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The HOPES Brain Tutorial (Text Version)

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The brain is a complex organ with many components. These multiple components work together to maintain basic life processes, like breathing, body temperature and blood pressure, as well as higher functions like creative thought and emotions. This is an introduction to some of the basic terms used when describing the brain and its major parts.

Central Nervous System^

The brain is a part of the central nervous system (CNS). It receives information from other parts of the body via the spinal cord and the peripheral nervous system and uses this information to control the body.

Brain Cells^

The brain is made up of two types of cells: neurons and glial cells. Neurons are nerve cells. They typically consist of dendrites that receive information, a cell body, and an axon that is used to transmit information throughout the nervous system. Glial cells have multiple functions, which include structurally supporting neurons, repairing the CNS, and regulating the biochemical balance of the brain. The blood-brain barrier is composed of astrocytes, a specific type of glial cell. This barrier prevents many substances in the blood from entering the brain.


The top of the brain is called the superior side, and the bottom is called the inferior side. Structures near the center are referred to as medial, and farther away from the center are referred to as lateral. The term anterior means ‘in front,’ while posterior means ‘behind.’


The brain is surrounded and protected by the rigid, bony skull and three membranes, or meninges. The tough, fibrous outer membrane is the dura mater. The intermediate membrane, named the arachnoid, is thin and weblike. The pia mater is the innermost covering and is the most delicate. It is molded to the shape of the brain. The cerebrospinal fluid (CSF) surrounds the brain and spinal cord and flows through open chambers in the brain, known as ventricles, and out an opening to the spinal cord. The brain actually floats in the shock-absorbing CSF, and is thus protected from trauma. The CSF also brings nutrients to the brain and removes wastes.

Cerebral Cortex^

The outermost and top layer of the brain is the cerebral cortex. The cerebral cortex is the most recently evolved and most complex part of the brain. As one moves lower into the brain, the parts have increasingly primitive and basic functions and are less likely to require conscious control.

Brain Hemispheres^

The cerebral cortex is divided down the middle, from front to back, into hemispheres, or halves. Each hemisphere has different functions. The left side of the cerebral cortex controls the right side of the body and speech. The right side controls the left side of the body and the perception of spatial relationships, such as where one’s foot might be located in relation to the ground.

Brain Tissue^

White matter, which consists of neuronal axons, makes up the inner core of the hemispheres. The outer layer is made up of gray matter, which consists of neuron cell bodies. The cortex contains ridges (gyri) and valleys (sulci).

The hemispheres are separated by a deep groove, but are connected deep in the brain by the corpus callosum, a thick bundle of nerve fibers through which information is passed between the left and right hemispheres of the brain.

Lobes of the Brain^

Two sulci – the central sulcus and the lateral sulcus – are used to divide each hemisphere into four sections known as lobes: the frontal lobe, parietal lobe, temporal lobe, and occipital lobe. (Below follows more information on each lobe.)

All of the lobes also contain areas for which specialized functions have not yet been identified. These areas are known as the association cortex and are thought to be involved in complex, higher-level mental activity.

Frontal Lobe^

The frontal lobe has a major role in the planning and execution of movements. It contains the pre-frontal, pre-motor and motor areas, listed from front to back.

The pre-frontal cortex is particularly associated with higher level thought, decision-making and planning. It has a significant inhibitory role over impulses and actions. People with HD sometimes have degeneration of the prefrontal cortex, leading to increased impulsiveness and changes in behavior.

The pre-motor and motor cortices process and transmit information regarding body movement. There are two pathways connecting the motor cortex and the basal ganglia to coordinate movement. As nerve cells in the basal ganglia die as a result of HD, both of these pathways are eventually damaged.

Parietal Lobe^

The parietal lobe is separated from the frontal cortex by the central sulcus. It lies posterior to (behind) the frontal lobe and superior to (above) the temporal lobe. The parietal lobe contains the primary sensory cortex through which sensations, such as touch and pressure, are felt. In addition, it has a key role in spatial orientation and information processing.

Temporal Lobe^

The temporal lobe is located inferior to (below) the frontal and parietal lobes. It is primarily involved with auditory processing and memory.

Occipital Lobe^

The occipital lobe is located posterior to (behind) the temporal lobe and is the visual center of the brain. Visual information from the eyes is processed here.

