Immunity and DNA Recombination Flashcards
What is the 12/23 rule?
a rule that states that gene segments to be recombined are usually adjacent to RSSs of different spacer lengths (i.e. one has a 12RSS and one has a 23RSS)
What is adaptive immunity?
a vertebrate-specific defence that is mediated by B lymphocytes (B-cells) and T lymphocytes (T-cells) and that exhibits specificity, memory, and self-nonself recognition
What is allelic exclusion?
a process by which only one allele of a gene is expressed while the other allele is silenced
What is an alpha chain?
One of the two chains of the T-cell receptor that make up the heterodimer. The α chain consists of a variable region, contributing to the antigen-binding site, and a constant region
What is an antibody?
a protein secreted by plasma cells (differentiated B-cells) that binds to particular antigens. All antibodies have the same Y-shaped structure and in their monomer form consists of two identical heavy chains and two identical light chains
What is an antigen?
a substance that elicits an immune response by binding to receptors of B- or T-cells
What is antigen presentation?
the process by which an MHC molecule binds to a fragments of an intracellular protein antigen and carries it to the cell surface, where it is displayed and can be recognised by a T-cell
What is a antigen-presenting cell?
a cell that upon ingesting pathogens or internalising pathogen proteins generates peptide fragments that are bound by class II MHC molecules and subsequently displayed on the cell surface to T-cells. Macrophages, dendritic cells, and B-cells are the primary antigen-presenting cells
What is an antigen receptor?
the general term for a surface protein, located on B-cells and T-cells, that binds to antigens, initiating adaptive immune responses. The antigen receptors on B-cells are called B-cell receptors (BCR), and the antigen receptors on T-cells are called T-cell receptors (TCR)
What is antigenic diversity?
the mechanism by which an infectious agent alters its surface proteins in order to evade a host immune response
What are B-cells?
The lymphocytes that complete their development in the bone marrow and become effector cells for the humoral immune response
What is Beta2-microglobulin?
a component of MHC class 1 molecules, which are present on all nucleated cells
What is a beta chain?
One of the two protein chains of T-cell receptors that make up the heterodimer. It is made up of a variable region, that contributes to the antigen-binding site, and a constant region
What is a biochemical assay?
an analytical in vitro procedure used to detect, quantify and/or study the binding or activity of a biological molecule, such an enzyme
What is Burkitt’s lymphoma?
a form of lymphoma in which the cancers starts in B-cells
What is cancer?
a group of diseases involving abnormal cell growth with the potential to invade or spread to other parts of the body
What is c-myc?
a regulator gene that codes for a transcription factor
What is cas9?
an RNA-guided DNA endonuclease enzyme associated with the CRISPR adaptive immunity system in some bacteria
What is a CD4 cell?
a type of T-cell that, when activated, secretes cytokines that promote the response of B-cells (humoral response) and cytotoxic T-cells (cell-mediated response) to antigens. Also called a helper T-cell.
What is a CD8 cell?
a type of lymphocyte that, when activated, kills infected cells as well as certain cancer cells and transplanted cells. Also known as a cytotoxic T-cell
What is a CDR?
complementary-determining region: a part of the variable chains in antibodies and T-cell receptors that binds to a specific antigen
What is a CDR1?
a complementary-determining region found in the variable region of a polypeptide chain
What is a CDR2?
a complementary-determining region found in the variable region of a polypeptide chain
What is a CDR3?
a complementary-determining region that include some of the variable region, all of the diversity region and some of the joining region, giving it the most variability out of the three CDRs
What is cell-mediated immunity?
the branch of adaptive immunity that involves the activation of cytotoxic t-cells, which defend against infected cells
What does chimeric mean?
a single organism composed of cells from different zygotes
What is clonal selection?
the process by which an antigen selectively binds to and activates only those lymphocytes bearing receptors specific for the antigen. The selected lymphocytes proliferate and differentiate into a clone of effector cells and a clone of memory cells specific for the stimulating antigen
What is the complement system?
a group of about 30 blood proteins that may amplify the inflammatory response, enhance phagocytosis, or directly lyse extracellular pathogens
What is a constant region?
