Chapter 1: Neuroscience – Past, Present, and Future
Neuroscience: the study of the brain, related to disciplines of medicine, biology,
psychology, physics, chemistry, mathematics, etc. where the brain can best be
examined through the combination of these disciplines.
Trepanation: producing a hole in the skull to produce therapeutic, curing effects in
ancient times. People during prehistoric time appreciated that the brain was vital to life.
The procedure showed evidence of healing afterwards, indicating it was done on live
subjects, possibly to treat headaches or mental disorders. However the heart was
considered the origin of the soul and consciousness until Hippocrates.
Hippocrates: 460-379 BC, the father of Western medicine who believed that the brain
was not only involved in sensation but also intelligence. This is known as the
cephalocentric or brain hypothesis.
Aristotle: 384-322 BC, Greek philosopher who believed that the heart was the centre of
sensation and intelligence and that the brain was responsible for cooling the blood
coming from the warm heart. This is known as the cardiac or cardiocentric hypothesis.
Galen: 130-200 AD, Greek physician who agreed with Hippocrates view of the brain.
He was involved with many gladiator injuries and animal dissections to try to discover
the functions of the cerebrum and cerebellum, proposing that sensations were received
by the cerebrum and muscle movements by the cerebellum, as the cerebrum was soft
enough to be imprinted on, and the cerebellum was harder and stronger. He also
discovered that the brain was hollow (ventricles) and filled with fluid which matches the
4 vital fluid (humors) model as the fluid moved through the nerves to interpret
sensations and initiate movements. The right conclusions were made for the wrong
Andreas Vesalius: 1514-1564, renaissance anatomist who added more details to the
structure of the brain except in the case of the ventricles. This brought on the idea that
the CSF was forced out into the muscles during a muscle contraction.
René Descartes: 1596-1650, French mathematician and philosopher who believed in
the fluid-mechanical theory of brain function except in the case of humans. This was
because he believed only humans had a soul, that behaviour was controlled by brain
mechanisms, and that mental capabilities existed outside of the brain with the mind,
known as dualism. The mind can only communicate with the brain through the pineal
gland since it lacks a left and right component. His theory could not account for
voluntary behaviour or the variability in behaviour.
18 t/19 thCentury Discoveries: during this time, white and gray matter were discovered, along with the CNS, the PNS, and that identical gyri and sulci existed in all
humans which allowed for distinguishing lobes for cerebral localization (different parts
have different functions). Also, it was examined that injury to the brain disrupted
sensation, movements and thoughts and even caused death. Also, nerves were
discovered to allow the brain to communicate with the body, and that the brain functions
as a machine according to the laws of nature.
Luigi Galvani and Emil du Bois-Reymond: Galvani discovered that the brain, muscle,
and nerve cells produce electricity and Reymond used the galvanometer to measure the
current in muscles to link it to movement when nerves were electrically stimulated.
Together they dismissed the idea of fluid-based neural communication, as the nerves
are ‘wires’ to conduct electrical signals to and from the brain. They did not find out the
same nerves for mechanoreceptors were also used in muscle contraction.
Bidirectional Communication: suggested as the ability for a neural impulse to move to
and from the brain in the same nerve, since when a nerve is cut the sensation and
movement is lost. At the same time it was known that within each nerve existed nerve
fibres that carried it’s own information in their own directions.
François Magendie and Charles Bell: discovered that the dorsal roots from the back
of the spine has sensory functions and the ventral roots from the front of the spine had
motor functions, which suggested that the brain could also be divided for functional as
well as anatomical reasons. This was tested by destroying the dorsal and ventral nerve
roots one by one. The nerve fibres of each root were either able to carry information into
the brain or out to the muscles. This solved the problem of bidirectional communication.
Bell proposed the origin of muscle fibres is the cerebellum and destination of sensory
fibres is the cerebrum.
Experimental Ablation Method: used to test for localization in the brain, by destroying
parts of the brain one by one to determine the sensory and motor deficits.
Marie-Jean-Pierre Flourens: Used the experimental ablation method was in 1823 in
animals, which provided strong experimental support for Bell and Galen’s ideas about
the cerebellum and cerebral functions and that the medulla was important to vital
processes. Flourens was also a strong critic of phrenology and did experiments with it.
For example if one who was good at music had a bump in the music centre of the head,
and another good at music didn’t, it was assumed that the second person was better at
a different aspect of music and therefore had the bump elsewhere showing that traits
are not isolated to one region and that skull shape ≠ brain shape. Also, he found that
regions with injury might restore function, not to the one area but to all areas, as he
believed the brain was equipotent and functioned as a whole because he resented Gall. It was later determined by Goltz that the size of the lesion, not the location affected
Franz Joseph Gall: states that the brain was divided into 27 different areas called
faculties, which could be found on the cortex of the brain. He also believed the cortex
acted as a muscle, where a larger area was associated with a larger function. This
increased size would cause a bump, which could be examined by cranioscopy. This
measurement along with personality became known as phrenology.
Paul Broca: French neurologist, examined a patient with a problem in producing
speech but not in understanding it. After death of the patient, he discovered a lesion or
soft tissue on the anterior left hemisphere. He discovered the deficit was in articulating
speech and comprehension, and that the left hemisphere in the frontal cortex of the
brain was responsible for speech in most people.
Gustav Fritsch and Eduard Hitzig: in 1870 showed that small electrical currents to a
region of the brain of dogs could elicit discrete movements. David Ferrier replicated the
experiment on monkeys, and showed that removal of that part of the brain caused
paralysis of the particular muscles. Hermann Monk used experimental ablation to
discover that the occipital lobe’s main function is vision.
Charles Darwin: assisted by Wallace, published the Origin of Species, which presents
the theory of evolution. He sailed on the HMS Beagle and travelled to the Galapagos
Islands for 5 years examining the finches there for isolation, different beak size and
function. Using Linnaeus’ classification supported ideas of evolution, William Smith’s
idea that the Earth was older than believed and that some species have changed or
gone extinct, Lyell’s idea that geological processes are still continuing, and Thomas
Malthus’s idea that populations grow exponentially until it reaches carrying capacity they
could propose the idea of natural selection. Organisms with traits that are favourable to
their survival will pass them on Ex. the response to fear in mammals is almost identical
which indicates evolution from a common ancestor with favourable behaviour retained
while other behaviours are adapted to allow the organism to survive in their
Theodore Schwann: German zoologist, proposed the cell theory, where all tissues are
composed of microscopic units called cells. This led to the recognition of the neuron as
the basic unit of the nervous system.
Levels of Neuroscience: there are 5 main levels involved with neuroscience. Breaking
down a problem into smaller levels of analysis is known as the reductionist approach:
• Molecular Neuroscience: brain matter consists of a variety of molecules, which
are mostly unique to the nervous system and which play different roles in communication, sentries controlling movement of materials in and out of neurons,
conductors controlling neuronal growth, and archive past experiences.
• Cellular Neuroscience: how the molecules in the brain work together to give the
neuron its properties. Types of neurons, differences in function, communication
etc is examined.
