Objectives and Vocabulary for Week Three Flashcards Preview

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Flashcards in Objectives and Vocabulary for Week Three Deck (36):

Know the four tenants of the clonal selection theory

1) Each lymphocyte bears a single type of receptor with a unique specificity.
2)Interaction between a foreign molecule and a lymphocyte receptor capable of binding that molecule with a high affinity leads to lymphocyte activation.
3)The differential effector cells derived from an activated lymhpocyte will bear receptor of identical specificty to those of the parental cell from which that lymphocyte was derived.
4)Lymhpocytes bearing receptors specific or ubiquitous for self molecules are deleted at an early stage in lymphoid cell development are are therefore absent from the repertoire of mature lymphocytes.


Differentiate between Ehrlichs side chain theory and the clonal selection theory

Ehrlich's side chain theory was one that proposed that each cell contained many receptors which linked to antigens like a key in a lock, and once the receptor—the “side chain”--was triggered by an antigen the cell would produce excess amounts of soluble receptor to neutralize said antigen.
The clonal selection theory is a theory which leads to the idea that there are numerous populations of B/T cell clones who each posses immunoglobulins which bind to different antigens with varying levels of specificity. Once a particular cell has encountered a particular antibody that cell then undergoes proliferation and a clonal expansion. These cells shall then produce the antibodies which destroy pathogens. This theory further states that immune cells that have immunoglobulins which bind to the cells of the host body will be destroyed early on in their development.


Be able to describe how antibody structure leads to function

Antibodies are essentially formed from two different molecules. These molecules are referred to as the heavy chain and the light chain. Both heavy chain and light chain contain regions which are constant—ie common to all immunoglobulin/antibodies—and regions which are variable between antibodies. Variable regions can be composed of an infinite number of amino acid sequences that allow binding of an equally high variety of antigens. The constant region, takes on of only four or five possible forms and confers effector function. There are four framework regions which form beta sheets, whereas areas of high variability (HV regions) form the outer loops. The V regions, especially those which are hypervariable, are the particular part of the V domain that localize to particular regions on the surface of the antigen it will bind. An antibody does not recognize the entirety of a molecule, rather due to it's structure, it can only recognize a small section of the antigen, it's epitope. Due to this, if an antigen becomes denatured, the antibody may not recognize the antigen in question, but it may be the case that the antibody can access and recognize an otherwise inaccessible section of the antigen. Due to the fact that an antibody has a Y shape, it has a hinge region which allows flexibility when binding to two determinants. The regions of H and L chains are paired, and therefore the combination of H and L chain CDRs determine antigen specificity, and this plays a role in combinatorial diveristy—wherein variability is produced by different H and L chain combinations.


Define the mechanisms leading to lymphocyte diversity and how the lymphocyte repertoire is generated.

There are four mechanisms which lead to the generated diversity seen in lymphocytes. There mechanisms are, combinatorial diversity, junctional diversity, different combinations of H and L chains that pair to the Ag binding site, and somatic hypermutation. Combinatorial diversity refers to the use of different gene segments for V(D)J and VJ recombination. Junctional diversity refers to the addition or subtraction of nucleotides at joining segments by TdT. The mechanism of somatic hypermutation entails inducing point mutations in the rearranged V region genes, leading to enhanced binding of antigens. There are multiple copies of the V, D, and J regions on each chromosome. There is a radom selection of one gene segment for each type, and this number of different V and J regions at the L chain locus promotes diversity. The combination of combinatorial diversity and junctional diversity combined can potentially create 1.3x108 combinations.


Discuss how somatic recombination occurs in B lymphocyte lineage genetic segments

Somatic recombination in B lymphocytes occurs through the process of combining different regions of DNA to form a single transcript and single protein chain that combines and acts as the B cell receptor. This process is carried out through the use of several enzymes and DNA sequences themselves. The enzymes are as follows, VDJ recombinase, RAG-1 and RAG-2, Ku70 and Ku 80, DNA-Pk, Artemis, TdT and DNA ligase. The signal spacer is referred to as an RSS, which is a conserved block of seven nucleotides with twelve or twenty-three base pair spacer followed by a conserved block of nine nucleotides. These spaces give rise to the 12/23rule, which states that a gene segment flanked by the twelve base pair spacer can only be joined to a gene segment flanked by a twenty-three base pair spacer. This orientations preludes direct V to J joining in the heavy chain. So, to begin, RAG1/2 complex binds to each of the RSS sequences. RAG makes single stranded DNA breaks, making two separate joints and are ligated to form hairpin structures. Then, Ku70/80 binds to the DNA ends after cleavage, recruits DNA-PK and Artemis which opens the hairpin structure. TdT adds more nucleotides randomly to the ends of the V and J regions, and DNA ligase joins the two ends, joining together the VDJ/VJ regions.


) Identify the four mechanisms in place that contribute to lymphocyte receptor diversity

1) Combinatorial Diversity, 2) Junctional Diversity, 3) Different combinations of H and L chains that pair to form the Ag binding site, and 4) Somatic hypermutation.


Clonal Selection Theory

A fundamental tenent of the immune system (no longer a hypothesis) stating that every individual possess numerous clonally derived lymphocytes, each clone having arisen from a single precursor, expresses one antigen receptor, and is capable of recognizing and responding to a distinct antigenic determinant. When an antigen enters, it selects a specific preexisiting clone and activates it.


Side Chain Theory

Theory proposed by Paul Ehrlich to explain the immune response in living cells. Where side chains link with a particular toxin “like a key in a lock.” These side chains would then break off and become antibodies which would circulate throughout the body. The thought was that the cell would then become activated and then produce more of the antibodies its side chain encountered.