Sections of both the B- and T-cell receptors that do not make up the antigen-binding site. In B-cell receptors, the constant region determines the mechanism used to destroy an antigen
What is CRISPR?
a genome editing technique that allows permanent modification of genes within organisms
What is the D (diversity) segment?
A section of polypeptide chain found in the β chain of theT-cell receptors and the heavy chains of B-cell receptors
What are dendritic cells?
an antigen-presenting cell, located mainly in lymphatic tissues and skin, that is particularly efficient in presenting antigens to helper T-cells (CD4), thereby initiating a primary immune response
What are effector cells?
a lymphocyte that has undergone clonal selection and is capable of mediating an adaptive immune response
What does endogenous mean?
genes that originate from within an organism
What is an epitope?
a small, accessible region of an antigen to which an antigen receptor or antibody binds
What is flow cytometry?
a laser-based biophysical technology employed in cell counting, cell sorting, biomarker detection and protein engineering, by suspending cells in a stream of fluid and passing them through an electronic detection apparatus
What is a fluorescence activated cell sorter (FACs)?
a specialised type of flow cytometry. It provides a method for sorting a heterogenous mixture of biological cells into two or more containers, one cell at a time, based upon the specific light scattering and fluorescent characteristics of each cell
What is a genome wide association study?
an examination of a genome-wide set of genetic variants in different individuals to see if an variant is associated with a trait
What are heavy chains?
one of the two types of polypeptide chains that make up an antibody molecule and B-cell receptor; consists of a variable region, which contributes to the antigen-binding site, and a constant region
What are helminths?
worm-like organisms living in and feeding on living hosts, receiving nourishment and protection while disrupting their hosts’ nutrition absorption, causing weakness and disease
What is heterologous recombination?
A recombination between DNA molecules with significantly different sequences, for example when a transgenic construct integrates randomly in the genome
What is histamine?
a substance released by mast cells that cause blood vessels to dilate and become more permeable in inflammatory and allergic responses
What is homologous recombination?
a type of geneticrecombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA
What is the humoural immune response?
the branch of adaptive immunity that involves the activation of B-cells and that leads to the production of antibodies, which defend against bacteria and viruses in body fluids
What is hyperproliferation?
an abnormally high rate of proliferation of cells by rapid division
What is the hypervariable (HV) region?
Another name for complementary-determining region (CDR)
What is IgA?
an type of antibody that plays a crucial role in the immune function of mucous membranes. It is secreted as a dimer
What is IgD?
an antibody isotype that makes up about 1% of proteins in the plasma membranes of immature B-cells
What is IgE?
a type of antibody that is secreted as a monomer and plays a big role in allergic responses and defence against helminths
What is IgG?
the most abundant type of antibody that is found in all body fluids and protects against bacterial and viral infections
What is IgM?
a type of antibody secreted as a pentamer and is the first antibody to appear in the response to initial exposure to an antigen
What is immortalisation?
a characteristic of a cancer cell in which cells are capable of diving indefinitely (but remain sensitive to constraints of growth e.g. contact inhibition)
What is an immunoglobulin (Ig)?
Another name for antibody
What is an inflammatory response?
an innate immune defence triggered by physical injury or infection of tissue involving the release of substances that promote swelling, enhance the infiltration of white blood cells, and aid in tissue repair and destruction of invading pathogens
What is innate immunity?
a form of defence common to all animals that is active immediately upon exposure to a pathogen and that is the same whether or not the pathogen has been encountered previously
What are interferons?
a protein that has antiviral or immune regulatory functions. Interferon-α and interferon-β, secreted by virus-infected cells, help nearby cells resist viral infection; interferon-γ, secreted by T-cells, helps activate macrophages
What is an isotype?
the slight variations between heavy chains of isotypes. There are 5 isotypes in human antibodies, each of which has a difference response mechanism to antigens
What is isotype switching?
a biological mechanism that changes a B-cell’s production of antibodies from one type to another. During which the constant region of the antibody heavy chain is changed, but the variable region of the heavy chain remains the same
What is a J (joining) segment?