• Systems Neuroscience: neurons forming complex circuits to carry out a larger
motor or sensory function and how these different circuits analyze sensory
information, form perceptions of the world, make decisions, and execute
• Behavioural Neuroscience: how neural systems work together to produce
larger behaviours, where different drugs act, how the different systems contribute
to mood and behaviour, where dreams come from.
• Cognitive Neuroscience: looks at the mechanisms involved with selfawareness,
mental imagery, and language. How brain activity creates the mind.
Neuroscientists: those that study the brain, where clinical neuroscience is conducted
by physicians, and experimental neuroscience is conducted by those with a M.D or
PhD. Clinical neuroscientists include neurologists, psychiatrists, neurosurgeons, and
neuropathologists where experimental neuroscience is much broader including
computational, developmental, neuroanatomists, neurophysiologists,
neuropharmacologists, molecular neurobiologists, neurochemists, neuroethologists,
neuropsychologists etc. Neuroscientists try to associate damage with behaviours and
come up with possible treatments.
Scientific Process: there are 4 major components to this process which allow
scientists to establish facts about the nervous system regardless of the level of analysis:
• Observation: made during experiments to test a hypothesis and by watching the
world around us, for example a human clinical case such as Broca observing his
patients speech problems.
• Replication: can be experimental or clinical, experiments must be replicated on
different subjects to ensure the results are consistent and valid and didn’t occur
due to chance.
• Interpretation: if the observation is correct it can then be interpreted based on
the knowledge of those carrying it out during the time period. Ex. Flouren’s
testing on birds gave different results than what was found in humans in terms of
localization and his beliefs were altered by his hate for Gall.
• Verification: when the results are very strong and the same experiment could be
done by others and produce the same results and therefore the observations can be accepted as a fact. Inaccuracies and insufficient replication due to slight
changes in variables such as time of day can prevent verification.
Animal Research: experiments on animals is crucial to what neuroscientists know
today. Less than 1% of animals used for food are also used for research and even less
for neuroscience. They are used due to low cost, accessibility, and imilarity to humans.
The animal used depends on what is being tested, the level of analysis, and how much
relatedness to humans there is. More basic processes can be observed in animals with
less evolutionary relation to humans. Animals must be treated well, are only used for
worthwhile experiments that promise advances in neuroscience, pain and distress is
minimized, and animal alternatives are considered. The Institutional Animal Case and
Use Committee with a vet, scientists, and others, then expert neuroscientists, then a
higher committee must review and evaluate the proposals to see if it is relevant.
Economic Costs of Brain Disorders: the costs are very large, as there are more
people suffering from these than from heart disease or cancer and billions are spent on
helping people with these disorders, on research, and producing effective treatments.
This requires neuroscientists to have a proper understanding of normal brain function,
though there is still much that is unknown.
Chapter 7: The Structure of the Nervous System
Anterior: also known as rostral, referring to locations towards the nose of the organism.
Posterior: also known as caudal, referring to locations towards the tail of the organism.
Dorsal: also known as superior, referring to locations towards the top/back.
Ventral: also known as inferior or basal, referring to locations the bottom/belly.
Bilateral Symmetry: referring to the fact that the brain has one axis of symmetry right
down the mid-sagittal line or midline. This separates the right and left hemispheres of
the brain. Most structures found in the brain come with a left and right component with
Medial: referring to structures of the body that are closest to the midline.
Lateral: referring to structures of the body that are furthest from the midline. In addition,
structures that are found on the same side of the body are ipsilateral and those found
on opposite sides are contralateral.
Section: slicing the brain into parts for examination purposes.
Anatomical Planes of Section: there are three planes of the body which are
perpendicular to each other in by which sections can be cut:
• Sagittal Plane: refers to the plane that cuts the body into left and right halves.
This can be along the midline, which is midsagittal, or off-centered which is
5 • Frontal Plane: also known as the coronal plane, refers to the plane that cuts the
body into anterior and posterior halves and is perpendicular to the ground.
• Horizontal Plane: also known as the transverse plane, refers to the plane that
cuts the body into superior and inferior halves and is parallel to the ground.
Central Nervous System (CNS): encased by bone, consists of the brain and spinal
cord. The cerebrum, cerebellum, and brain stem are common in both rats and humans.
The brain has 3 major sections:
• Forebrain (prosencephalon): makes up most of the brain, the diencephalon and
• Midbrain (mesencephalon): has 2 subdivisions, tectum and tegmentum.
• Hindbrain (rhombencephalon): the area between the brain and the spinal cord,
divided into the metencephalon and the myelenchephalon.
Cerebrum: the most rostral and largest part of the brain, consists of 2 cerebral
hemispheres separated by the mid-sagittal fissure and held together by the corpus
callosum. Usually, these hemispheres receive information from and control contralateral
parts of the body.
Cerebellum: part of the hindbrain or metencephalon, behind the cerebrum responsible
for coordinating and initiating movement, also involved in learning and language
processing. The cerebrum contains as many nerves as both cerebral hemispheres
combined. Information it receives and where it controls is ipsilateral. It has 3 zones:
lateral (in each hemisphere, multijoint movements), intermediate (in each hemisphere,
guides limb movement), and vermis (centre, for posture/body movement). Within these
zones there are 3 nuclei called deep cerebellar nuclei: fastigial receives from vermis,
interpositus receives from intermediate, and dentate received from lateral.
Fissure: deep sulci that reach far into the cortex. The longitudinal fissure runs sagittal
separating hemispheres, the central fissure runs coronal separating the frontal and
parietal lobes, and the lateral or Sylvian fissure separates the temporal lobe in humans.
Brain Stem: the remaining part of the brain, forming a stalk where the cerebellum and
cerebrum branch out. It is made of a nexus of fibres and cells to relay information from
the spinal cord to the cerebrum and cerebellum and vice versa. This is where vital
information is processed such as breathing, heart beat, heart rate, consciousness etc
therefore although primitive, is vital to life. There are 2 main sections:
• Medulla Oblongata: lowest part of the hindbrain, helps regulate involuntary
processes such as sleep, breathing, heart rate, etc.
• Pons: a bulge above the medulla above the metencephalon and
myelencephalon, relays sensory information from the spinal cord to the
cerebellum and other brain structures, through the thalamus.
Spinal Cord: encased in bone and attached to the brain stem. This relays information
from the PNS to and from the brain and all over the body. The spinal cord has 31
sections with 2 spinal nerve projections each (left/right). This is divided into cervical,
thoracic, lumbar, sacral, and coccygeal. If one of these is damaged that section and
below (caudal) loses sensation and control (paralysis). The muscles are functional but
the brain cannot control them after this.
Spinal Nerves: how the spinal cord communicates with the body. These are a part of the PNS and exit the vertebrae through notches between each vertebrae. The spinal
nerves connect to the spinal cord through the dorsal and ventral roots carrying sensory
and motor information respectively.
Peripheral Nervous System (PNS): efferent systems, the portion of the nervous
system existing outside of bone (skull and vertebrae). It has 2 major divisions, the ANS
(visceral PNS) and the sPNS.
Autonomic Nervous System (ANS): also known as the visceral PNS, part of the PNS
that is involved with regulating neurons which innervate blood vessels, organs, and
glands to control internal states (ex. Temperature, blood pressure, heart rate etc). It
conveys information from the body’s organs to the CNS. There are 2 types of ANS
efferent nerves, which are:
• Sympathetic: form a network that prepares the body for vigorous activity (ex.
