's, lathyrism, domoic acid poisoning).

$GABA_A$ Receptors

Gate $Cl^-$ channels. Modulated by:

• Benzodiazepines (e.g., Valium): Increase channel opening frequency in the presence of GABA.

• Barbiturates: Increase channel opening duration.

• Ethanol and Neurosteroids (cholesterol metabolites).

G-Protein-Coupled Receptors and Effectors

Structure: Single polypeptide with 7 transmembrane alpha helices.

G-Protein Operation

1. Heterotrimeric ($α$, $β$, $γ$ subunits). Inactive state: GDP bound to $G_α$.

2. Receptor activation exchanges GDP for GTP on $G_α$.

3. $G_α\text{-GTP}$ splits from $G_{βγ}$. Both subunits activate effectors.

4. $G_α$ intrinsically hydrolyzes GTP back to GDP, reassociating with $G_{βγ}$.

• $G_s$ = Stimulatory; $G_i$ = Inhibitory.

Effector Cascades

• Shortcut Pathway (Membrane-Delimited): $G_{βγ}$ binds directly to nearby ion channels (e.g., Muscarinic AChR in cardiac muscle or $GABA_B$ receptors opening $K^+$ channels). Fast ($30\text{--}100\text{ ms}$), localized.

• cAMP Second Messenger Cascade: $G_s$ activates adenylyl cyclase, converting ATP to cAMP, activating PKA. $G_i$ inhibits adenylyl cyclase.

• Phospholipase C (PLC) Cascade: $G_q$ activates PLC, which cleaves membrane $PIP_2$ into:

  1. Diacylglycerol (DAG): Remains in membrane, activating Protein Kinase C (PKC).

  2. Inositol-1,4,5-triphosphate ($IP_3$): Diffuses in cytosol, opening $IP_3$-gated $Ca^{2+}$ channels on smooth ER, raising cytosolic $Ca^{2+}$ and activating CaMK.

• Protein Kinases phosphorylate target proteins; Protein Phosphatases dephosphorylate them.

• Signal Amplification: Single receptor activates multiple G-proteins, producing cascade amplification at each enzyme step.

Divergence vs. Convergence

• Divergence: One transmitter activates multiple receptor subtypes and effector pathways.

• Convergence: Multiple transmitters activate distinct receptors that converge on the same effector system.

Gross Organization and Development of the Central Nervous System

Anatomical Terminology

• Anterior / Rostral: Toward the nose.

• Posterior / Caudal: Toward the tail.

• Dorsal: Toward the back/top.

• Ventral: Toward the belly/bottom.

• Midline: Invisible dividing line down the middle of the body.

• Medial: Closer to the midline.

• Lateral: Farther from the midline.

• Ipsilateral: On the same side.

• Contralateral: On opposite sides.

• Planes of Section: Midsagittal (splits right/left equal halves), Sagittal (parallel to midsagittal), Horizontal (parallel to ground, dorsal/ventral halves), Coronal (perpendicular to ground, anterior/posterior halves).

Gross Organization of the CNS

• Brain:

  • Cerebrum: Paired hemispheres divided by sagittal fissure. Right hemisphere controls/senses left body; left controls/senses right body.

  • Cerebellum: Movement control center. Right side controls right body; left controls left body.

  • Brain Stem: Relays information between cerebrum/cerebellum and spinal cord. Controls vital functions (breathing, body temperature, consciousness).

• Spinal Cord: Attached to brain stem. Encased in vertebral column. Communicates via spinal nerves.

  • Dorsal Root: Contains sensory afferent axons (cell bodies in dorsal root ganglia).

  • Ventral Root: Contains motor efferent axons.

Peripheral Nervous System (PNS)

• Somatic PNS: Voluntary control. Innervates skin, joints, muscles.

• Visceral PNS (Autonomic Nervous System / ANS): Involuntary. Innervates internal organs, blood vessels, glands.

• Afferent Axons: Carrying information toward a reference point in the CNS.

• Efferent Axons: Carrying information away from the CNS.