A section of polypeptide chain found in T-cell receptors and both the heavy and light chains of B-cell receptors
What is a knockout?
a genetic technique in which one of an organism’s gene is made inoperative
What are light chains?
one of the two types of polypeptide chains that make up an antibody molecule and B-cell receptor; consists of a variable region, which contributes to the antigen-binding site, and a constant region
What are lymphocytes?
a type of white blood cell that mediates immune responses. The two main types are B-cells and T-cells
What is a lysozyme?
an enzyme that destroys bacterial cell walls; in mammals, it is found in sweat, tears and saliva
What are macrophages?
a phagocytic cell present in many tssues that functions in innate immunity by destroying microbes and in acquired immunity as an antigen-presenting cell
What is a major histocompatibility complex (MHC)?
a host protein that functions in antigen presentation. Foreign MHC molecules on transplanted tissue can trigger T-cell responses that may lead to rejection of the transplant
What are mast cells?
a vertebrate body cell that produces histamine and other molecules that trigger inflammation in response to infection and in allergic responses
What are memory cells?
one of a clone of long-lived lymphocytes, formed during the primary immune response, that remains in a lymphoid organ until activated by exposure to the same antigen that triggered its formation. Activated memory cells mount the secondary immune response
What is metastasis?
the ability of a cancer cell to invade normal, healthy tissue
What are natural killer cells?
a type of white blood cell that can kill tumour cells and virus-infected cells as part of innate immunity
What are neutrophils?
the most abundant type of white blood cell. Neutrophils are phagocytic and tend to self-destruct as they destroy foreign invaders, limiting their life span to a few days
What is a parasite?
an organism that lives in or on another organism (its host) and benefits by deriving nutrients at the host’s expense.
What is parasitology?
the study of parasites, their hosts, and the relationship between them
What is phagocytosis?
a type of endocytosis in which large particulate substances or small organisms are taken up by a cell. It is carried out by some protists and by certain immune cells of animals (in mammals, mainly macrophages, neutrophils and dendritic cells
What are plasma cells?
an antibody-secreting effector cells of humoral immunity. Plasma cells arise from antigen-stimulated B-cells
What is a plasmodium?
A unicellular parasite that causes malaria in humans
What is a primary immune response?
the initial adaptive immune response to an antigen, which appears after a lag of about 10-17 days
What are proto-oncogenes?
A normal gene which, when altered by mutation, becomes anoncogenethat can contribute to cancer
What does pseudopregnant mean?
false pregnancy - the appearance of clinical signs and symptoms associated with pregnancy when the organism is not actually pregnant
What is RAG 1 and 2?
recombination-activating genes: genes that encode enzymes that play an important role in the rearrangement and recombination of the genes of immunoglobulin and T-cell receptor molecules
What are recombination signal sequences (RSS)?
conserved sequences of noncoding DNA that are recognised by the RAG 1 and 2 enzyme complex during V(D)J recombination in immature B- and T-cells
What is the secondary immune response?
the adaptive immune response elicited on second or subsequent exposures to a particular antigen. The secondary immune response is more rapid, of greater magnitude, and of longer duration than the primary immune response
What are T-cells?
the class of lymphocyte that mature in the thymus; they include both effector cells for the cell-mediated immune response and helper cells required for both branches of adaptive immunity
What is terminal deoxylnucleotidyl transferase (TdT)?
a specialised DNA polymerase expressed in immature B- and T-cells responsible for adding nucleotides to the V, D, and J exons of the TCR and BCR genes during junctional diversity antibody gene recombination
What is the thymus?
a small organ in the thoracic cavity of vertebrates where maturation of T-cells is completed
What are toll-like receptors (TCR)?
a membrane receptor on phagocytic white blood cells that recognise fragments of molecules common to a set of pathogens
What is transformation (cancer)?
a characteristic of cancer cells where they fail to observe the normal constraints of growth (no longer sensitive to contact inhibition and grow on top of each other)
What are transgenes?
a gene or genetic material that has been transferred naturally, or by any of a number of genetic engineering techniques from one organism to another
What are trypanosomes?
unicellular parasites that causes disease in host organisms
What is a V (variable) segment?
A section of polypeptide chain found in T-cell receptors and both the heavy and light chains of B-cell receptors
What is a variable region?