Limbic System^

Fig AB-16: Limbic System

The limbic system wraps around the brain stem and is beneath the cerebral cortex. It is a major center for emotion formation and processing, for learning, and for memory. The limbic system contains many parts, including the cingulate gyrus, a band of cortex that runs from the front of the brain to the back, the parahippocampal gyrus, the dentate gyrus, and most notably, the hippocampus and amygdala. The hippocampus is involved in memory storage and formation. It is also involved in complex cognitive processing. The amygdala is associated with forming complex emotional responses, particularly involving aggression. The limbic structures are also connected with other major structures such as the cortex, hypothalamus, thalamus, and basal ganglia.

Fig AB-17: Limbic System (Cross-Coronal Section)

HD affects the communication of the limbic system with the frontal lobes by damaging the caudate nucleus, a relay station between them. As the connections degenerate, the activity-initiating frontal lobes are disconnected from the emotion processing center of the brain, producing apathy, a common symptom of HD.

Basal Ganglia^

Fig AB-18: Basal Ganglia

Deep in the gray matter of the brain are the basal ganglia. The basal ganglia, along with the cerebral cortex and diencephalon, compose the region of the brain called the forebrain. The basal ganglia connect to the cortex and thalamus and organize muscle-driven “motor” movements of the body. They are the parts of the brain most affected by HD and many of the symptoms of HD result from damage to them.

The major divisions of the basal ganglia are the caudate nucleus, putamen, globus pallidus and substantia nigra.

Caudate Nucleus^

The caudate nucleus is a collection of neuronal bodies that connects to many parts of the brain. Together with the putamen, it comprises the neostriatum. Its neurons are most affected by HD, and the deterioration of its connections result in behavioral changes and the inability to control emotions, impulses, thoughts or movements. Damage to the caudate may also result in the inability to experience intense feelings of embarrassment, guilt or shame. Individuals with caudate damage may become “stuck” on one idea or activity, resulting in a lack of self-awareness and inability evaluate their own behavior. This decreased self-awareness may cause individuals to be unaware of mistakes that are evident to others. It may also impair their ability to experience a range of subtle emotions and see other points of view, making social and personal relationships more difficult.

The caudate organizes and filters information that is sent to the frontal lobe, particularly information from the limbic system. Caudate malfunction can affect the functioning of the frontal lobes through a lack of information or an improper amount of information. The caudate assists the frontal lobes in prioritizing the transfer of information to other parts of the brain. Damage to the caudate makes it difficult for people with HD to prioritize tasks and organize their day, as well as to handle many simultaneous stimuli. Along with the putamen, the caudate also controls voluntary movement.


The putamen and caudate are collectively known as the neostriatum. Together, they control voluntary movement. The cells of the neostriatum are the first to die as a result of HD, disrupting both the indirect and direct pathways controlling movement. The death of neostriatal neurons in the direct motor pathway leads to the under-stimulation of the motor cortex, causing the slow speed of motor movement often seen in persons with HD. The death of neostriatal neurons in the indirect motor pathway leads to over-stimulation and chorea.

(For more information about these motor pathways, click here.)

Fig AB-19: Basal Ganglia Pathways

Neostriatum / Striatum^

The neostriatum, comprised of the caudate and putamen, transmits information to the subthalamic nuclei that modulate motor control. Together, the neostriatum and globus pallidus make up the striatum.

Globus Pallidus^

The globus pallidus relays information from the caudate and putamen to the thalamus and is part of the striatum. In HD, both its external and internal regions suffer neuronal loss. Gliosis, the excessive growth of cells that normally support and protect neurons in the globus pallidus, is implicated in juvenile HD. Individuals who experience rigidity rather than chorea may also have damage to the globus pallidus.

Substantia Nigra^

The substantia nigra is generally considered part of the basal ganglia due to its similar neuronal structure and related function of motor control, but may also be considered part of the midbrain due to its location. It contains most of the neurotransmitter dopamine in the brain and also participates in motor coordination.


Fig AB-20: Diencephalon

The diencephalon is part of the forebrain and is located above the midbrain. It contains two major organs: the thalamus and the hypothalamus.


Fig AB-21: Thalamus

The thalamus is a major relay center to the cortex for all sensations except for smell. It consists of many nuclei, including the lateral geniculate nucleus, which transmits visual information, and the medial geniculate nucleus, which transmits auditory information.


Fig AB-22: Hypothalamus, MFB, & Pituitary Gland

The hypothalamus controls many functions including hunger, thirst, pain, pleasure and the sex drive. Another key function of the hypothalamus is to regulate the pituitary gland, which in turn, regulates hormonal levels in the body.