Naive Lymphocyte

: Mature T or B cells which have not been exposed to an antigen. Some of these cells circulate through the lymphatic system When these cells encounter an antigen, or an antigen is presented to them through an APC, the cell then becomes activated and undergoes a clonal expansion.


Effector Cell

The cells that perform effector functions during an immune response, such as secreting cytokines (ie helper T cells), killing microbes, killing microbe-infected host cells, or secreting antibodies



The increase in the number of cells due to some facet of the immune response, often due to cytokines or antigens activating lymphocytes


Clonal Deletion

A mechanism of lymphocyte tolerance in which an immature T cell in the thymus or an immature B cell in the bone marrow undergoes apoptotic death as a consequence of recognizing a self-antigen


Heavy Chain

The large polypeptide subunit of an antibody. The heavy chain defines the isotype of an antibody and are composed of one variable domain, one diversity domain, and several constant domains.


Light Chain

The small polypeptide subunit of an antibody, of which there are two types kappa and lambda chains. These are encoded on chromesome 2 and 22 respectively. Light chain class remains fixed for the life of the B lymphocyte.


Constant (C) Region:

: The portion of Ig or TCR polypeptide chains that does not vary in sequence among different clones and is not involved in antigen binding.


Hypervariable Region

Short segments of about 10 amino acid residues within the variable region of antibody or TCR proteins that form loop structures that contact antigens. Three hypervaraible loops, aka CDRs, are present in each antibody heavy chain and light chain and in each TCR chain. Most of the variability between different antibodies or TCRs is located within these loops.


Variable Region

The extracellular, N-terminal region of an Ig heavy chain or light chain or a TCR alpha, beta, lambda, or sigma chain that contains variable amino acid sequences that differ between every clone of lymphocytes and that are responsible for the specificity for antigen. The antigen binding variable sequences are localized to extended loop structures or hypervariable segments.


F(ab) fragment (antigen biding fragment)

A proteolytic fragment of an IgG antibody molecule that includes one complete light chain paired with one heavy chain fragment containing the variable domain and only the first constant domain. Fab fragments retain the ability to monovalently bind an antigen but cannot interact with IgG Fc receptors on cells or with complement. Therefore, Fab preparations are used in research and other therapeutic applications when antigen binding is desired without activation of effector functions. (The fab' fragment retains the hinge region of the heavy chain).


Fc Fragment (fragment crystalline)

A proteolytic fragment of IgG that contains only the disulfide-linked carboxyl terminal regions of the two heavy chains. Fc is also used to describe the corresponding regoin of an intact Ig molecule that mediates effector functions by binding to cell surface receptors or the C1q complement protein. (Fc fragments are named such due to their tendency to crystallize out of solution).



Complementary Determining Region; : Part of the variable chains in immunoglobulins and T cell receptors generated by B cells and T cells where these molecules bind to their specific antigen. The most variable parts of the molecules, are crucial to the diversity of antigen specificities generated by lymphocytes.


Combinatorial Diversity

The diversity of Ig and TCR specificities generated by the use of many different combinations of different variable, diversity, and joining segments during somatic recombination of DNA in the Ig and TCR loci in developing B and T cells. Combinatorial diversity is one mechanism which works together with junctional diversity, for the generation of large numbers of different antigen receptor genes from a limited number of DNA segments.


V(D)J recombination

Aka somatic recombination is the unique mechanism of genetic recombination that occurs only in developing lymphocytes during the early stages of T and B cell maturation. The process results in the highly diverse repertoire of antiboides/immunoglobulins (Igs) and T cell receptors (TCRs) found on B cells and T cells, respectively. It occurs in the primary lymphoid organs, bone marrow and thymus, and in a nearly random fashion rearranges Variable (V) regions with joinging (J) regions and in the case of heavy chains with the diversity (D) gene segments.


12/23 rule

A gene segment flanked by the 12bp spacer can only be joined to a gene segment flanked by a 23bp spacer.



Recombinational Signal Sequences; Specific DNA sequences found adjacent to the V, D, and J segments in the antigen receptor loci and recognized by the RAG-1/RAG-2 complex during V(D)J recombination. The recognition sequences consist of a highly conserved stretch of seven nucleotides called the heptamer, located adjacent to the V, D, or J coding sequence, followed by a spacer of exactly 12 or 23 non-conserved nucleotides and a highly conserved stretch of nine nucleotides, called the nonamer.



Lymphocyte specific enzymes expressed during lymphocyte development only when recombination is taking place. It has endonuclease activity and makes ssDNA breaks. The clevage during recombination leads to coding and signal joins.



An ubiquitous DNA modifying enzyme which form a heterodimer that binds DNA and associates with DNA-PK.



DNA dependent protein kinase is a ubiquitous DNA modifying enzyme which must bind to Ku70/80 in order for non-homologus end joining.



An ubiquitous DNA modifying enzyme which opens hairpins (endonuclease activity). Artemis is activated when DNA-PK phosphorylates it


DNA ligase

An ubiquitous DNA modyfing enzyme which ligates (joins) two open ended strains, in the case of recombination to join V, J, and D regions together.



Terminal deoxynucleotidyl transferase ;An enzyme which is ubiquitous to DNA repair which adds random nucleotides to the ends of V and J regions in multiples of three.


IgM, IgD, IgA, IgG, IgE

Various immunoglobulins which are synonymous with antibodies, which are a type of glycoprotein produced by B lymphocytes that bind antigens. They are composed of two identical heavy light chains and two identical light chains Note: The constant region determine the functions of antibodies.



Mucosal Immunity



Naive B cell antigen receptor, present with IgM on mature B cells.



Defense against helminthic parasites, immediate hypersensitivity.



Opsonization, complement activation, antibody-dependent cell-mediated cytotoxicity, neonatal immunity, feedback inhibition of B cells.



Naive B cell antigen receptor, complement activation

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