Foundational Concepts in Neuroscience

Photo by Jez Timms |
Photo by Jez Timms |

The following article is part one of our four-part introduction to neuroscience series. The articles will be released separately, but together will seek to produce a coherent story of the brain. We will begin at the cellular level; then explore the five senses; then discuss the systems involved in generating movement; and finally we will end with a discussion of emotion, language, and consciousness.

Even an abridged functional neuroanatomical atlas of the human brain could fill numerous dictionary-thick textbooks. The following articles will present a truncated rendering of the abridged version of human functional neuroanatomy. By definition, our much-abridged version will be necessarily incomplete. We will provide citations for the unabridged source material so that the interested reader may investigate the various topics further. We will attempt to maintain a clear and accurate description of the functional neuroanatomy of the human brain, but we readily admit that simplification is the next-door neighbor of oversimplification, and that the former shares the risks of inaccuracy inherent to the latter.


By BruceBlaus | CC License
By Bruce Blaus | CC License

Our abridged version of the functional neuroanatomy of the human brain begins with two types of cells known as neuronal and glial cells. Neurons and glia account for the vast majority of cells that form the central nervous system (CNS).1 The CNS includes the brain and spinal cord, with the spinal cord acting as a go-between, connecting body and brain. Neurons use chemicals known as neurotransmitters to trigger action potentials (electrical signals) in other neurons. Action potentials propagate down the neuron’s axon (a long, thin projection off of the neuronal cell body) and start the whole process over again, releasing new neurotransmitters and thus passing on the electrochemical signal.2

Glial cells support the hardworking neuronal cells. Glial cells insulate axons with a material known as myelin, provide oxygen and nutrients to neurons, and destroy pathogens and old neurons.1 For the abridged version of our functional neuroanatomical atlas, neuronal and glial cells will complete our investigation of the cellular level of neurological organization.

Anatomical Terms of Location

Derived from Bachforelle Zeichnung |Public Domain
Derived from US Fish & Wildlife | Public Domain

A quick note regarding neuroanatomical nomenclature: the adjective anterior indicates that a structure is towards the front (face side) of the brain, while posterior indicates that the structure is towards the back. Superior indicates that a structure is towards the top (crown) of the head, while inferior means that the structure is towards the bottom of the brain. In the brain, dorsal can be considered synonymous with superior (like a dorsal fin), and ventral is synonymous with inferior. Medial suggests that a structure is towards the middle of the brain, while lateral indicates that a structure is towards the outside of the brain. A final word of clarification: these descriptors are often used to describe a structure’s relationship to another structure. For example, the brain is superior to the spinal cord.

Brainstem, Cerebellum, Interbrain, and Cerebral Cortex

Labeled for reuse with modification. Retrieved from Google image 01/13/15. Image credit attributed to PIXABAY p-303186/?no_redirect
Labeled for reuse with modification |

Moving from the microscopic cellular level to the macroscopic structural level, we can subdivide the brain into brainstem (most inferior), cerebellum, interbrain, and cerebral cortex (most superior). For some commonly used structures we will use a terminological shorthand to improve recall. For example, the brainstem can be thought of as the “central processing unit” (CPU) of the brain. A computer’s CPU carries out the instructions of a given computer program by performing basic algorithmic operations. Similarly, the brainstem/CPU synthesizes and executes instructions provided by the higher brain structures and mediates between the body and brain.3 The mnemonic device of physically joining the structure and the analogical construct with a slash (/) is meant to help the reader recall the original description of a given structure’s function without having to return to the original context.

The brainstem/CPU executes the neurophysiological programs that regulate heartbeat, breathing pattern, metabolism, sleep-wake cycle, and general alertness.1 Higher cortical “programs” can augment the output of the brainstem/CPU based on environmental need, dialing the aforementioned processes up or down as required. The brainstem/CPU also serves as a conduit between the body and the rest of the brain, transmitting vital input and output messages between the two.

In general, the roles of each subdivision increase in complexity as one moves more superiorly. Sitting next to the brainstem/CPU, the cerebellum (Latin for “little brain”) is primarily involved in motor control, coordination, and balance. Superior to both the brainstem and the cerebellum, the interbrain consists of structures such as the thalamus, the basal ganglia, the hypothalamus, and the pituitary gland.1 The thalamus relays, filters, and processes sensory and motor information from the body to the brain and from one part of the brain to another;2 because of this role we will use the mnemonic thalamus/relay to recall the thalamic function. The basal ganglia (BG) stores and helps to execute the cognitive and motor patterns that allow for habitual and learned behavior;1 because of this role we will use the mnemonic BG/pattern-generator.

