School biology notes: Introduction to the structure & functioning of the BRAIN

The BRAIN - what the different parts do, investigating brain function and the dangers if the brain is damaged

 Doc Brown's school biology revision notes: GCSE biology, IGCSE  biology, O level biology,  ~US grades 8, 9 and 10 school science courses or equivalent for ~14-16 year old students of biology

 This page will help you answer questions such as ...

 What is the function of the cerebral cortex?  What is the function of the medulla?

 What is the function of the cerebellum?  What is the function of the spinal cord?

 What is an MRI scanner used for? The consequences of brain injury?

Sub-index for this page

(a) The spinal cord and the main parts of the brain and their function

(b) How can we study the brain? How can this help in medical diagnosis?

(c) What are the causes, risks, consequences and treatment of brain damage

See also An introduction to the nervous system including the reflex arc

(a) The spinal cord and the main parts of the brain and their function

The brain and spinal cord are all part of the central nervous system.

The brain is extraordinarily complex, consisting of billions of interconnected neurones.

Using these interconnected neurones pathways the brain is responsible for the control and coordination of all our complex behaviour - everything that happens to us, either consciously, unconsciously. Its the boss!

Research over many years has shown that different parts of the brain perform different functions.

VERY simplified diagram of the brain!

The brain can be considered to have three main regions

The cerebral cortex

The cerebellum

The medulla


The cerebral cortex of the brain (part of the cerebrum - cerebral hemispheres)

The highly folded cerebral cortex is found in the upper outer regions of the brain and it dominates the mammalian brain both physically and functionally.

The cerebrum is largest part of the brain, rather wrinkly in nature and split into two halves called cerebral hemispheres.

The right hemisphere controls muscles on the left side of your body and the left hemisphere controls the muscles on the right side of your body.

The cerebral cortex is associated with all the higher functions of the brain - in a very real way, it makes you who you are as an individual.

The cerebral cortex is responsible for the coordination of many things including consciousness, intelligence, language, memory, movement and vision.


The cerebellum of the brain

The cerebellum is in the lower part of the brain near where it connects with the spinal cord.

The cerebellum is responsible for conscious movement - muscle coordination and posture-balance.


The medulla oblongata, part of the brain stem

The medulla oblongata is at the base of the brain where the brain connects with the spinal cord.

The medulla oblongata is the lower part of the brain stem.

The medulla oblongata controls unconscious activities like breathing and your heartbeat.

These are bodily functions you wouldn't normally think about - they just happen thanks to the medulla.


The hypothalamus of the brain

The hypothalamus, in the centre of the brain, is involved with keeping body temperature constant - so involved with aspects of homeostasis.

The hypothalamus produces hormones that control the functioning of the pituitary gland.


The pituitary gland in the brain - adjacent to the hypothalamus

The pituitary is a gland that produces many important hormones e.g. those involved in the menstrual cycle. It communicates with the hypothalamus (see above).


The spinal cord

The spinal cord connects the brain to the rest of the central nervous system.

The brain stem links the cerebellum to the top of the spinal cord.

The spinal cord is built of a long column of nerve cells (neurones) that run from the base of the brain down through the spine of your body.

The spinal cord consists of tracts of ascending sensory nerve fibres and descending effector nerve fibres. These of course work together in negative feedback systems and reflex arcs - so any damage to the spinal cord has serious consequences.

At various points down the spine, neurones branch off and connect with all the rest of the parts of the body.

The spinal cord relays all the nerve pulses of information between the brain and the rest of the body.


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(b) How do we study the brain?  How can this help in medical diagnosis?

and the development of diagnostic techniques to help treat patients with brain disorders

We understand quite a lot of how the brain works, but there is still an awful lot we don't know about brain functions.

Because of its complexity and delicate nature, investigation brain function is tricky and difficult to do without great caution (its like a thick jelly).

To investigate brain function we need to 'get inside' the brain and observe in some direct, but safe way, and preferably not by surgical methods - cutting the skull open to examine brain tissue carries a high risk of permanent brain damage!


(i) Patients with brain injuries

Much has been learned historically from people who have suffered in some small way with brain damage - in other words damage to one small part of the brain.

The effect of this brain damage on the patient can tell a clinician what the function of the damaged part of the brain was responsible for.

e.g. if an area at the back of the brain was damaged by a stroke and the patient went blind, you would know that part of the brain was involved with vision.

A stroke in the brain stem or cerebellum of a patient can affect breathing and heartbeat. It can also cause speech impairment, hearing and cause vertigo (difficulty in balancing).

People who have suffered massive brain injury, but survive, would give us some insight, but, would it be ethical to study someone who might not be in a position to grant (informal consent) the brain investigation?

