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A Guide to Your Immune System: How it Works, What It Does and How It Keeps Us Healthy

The human body is a very robust, complicated system. In the United States, the average life span is about 80 years, which is an astounding feat when we consider that the body is exposed to thousands of organisms that could subvert our bodies’ normal functions and ruin this complicated system.

We have our immune systems to thank for keeping us running. While these systems protect us on a daily basis, most of us lack a working knowledge of what the immune system does and how it works. It’s not important to be a scientific expert, but a brief working knowledge helps one understand inflections, the flu, colds, etc. This information will help explain some of the basics regarding immune system function and is also of great value when attempting to understand a doctor’s comments when and if needed.

The immune system is even more complicated than the heart, which uses electrical signals to cause roughly one billion heart beats over the course of one’s life. It’s also more complicated than the kidneys, which filter blood. It is more complicated than almost every other part of the body. The immune system is complex because it is a coordinated whole-body system.

What does the immune system really do?

The immune system is built to recognize the difference between self and non-self. The self is anything that is naturally in the body, while non-self is a particle or cell that is not naturally present in the body. A properly functioning immune system doesn’t attack other parts of the body, but does attack anything foreign to the body. Alternatively, it has been suggested that the immune system determines when the body is in danger, for instance when there are cancerous cells or a viral infection. In either case, the immune system’s primary job is to protect our bodies from anything that can cause them harm.

What Exactly is the Immune System?

The immune system is a whole-body system affecting all of our organs. It includes:

  • The skin, which is a physical barrier against foreign particles.
  • The , which circulates immune cells and provides areas (, the , in the gut) where immune cells can communicate with each other.lymphatic systemlymph nodesspleen Peyer’s Patches
  • The thymus, located in the upper part of the chest, where some types of immune cells mature.
  • Bone marrow, where other types of immune cells are produced and mature.

The immune system has many parts, many of which circulate throughout the body. There are a number of different types of cells that work in this coordinated effort. Some of these may sound familiar to those who have recently had a complete blood count (CBC) per the doctor’s recommendation. These cells provide medical professionals with information on how the immune system is functioning and include:

  • Granulocytes, which include neutrophils, eosinophils, basophils, and mast cells. These cells have many different properties, including clearing the body of debris, killing parasites, and producing inflammatory responses.
  • Lymphocytes, which are a number of different cell types that work around the body with many different functions. For example, B cells produce antibodies and T cells can kill infected cells or they can help other immune cells function.
  • Monocytes, include macrophages and dendritic cells. These cells are called antigen presenting cells, and can stimulate lymphocytes to produce an immune response. Macrophages also help clear foreign particles from our bodies.

For these components to coordinate, they must communicate through either direct or indirect contact. In direct communication the cells touch one another to convey information. This produces signals to both cells, prompting one to perform a function or change its action. There is also indirect communication, in which a cell releases molecules as a way to send information to other cells. These molecules are called cytokines or chemokines and they can travel long distances in the body like messengers, causing other cells to react.

How Does the Immune System Protect Us?

Our cells have molecules on their surface called Human Leukocyte Antigens (HLA molecules) which signal to the immune system that they belong in the body. These molecules are the most variable of all human proteins, meaning that each person has a different mix that make their “HLA type” different from others.

Examining HLA molecules is one of the ways in which the body can locate foreign particles. When a cell becomes infected, it cuts up parts of the antigen (the foreign particle) and includes them in its HLA molecule. This new HLA type is called antigen presentation, and it’s one of the primarily ways the immune system distinguishes between self and non-self cells. When immune cells encounter a cell with a foreign HLA type, they start an immune response to rid the body of the invader.

When doctors talk about transplant matches, they are really talking about matching HLA types between the donor and the recipient. Since HLA molecules help the immune system determine between self and non-self, a difference in HLA molecules can trigger transplant rejection.

The Innate Immune Response

The innate immune response is the first step in protecting our bodies from foreign particles. It is an immediate response that’s “hard-wired” into our immune system. The innate immune response is non-specific immunity against infection-carrying viruses, meaning that it’s generalized. Here are some of the components of the innate response:

General barriers to infectioninclude:

  • Physical (skin, mucous, tears, saliva, and stomach acid)
  • Chemical (specific proteins found in tears or saliva that attack foreign particles)
  • Biological (microbiota or good bacteria in the gut that prevents overgrowth of bad bacteria)

Antigen-independent responses to foreign particles:

  • Bacteria, viruses, and parasites contain molecules called pathogen associated molecular patterns (PAMPs) that are not made in our bodies. Some immune cells, like antigen-presenting cells, have pattern-recognition receptors (or PRPs) on their surface so that they can recognize PAMPs. When an immune cell comes into contact with a PAMP, it produces a response to protect the body. Often, it stimulates cells to produce molecules like interferons which make the cell inhospitable to pathogens
  • The can label, neutralize, and destroy pathogens, as it involves more than 20 different proteins and cell types. The complement system can also initiate several responses that appear in the body as illness symptoms, such as inflammation. People who are born with complement deficiencies are often more susceptible to bacterial infection.complement system

Cellular response to foreign particles:

  • Cytokine or chemokine signals recruited different cells to an infection site: Neutrophils and macrophages ingest foreign organisms and kill them, natural killer cells destroy infected cells, and eosinophils help kill parasites.