• Parasympathetic: form a network to sustain non-emergency behaviour,
opposes the sympathetic system to create balance.
Somatic Nervous System (sPNS): contains all spinal nerves, which innervate the skin,
joints, and muscles under voluntary control. Somatic motor axons derive from motor
neurons in the ventral spinal cord and where the cell bodies lie in the CNS and somatic
sensory axons derive from sensory neurons in the dorsal roots where cell bodies lie
outside of the spinal cord in dorsal root ganglia. There is one dorsal root ganglia per
spinal nerve. The visceral nervous system projects to smooth and cardiac muscle.
Cranial Nerves: there are 12 pairs of nerves that are visible on the cranial surface,
many of which attach at the medulla and innervate the head. Some are part of the CNS
and others are part of the sPNS or ANS: ooottafvgvsh ssmmbmbsbbmm
I olfactory: special sensory, smell
II optic: special sensory, vision
III oculomotor: somatic/visceral motor,
eye motion, pupil dilation
IV trochlear: somatic motor, eye
V trigeminal: somatic sensory/somatic
motor, somatosensory info (face),
muscle movement during mastication
VI abductens: somatic motor, eye
movement. VII facial: somatic sensory/special
sensory, movement of muscles of facial
expression, sensation of anterior
VIII acoustic (vestibulocochlear): special
sensory, hearing and balance.
IX glossopharyngeal: somatic
sensory/visceral sensory, movement of
throat muscles, parasymp control of
salivary glands, post. tongue, blood
pressure change detection.
X vagus: visceral motor/visceral
sensory/somatic motor, control of
XI spinal accessory: somatic motor,
XII hypoglossal: somatic motor, tongue
NOTE: throat = oropharynx
Cranial Nerve Damage: can result in Parry Romberg Syndrome where the trigeminal
nerve is damaged and severe pain in facial tissues. Vestibular neuritis can also occur
when the vestibular nerve is inflamed causing vertigo and dizziness.
Meninges: Greek for hard covering, doesn’t allow the CNS to come into direct contact
with the bone. This provides protection and support for the brain. This is composed of 3
• Dura Matter: Latin for hard mother, the layer closest to the skull, a thick fibrous,
inelastic layer. There is no space between this and the arachnoid layer.
• Arachnoid Matter: Greek for spider, the middle layer, web-like, spongy matter
where blood vessels run from the outer brain.
• Pia Matter: ‘gentle mother’, very thin layer closest to the brain. Many blood
vessels run along this layer.
Subarachnoid Space: below the arachnoid matter (between the arachnoid and pia
matter) contains cerebrospinal fluid, which helps excrete wastes, maintaining the CNS
environment. The CSF can be absorbed into blood vessels by arachnoid villi.
Subdural Hematoma: when a blood vessel passing through the dura breaks causing a buildup between the dura and arachnoid matter and can compress on the CNS causing
damage therefore must be drained.
Ventricles: four hollow areas in the brain filled with cerebrospinal fluid, the lateral (1 st
and 2 nd) and 3rdventricle (in midline of brain) are connected by the interventricular
foramen, and the 3 rdand 4 thare connected by the cerebral aqueduct (aqueduct of
Sylvius) and central canal connects to the spinal cord. They are lined with CSFproducing
ependymal cells. The massa intermedia passes through the centre of the 3 rd
ventricle. The cerebrospinal fluid is able to flow from the ventricular system to the
subarachnoid space through small openings near where the cerebellum attaches to the
brainstem. If the flow of CSF is disrupted it can be harmful.
Cerebral Spinal Fluid: CSF functions to maintain the ion concentration/pH balance of
the brain, protection, cleans the brain/excretion of waste, lubricates it/buoyancy,
Choroid Plexuses: a network of blood vessels in the floor of the lateral ventricles and
roof of the 3rd/4thventricles produce the cerebrospinal fluid. This fluid is absorbed by
arachnoid granulations in the sagittal sinus.
Interventricular Foramen: the foramen of Monroe, connects the lateral and 3 rd
Hydrocephalus: water on the brain, a developmental disorder. Causes an enlarged
skull and ventricles causing the brain to be compressed.
Alzheimer’s Disease: neurodegenerative disease where neurons die and shrink so
ventricles fill up to take up the extra space, causing the sulci to be enlarged as well.
Schizophrenia and hydrocephalus also causes enlarged ventricles. This is caused by a
disruption of the cytoskeleton in neurons in the cerebral cortex and the formation of
neurofibrillary tangles involving microtubule-associated protein tau. Microtubules usually
run parallel to each other, but when tau detaches and accumulates in the soma, the
axons wither since materials aren’t being transported properly, impeding the flow of
information. The cause is uncertain but can be linked to amyloid plaques.
Structural Imaging: a test that provides an image of the brain structure, which helps
clinicians find the location of an injury or abnormality.
• Computed Axial Tomography (CAT/CT scans): developed by Hounsfields and
Cormack, give a non-invasive view of the brain involving computing and x-rays. It
involves sending X-rays into the body at different angles then computed into a 3-
D image and brain slices where dense areas are bright and the rest is dark, and
where ventricles can be seen. The problem is this technology cannot differentiate
between white and grey matter. The axial version scans in one plane. These
8 scans help identify abnormalities in the brain shown by changes in density on the
scan (except for tumors similar in density to normal cells) so they could be
related to behavioural defects.
• Magnetic Resonance Imaging (MRI): produced an image using nuclear
magnetic precision measurement, similar to CT scans, however they have better
resolution, don’t use X-ray, and produces images in any plane. Since hydrogen is
a common element in the body with poles facing random directions, this scan
places a strong magnetic field near the brain so the atoms poles become aligned
and polarized. The machine measures the relaxation time (time it takes for the
atoms to return to their low-energy normal positions) therefore measures H
density. The image shows brain, bone, air and water as dark and with fluid as
bright. The receiver coil (measures intensity) and gradient field produce the 3-D
image. The limitations are that any internal metal in the body will be attracted to
the magnet, which is dangerous ex bits of needle from tattoos or metal salts in
Functional Imaging: collects brain information without measuring electrical currents or
magnetic fields. These tests measure changes in blood flow. No oxygen and little
glucose is stored in the brain therefore the brain works on blood flow.
• Positron Emission Tomography: invasive test capable of blood flow scans
with higher resolution, as well as testing utilization of substances such as
dopamine. A compound must be radioactively labeled with a substance that
emits positrons and gamma rays and injected into the person while a machine
scans for positrons emitting in the brain and creates a 3-D image.
• Functional Magnetic Resonance Imaging: an MRI scan that detects changes
in the positions of H atoms since they are found in water and blood, which is
constantly moving in the brain by alternating magnetic gradients very quickly.
Since oxygenated and deoxygenated blood have different magnetic properties
the MRI shows that oxygenated blood flow increases in part of the brain being
used. It gives better photos and resolution however has the same limitations as
Gray Matter: collection of neuronal cells bodies in the CNS, seen in a freshly dissected
brain. The brain is grey on the outside and the spinal cord is grey on the inside. This is
mostly composed of neuron cell bodies and blood vessels.