You can study the brains of people who have died - in your will or donor card system, you can leave parts or all of your body for medical research.


(ii) Connecting electrodes to the brain

You can push tiny electrodes into brain tissue and give it a tiny electrical stimulus.

You can then observe what happens on stimulating various parts of the brain.

You can then relate that part of the brain with what happens.

e.g. If you stimulate the part of he brain called the motor area, it causes muscle contraction and movement.

An electroencephalogram (EEG) is a test that detects electrical activity in your brain using small, metal discs (electrodes) attached to your scalp - the electrodes pick up patterns of electrical activity in the brain.

Your brain cells communicate via electrical impulses and are active all the time, even when you're asleep. With electroencephalography you can monitor this activity, which shows up as wavy lines on an EEG recording.

(iii) Modern technology

Non-invasive scanning-mapping techniques external to the body

The advancement in new technology is helping academics research the brain with plenty of spin-offs to help patients with brain conditions. We can now examine the brain without intrusive surgery using various 'high-tech' scanning machines.

A magnetic resonance imaging scanner (MRI machine) is a complex and costly way of producing a very detailed picture of the brain's structure.

MRI uses strong magnetic fields and radio waves to produce a highly detailed image of the nervous system of the brain (and any other part of the body too).

You can monitor the brain's activity while a person is doing particular things e.g. solving a problem, doing a skilled or unskilled physical task or doing a memory test and while they are enclosed in the MRI scanner.

An fMRI scanner (functioning magnetic resonance imaging) is a more advanced MRI scanner which is able to detect increased blood flow in the activated areas of the brain, an MRI scanner cannot.

MRI is a very safe non-invasive technique that doesn't use ionising radiation, so safer than CF scanning and PET scans (both briefly described next).

A CT scanner uses X-rays to produce an image of the main structures of the brain.

However, a CT scanner cannot show the functioning of the imaged parts of the brain.

BUT, the CT scan can show a damaged or diseased part of the brain which can be related to some loss of function by the patient.

e.g. loss of mobility or loss of vision can be related to damaged areas of the brain in the CT scanner image.

PET scanners are much more sophisticated and involve the use of radioactive tracer

Positron emission tomography (PET) scans are used in medicine to produce highly detailed three-dimensional images of the inside of the human body.

PET images can clearly show the part of the body being investigated e.g. brain function, including any abnormal behaviour.

The patient is injected with a radioisotope, whose emitted radiation is monitored by detection screens. The radioisotope (radioactive tracer) atom is incorporated in a molecule that moves around the body e.g. a derivative of glucose. This molecule accumulates in more active cells.

You can actually monitor the patient's brain activity while they are in the PET scanner.

The PET scan can show which parts of the brain are active and behaving normally or abnormally - unusual reduced activity or not functioning at all.

PET scans are so detailed you can investigate brain structure in real time and see how the patient's brain is functioning while they are in the PET scanner.

This means PET scans can be used to study disorders that change the brain's activity like Alzheimer's disease.

Here, certain parts of the brain become less active e.g. the memory region, and the PET scan can be compared with that of a normal brain.

For more details on pet scans see Uses of radioactive isotopes in medicine

PET scans are often combined with computerised tomography (CT) scans to produce even more detailed 3D images, known as PET-CT scans.

PET scans may also occasionally be combined with a magnetic resonance imaging (MRI) scan, known as a PET-MRI scan.

Techniques are getting increasingly sophisticated and costly, but all for the patient's benefit.

Transcranial magnetic stimulation (TMS) uses a magnetic field to change brain activity in targeted areas of the brain.

TMS uses magnetic fields to stimulate selected nerve cell activity and has been used to treat depression.


Footnotes on scanners: Despite the wonderful technology, interpreting these scans for diagnostic purposes is not always clear cut i.e. it can inform to help in a prognosis and affect a treatment decision, but its not always that 'simple'.

One problem is that the brain function observed in the scanner, might not be what you would 'theoretically' observe in real life outside the scanner. The mere fact that you are lying down and enclosed inside the scanner means you are not in an everyday state!

Another problem is that our knowledge is still inadequate in knowing how treat certain brain conditions and we cannot adequately access some areas of the brain - so test results can be hard to fully interpret for the benefit of the patient.

For more see the uses of radioactive materials in medicine notes


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(c) What are the causes, risks, consequences & treatment of brain damage?

As our knowledge of how the brain works increases, so it is possible to devise appropriate treatments for different disorders of the brain.

The brain is so delicate and complex that there are many causes of brain damage.

Sadly, its hard to repair damage to any part of the central nervous system - anything faulty in spinal cord or brain.