The segment of BCRs and TCRs that determine the antigen specificity of that receptor
What is a variant surface glycoprotein (VSG)?
a protein found on the surface of trypanosomes that allows the parasite to evade the host immune system
True or False: VDJ recombination uses the same mechanisms as the recombination events that cause isotype switching. The two events occur at the same time.
False:
- Isotype switching does not use RAG genes
- Isotype switching occurs only after B-cells have been activated by contact with antigen. Thus, by definition, it must occur later than VDJ recombination
True or False: TCR and BCR are both formed as a result of VDJ recombination. The regions of the receptors that bind antigen and determine specificity are small and confined to the 3 CDR regions. Therefore the function of the TCR and BCR is identical
False:
- After activation the BCR is secreted (antibody), the TCR is never secreted
- The TCR recognises only peptide antigen presented in MHC molecules
True or False: Making a mutant mouse by either transgenic
or gene knockout technology uses the same
biological process of homologous
recombination
False:
• A gain of function transgenic mouse
– does not use homologous DNA (think of the
jellyfish DNA into mice or plants).
– The transgene inserts randomly into the
genome….perhaps multiple times.
• In contrast a loss of function knockout mouse
must have homologous DNA.
– This technique works by the endogenous gene
being replaced by the mutant by homologous
recombination
True or False: T. brucei switches expression of its VSG genes as a
result of selection pressure from the immune system.
Antibodies recognise the VSG, kill the parastie which
forces the parasite to switch VSG genes
False:
It is true that the immune system is important in
giving a parasite that has recently switched its VSG
gene a selective advantage over non-switched
counterparts. However, the switching/gene
conversion process itself is random, and occurs
spontaneouly during mitosis
Cells of the immune system: A. Originate within the spleen B. Respond only to contact with other immune cells C. Can communicate with one another D. Act independently of each other E. Are generated at the site of need
C. Can communicate with one another
MHC molecules: A. Are not expressed by immune cells B. Are an important component of the innate immune system C. Regulate the composition of mucus in the gastrointestinal tract D. Present peptide to the antigen receptors of B cells E. Present peptide to the antigen receptors of T cells
E. Present a peptide to the antigen receptors of T-cells
The immune system is said to be very diverse in terms of cells types. One such cell, the B cell: A. Is not necessary any more because of T cells B. Is useful because it can identify and kill virus infected cells C. Is useful because it can produce toxin blocking molecules D. Is restricted to the bone marrow and protects the haematopoietic stem cells from destruction E. Is associated with the innate immune system
C. Is useful because it can produce toxin blocking molecules
T cell receptors: A. Bind directly to surface of bacteria B. Can only bind peptides presented by MHC class I molecules C. Interact with MHC and peptide complexes D. Expressed by a single cell are diverse and quite different E. Once formed can mutate to produce stronger binding receptors
C. Interact with MHC and peptide complexes
The number of V, D and J regions for the TCR b-subunit is 50, 2 and 12 respectively and the number of V, and J regions for the TCR a-subunit is 45 and 55 respectively. Based on this information, the number of different TCR a-chains that can be formed is: A. 50 x 2 x 12 x 45 x 55 B. (45 x 55) + (50 x 2 x 12) C. 45 x 55 D. about 1,000,000,000,000 E. 45 + 55
C. 45 x 55
The isotype of an antibody molecule is: A. governed by the binding sites produced B. indicates what kind of antigen it will bind to C. is governed by the constant domain D. has no influence on the function of the antibody E. is by default IgA
C. governed by the constant domain
Knock out mice are produced by mutating a known gene and thus eliminating the action of a particular gene. Using this technology, it has been shown that: A. RAG genes are not required for TCR and BCR rearrangement B. CD4 T cells bind MHC class I C. Mice lacking MHC class I do not produce CD8 T cells D. All genes are required for life E. Gene repair mechanisms efficiently replace the deleted gene
C. Mice lacking MHC Class I do not produce CD8 T-cells
Concentrating on the B cell receptor, the genes that encode the receptor: A. Will be rearranged in all the cells of the body B. Are rearranged identically in T and B cells C. Will be different in B cells compared to liver cells. D. Are rearranged only when required to produce antibodies E. Are fixed at birth and does not
C. Will be different in B-cells compared to liver cells
Gene rearrangement or recombination: A. Can be associated with disease B. Is confined to the generation of antigen receptors in the immune system C. Is confined to meiosis D. Results in cell death because of gene destruction E. Results in tissue rejection
A. Can be associated with disease
PCR can be used to specifically detect the
chromosomal translocation event that occurs between the
Ig Heavy chain gene and the c-myc proto-oncogene in
Burkitt’s lymphoma. The two important facts (ie choose 2
options) that make this PCR a useful specific diagnostic
tool are:
A. c-myc and the Ig Heavy Chain are always in close proximity to
one another, on the same chromosome, in normal cells.