Cortex: Latin for bark, a collection of neurons that form a thin sheet at the brain’s
surface, just under the surface of the cerebrum.
Nucleus: Latin for nut, a clearly distinguishable mass of neurons, usually deep in the
brain. ex. the lateral geniculate nucleus, which receives signals from the visual system
before being relayed to the occipital lobe.
Substantia: a group of related neurons within the brain, but less distinct borders as in a
nucleus ex. substantia nigra, involved with control of voluntary movements.
Locus: a small, well-defined group of cells ex. locus coeruleus, involved with
wakefulness and arousal.
Ganglion: Greek for knot, a collection of neurons in the PNS, ex. dorsal root ganglia,
which contains cell bodies of axons entering the spinal cord. The only one found in the CNS is the basal ganglia, which is part of the telencephalon and involved with
Nerve: a bundle of axons in the PNS, one collection of CNS axons (optic nerve).
White Matter: a collection of CNS axons, appear white in a freshly dissected brain. The
brain is white on the inside and the spinal cord is white on the outside. This is mostly
composed of myelinated axons.
Tract: a collection of CNS axons with a common origin and destination, ex.
Bundle: collection of axons that run together, but do not have the same origin and
destination as a tract does.
Capsule: collection of axons that connect the cerebrum with the brain stem.
Commissure: collection of axons that connect one side of the brain with the other, ex.
corpus callosum is the largest commissure.
Lemniscus: a tract that exists through the brain as a ribbon, ex. medial lemniscus,
which bring touch information to the brain from the spinal cord.
Hypothalamus: composed of 22 nuclei, part of the diencephalon, involved with feeding,
hormone regulation, satiety, homeostasis, and sex.
Thalamus: a miniature brain with gyri (bumps) and sulci (grooves), relays sensory
information between the cortex and sensory organs. Forms a heart shaped structure in
the mid-thalamus junction and is dorsal to the hypothalamus and contains 2 nuclei
known as the ventral posterior nucleus of the somatic sensory system, which projects to
the postcentral gyrus and the ventral lateral nucleus, which is related to the ventral
anterior nucleus, which relays to the motor system. The different nuclei relay
information to different areas of the cortex.
Pituitary Gland: Involved with hormone secretion, attached to the hypophysis, close to
the cranial nerves. Infundibulum stalk is left after the pituitary is removed.
Corpus Callosum: the largest commissure in the brain, consisting of white matter. It
contains homotopic and hetertopic connections (connections between similar and
dissimilar cortical areas respectively). Posterior to anterior is the splenium, then genu,
Tectum: part of the midbrain that contains a number of motor nuclei, including the red
nucleus and substantia nigra, relays visual and auditory sensory information. There are
4 small bumps on the dorsal midbrain (2 inferior colliculi and 2 superior colliculi):
• Superior Colliculus: also called the optic tectum, receives direct input from the
eye to control eye movements with motor neurons that innervate the muscles of
the eye. • Inferior Colliculus: receives sensory information from the ear to relay it to the
Tegmentum: located ventral to the tectum, contains the substantia nigra (black matter),
red nucleus (motor nuclei) to control voluntary movement, the periaqueductal gray for
Frontal Lobe: the most anterior part of the brain, containing many important gyri and
sulci, involved in control of movement, memory, thinking, awareness, regulating social
behaviour, and personality.
Temporal Lobe: separated by the Sylvian fissure and parietooccipital sulci, containing
many important gyri and sulci. It is involved with language processing, memory, object
recognition, and emotion.
Parietal Lobe: bordered by the central, lateral, and parietooccipital fissures, again
contains many important gyri and sulci. It plays a role in sensory and somatosensory
function, spatial cognition, and sensory integration.
Occipital Lobe: bordered by the parietooccipital sulci, and contains the calcarine
fissure, which is surrounded by the primary visual cortex. The most posterior portion is
the occipital pole.
Cerebral Cortex: the main part of the brain consisting of the frontal, parietal, occipital,
and temporal lobes. This structure has 7 different layers, where the neurons closest to
the surface are separated by a layer with no neurons (layer I). Deeper layers have cells
with large dendrites which penetrate layer I. The layer covering the first layer is the pia
matter and the darker regions are denser. Layer 5 has large pyramidal cells compared
to layer 3. Layer 6 has a mixture of cells with stellate, Golgi, spindle, pyramidal etc.
Below this layer is the corpus callosum. These are anatomically and can be functionally
different. These layers can range in depth depending on where in the brain they are.
Hippocampus: medial to the lateral ventricle, a structure in the temporal lobe involved
with the limbic system, learning, and memory but not storage of memories.
Olfactory Cortex: connected ventrally to the hippocampus and continuous with the
olfactory bulb. This is separated from the neocortex by a sulcus known as the rhinal
Neocortex: only found in mammals, since the brain has expanded over time by
evolution, however its structure and shape has remained constant. This is separated
from the hippocampus and olfactory bulb by the rhinal fissure. This has 6 layers and the
most amount of laminae
Cytoarchitectural Map: can be used to divide the brain and its parts into different
zones, similar to how Korbinian Brodmann did, where each area of cortex is labeled by a number. He was unable to show that cortical areas that looked different performed
different functions but there were 52 areas.
Chapter 7: Appendix
Gross Features: gross features of the brain seen lateral include, the cerebrum (which
includes the frontal, parietal, occipital, and temporal lobes), the brain stem (pons and
medulla) and the cerebellum. The olfactory bulb of the cerebrum can also be seen.
Gyri, Sulci, and Fissures: where gyri are bumps, sulci are grooves, and fissures are
deep grooves, which form patterns common to all humans with slight differences. The
postcentral gyrus lies posterior the central sulcus and is involved with somatic sensation
and the precentral gyrus is located anterior to the central sulcus and is involved with
voluntary movement. The superior temporal gyrus is located ventral to the
Sylvian/lateral fissure and contains the primary auditory cortex. Gyrencephalic refers to
organisms with gyrated brains and lissencephalic are organisms with smooth brains ex.
Insula: a buried piece of cerebral cortex, can be seen if the Sylvian/lateral fissure is
pulled apart. This borders and separates the frontal and temporal lobes.
Cortical Sensory Areas: organized by Brodmann into areas, where visual areas 17,
18, and 19 are in the occipital lobe, sensory areas 1, 2, and 3 are in the parietal lobe,
and auditory areas 41 and 42 are in the superior temporal gyrus of the temporal lobe.
On the inferior parietal lobe (operculum) on the insula is gustatory area 43 for taste.
Cortical Motor Areas: also organized by Brodmann into areas, where primary motor
cortex area 4 and anterior to that, premotor (lateral) and supplementary motor (medial)
area 6 lie in the frontal lobe anterior to the central sulcus.
Association Areas: areas 5, 7, 20, 21, 37, Involved in higher order processing for
single separate sensory/motor modalities (unimodal) ex. smelling a muffin, as well as
the integration of multiple modalities (multi/heteromodal) ex. smelling/tasting/seeing a
muffin. Association areas are more wide spread, lots of regions are involved with this
activity including the prefrontal cortex, posterior parietal cortex, and inferotemporal
Midsagittal Structures: midsagittally, the parts of the brain stem can be seen, as well
as the diencephalon thalamus and hypothalamus, the midbrain’s mesencephalon
tectum and tegmentum, and the hindbrain’s mylencephalon pons and medulla and
metencephalon the cerebellum.