• Cranial Nerves: 12 pairs numbered I to XII arising from brain stem.

Meninges and Ventricular System

• Meninges:

  1. Dura Mater: Tough, inelastic outer leathery bag. Ruptured vessels form subdural hematomas.

  2. Arachnoid Membrane: Middle spider-web-like layer.

  3. Pia Mater: Thin inner membrane adhering to brain surface. Separated from arachnoid by subarachnoid space filled with cerebrospinal fluid (CSF).

• Ventricular System: CSF produced by choroid plexus in ventricles. Flows through ventricles, exits apertures into subarachnoid space, absorbed by arachnoid villi.

  • Hydrocephalus: Impaired CSF drainage causes fluid backup and ventricle expansion. Treated by inserting a ventricular shunt tube.

Neuroimaging Methods

• CLARITY: Replaces light-absorbing lipids with a water-soluble hydrogel, rendering brain tissue transparent.

• Computed Tomography (CT): Rotating X-ray source and sensors create digital cross-sectional slice reconstructions (Godfrey Hounsfield & Allan Cormack, 1979 Nobel Prize).

• Magnetic Resonance Imaging (MRI): Maps hydrogen atom response to radio-frequency pulses in a magnetic field.

• Diffusion Tensor Imaging (DTI): Variant of MRI measuring water diffusion along axon tracts to visualize white matter bundles.

• Functional Brain Imaging: Measures regional blood flow and metabolic activity.

  • Positron Emission Tomography (PET): Injects 2-deoxyglucose labeled with positron-emitting isotopes (Ter-Pogossian, Phelps, Cho).

  • Functional MRI (fMRI): Measures Blood Oxygen Level Dependent (BOLD) signal changes (oxyhemoglobin to deoxyhemoglobin ratio, Seiji Ogawa).

CNS Development

Early Neurulation

1. Embryo forms three germ layers: Endoderm (viscera), Mesoderm (skeleton, muscles, somites), Ectoderm (nervous system, skin).

2. Ectoderm forms the neural plate.

3. Neural plate forms the neural groove flanked by neural folds.

4. Neural folds fuse dorsally at day 22 to form the neural tube (entire CNS).

5. Ectoderm pinched off lateral to the tube forms the neural crest (entire PNS).

6. Mesoderm forms somites (33 vertebrae and skeletal muscles).

Neural Tube Defects (Box 7.4): Folic acid (folate) deficiency in maternal diet causes incomplete closure. Anencephaly (failure of anterior closure, degeneration of forebrain, fatal); Spina Bifida (failure of posterior closure).

Primary Brain Vesicles

• Prosencephalon (Forebrain): Rostral-most swelling.

• Mesencephalon (Midbrain): Middle swelling.

• Rhombencephalon (Hindbrain): Caudal swelling connecting to spinal cord.

Differentiation of the Forebrain

• Secondary Vesicles: Optic vesicles (form optic stalk/nerve and optic cup/retina) and Telencephalic vesicles (form telencephalon/cerebral hemispheres and olfactory bulbs). Central remaining structure is the Diencephalon.

• Ventricles: Lateral ventricles (telencephalon), Third ventricle (diencephalon).

• Telencephalon Gray Matter: Cerebral cortex and Basal telencephalon (basal ganglia, amygdala).

• Diencephalon Gray Matter: Thalamus (gateway to cortex) and Hypothalamus (controls ANS and pituitary gland).

• Forebrain White Matter Systems: Cortical white matter, Corpus callosum (interhemispheric bridge), Internal capsule (links cortex with thalamus/brain stem).

Differentiation of the Midbrain

• Tectum (dorsal): Differentiates into Superior Colliculus (optic tectum, eye movements) and Inferior Colliculus (auditory relay).

• Tegmentum (ventral): Contains Substantia Nigra and Red Nucleus (motor control).

• Cerebral Aqueduct: Constricted CSF canal connecting 3rd and 4th ventricles.