B. C-myc is translocated to the Ig Heavy chain gene locus in
Burkitt’s lymphoma B cells. Therefore, in these B cell tumors,
the two genes are brought into close proximity
C. C-myc and the Ig Heavy chain gene are always located on
different chromosomes, in both normal B cells and Burkitt’s
lymphoma cells.
D. In normal B cells c-myc is located on chromosome 8 and the
Ig Heavy chain gene chromosome 14.
E. The Ig Heavy chain gene enhancer element drives and
dysregulates the expression of the c-myc proto-oncogene.
- B. C-myc is translocated to the Ig Heavy chain gene locus in
Burkitt’s lymphoma B cells. Therefore, in these B cell tumors,
the two genes are brought into close proximity - D. In normal B cells c-myc is located on chromosome 8 and
the Ig Heavy chain gene chromosome 14.
How is antigen receptor diversity created in the immune system?
Somatic recombination
What does innate immunity consist of?
Physical barriers (i.e. skin), cellular (phagocytic cells) and soluble components (complement system)
How do we obtain our innate immune system?
We inherit it from our parents
What pathogenic structures does the innate immune system recognise?
Viral DNA
Viral RNA
Bacterial specific carbohydrates
Pathogen specific wall components
How do we obtain our adaptive immunity?
It develops when lymphocytes encounter a specific pathogen
True or False: Specific antigens are generated during development prior to exposure to pathogens
True
What somatic recombination occurs in the heavy chain of B-cells?
D-J joining and then V-D-J joining
What type of somatic recombination occurs in the light chain of B-cells?
V-J joining
True or False: Lymphocytes have the same genetic material as a liver cell
False - each lymphocyte rearranges its immunoglobulin genes and retains its own unique section of immunoglobulin gene elements
What are the highly variable domains of the amino acid composition of antibody molecules called?
Complementary determining regions (CDR)
How many complementary determining regions are found in each chain of an antibody molecule?
Three in each
How many CDRs do antibody molecules have in total?
12
Which CDR has the greatest variability?
CDR 3
What does the binding site of antibody molecules consist of?
The binding site is formed by the coming together of the complementary determining regions of the heavy and light chains
Which immunoglobulin gene segment encodes CDR 1?
V segment
Which immunoglobulin gene segment encodes CDR 2?
V segment
Which immunoglobulin gene segment encodes CDR 3?
V, D and J
What are the 3 mechanisms of diversity in immunoglobulin molecules?
Recombination of Ig genes
Nucleotide deletion at junctions
Addition of nucleotides at junctions
In which cells are RAG 1 and 2 enzymes expressed?
Developing T- and B-cells
How does Ig gene recombination occur?
RAG 1 and 2 recognise specific recombination signal sequences (RSS) in the genome to initiate recombination. They then bind to the 12 and 23bp spaced RSS. The enzymes then bind to each other, bringing together the segments to be joined, allowing the DNA to be cleaved to create hairpin structures at the end of the Ig gene segments. DNA ligase then reconnects the remaning genes
Where are the recombination signal sequences (RSS) found?
3’ end of each V gene segment, 5’ end of each J gene segment and both sides of each D gene segment
What do recombination signal sequences (RSS) consist of?
They consist of a conserved 7 nucleotide heptamer and a 9 nucleotide nonamer with either a 12 or 23 non-conserved nucleotide spacer in between
Which enzyme is capable of adding nucleotides not encoded in the genome?
Terminal deoxynucleotidyl transferase (TdT)
What is junctional diversity?