• Corpus Callosum: the largest commissure in the brain, consisting of white
matter. It contains homotopic and hetertopic connections (connections between similar and dissimilar cortical areas respectively). Posterior to anterior is the
splenium, then genu, then rostrum. From a thalamus-telencephalon junction, it is
seen connecting the 2 hemispheres in white.
• Fornix: can also be seen, which connects the hippocampus on each side with
the hypothalamus and mammillary bodies and functions to regulate memory
storage. This shows as a stalk between the lateral ventricles and on each side
lateral to where the lateral and 3 rdventricles meet and dorsal to the thalamus,
ventral to the septal area, which connects it to the corpus callosum.
• Mammillary Bodies: nuclei, small protrusions along the ventral brain surface,
which play a role in memory as they receive information from the fornix. These
can be seen in the mid-thalamus junction and exist ventral to the subthalamus
• Amygdala: a small almond-shaped structure in the temporal lobe, part of the
limbic system involved with emotions and memory. Cannot be see midsagittally
because it lies deep within the cortex. This is located near the ventral surface in
each hemisphere and can be seen in the mid-thalamus junction.
• Hippocampus: a structure in the temporal lobe involved with the limbic system,
learning, and memory but not storage of memories. Cannot be see midsagittally
because it lies deep within the cortex.
Ventricles: the lateral walls of the 3rdand 4 thventricles, as well as the cerebral
aqueduct and spinal canal can be seen from a midsagittal view. The thalamus and
hypothalamus lie next to the 3 rdventricle, the midbrain is next to the aqueduct, the pons,
medulla, and cerebellum are next to the 4 thventricle, and the spinal cord forms the walls
of the spinal canal. The lateral ventricles (1 and 2) extend from the 3 rdventricle but can’t
be seen midsagittally. A thalamus-midbrain coronal cut will intersect the horns of the
lateral ventricles twice in each hemisphere.
• Lateral Ventricle: associated with the cerebral cortex and telencephalon
• Third Ventricle: associated with the thalamus and hypothalamus
• Cerebral Aqueduct: associated with the tectum and tegmentum
• Fourth Ventricle: associated with the cerebellum, pons, medulla
Ventral Surface: from this view, the 12 cranial nerves of the brain can be seen, as well
as the optic chiasm where optic nerves from the eyes may cross over anterior to the
hypothalamus. Posterior to the chiasm is there the optic tract begins and disappears
into the thalamus. The mammillary bodies, 2 nuclei of the hypothalamus, are visible
anterior to the pituitary and infundibulum and are a target of the axons of the fornix. The
olfactory bulbs and tracts, pons, medulla, and midbrain can also be seen. Dorsal Surface: from here, the frontal and parietal lobes can be seen, as well as the
corpus callosum deep within the medial latitudinal fissure between the two
hemispheres. If the cerebrum is removed, the cerebellum dominates the dorsal view
and controls movements and balance, with 2 lateral structures and a midline called the
vermis. If the cerebellum is also removed, the brain stem is exposed, including the
pineal body on top of the thalamus, which secretes melatonin to regulate circadian
rhythm and sexual behaviour. Also, the superior and inferior colliculi, for eye
movements and audition respectively can be seen posterior to the pineal body. The
cerebellar peduncles on either side can be seen and used to connect the cerebellum to
the brain stem.
Cross Sections: usually best when perpendicular to the neuraxis, can be made with a
knife or with brain imaging techniques such as MRI or CT scans.
Thalamus-Telencephalon Junction: the telencephalon surrounds the lateral
ventricles, and the thalamus surrounds the 3 rdventricle. From a slice, the third ventricle
appears as a slit and the lateral ventricles branch out dorsally from it. The hypothalamus
forms the floor beneath the 3 rdventricle. The insula is found at the base of the Sylvian
fissure separating the frontal and temporal lobe. The basal forebrain lies in the
telencephalon lateral to the 3 rdventricle and thalamus and medial to the insula.
Internal Capsule: a large collection of axons connecting the cortical white matter with
Septal Area: the neurons associated with this contribute axons to the fornix and are
involved with memory storage.
Basal Ganglia: a division of the telencephalon, important to initiating movements and
maintaining muscle tone. This is made of 3 parts:
• Caudate Nucleus: along with the putamen, is called the striatum, extends from
putamen. This is part of the basal ganglia and is located lateral to the lateral
• Putamen: along with the globus pallidus, is called the lentiform nucleus, encase
the globus pallidus. Part of the basal ganglia and is located lateral to the globus
• Globus Pallidus: part of the basal ganglia, forms the lentiform nucleus with the
putamen and is located medial to the putamen.
Mid-Thalamus Junction: more caudal than the Thalamus-Telencephalon Junction,
where the thalamus is heart-shaped in the centre of the brain surrounding the end of the
3rdventricle and dorsal to the hypothalamus. The lateral fissure separates the parietal
and temporal lobe.
Subthalamus: part of the motor system, can be seen in the mid-thalamus junction just
dorsal to the mammillary bodies and the hypothalamus.
Substantia Nigra: means black substance, part of the tectum of the midbrain, can be
seen in the mid-thalamus junction. This is located near the base of the brain lateral to
the mammillary bodies and is involved with voluntary movements. Parkinson’s results
when this structure is degenerated.
Thalamus-Midbrain Junction: at this junction the third ventricle connects to the
cerebral aqueduct. The thalamus is surrounding this 3 rdventricle and the midbrain
surrounds the aqueduct. The lateral ventricles exist here still but are now separated and
the 2 horns in each hemisphere can be seen.
Medial Geniculate Nuclei: a nucleus of the thalamus, which relays information to the
auditory cortex. This is medial to the ventral horn of the lateral ventricles.
Lateral Geniculate Nuclei: a nucleus of the thalamus, which relays information to the
visual cortex. This is dorsal to the ventral horns of the lateral ventricles and lateral to the
medial geniculate nucleus.
Hippocampus: medial to the lateral ventricle, a structure in the temporal lobe involved
with the limbic system, learning, and memory but not storage of memories. This is
located lateral to the ventral horn of the lateral ventricle and beneath the lateral
Rostral Midbrain: cuts across the midbrain perpendicular to the neuraxis. This includes
the cerebral aqueduct and the roof of the midbrain (tectum) contains the superior
colliculus and the substantia nigra, as well as the red nucleus and the periaqueductal
Red Nucleus: part of the periaqueductal gray and controls somatic pain sensations.
Both are located ventral to the superior colliculi and lateral to the cerebral aqueduct, but
the red nucleus is more ventral.
Caudal Midbrain: this is a cut below the rostral midbrain and contains the inferior
colliculus, cerebral aqueduct, the periaqueductal gray, and the substantia nigra. The
roof is formed by the inferior colliculus instead of the superior colliculus as in the rostral
Pons and Cerebellum: cuts right through the cerebellum and pons and contains the 4 th
ventricle, the deep cerebellar nuclei which receive output from the cerebellum, and
pontine reticular formation, the pontine nuclei which sends information to the
cerebellum, and the cerebellar cortex.