Differentiation of the Hindbrain

• Rostral Hindbrain (Metencephalon): Rhombic lips grow dorsally to form the Cerebellum. Ventral wall swells to form the Pons (bridge relaying cortical input to cerebellum).

• Caudal Hindbrain (Myelencephalon): Diencephalon forms Medulla Oblongata. Ventral bundles form Medullary Pyramids (corticospinal tract undergoing pyramidal decussation).

• Fourth Ventricle: Central cavity.

Differentiation of the Spinal Cord

• Central channel becomes the spinal canal.

• Gray Matter: Dorsal horn (sensory input), Ventral horn (motor output), Intermediate zone (interneurons).

• White Matter Columns: Dorsal columns (ascending touch), Lateral columns (corticospinal tract), Ventral columns.

Human Neocortex Specializations

Surface area expanded to $1100\text{ cm}^2$, folded into gyri (bumps) and sulci (grooves).

• Four Lobes: Frontal, Parietal, Occipital, Temporal.

• Cortical Features: Layered cell organization parallel to surface, Layer I (molecular layer lacking cells), Pyramidal cells with apical dendrites extending to Layer I.

• Types: Hippocampus (1 cell layer), Olfactory cortex (2 cell layers), Neocortex (6 cell layers, unique to mammals).

• Brodmann's Cytoarchitectural Map: Area 17 (primary visual cortex V1), Area 4 (primary motor cortex M1).

• Neocortical Column: Functional cylinder $2\text{ mm}$ high, $0.5\text{ mm}$ diameter containing $∼10,000$ neurons and $10^8$ synapses.

• Connectome: Map of neural connectivity (C. elegans wiring map completed by Sidney Brenner: 302 neurons, 7000 synapses; Sebastian Seung EyeWire project).

Sensory Physiology of the Chemical Senses: Taste and Smell

Chemoreceptors detect environmental and internal chemicals. Taste (gustation) and smell (olfaction) combine to produce perception of flavor.

Taste (Gustation)

Five basic tastes: Saltiness, Sourness, Sweetness, Bitterness, Umami (savory taste of glutamate/MSG). (Box 8.1: Candidates for fat, starch, carbonation, calcium, water receptors).

Taste Organs and Cells

• Organs: Tongue, palate, pharynx, epiglottis. Papillae: Foliate (ridge), Vallate (pimples), Fungiform (mushroom).

• Taste Buds: Each papilla has 1 to several hundred taste buds; total 2000–5000 per person. Each bud has 50–150 taste receptor cells plus basal cells.

• Taste Cells: Apical microvilli project into the taste pore. Life span of $∼2\text{ weeks}$. Depolarizing receptor potential triggers transmitter release onto primary gustatory afferents.

  • Sour and Salty cells release Serotonin.

  • Sweet, Bitter, and Umami cells release ATP via ATP-permeable membrane channels.

Transduction Mechanisms

• Saltiness: Amiloride-sensitive $Na^+$ channels. $Na^+$ flows directly into the cell down its gradient, depolarizing the membrane and opening voltage-gated $Na^+$ and $Ca^{2+}$ channels.

• Sourness: High acidity ($H^+$ ions). Protons block K+-selective channels or permeate TRP channels, causing depolarization.

