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The molecular switch from welcoming to attacking a pathogen?

  1. Mar 2, 2016 #1
    I watched many videos and read bunch of answers about this, but I was having a hard time finding an answer to this one point:

    What is the exact moment an organism realizes that it is under an attack? I understand that there might be a few different types of ways a body can react too.

    So far, this is my understanding:
    - Certain amounts of white cells swim around the body, scanning for different movement and chemical "patterns".
    - They do this by making their own proteins from the DNA that they are being coded from, which look for these "patterns".
    - When there is anything that they don't recognize, they make the white blood cell attack.
    - Additionally they are able to call other cells "for help", and they all collectively absorb pathogens and try to dissolve them with their enzyme proteins (with a little help from antibody proteins that bind and neutralize the pathogens).
    - Plus some of them can remember these patterns by retaining the genetic information of the pathogens, through which they generate the appropriate proteins.

    I hope I presented the "simplified" picture as good as possible.

    My question is:
    What is the exact thing that happens when the antibody protein "recognizes" the antigen entity? Or better, "how" does the antibody "make" the cell (or some other cell) attack?

    Does it send some kind of a signal back to the cell (or nucleus) in some way? If yes, in what way?
    Once that "signal" is received by the cell/nucleus, would then the nucleus start coding for new proteins that will do a different action for the cell to get rid of the antigen?
    Or is this all automatically done by the same protein in the first place?

    I hope the question makes sense and that I am even thinking of it in the right way.

    Any thoughts welcome!
  2. jcsd
  3. Mar 4, 2016 #2


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    Staff: Mentor

    Well, the first thing to remember is that the processes used detect pathogens and communicate this information to other cells are extremely complex. They involve everything from the shape and chemical properties of celluar membrane surface receptors to the details of how the molecular machinery inside cells communicates and functions.

    I believe that antibodies bind to a pathogen and either directly neutralize it or signal to the rest of the immune system that this pathogen is a valid "target". The details of how this happens have to do with the exact shape and chemical properties of the antibody's antigen-binding site and the antigen itself. Common analogies are that the antigen and the binding site function like a lock and key. Wiki states the following:

    Antibody and antigen interact by spatial complementarity (lock and key). The molecular forces involved in the Fab-epitope interaction are weak and non-specific – for exampleelectrostatic forces, hydrogen bonds, hydrophobic interactions, and van der Waals forces. This means binding between antibody and antigen is reversible, and the antibody'saffinity towards an antigen is relative rather than absolute. Relatively weak binding also means it is possible for an antibody to cross-react with different antigens of different relative affinities.

    Some signaling has to be done, otherwise the cell won't know that about the antibody, but I'm not sure of the details.

    I think it depends on what exactly the cell is supposed to do. If it's a phagocyte, the antibody may simply stimulate the cell into phagocytosis through signaling processes that don't involve the nucleus (though that's more of a wild guess unfortunately).

    Note that DNA is not a literal blueprint or set of instructions for the cell. I believe most cellular functions occur without needing to have DNA read and proteins constructed.
  4. Mar 8, 2016 #3
    I think your asking about immediate responses where as most antibody responses are delayed unless there is prior experience of the pathogens. remember whenever tissues are damaged regardless of the cause, they release a range of chemicals that cause inflammation, this increases the blood flow into the area and increases the permeability of the capillaries. These chemicals activate the white cells in the area, they attract other white cells and the inflammation facilitates their movement, there are a number of cells involved in dealing with damage. Phagocytes engulf anything they think is foreign and anything that is damaged, some of these will take pieces of any bacteria to collections of lymphatic tissue for them to start work on antibodies. If the attacker is viral the cell itself puts markers on its cell wall, other white cells are constantly checking cells, if they find one that is infected with a virus, they order it to self destruct to prevent the virus maturing.
    If an infection is not rapidly controlled stem cells in the bone marrow are instructed to increase production of white cells, some white cells might try to wall off an area of infection and an abscess might form. After this it gets progressively more specific, lots of pathogens require particular strategies to manage our immune system learns and remembers these so that its responses to similar infections are quicker and more effective. Antibody production takes some time but a range of these might be produced and get progressively more effective over time, some might simply tag the bacteria making them more obvious, they might cause them to clump together for easier phagocytosis or they might attack the bacteria directly causing its death. Other antibodies might be produced to neutralise toxins that the bacteria might produce.
  5. Mar 8, 2016 #4
    Thanks for the responses, super helpful!
    So the way that cells communicate in the body amongst each other is by releasing different chemicals (e.g. tissue cells), which then activate the appropriate cells that are floating around to take action. Does the process of "taking action" involve the chemical each time activating a specific gene in white blood cells that creates mRNA, creating the right protein that executes a specific defensive functions? And furthermore, do white blood cells do the same to notify stem cells?

    Basically, is this the process that happens every time we say that the body, or the cells are "instructing" some other part of the body to do something?

    I've also heard that some this signaling is on a pure physical basis, not chemical.
  6. Mar 8, 2016 #5
    Remember there are a number of different white cells and they have a variety of functions, there are also other cells throughout the body that are also involved in its defence
    Its worth reading about the innate immune system – https://en.wikipedia.org/wiki/Innate_immune_system and the adaptive immune system, a lot of your questions appear to relate to the innate, the first responders as it were.
    I would highly recommend this video which describes the responses to viral attacks, its brilliant and shows some of the responses.
    Describing the immune system is actually quite difficult, the response to infections becomes very specific to each pathogen though it is fascinating. I'm not sure we are in a position to describe a lot of the functions at the level of the gene but I would think there are a lot of generalised responses, when white cells are activated they don't just attack pathogens, they become a bit overzealous, attacking anything even vaguely suspect and ordering cell suicides unnecessarily. Some areas of the body have to be protected from these reactions, which can cause more damage than the infection. Hope this helps.
  7. Mar 8, 2016 #6
    Great, thank you!
  8. Mar 9, 2016 #7
    That movie just blew my mind. And yes, it explained a whole lot!! Thank you!
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