Medial Forebrain Bundle^

The medial forebrain bundle (MFB) is a bundle of axons that passes through the hypothalamus, and is rich in dopamine neurons. When stimulated, the neurons produce reinforcing, pleasurable feelings.>

Pituitary Gland^

The pituitary gland is attached to the inferior hypothalamus via a stalk containing blood vessels and neurons. The pituitary gland is divided into two distinct regions, the anterior and the posterior pituitary. The posterior pituitary is composed of neural tissue and considered an extension of the hypothalamus, while the anterior has a more extensive endocrine role, meaning that it regulates the levels of hormones in the body.


Fig AB-23: Cerebellum

At the back of the head, in between the brain stem and cerebral cortex, is the cerebellum. The cerebellum controls balance and coordination and is where learned movements are stored. Purkinje neurons that control the refinement of motor movements are found in the cerebellum. The cerebellum receives input from many parts of the brain (especially from granule cells) regarding pressure on the limbs, limb movement, and the position of the limbs in space. The dentate nucleus, located within the cerebellum, coordinates skilled movement. Damage to this region, as a result of HD, causes movements that were once smooth and refined to become jerky. Movements must also be constantly relearned.

Reticular Activating System^

Fig AB-24: Reticular Activating System

The reticular formation aids in regulation of the sleep-wake cycle as well as the level of arousal when awake.


Fig AB-25: Brainstem

The bottom-most part of the brain is the brain stem. The brain stem is attached to the spinal cord. It relays information between parts of the brain or between the brain and body and regulates basic body function. It is made up of the midbrain, medulla and the pons.

Midbrain: The midbrain contains the major motor supply to the muscles controlling eye movements and relays information for some visual and auditory reflexes.

Pons: The pons is a mass of nerve fibers that serves as a bridge between the medulla and midbrain above it. The pons is associated with face sensation and movement.

Medulla: The medulla (also known as the medulla oblongata) is located at the base of the brain stem and controls many of the mechanisms necessary for life, such as heartbeat, blood pressure and breathing.

Build A Brain^

Now that we’ve finished our tour of the brain, let’s see how all the different sections fit together.

Fig AB-26: Build A Brain, Step 1
Fig AB-27: Build A Brain, Step 2
Fig AB-28: Build A Brain, Step 3
Fig AB-29: Build A Brain, Step 4
Fig AB-30: Build A Brain, Step 5
Fig AB-31: Build A Brain, Step 6
Fig AB-32: Build A Brain, Step 7
Fig AB-33: Build A Brain, Step 8
Fig AB-34: Build A Brain, Step 9
Fig AB-35: Build A Brain, Step 10
Fig AB-36: Build A Brain, Step 11
Fig AB-37: Build A Brain, Step 12


We hope that this tutorial has proven useful and informative to you. To leave comments or feedback, click here. Thanks for viewing the HOPES brain tutorial.

This tutorial is brought to you by:

The Huntington’s Outreach Program for Education, at Stanford

Text by Vinita Kailasanath
Drawings by Kristel Bugayong and Shawn Fu
Programming & Design by Shawn Fu

Special Thanks to:
Belinda Fu, Bill Durham, Ron Barrett, and the rest of the HOPES team for their countless edits & unending patience!

Images Adapted from…

Bloom, F.E. & A. Lazerson. Brain, Mind, and Behavior. 2nd Ed. New York: W.H. Freeman, 1988.

Nieuwenhhuys, R., J. Voogd, & C. Van Huijzen. The Human Central Nervous System: A Synopsis and Atlas. 2nd Ed. Berlin: Springer-Verlag, 1981.

Nolte, J. & Jay Angevine, Jr. The Human Brain: in Photographs and Diagrams. 2nd Ed. St. Louis: Mosby, 2000.

Ornstein, R., R.F. Thompson, & D. Macaulay. The Amazing Brain. Boston: Houghton Mifflin, 1984.

Purves, W.K., D. Sadava, G.H. Orians, & H.C. Heller. Life: The Science of Biology. 6th Ed. Gordonsville: W.H. Freeman, 2001.

Sherwood, L. Human Physiology: From Cells to Systems. 4th Ed. Pacific Grove: Brooks/Cole, 2001.

Copyright 2003, HOPES

-V. Kailasanath & S. Fu, 7-15-03