The addition or subtraction of nucleotides at the ends of cut DNA fragments, creating even more diversity in the CDR 3 region of antibody molecules
Which enzymes can remove nucleotides before the V (D) and J segments are joined?
DNA exonucleases
When are antibodies secreted?
Antibodies are secreted from mature B-cells after they have been activated
What does the constant region of the Ig genes encode for?
The isotype of the antibody
When does isotype switching occur?
It occurs separately and after the recombination process that produced the antigen receptor and after the B-cell has been activated by encountering an antigen
What is the most common isotype of antibody?
IgA
What is the only antibody secreted without the assistance of Th cells?
IgM
True or False: class switching involves signal sequences and DNA repair enzymes
False - while the mechanism is not well understood, we know that it is different to varaible region rearrangement
What is a T-cell receptor (TCR) made up of?
One alpha chain and one beta chain
What are each alpha and beta chain composed of?
Variable region
Constant region
Transmembrane and short cytoplasmic region
True or False: TCRs can only recognise antigens when it is presented by MHC molecules
True
What type of MHC does CD4 cells recognise?
MHC class II
What type of MHC does CD8 cells recognise?
MHC class I
How many CDRs in total are on each TCR?
6; 3 one the alpha chain and 3 on the beta chain
Which gene segments encodes the alpha chain?
V and J regions
Which gene segments encodes the beta chain?
V, D and J regions
True or False: recombination of TCR genes involves the same genes and enzymes as BCR recombination
True
What does the basic transgene require?
A promoter and a coding region
How do you make a transgenic mouse?
Replace the gene of interest with the transgene via homologous recombination in an isolated newly fertilised zygote. The zygote can then be introduced into a pseudopregnant mother
How are transgenic mice identified?
Polymerase chain reaction
Protein expression
Phenotype
What is needed for homologous recombination to occur?
Similar (homologous) regions of DNA
What can happen if a stretch of DNA homologous to a known gene is introduced into a cell?
Nothing Random integration (heterologous) Specific integration (homologous)
True or False: The frequency of homologous recombination is high
False - it is very difficult to insert a transgene into a specific site
How do you determine whether homologous or heterologous recombination has occurred?
- A marker gene will be inserted into the endogenous gene being targeted (i.e. antibiotic resistance)
- Another gene (thymidine kinase) is introduced at one end that will produce a toxic effect when exposed to another drug (ganciclovir). TK will not be incorporated in specific integration
What is interesting about MHC class I KO mice?
They do not generate CD8 cells
Why don’t MHC class I KO mice produce CD8 cells?
For CD8 cells to fully develop they must be able to recognise MHC class I markers. If there are no MHC class I markers, they cannot fully develop so they are destroyed
What three changes occur during tumourgenesis?
Immortalisation (failure to die)
Transformation (no contact inhibition)
Metastasis (invade normal tissue)
What does rearrangement of oncogenes result in?
Sequence alterations (different product produced)
Dysregulation of expression
Combination of above
What happens to the c-myc gene in patients with Burkitt’s Lymphoma?
The c-myc is relocated next to the regulatory region of Ig genes. Because Ig genes are constantly expressed they drive the expression og c-myc
What does overexpression of c-myc cause?
Hyperproliferation of B-cells which leads to lymphoma
True or False: the recombination between c-myc and the Ig gene occurs between two chromosomes
True
How do trypanosomes protect themselves from B-cells?
They are covered by a variant surface glycoprotein (VSG) controlled by the VSG gene. Trypanosomes can switch the expression of VSG genes, altering the antigen so antibodies cannot recognise them
What are the mechanisms of VSG switching?
Gene conversion
Telomere exchange
In situ switch
What is gene conversion VSG switching?
Replacement of the expressed VSG gene by a pre-exisitng silent copy
What is telomere exchange VSG switching?
Homologous recombination between telomeres
What is in situ VSG switching?
Activation of another VSG expression site
How do malaria parasites avoid splenic clearance?
A major protein on infected red blood cell surface is PfEMP1 which can bind the cell to the endothelium of blood vessels allowing them to avoid splenic clearance
True or False: antibodies cannot recognise the PfEMP1 protein
False - but the protein can be altered through switching between difference expression of the var gene allowing them to avoid detection