• Bitterness: $T2R$ G-protein-coupled receptor family ($∼25$types). Tastant binding activates Phospholipase C (PLC)$&rightarrow$generates$IP_3$$&rightarrow$opens taste-specific$Na^+$channels and releases$Ca^{2+}$from ER stores$&rightarrow opens ATP-permeable channels.\n- **Sweetness**: T1R2 + T1R3$heterodimer receptor. Uses the same PLC /$IP_3 / ATP-release pathway as bitterness, expressed in sweet-specific cells. (Cats lack T1R2).\n- **Umami**: T1R1 + T1R3$heterodimer receptor. Detects amino acids. Uses the same PLC /$IP_3 / ATP-release pathway in umami-specific cells. (Vampire bats lack T1R1).\n\n### Central Taste Pathways\n- Cranial Nerves: CN VII (Facial; anterior 2/3 of tongue, palate), CN IX (Glossopharyngeal; posterior 1/3 of tongue), CN X (Vagus; throat, epiglottis).\n- Path: Cranial Nerves &rightarrow$Gustatory Nucleus (medulla)$&rightarrow$Ventral Posterior Medial (VPM) Nucleus of Thalamus$&rightarrow Primary Gustatory Cortex (Brodmann's area 36, insula-operculum). Primarily ipsilateral.\n- Loss of taste perception = Ageusia.\n- Conditioned Taste Aversion (Garcia Effect, Box 8.2): Robust single-trial associative learning linking taste to nausea.\n\n### Coding Mechanisms\nUses a combination of roughly labeled lines and **population coding** (evaluating responses across a broad ensemble of broadly-tuned cells).\n\n## Smell (Olfaction)\n\n### Olfactory Epithelium\nLocated high in the nasal cavity (10 ext{ cm}^2$in humans,$>170 ext{ cm}^2 in dogs). Three cell types: Olfactory receptor cells (genuine neurons, replaced every 4–8 weeks), Supporting cells, Basal cells. Mucus layer secreted by supporting cells contains odorant binding proteins and antibodies.\n\n### Olfactory Receptor Neurons\nHave a single dendrite ending in a knob with cilia extending into mucus. Unmyelinated axons form the olfactory nerve (CN I), penetrating the bony **cribriform plate** to enter the olfactory bulb. Traumatic severing causes **anosmia**.\n\n### Olfactory Transduction Cascade\n ext{Odorant} → ext{G-protein-coupled receptor} → G_{ ext{olf}} → ext{Adenylyl cyclase} → ext{cAMP} → ext{cAMP-gated cation channel} → ext{Inward } Na^+ ext{ and } Ca^{2+} ext{ current} → Ca^{2+} ext{-activated } Cl^- ext{ channel opens} → Cl^- ext{ efflux} → ext{Depolarization}\n\nLinda Buck and Richard Axel (2004 Nobel Prize) discovered ∼1000$odorant receptor genes in rodents and$∼350$in humans. Each olfactory neuron expresses only 1 receptor gene. Adaptation occurs within$∼1 ext{ minute}.\n\n### Central Olfactory Pathways\n- Primary axons terminate in spherical **glomeruli** (50 ext{--}200 ext{ }μm$diameter) in the olfactory bulb.$∼25,000$receptor axons converge onto$∼100 second-order neurons per glomerulus.\n- Precision Mapping: All receptor neurons expressing a specific receptor gene project to the exact same 2 glomeruli per bulb.\n- Olfactory tract projects directly to the **Olfactory Cortex** and temporal lobe structures (bypassing the thalamus), and indirectly via the olfactory tubercle &rightarrow$medial dorsal nucleus of the thalamus$&rightarrow orbitofrontal cortex.\n\n### Olfactory Coding\n1. **Population Coding**: Combinatorial code across broadly tuned receptors.\n2. **Sensory Maps**: Spatial arrangement of active glomeruli in the bulb and specific neural ensembles in cortex.\n3. **Temporal Coding**: Spike timing, oscillation synchrony, and temporal patterns encode odor quality.\n\n---\n\n# Ocular Optics and Retinal Visual Processing\n\n## Properties of Light\nLight is visible electromagnetic radiation (400 ext{--}700 ext{ nm} wavelength).\n- **Wavelength**: Distance between peaks.\n- **Frequency**: Waves per second. Higher frequency = higher energy.\n- **Optics**: Reflection (bouncing), Absorption (energy transfer), Refraction (bending of light at interfaces between media with different light speeds).