Reticular Formation: means net, runs from the midbrain to the medulla at the core of
the brain stem under the cerebral aqueduct and 4 thventricle, regulates sleep and
Pontine Reticular Formation: located anterior to the 4 thventricle on each side, is
involved with controlling body posture.
Rostral Medulla: a cut located right below the pons, where the brain surrounding the
4thventricle is the medulla. This also contains the dorsal and ventral cochlear nuclei
lateral to the 4thventricle and the superior and inferior olive for motor control, and the
raphe nucleus for the modulation of pain, mood, and wakefulness.
Medullary Pyramids: lie at the floor of the medulla, where huge bundles of axons from the forebrain meet the spinal cord. These pyramids have corticospinal tracts involved in
Mid-Medulla: cuts below the rostral medulla, with the same structures as the rostral
medulla but also includes the medial lemniscus.
Medial Lemniscus: located along the ventral median fissure to bring information about
somatic sensation to the thalamus.
Gustatory Nucleus: serves for sense of taste, part of the larger nucleus of the solitary
tract, which regulates visceral function, located ventral to the vestibular nucleus and
dorsal to the medullary reticular formation.
Vestibular Nuclei: serves for sense of balance, located dorsal to the other structures.
Medulla-Spinal Cord Junction: the cut right above the brainstem, where the 4 th
ventricle disappears as well as the medulla, where the spinal cord begins. This contains
the dorsal column nuclei and medial lemniscus with the medullary pyramids.
Dorsal Column Nuclei: receives somatic sensory information from the spinal cord.
Axons from here cross to the other side of the brain (decussate) and ascend to the
thalamus by the medial lemniscus.
Spinal Nerves: part of the somatic PNS that communicate with the spinal cord through
notches between the vertebrae. These are named according to the vertebrae directly
above, where the first 7 are cervical, next 12 are thoracic, next 5 are lumbar, and the
rest are sacral and coccygeal, however the cord ends at the 3 rdlumbar vertebrae since
it doesn’t grow after birth as the vertebrae does.
Cauda Equina: ‘horse’s tail’ the bundles of spinal nerves streaming down within the
lumbar and sacral vertebral column.
Ventral-Lateral Spinal Cord: when the nerve branches off of the spinal cord and
through the vertebral notch, it splits into the dorsal root carrying sensory axons with cell
bodies in he dorsal root ganglia and the ventral root which carries motor axons from the
gray matter in the ventral spinal cord.
Spinal Gray Matter: forms a butterfly shape, with neuronal cell bodies. There are
dorsal, ventral, and lateral horns. The white matter with axons run up and down the cord
is divided into 3 columns: dorsal between the dorsal horns, lateral between the dorsal
and lateral horns, and ventral between the ventral horns.
Spinothalamic Tract: carries information about painful stimuli and temperature, located
surrounding the ventral ad lateral horns of the gray matter. This is part of the ascending
sensory pathways leading to the brain.
Ascending Sensory Pathway: includes the spinothalamic tract, and where the whole
dorsal column consists of sensory axons to the brain. Descending Motor Pathways: contributes to 2 different pathways: lateral pathway for
commands for voluntary movements and ventromedial for the maintenance of posture
and reflexes. This includes the vestibulospinal tract, which originates in the vestibular
nuclei of the medulla and ends in the spinal cord.
Sympathetic Ganglia: appears as a chain of ganglia that runs along the vertebral
column, communicating with spinal nerves, with each other, and with internal organs.
Parasympathetic Fibres: arises from the vagus nerve to innervate viscera, and the
sacral spinal nerves.
Vertebral Arteries: 2 arteries that enter the back of the brain from the vertebral column.
They supply the posterior and anterior inferior cerebellar arteries before joining the
basilar artery. This branches into the posterior cerebral arteries and the superior
cerebellar arteries, where the posterior cerebral artery branches into the posterior
communicating artery, which connects to the internal carotid arteries.
Carotid Arteries: 2 arteries that supply blood to the anterior hemispheres of the brain.
These separate into the anterior cerebral arteries. The 2 carotid arteries are joined by
the anterior communicating artery of the circle of Willis and branch off from the posterior
Basilar Artery: receives blood from the vertebral arteries, which give rise to the
posterior cerebral arteries and the superior cerebellar arteries.
Circle of Willis: a circular region where the arteries join in the brain. If one section
becomes blocked, this compensates. This is made up of the anterior and posterior
communicating arteries. Also equalizes blood pressure in the brain.
Anterior Cerebral Arteries: supplies the anterior cerebral cortex, supplies the frontal
lobe, and the medial wall of the cerebral hemisphere.
Middle Cerebral Arteries: supplies the midsection of the cerebral cortex, frontal and
parietal lobes, the lateral sides of the cortex, and the deep basal forebrain, branches off
of the internal carotid arteries.
Posterior Cerebral Arteries: branches off of the basilar artery, supplies the posterior
cerebral cortex, the medial wall of the occipital lobe, and the inferior part of the temporal
Stroke: neurons are very sensitive to oxygen and glucose and wont survive for long
without it. And ischemic stroke (short disruption) this can cause permanent cell death.
The severity depends on how long the brain region goes without blood. There are
• Thrombotic: ischemic, occlusion of cerebral blood vessels due to plaque
buildup. • Embolic: ischemic, plugging of the cerebral artery with a dislodged embolus
from heart/plaque buildup from vertebral arteries.
• Hemorrhagic: rupturing of a cerebral blood vessel from hypertension,
aneurysms etc. This can cause pressure build up, causes 20% of stroke but
can damage tissues.
Broca’s Aphasia: affects Broca’s area, where speech is highly impaired, including long
pauses and anomia (difficulty finding words), mainly content words such as nouns,
adjective, and verbs are used but not function/connecting words (no grammar structure
or grammatically correct speech, agrammatism). Comprehension is still normal.
Chapter 2: Neurons and Glia
Neurons: cells in the nervous system that are responsible for communication of neural
impulses and therefore behaviour. There are 100 billion with a total surface area of
25,000m 2. They sense changes in the environment and communicate these changes
with other neurons to command a response. They learn and store information about
their external environment. The neuron shape allows it to receive, conduct, and transmit
signals. There are 3 types based on the number of neurites extending from the soma:
• Unipolar: have only one process coming from the cell body.
• Bipolar: have only 2 processes coming from the cell body.
• Multipolar: have numerous processes coming from the cell body. These are
the most common.
• Interneurons: most common, relay information within structures instead of
between structures (ex. Connect the sensory and motor neurons of the reflex arc
to connect the responses).
• Afferent Neurons: also called primary sensory neurons, send information to the
brain from sensory surfaces.
• Efferent Neurons: also called motor neurons, send information away from the
brain to muscles and release acetylcholine making them cholinergic.
• Golgi type I Neurons: also called projection neurons, have long axons that
extend from one part of the brain to another, usually are pyramidal.
• Golgi type II Neurons: also called local circuit neurons, have short axons and
do not extend beyond the vicinity of the cell body usually are stellate.
