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My professor said that in human body nearly 10$^9$-10$^1$$^2$ antibodies are produced by VDJ recombination and all the antigens that a person encounters in his lifetime are dealt by antibodies already present in his body. But he didn't explain what if the body in infected by a new mutated microbe(antigen) whose corresponding antibody is not present in the body.

My question is does our body have the mechanism to judge the epitope of the new antigen and synthesise an antibody with completely new paratope? If so what is it?

After reading the following I was forced to wonder whether the specificity of the antibodies improve(improve by synthesising new paratopes) after encountering antigens in the course of response.

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    $\begingroup$ The human immune system is capable of producing far more than 1e9 antibodies - it's more on the order of 1e12. $\endgroup$ – MattDMo Oct 4 '16 at 15:14
  • $\begingroup$ "Holes" in peoples' antibody repertoire are quite common -- that is, it isn't unusual for individuals to fail to make an antibody for a particular epitope. However, pathogens generally have dozens to thousands of epitopes (many per protein) and it's rare that a person fails to make antibodies to enough epitopes to protect against the pathogen. $\endgroup$ – iayork Oct 4 '16 at 19:19
  • $\begingroup$ Sanjukta, your English is usually better than this. I don't understand what you are trying to say in the phrase "does our body have (not has) the mechanism to JUDGED the epitope". "Judged" is wrong. Can you clarify what you are actually asking. And when you say "child" and then "lifetime", do you mean "individual" (baby, child, adult) or are you talking about early life? $\endgroup$ – David Oct 4 '16 at 22:44
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    $\begingroup$ That's clearer. There's nothing against the rules in your question so I've cut that bit out. Accepted answer seems OK. But be clear that the immune system is not "judging" the antigen or using it as a template in any way. Those pre-existing cells the antibodies of which can bind to some extent will expand and mutate, makingit likely that some of those produced will have higher affinity. $\endgroup$ – David Oct 6 '16 at 21:34
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    $\begingroup$ @SanjuktaGhosh I just read your updated question, and the idea that the innate response is not highly specific is getting out of date, as is the strong dichotomy between innate and adaptive responses. Surface and intracellular receptors for PAMPs are incredibly specific for their targets, and have a broad range of effects that varies greatly from receptor to receptor, depending on the type of microbe associated with each PAMP. More understanding about NK, NKT, and γ-δ T cells (among others, such as the interaction of immature B cells with subcapsular sinus macrophages in the spleen to (...) $\endgroup$ – MattDMo Oct 7 '16 at 17:01
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In case of T-cells and Abs our organism first generates a great diversity of T- and B-cell receptor variants so that any new foreign antigen is likely to be recognized by some of them. When a B-cell encounters its antigen it begins proliferating and changes it phenotype. Additionally, B-cell (but not T-cell) receptor starts to mutate (so-called somatic hypermutation) generating new B-cell receptor variants that differ a bit from the original one. This process acts like evolution, with B-cell carrying a receptor with higher affinity being more likely to proliferate. So the specificity of antibodies improves indeed, this is called affinity maturation.

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  • $\begingroup$ Could you please add some references? $\endgroup$ – L.B. Oct 5 '16 at 16:39
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    $\begingroup$ I've added the wikipedia link to Somatic hypermutation. Hope you don't mind. Besides welcome to Bio stackexchange and thank you very much for the life-saving answer. :) Hope you have a nice experience here. $\endgroup$ – Tyto alba Oct 5 '16 at 17:07
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    $\begingroup$ @L.B. This topic is nicely covered in Janeway Immunobiology garlandscience.com/product/isbn/9780815342434 . This book really helped me when I've transferred to the immunology field having a pure physics background. $\endgroup$ – 51102 Oct 5 '16 at 18:43
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    $\begingroup$ @51102 that's not the point. We require answers on this site to include relevant citations to the scientific literature to back up non-obvious claims. Of course there's always some disagreement about what "non-obvious" means, but it's often interpreted to mean things that a person who's had a basic biology course wouldn't understand. So, you don't need to provide evidence that DNA is the carrier of genetic information, but a link to the Wikipedia pages for T cells, B cells, and antigens (maybe) would be appreciated. Somatic hypermutation would definitely need a citation. $\endgroup$ – MattDMo Oct 7 '16 at 16:48
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    $\begingroup$ Also, you can find an older version (the 5th edition from 2001, unfortunately) of Janeway on the NCBI Bookshelf here if you have a particular passage or figure that would illustrate your point well. $\endgroup$ – MattDMo Oct 7 '16 at 16:50

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