\n\n## Gross Anatomy of the Eye\n- **Pupil**: Opening allowing light to enter.\n- **Iris**: Pigmented ring containing pupillary muscle controls.\n- **Cornea**: Glassy transparent front surface.\n- **Sclera**: Tough white wall of eyeball.\n- **Extraocular Muscles**: Three pairs inserted into sclera moving the eye.\n- **Conjunctiva**: Membrane folding back from eyelids.\n- **Optic Nerve**: Axons exiting the back of the eye.\n\n### Ophthalmoscopic Features\n- **Optic Disk**: Origin of retinal vessels; exit point of optic nerve. Contains no photoreceptors (**blind spot**).\n- **Macula**: Central retina region specialized for central vision, lacking large blood vessels.\n- **Fovea**: 2 ext{ mm} central pit in macula marking retinal center.\n\n### Internal Cross-Sectional Anatomy\n- **Aqueous Humor**: Watery fluid nourishing the cornea, located in the anterior chamber.\n- **Lens**: Transparent lens suspended by **zonule fibers** attached to the **ciliary muscle**.\n- **Vitreous Humor**: Viscous jelly between lens and retina maintaining spherical eye shape.\n\n*Eye Disorders* (Box 9.2): Strabismus (misalignment; esotropia [cross-eyed], exotropia [wall-eyed], leading to amblyopia if uncorrected); Cataract (lens clouding); Glaucoma (elevated intraocular pressure damaging optic nerve); Retinitis pigmentosa (photoreceptor degeneration starting peripherally); Macular degeneration (loss of central vision).\n\n## Image Formation\n\n### Refraction by the Cornea\nCornea provides ∼42 ext{ diopters}$of refractive power ($ ext{Diopters} = rac{1}{ ext{focal distance in meters}}). Most refraction occurs at the air-cornea interface.\n\n### Accommodation by the Lens\nProvides an additional ∼12 ext{ diopters}$for focusing objects closer than$9 ext{ m}.\n- **Near Vision**: Ciliary muscle contracts, swelling inward, relaxing tension on zonule fibers. The elastic lens becomes rounder/thicker, increasing refractive power.\n- **Distant Vision**: Ciliary muscle relaxes, increasing tension on zonule fibers and flattening the lens.\n\n*Refractive Errors* (Box 9.3):\n- **Emmetropia**: Normal eye focusing parallel light on retina.\n- **Hyperopia (Farsightedness)**: Eyeball too short; light focuses behind retina. Corrected with convex lens.\n- **Myopia (Nearsightedness)**: Eyeball too long; light focuses in front of retina. Corrected with concave lens.\n- **Presbyopia**: Age-related loss of lens elasticity.\n- **LASIK**: Laser reshaping of internal corneal tissue.\n\n### Pupillary Light Reflex and Visual Field\n- **Pupillary Light Reflex**: Consensual constriction of both pupils in response to light in one eye. Increases depth of focus.\n- **Visual Field**: Total space viewed by one eye (150^ ext{o}$total:$100^ ext{o}$temporal,$60^ ext{o} nasal). Images are inverted and reversed on the retina.\n- **Visual Acuity**: Ability to distinguish two points near each other. Snellen chart 20/20$vision resolves letters subtending$0.083^ ext{o}$($5 ext{ minutes of arc}).\n\n## Microscopic Anatomy of the Retina\n\nDirect pathway: ext{Photoreceptors} → ext{Bipolar cells} → ext{Ganglion cells}. Horizontal and amacrine cells mediate lateral interactions. Only ganglion cells fire action potentials and project axons out of the retina.\n\n### Laminar Organization (Inside-Out)\n1. **Ganglion Cell Layer**: Cell bodies of ganglion cells.\n2. **Inner Plexiform Layer**: Synapses between bipolar, amacrine, and ganglion cells.\n3. **Inner Nuclear Layer**: Cell bodies of bipolar, horizontal, and amacrine cells.\n4. **Outer Plexiform Layer**: Synapses between photoreceptors, horizontal, and bipolar cells.\n5. **Outer Nuclear Layer**: Cell bodies of photoreceptors.\n6. **Layer of Photoreceptor Outer Segments**: Light-sensitive membranous disks embedded in the pigmented epithelium (absorbs stray light; tapetum lucidum in nocturnal animals reflects light).