Glia: means glue, cells in the nervous system that are responsible for support,
maintenance, insulation, and nourishment of neurons. There are 3 types:
• Astrocytes: large star shaped glia, which fills the space between neurons. There
is a small gap between these and the neuron probably allowing the neurite to
contract/grow. These are also involved in the blood-brain barrier supply nutrients to neurons, regulate the chemicals and ions in extracellular space, keep
neurotransmitters within the synaptic gap, regulate and store neurotransmitters
(especially when in excess). These also have receptors where neurotransmitters
can bind and create electrical activity.
• Oligodendrocytes: glia and Schwann cells to make myelin. They wrap around
axons of the CNS to insulate the axons. It is a sheath because it covers the
whole axons with small interruption at the nodes of Ranvier. The glia are found in
the CNS and the Schwann cells are found in the PNS.
• Microglia: small glia made outside the CNS by microphages, which are
phagocytes that remove debris from dead neurites and glia in the nervous
system. Excessive microglia can cause neurodegenerative diseases.
Ependymal Cells: provide the lining of the ventricles and direct cell migration during
Blood-Brain Barrier: a specialized system of capillary endothelial cells connected by
tight junctions, different than found in the peripheral tissue, separating the brain from the
rest of the body. This creates a protective barrier against other molecules and toxins
except those which are fat soluble such as glucose, oxygen, small fat-soluble
molecules, ions involved with critical neuron activity, and few water-soluble molecules.
This prevents most toxins from getting in except lead. It is also essential to homeostasis
by preventing large fluctuations in concentration of ions. Ex by buffering K + ions into
extracellular brain fluid preventing premature/sustained neuron depolarization. The
barrier is not well developed in young children so lead can accumulate and impair
learning and memory even in pregnant women it may not affect the mother but it can
pass into the placenta. Drugs sometimes cannot get in and influence the CNS but
researchers to modify drugs to have similar structures to molecules, which can enter the
blood-brain barrier, such as L-DOPA for PD, which is similar to dopamine. Antiretroviral
drugs for HIV can’t cross the barrier.
Axon: there is usually one per neuron, extends from the cell body of the neuron at the
axon hillock into the axon proper and transmits action potentials to other neurons over
great distances. The diameter is uniform along its length and is proportional to the
speed of the signal it sends. Axons may be branched, with branches at right angles
called axon collaterals. These may connect to the same neuron or neighbouring
neurons and are called recurrent collaterals. No rough ER extends into the axon but few
free ribosomes may exist but means there is no protein synthesis in the axon and all
proteins must originate from the soma. These also contain cytoskeleton (except the
terminal), mitochondria, and vesicles. Also, the proteins in the membrane of the axon may differ from those in the soma.
Dendrites: means tree, only about 2mm in length, extend from the neuron cell body
and are the component of the neuron that receives information from other neurons and
transmit it to the cell body. These contain some major organelles. They are highly
branched to increase the surface for receiving signals and to indicate how many axons
it may be connected with. The diameter is not constant along its length, as these
generally taper into a point at the tips. These have receptors on them to receive
neurotransmitters from the synaptic gap and may contain polyribosomes. All the
dendritic branches on a single neuron are known as the dendritic tree. There are 2
• Stellate Cells: neuron cells in which the dendritic trees are star-shaped. These
neurons can be spiny or aspinous and are usually Golgi type II neurons. These
usually respond to steady depolarizing current injected into the soma by firing
action potentials at a steady frequency.
• Pyramidal Cells: neuron cells in which the dendritic trees are pyramid-shaped.
These neurons are spiny and are usually Golgi type I neurons. These can’t
usually sustain a steady firing rate, as they fire rapidly at the beginning of the
stimulus and then slow down even if the stimulus is steady. This is due to
adaptation because of the many ion channels. Large pyramidal cells can also
respond with bursts of fast firing with breaks in between.
Dendritic Spines: growths on the outside of the dendritic branches that receive
synaptic input. The number of spines is also related to the environment the organism
was exposed to during development. Neurons with spines are known as spiny, those
without are aspinous. New spines can form to store new knowledge and memories, or
they can be modified to do so or change existing memories. Structural appearance and
function may be modified by experience, learning and memory, environment,
development, and stress. Change in number can occur with estrogen or hormones to
make more synapses, they can decrease with age and not being used, a result of
Down’s Syndrome, Schizophrenia, Huntington’s Disease, Fragile X (more immature
spines such as filopodia). The outgrowths can be simple including long and thin
(filopodium, immature), simple, stubby, or crook sessile, thin, mushroom, or gemmule
pedunculated, or branched.
Formaldehyde: a chemical used to ‘fix’ or harden tissues so that the brain could be cut
into thin slices for examination. This is not possible otherwise because the consistency
of the brain is similar to Jell-O and is not firm enough to be sliced. However, this
technique stains all tissues the same colour making it hard to view different types of
Histology: the microscopic study of the structure of tissues. This is difficult to do when
the brain has been fixed in formaldehyde, therefore stains must be used to colour some
but not all parts of the brain cells.
Nissl Stain: developed by Franz Nissl, a German neurologist. He showed that certain
dyes could be used to stain nuclei of the brain and clumps of material surrounding the
nuclei of neurons called Nissl bodies. The stain is purple/blue and doesn’t stain
dendrites or axons like the Golgi stain. This is used to distinguish neurons and glia from
each other and allows histologist to study the cytoarchitecture of neurons in different
parts of the brain. This allowed for the realization that the brain has many specialized
regions with different functions.
Golgi Stain: developed by Camillo Golgi, an Italian histologist who stained brain tissue
with silver chromate solution where some neurons (including dendrites and axons)
become darkly coloured in their entirety, instead of just a lump around their nucleus as
with the Nissl stain. This stain shows that the neuron has a central part with a nucleus
known as the cell body, as well as thin tubes, which radiate away from it known as
neurites, which includes a single axon and the dendrites. Golgi believed that neurites of
different cells are fused together to form a continuous network, and that the brain is an
exception to the cell theory. 1 in 700 or 1400 are stained, but the reason it is stained is
Santiago Ramón Y Cajal: Spanish histologist, used Golgi stain to trace connections
and circuitry to the brain, and examine dendrites. He proposed neurons are not
continuous and must communicate by contact not continuity (neuron doctrine) and
adheres to the cell theory, opposite to Golgi’s theory. He noted that neurons come in all
shapes and sizes that correspond to certain parts of the brain known as
cytoarchitecture. This was later proven when the electron microscope was invented.
The Neuron Doctrine: states that the brain is composed of separate neurons and cells
that are structurally, metabolically and functionally independent and that information is
transmitted from cell to cell across tiny gaps called synapses.
Soma: also known as the cell body or perikaryon, the spherical central part of the
neuron, about 20μm in diameter containing cytosol rich in sodium and potassium all
surrounded by the neuronal membrane. Like other cells the soma contains organelles.
Nucleus: means ‘nut’, located within the neuron soma contained within the nuclear
envelope, a perforated membrane which holds in the chromosomes which contain DNA
identical to the DNA found in all cells of the body however different genes are
expressed in each type of cell.