The hypothalamus helps to regulate metabolic and autonomic functioning in addition to its role in modulating neurohormonal release from the pituitary gland.1 The autonomic nervous system is comprised of the sympathetic and parasympathetic nervous systems. If the human body were a car, then the sympathetic nervous system (SNS) would be the gas pedal, responsible for increasing heart rate and blood pressure, dilating bronchioles (airways), and diverting blood to skeletal muscles to generate the “fight-flight-or-freeze” response.1 We will use the mnemonic SNS/gas to recall the sympathetic nervous system. The yin to the SNS/gas’s yang is the parasympathetic nervous system (PSNS), which decreases heart rate, increases intestinal motility and digestion, and increases glandular (sweat, tears, etc.) activity; because of its role in “rest-and-digest” (or “feed-and-breed”) functions we will use the mnemonic PSNS/brake. Importantly, each system is never all the way off or all the way on; homeostasis depends on a balancing act between the two.2

Brain_MedialReturning to the hypothalamus and its capacity to regulate the autonomic nervous system (SNS/gas and PSNS/brake), let’s use the mnemonic hypothalamus/cruise control to recall its role in increasing or decrease the metabolic and autonomic “speed” of the body.

And finally, superior to the brainstem/CPU, cerebellum, and the interbrain sits the cerebral cortex (“cortex” for short). The cortex can be divided into four lobes: the occipital, temporal, parietal, and frontal lobes. The cortex is involved in higher-order processing of sensory, emotional, and abstractive information.

Now that we have reviewed the foundational components of the human brain, we will spend the majority of remaining of our series examining how the CNS organizes itself into neuroanatomically distinct, but highly integrated, functional units.

Wake Up!

As it turns out, keeping the brain awake is a tremendously complex task. The ascending reticular activating system includes a variety of nuclei (i.e. groups of neurons that have similar functions) and plays a central role in maintaining wakefulness.1

Neurons in the lateral tegmental group and the locus coeruleus in the brainstem send norepinephrine-releasing axonal projections throughout the cortex.1 Norepinephrine is a catecholamine neurotransmitter that promotes attention and alertness.4

Serotonin, another neurotransmitter, is also widely distributed throughout the cortex by a set of brainstem/CPU nuclei known as the raphe nuclei. Serotonin’s role in maintaining the waking state is somewhat controversial, but current evidence suggests that the raphe nuclei are more active during wakefulness, suggesting that serotonin is involved in the maintenance of the waking state.4

The basal forebrain (also known as the “basal nucleus of Meynert”) and the brainstem/CPU send acetylcholine-releasing projections throughout the cortex. Acetylcholine plays a central role in maintaining attention and vigilance. Acetylcholine also is intimately involved in learning and memory.4

The ventral tegmental area contains neurons that project dopamine-releasing axons throughout the cortex. Dopamine has many functions within the CNS, including the modulation of reward, facilitation of movement, and the production of general salience (assigning subjective importance to various stimuli);1 because of the aforementioned roles in the CNS we will recall dopamine (DA) with the mnemonic DA/motivation. And because the ventral tegmental area (VTA) contains DA/motivation-releasing neurons, we will use the mnemonic VTA/motivator for recall. In regards to our current discussion of wakefulness, it is important to be aware that DA/motivation is particularly important to the maintenance of alertness.1

The hypothalamus/cruise control contributes the neurotransmitters orexin and histamine to the mix.1 Histamine helps to maintain the level of arousal necessary for wakefulness. Thus, first-generation antihistamines produce sleepiness as a side effect of blocking histamine receptors. Orexin is a powerful neuropeptide that preserves wakefulness. The most common form of narcolepsy, a disorder characterized by abnormal sleepiness, is caused by a deficiency of orexin.1

The hypothalamus/cruise control also contains a region known as the suprachiasmatic nucleus (SCN). The SCN establishes our circadian rhythm, or natural sleep-wake rhythm, based on the amount of light that makes contact with the retina within our eye.1 In the absence of retinal light stimulation (i.e. at night), the SCN triggers the pineal gland to produce melatonin. Melatonin promotes sleep and is often used as an over-the-counter sleep aid.

Photo by Blake Richard Verdoorn |
Photo by Blake Richard Verdoorn |

A final piece in the wakefulness puzzle is the chemical adenosine. Adenosine is a byproduct of cellular metabolism in the brain and builds up over the course of our wakeful period.2 When adenosine binds to adenosine receptors it contributes to our experience of drowsiness. The popular drug caffeine is an adenosine receptor antagonist (among other things) and blocks the natural sedating side effect of adenosine accumulation throughout the day.1

This completes the first part of our four-part introduction to neuroscience series. In our next article, we will explore the five senses and why our sense of smell is such an emotionally powerful and evolutionarily ancient sense.


  1. Squire LR, ed. Fundamental Neuroscience. 4th ed. Amsterdam; Boston: Elsevier/Academic Press; 2013.
  2. Haines DE, Ard MD, eds. Fundamental Neuroscience for Basic and Clinical Applications [study Smart with Student Consult]. 4th ed. Philadelphia: Elsevier, Saunders; 2013.
  3. Vanderah TW, Gould DJ, Nolte J. Nolte’s The Human Brain: An Introduction to Its Functional Anatomy. Seventh edition. Philadelphia, PA: Elsevier; 2016.
  4. Baynes J, Dominiczak MH. Medical Biochemistry.; 2014. Accessed July 9, 2016.

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