\n\n### Photoreceptors\n- **Rods**: Long cylindrical outer segments with many disks. High photopigment concentration makes rods 1000 times more sensitive to light. ∼92 ext{ million} per retina. Nighttime (**scotopic**) vision.\n- **Cones**: Short tapering outer segments with fewer disks. ∼5 ext{ million} per retina. Daytime (**photopic**) and color vision.\n- **Foveal Specialization**: High density of cones, no rods in the central fovea. Cellular layers above photoreceptors are displaced laterally (foveal pit), minimizing light scattering and maximizing visual acuity. Peripheral retina has high rod density and high convergence (many photoreceptors per ganglion cell), increasing light sensitivity at the cost of acuity.\n\n## Phototransduction\n\n### Rod Phototransduction\nIn the dark, rods are continuously depolarized (V_m ≈ -30 ext{ mV}$) due to an inward$Na^+$current (**dark current**). Cyclic GMP (cGMP) produced by guanylyl cyclase holds$Na^+ channels open.\n\nLight-activated cascade:\n1. Light activates (bleaches) **rhodopsin** (opsin protein + prebound 11-cis retinal agonist).\n2. Retinal changes conformation, activating opsin.\n3. Opsin activates G-protein **transducin**.\n4. Transducin activates **phosphodiesterase (PDE)**.\n5. PDE breaks down cGMP to GMP.\n6. cGMP levels drop, cGMP-gated Na^+ channels close, and the cell hyperpolarizes.\nSignal amplification allows a rod to respond to a single captured photon.\n\n### Cone Phototransduction and Color\nCones use 3 distinct opsins with different spectral sensitivities:\n- **Blue (Short wavelength)**: Peak sensitivity ∼430 ext{ nm}.\n- **Green (Medium wavelength)**: Peak sensitivity ∼530 ext{ nm}.\n- **Red (Long wavelength)**: Peak sensitivity ∼560 ext{ nm}.\nYoung-Helmholtz Trichromacy Theory: Brain assigns colors based on the relative readout across all 3 cone types. Red-green colorblindness is X-linked (Box 9.5).\n\n### Calcium's Role in Light Adaptation\nCa^{2+}$enters through open cGMP-gated channels in the dark and inhibits guanylyl cyclase. Light closes channels, stopping$Ca^{2+}$influx. Reduced internal$Ca^{2+}$disinhibits guanylyl cyclase, increasing cGMP synthesis and reopening channels to allow adaptation over a$10^6-fold light intensity range.\n\n## Retinal Processing and Output\n\nPhotoreceptors hyperpolarize to light, releasing less glutamate.\n\n### Bipolar Cell Receptive Fields\nConcentric **antagonistic center-surround** receptive fields:\n- **OFF-Center Bipolar Cells**: Have ionotropic glutamate receptors. Glutamate depolarizes them in the dark; light in the center hyperpolarizes them.\n- **ON-Center Bipolar Cells**: Have metabotropic glutamate receptors. Glutamate hyperpolarizes them in the dark; light in the center depolarizes them.\n- Receptive field surrounds are mediated via indirect horizontal cell circuits that invert the signal.\n\n### Ganglion Cell Output\nGanglion cells fire action potentials. Center-surround organization leads to neural output emphasizing **light-dark contrast edges** rather than uniform illumination.\n\nGanglion Cell Subtypes:\n1. **M-type (Magno)**: Large (∼5 ext{\%} of population). Large receptive fields, rapid conduction, transient response bursts, sensitive to low contrast.\n2. **P-type (Parvo)**: Small (∼90 ext{\%}$of population). Small receptive fields, sustained responses, sensitive to fine detail.</p></li></ul><ol><li><p><strong>Color-Opponent Ganglion Cells</strong>: P-type and nonM-nonP cells displaying red-green ($R^+G^-$) or blue-yellow ($B^+Y^-$$) opponency in center vs. surround.

• Intrinsically Photosensitive Retinal Ganglion Cells (ipRGCs): Use melanopsin photopigment. Depolarize directly to light, have large receptive fields, and project to subcortical centers regulating circadian rhythms.