Immune system (innate and adaptive immune system)

Innate immune system work by detecting pathogen associated molecular pattern (PAMP). Pathogen can't escape innate immune system easily because it detect whole structure like LPS, double stranded rna etc. and variation inside them actually don't count. So the only option the pathogen has is to discard the whole structure.

Adaptive immune system helps the body to detect pathogen which body has never even encountered in evolutionary history. It is capable of detecting every non-self structure
very specifically. It is this specificity that characterize adaptive immune system. Like a species can adapt itself to changing condition through natural selection, there is a part of immune system which can adapt itself with the invader (theoretically any invader). That part of immune system is called adaptive immune system. Adaptive immune system has other important property which can be called memory. It can recognize a previously encountered entity and this recognition bring more rapid and strong response than virgin encounter.
Invader's can escape and confuse adaptive immune system by slightly changing their antigenic molecule but not innate immune system. So adaptive immune system confer lasting immunity against a pathogen it has encountered before but this immunity is a specific one- which can be beaten by mutating the corresponding antigenic molecule.

T cells recognize MHC 1 bound antigen.
B cells recognize antigen and the antigen don't have to be bound with MHC protein.

Cytotoxic T cells is specialized to kill infected cells so it must make sure it binds with infected cell. Simultaneous binding with MHC and antigen ensure this.

Innate and adaptive immune system work together. When a macrophage binds with microbial component it release soluble proteins which stimulate and direct adaptive immune response. Adaptive immune system also secrete substance that increase the sensitivity of macrophage and their ability to kill the digested microbes.

Innate immunity can only detect pathogen specific molecular pattern. It can't distinguish say, variation in the same species. So the phenomenon of tissue rejection in tissue transplant is not due to innate immunity but because of adaptive immunity.
Actually the different individual in the same species are likely to have different MHC(major histocompatibility factor) molecules. This leads to tissue rejection.

MHC 1
MHC class I molecules are loaded with peptides generated from the degradation of ubiquitinated cytosolic proteins in proteasomes. As viruses induce cellular expression of viral proteins, some of these products are tagged for degradation, with the resulting peptide fragments entering the endoplasmic reticulum and binding to MHC I molecules. In this way, the MHC class I-dependent pathway of antigen presentation is the primary way for a virus-infected cell to signal T cells that abnormal proteins are being synthesized as a result of infection.

The fate of the virus-infected cell is almost always induction of apoptosis through cell-mediated immunity, reducing the risk of infecting neighboring cells. As an evolutionary response to this method of immune surveillance, many viruses are able to down-regulate or otherwise prevent the presentation of MHC class I molecules on the cell surface. In contrast to cytotoxic T lymphocytes, Natural killer (NK) cells are normally inactivated upon recognizing MHC I molecules on the surface of cells. Therefore, in the absence of MHC I molecules, NK cells are activated and recognize the cell as aberrant, suggesting they may be infected by viruses attempting to evade immune destruction. Several human cancers also show down-regulation of MHC I, giving transformed cells the same survival advantage of being able to avoid normal immune surveillance designed to destroy any infected or transformed cells

Class switching in B cells:

usually IgM to IgG
variable region (so the antigen specificity) does not change but the constant region of the heavy chain change
class switching occurs at DNA level

Molecular nature of cell signals

Cells usually communicate with each other by sending signals. These signals are not like any signal we are used to send. They are not electromagnetic or they don’t flow through a cable. Signals are in the form of molecules and the process they are transmitted is diffusion. These molecules reach their target through diffusion. The process of diffusion requires a continuous liquid medium from source to target.

Diffusion is a passive process, molecules don’t know where they are going- actually they go to every possible direction. In this aspect they are like electromagnetic wave and become weaker (less concentrated) as distance increases.