The symptoms that surface with an illness (fever, inflammation, achiness, runny nose, etc.) are actually the effects of an innate immune response. Our bodies react in this way to make it difficult for infections to spread within the body. For example, acute inflammation is the result of increased blood flow into the infected area, as well as the swelling of some cells.

The Adaptive Immune Response

The innate immune response leads to the pathogen-specific adaptive immune response. While this response is more effective, it takes time to develop—generally about a week after the infection has occurred.

During an innate immune response, antigen-presenting cells ingest foreign particles then move toward the lymph nodes. While there, the antigen-presenting cells interact with lymphocytes. Lymphocytes (B cells and T cells) have proteins on their surface that match with specific antigens. When a lymphocyte recognizes an antigen brought by an antigen-presenting cells, it begins the adaptive immune response. Once activated, the lymphocytes undergo multiple rounds of mutation and expansion until they can quickly recognize the specific foreign particle launching an attack on the body. There are two types of lymphocytes: B cells and T cells.

B cells (or plasma cells) produce antibodies, which are a type of protein secreted by the lymphocyte. Though antibodies are very small compared to bacteria and viruses, they are highly specific and attach tightly to pathogens. Large numbers of antibodies can coat the pathogen and prevent it from functioning properly. They are then able to mark the pathogen so that immune cells know to destroy it.

There are two main types of T cells: Killer T cells and Helper T cells. As one might imagine, Killer T cells recognize infected cells and kill them by puncturing the cell membrane. Helper T cells, on the other hand, aid other immune cells by releasing cytokines. This coordinates the immune response and tailors it to the specific infection.

Once the body creates an antigen-specific lymphocyte to combat a particular virus or bacteria, it will always be able to defend against that virus. While most of the antigen-specific cells die off after an infection goes away, a small number remain and become memory cells. So, the next time the body encounters the same infection, instead of waiting a week to produce a highly-specific, targeted attack, it can now produce this response in a matter of hours or days. This is the why vaccines can protect individuals against specific illnesses. A small amount of the disease is inserted into the body through the vaccine so that the immune system can build up antigen-specific cells to defeat it. When the body encounters that illness in the future, it will remember the specific virus and quickly defeat it.

When the Immune System Malfunctions

Since the immune system affects so many of our bodies’ processes, it’s not surprising that immune system function or dysfunction is an issue in virtually every disease.

The immune system is most notably involved in autoimmune diseases. Autoimmune diseases occur when the immune system mistakenly recognizes our own body’s cells as foreign or dangerous. In diseases such as multiple sclerosis, rheumatoid arthritis or Crohn’s Disease, the immune responses that would normally protect the body from a foreign invader mistakenly launch an attack on an otherwise healthy body. The ability to recognize “self” fails. The cause of immune dysfunction is unclear, but it appears that genetics, environment, and long-term chronic inflammation state can all cause autoimmune diseases.

A similar breakdown occurs in allergies and asthma, except in this case the mistake immune response is against non-harmful foreign particles such as dust or peanut proteins. In these cases, the immune system fails at recognizing the particle as non-harmful, so it mounts an unwanted attack causing cold-like symptoms such as coughing, sneezing or tear production. In the worst case scenario, the allergic inflammation can be so severe that the body’s airways close or the person goes into shock.

The immune system also plays a role in cancer. Since the immune system can find and attack tumor cells, when this function breaks down it can cause cancers and tumors to develop. There are also cancers of the immune system (leukemias and lymphomas), that cause immune cells to grow uncontrolled. Researchers are currently exploring experimental therapies in which they attempt to prime the immune system to recognize tumor cells and mount a specialized attack to help clear the cancer.

These are just a few examples of how a malfunctioning immune system can cause big problems for the body. Not only does the immune system protect us from viruses and bacteria, it also makes sure our cells aren’t growing uncontrolled.

Additional Resources

There are literally volumes of work and hundreds of thousands of articles that describe the immune system and the many ways it functions in the body. For a more in-depth look at the immune system, here are a few good resources.

National Cancer Institute

The Immune System

Howard Hughes Medical Institute

Immunology Primer


The American Academy of Allergy, Asthma, and Immunology


Last Updated: 1/16/17 

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