Gene Expression: the reading of DNA, where the product is proteins of all shapes,
sizes, and functions by protein synthesis in the cytoplasm.
Transcription: occurs because DNA cannot leave the nucleus, therefore mRNA makes
a copy so it can enter the cytoplasm through the nuclear pores and initiate protein
synthesis. The sequence of nucleotides in the mRNA chain represents the information
in the gene, the code for a specific protein to be made. The promoter exists at one end
of the gene, where RNA-polymerase binds to initiate transcription, all of which is
regulated by transcription factors. The terminator is a sequence, which the RNApolymerase recognizes to stop transcription.
Introns: although some portions of DNA do not code for anything (junk DNA), there are
also regions of genes that code for proteins. Introns, and they exist within the coding
sequences called exons. Introns are spliced out during posttranscriptional modification
in a process called RNA splicing. Parts of exons may also be spliced in some cases to
produce an mRNA strand coding for a different protein. This means transcription of one
gene can code for many types of proteins and mRNA’s.
Translation: when the mRNA enters the cytoplasm and binds to a ribosome to initiate
protein synthesis, where amino acids are added on by tRNA molecules according to
their anticodon sequence (sequence opposite to the codons found on the mRNA). Many
ribosomes can act on a single mRNA molecule.
NOTE: transcription and translation are a part of the central dogma, by Watson and
Rough Endoplasmic Reticulum: outside of the nucleus, and dotted with ribosomes,
mostly found in neurons compared to glia and other brain cells. These are also the Nissl
bodies found as stained surrounding the stained nucleus. This is a major site of protein
synthesis, along with free ribosomes, and polyribosomes, which are ribosomes attached
to an mRNA strand. Free ribosomes make the proteins used in the cytosol and rough
ER make the proteins destined to be inserted into the cell or organelle membranes.
Smooth Endoplasmic Reticulum: fills the cytosol and performs different functions in
different locations and in some cases is also connected to the rough ER. One function is
to regulate internal concentrations of substances (ex. calcium). The one furthest from
the nucleus is the Golgi apparatus for post-translational processing and protein sorting.
Mitochondria: enclosed by 2 membranes and contain folds known as cristae with the
inner space known as the matrix. This is the site of cellular respiration, taking in
pyruvate and oxygen, which enter the Kreb’s cycle, to yield ATP (17 molecules per
Neuronal Membrane: a barrier to enclose the cytoplasm inside the neuron from the
fluids existing outside the neuron. This membrane, like other cells has embedded
proteins for transport.
Cytoskeleton: scaffolding inside the cell, giving the cell it’s characteristic shape.
Microtubules, microfilaments, and neurofilaments make up this structure, though they
are not stiff, but dynamic:
• Microtubules: big, straight, hollow pipe, run longitudinally down neurites, walls
are made of smaller braided strands made of globular tubulin monomer units to
form a polymer (resembles pearls connected on a necklace). They are regulated by microtubule-associated protein (MAPs), which anchor them to each other and
parts of the neuron. Changes (tau) are associated with Alzheimer’s.
• Microfilaments: same thickness as the cell membrane, found all over the
neuron but mainly in the neurites, a braid of 2 thin strands (polymers) of actin
involved in changing the cell shape. These are also bound to the membrane of
• Neurofilaments: intermediate sized filaments of neurons, found in all other cells
of the body as intermediate filaments. Consist of multiple subunits organized like
sausage links, where each unit has 3 long protein strands woven together (not
strands of monomers as in microtubules and filaments) making it very strong.
Terminal Button: the end of the axon or axon terminal, from which information is sent
to the synapse and dendrites of other neurons. This contains several vesicles
containing neurotransmitters located near areas high in proteins called active zones.
When the action potential is received, as Ca +ions channels open allowing Ca + ions to
enter to stimulate proteins to fuse the vesicles to the cell membrane and release
(exocytose) the neurotransmitters into the synaptic gap at the active zones. When the
stimulus stops, the Ca are pumped back out to prevent more neurotransmitters from
entering the synaptic gap. Reuptake occurs for neurotransmitters remaining in the gap
or are broken down. Innervation is when an axon terminal comes into contact with
another cell. The cytoplasm here has no microtubules, and many mitochondria due to
Terminal Arbor: when axons branch out on the ends and connect to the same region
on another neuron’s dendrites or soma.
Boutons En Passant: when axons form synapses at swollen regions along their length
and then continue on to terminate elsewhere.
Synapse: the gap between the axon terminal of one neuron and the dendrites of
another where information is passed. Presynaptic events are those that occur before
the synapse in the axon terminal and postsynaptic are those that occur after the
synapse in the dendrites or soma. There are 2 types:
• Electrical Synapse: when the membranes the pre and post synaptic cells are
touching and connected by junctions allowing electrical impulses to flow between
cells uninterrupted for fast transmission.
• Chemical Synapse: more common synapse, when the membranes of pre and
postsynaptic cells are separated by a gap (synaptic gap/cleft). The axon terminal
releases neurotransmitters when the electrical signal is received, which are sent
to the dendrite receptors which stimulates a new electrical impulse equal in magnitude. Transfer of information across the gap is called synaptic
Neurotransmitter: a chemical substance used in neuronal communication at synapses.
It is released from the active zone of the terminal button and diffuses across the
synapse to the dendrite where it binds to its specific receptor protein. There are 2 types:
• Direct: bind directly to a ligand-gated ion channel in the postsynaptic membrane,
which changes the flow of ions in the postsynaptic cell.
• Indirect: work slowly as 1stmessengers, bind to G protein-coupled receptors
which then activate receptors to trigger the generation of 2 ndmessengers such as
cyclic AMP. The 2 ndmessenger then controls ion channels.
Wallerian Degeneration: discovered by English physiologist Waller, that when the
axon is separated from the parent cell body, the axon degenerates and cannot be
sustained. This is because the proteins the axon needs are synthesized in the soma
and shipped over which cannot occur if the connection is lost. This is a way to trace
axonal connections in the brain using stains.
Axoplasmic Transport: the movement of materials down the axon, as determined by
Weiss, where tying a string around the axon interrupted the flow and caused a buildup
of materials on the side proximal to the soma and removing the string allowed the
materials to continue. It was found that the movement was slow until radioactive amino
acids were injected, built into proteins and then observed to the rate it moved into the
axon. Grafstein discovered that along with the slow axoplasmic transport there was also
a fast axoplasmic transport.
Anterograde Transport: movement of materials in the direction from the soma to the
axon. Materials are moved inside of vesicles, which move along microtubules and
kinesin using ATP.
Retrograde Transport: movement of materials in the direction from the axon to the
soma, to provide signals to the soma about changes in the metabolic needs of the axon
terminal. The movement of materials is also done on vesicles moving along
microtubules using ATP but dynein is used instead of kinesin.
Chapter 3: The Neuronal Membrane at Rest
Long Distance Signaling: while telephone wires are copper (good conductor)
suspended in air (bad conductor) and well insulated, electrons can be transferred
extremely quickly, however in the axon, it is not as well insulated, it is surrounded by
salty ions which can also conduct electricity, and the charge is carried by atoms instead
of electrons making it less efficient.
Excitable Membrane: found on cells capable of generating and