Lots of things can go wrong with the central nervous system e.g. physical injuries to the brain or spinal cord from severe impacts in accidents, tumours from pathogen caused mutations, diseases like Alzheimer's and Parkinson's disease.

All of these are difficult to treat, one reason being the difficulty in repairing damage to the neurones in the CNS, the neurones cannot repair themselves and we have not yet devised techniques to repair damaged nerve tissue.

Any operation to remove a brain tumour is tricky, and it is difficult to avoid damage to surrounding areas of otherwise healthy brain tissue.

Such damage can leave the patient with problems with speech or vision.

In some cases, no treatment is impossible e.g. it is not possible to remove tumours growing certain regions of the brain.

Surgery on a patient with spinal cord damage risks further damage to the spinal cord, which can cause permanent paralysis - loss of movement capability because nerve signals from the brain can't get through to the effector cells.

Neurones in the nerve systems cannot readily repair themselves and medical science hasn't found a way yet to repair nerve tissue.

Cell differentiation is the process by which a less specialized cell becomes a more specialized cell type. Once neurones have differentiated they don't undergo mitosis - they can't divide to replace lost neurones.

Medical research scientists are investigating the use of stem cells to replace damaged tissues of cells in the nervous system - the idea being to get stem cells to differentiate and change into neurones.

The use of stem cells raises ethical issues - the use of embryonic stem cells offends many people because destroying an embryo is destroying a potential life. Others would argue curing somebody of a very disabling medical condition should override other moral considerations - a tricky one! and lots more dilemmas to come as medical science gets cleverer and cleverer!

Any treatment of a central nervous system disorder carries risks of further permanent damage.

A stroke in the brain may be caused by a blocked artery or the leaking or bursting of a blood vessel causing brain damage. Some people may experience only a temporary disruption of blood flow to the brain. The former is much more serious and can lead to permanent brain damage.

After a stroke, depending on which area of the brain is affected, you can be left with paralysis down one side of your body - mobility problems, speech, vision and memory impairment.

If treatment is initiated rapidly, its amazing how good patient recovery can be.

Parkinson's disease is a progressive disease of the nervous system characterised by involuntary shaking of the body - tremors, muscular rigidity, and slow imprecise movement. It mainly affects middle-aged and elderly people. It is caused by the brain becoming progressively damaged by loss of nerve cells over a period of many years.

Although there's currently no cure for Parkinson's disease, treatments are available to help reduce the main symptoms and maintain quality of life for as long as possible.

These include:

supportive treatments such as physiotherapy and occupational therapy


in some cases, brain surgery

electrical stimulation using tiny electrodes has been used to reduce muscle tremors in nervous system disorders like Parkinson's disease.

Serious head injuries from a physical impact to the head in an accident can lead to brain damage.

Alzheimer's disease is a progressive degenerative condition of the brain, which means the symptoms develop gradually over many years and eventually become more severe.

It affects multiple brain functions e.g. memory problems, confusion, disorientation and getting lost in familiar places, difficulty planning or making decisions, problems with speech and language, problems moving around or performing self-care tasks and personality changes. Its basically the brain degenerating as you get older and difficult to treat.

Spinal cord injuries in an accident can cause paralysis of the lower body.

Surgery for a spinal cord injury carries the risk of permanent and greater injury e.g. paralysis.

Brain cancer tumours will cause disruption of brain function and the surgery to remove them carries high risks of further brain damage.

Depending on the part of the brain affected where the tumour is growing, some tumours can be treated with radiotherapy or chemotherapy, other tumours can be removed surgically, but others cannot be dealt with at all.

Since you cannot be always sure of completely removing all of the cancerous tissue of a tumor, post-surgery treatment may include radiation therapy or chemotherapy.

In removing a brain tumour you might, however inadvertently, damage other areas of the brain adjacent to where the tumour was.

As with any invasive surgery, there is always a risk of infection.

Whatever the treatment on offer, you have to make a decision based on benefits (potentially increasing life span) versus risk (brain damage and limited capability of life).

Medical scientists are always looking for safer and more effective treatments e.g.

monoclonal antibodies and gene therapy might used to treat brain cancer,

and stem cell culture techniques may help to repair damaged nerve tissue.

Boxers are particularly susceptible to brain damage because of the repeated bangs to the head. Over a period of time brain damage can accumulate as nerve cells are destroyed.


The sheer complexity of the brain and its delicate nature means any procedures like surgery that impact directly on the brain does increase the risk of brain damage. With intrusive procedures the risk of brain damage is always there and its effect on brain function e.g. inhibited limb movement, speech problems etc.

BUT, it may be the case where you are balancing risk of brain damage versus saving someone in a life threatening situation - difficult decisions!


See also An introduction to the nervous system including the reflex arc  gcse biology revision notes

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