Immuno Chapter 5

MHC molecule is important for what

important for how the T cell recognizes antigen

what does the MHC gene provide

genetic polymorphisms and diversity in population

what is a T cell receptor (TCR)

a membrane bound glycoprotein made of amino acids (has protein chains and sugars)

what does the TCR resemble

the arm of the antibody

how many protein chains is TCR made of

two- alpha and beta

what do the TCR protein chains form when they come together

an antigen binding site at the top of the protein chains

what holds together the antigen binding site on TCR

a sulfide bond

what is the top domain of the TCR protein chains

two variable regions that differs in amino acid sequences between TCRs

what is the bottom domain of the TCR protein chains

2 constant regions. no soluble form, so constant regions rarely interact.

what function does the transmembrane region of TCR proteins serve

extends into the membrane to keep it as a receptor

what does the TCR have in its molecular structure just like BCR

beta sheets held together by disulfide bonds

what do TCR antigen binding sites have that BCR also has

hypervariable loops

how many hypervariable loops does the TCR have? where do they form?

3 on alpha, 3 on beta. form at the end of the variable domain

where does the most variability in the amino acid sequence come from

the area that interacts with the antigen the most

when does somatic recombination of a T cell occur?

while T cell is still developing, prior to antigen exposure

where does somatic recombination of TCR occur?

in the thymus

what segments makes up the TCR alpha chain

Variable and Joining segments

what segments makes up the TCR beta chain

Variable, Joining, and D segments

what chromosome is associated with alpha chain

chromosome 14

what chromosome is associated with beta chain

chromosome 7

how many constant segments does alpha chain have

1

how many constant segments does the beta chain have

2, but they are identical and express the same protein

why does TCR somatic recombination occur

if structure that is fragmented needs to be selected to be put back together to get a functional gene to express.

describe the steps of somatic recombination in TCR

alpha chain goes first and does 1 somatic recombination event. it picks a V, J, brings them together, and cuts DNA. Junctional diversity then fixes the break, and a functional gene is made. beta chain is next. picks a D and J, brings it together, and then does another somatic recombination event to pick a V. brings together and makes a functional gene, and constant codes for variable in constant domain on protein.

what is the function of junctional diversity

repair the break from somatic recombination

describe junctional diversity of TCR

once cut is made from somatic recombination, P and N nucleotides are added using TdT enzyme. looks for base pairing, removes anything that doesnt match, and fills in the gaps

why are RAG enzymes so important

they help us do somatic recombination and junctional diversity. they give us BCR and TCR, which are the most important parts of adaptive immune response to recognize antigen.

what is the difference between introns and exons

exons are coding information, and introns are noncoding information that is removed in RNA splicing

what do RAG genes NOT contain

introns

what do RAG genes resemble

a transposon, a mobile genetic element

what are transposons? what do they do?

sequence of nucleotides that move throughout genome, insert themselves into a particular chromosome, cut themselves out and move to a different location to another, repeated cycle, naturally occurring. they make transposase gene

what does transposase gene do

codes for enzyme transposase

what does the enzyme transposase do

cuts DNA, and has terminal repeat sequence to integrate themselves into the genome.

what is the working hypothesis about transposons

100 millions years ago a transposon cut itself into an innate immune receptor gene and over hundreds of millions of years by cutting in receptor, and out it fragmented the receptor gene that evolved into the BCR and TCR, left behind terminal repeat sequence that evolved into RSSs, transpose gene evolved into RAG1 and RAG2. the evidence lacks introns

cannot make BCR or TCR without…

RAG genes

describe SCIDS

Severely combined immunodeficiency. this is an inherited disease and and RAG is completely defective. without treatment, patient will not like beyond 6-12 months of life as they are susceptible to every opportunistic pathogen

defective RAG gene treatment

gene therapy developed over the past decade that has good results. genetic screening in utero must be done to see defective copy of RAG is seen and plan made so they can receive gene therapy early in life

define omenn syndrome

missense mutation in RAG gene that causes partial function loss. have about 20% RAG enzyme activity. can make some BCR and TCR, however the receptors made are usually autoimmune that attack own cells and tissues which causes massive inflammation. patients cannot survive beyond 6-12 months unless gene therapy treatment

unlike BCR and B cells, what do T cells not go through

somatic hypermutation and class switching

what is a good result of somatic recombination and junctional diversity of TCR

diversity

when do t cells go through somatic recombination and junctional diversity

before presence of antigen

what happens after TCR genes go through somatic recombination and junctional diversity?

a functional gene receptor is made. alpha and beta chains are transcribed and translated. protein chains go to endoplasmic reticulum. when alpha meets beta, it forms a disulfide bond making TCR.

what does TCR have that BCR does not?

help. TCR has other protein chains that join the alpha and beta chain at the surface to make true TCR

what are the protein chains that help TCR?

CD3gamma, CD3delta, CD3epsilon, zeta chain. they all combine with alpha and beta making a fully functional TCR

why are alpha and beta chains most important

because they recognize the antigen. known as TCR proper

what CD3 complexes are next to the alpha and beta chains of TCR

epsilon and gamma next to alpha, epsilon and delta next to beta (both extracellular)

describe the zeta chain of the TCR

homodimer. found in cytoplasm of cell in intracellular environment. its function is to signal and activate signaling cascades.

what chains are present every time TCR is?

CD3 complex (epsilon, sigma, delta) and zeta chain

what is the second class of TCR

gamma delta

gamma delta TCR structure

two chains with variable constant and transmembrane regions. loop structure.

does alpha beta or gamma delta have more diversity

alpha beta

what chromosome is the gamma chain associated with

7

what chromosome is the delta chain associated with

14

what is the reason why alpha beta is made more than gamma delta

when alpha chain is doing somatic recombination picking V and J, everything in the middle is part of a hairpin look that is degraded with delta gene in hairpin loop

TCR cannot recognize a pathogen directly like BCR. what does it need?

needs the pathogen processed and presented.

describe TCR antigen processing

cells break down the antigen/pathogen inside of the cell. this takes place in immune cells and other body cells

describe antigen presentation

antigen must be presented to TCR. once processed and broken down, protein MHC found on surface of cell will present. holds the T cell and TCR so they can evaluate the antigen and determine if they can bind or not

antigen processing and presenting basic steps

pathogen protein in a human cell is broken down into small pieces. one of the pieces is picked up by the MHC molecule and brought to the surface of the cell to present the antigen peptide to the T cell

what are the two types of antigens

extracellular and intracellular

how do extracellular antigens replicate in the body?

bacteria is brought into the macrophage and is phagocytized. the pathogen is degraded into tiny pieces in a vesicle (phagolysosome)

how do intracellular antigens replicate in the body

virus is brought in and degraded in cytoplasm of host cell. degradation is done by enzyme complex that generates tiny pieces of pathogen

what T cells are best at fighting extracellular antigens

CD4 T cells

what T cells are best at fighting intracellular antigens

CD8 cytotoxic killer T cells

what is the CD4 T cell co receptor

single protein chain made up of different domains. also has a transmembrane domain anchoring into membrane

what do Helper 1 CD4 T cells do

activate macrophages

what do Helper 2 CD4 T cells do

activate B cells

what is the goal of helper cells

help other cells become activated to perform their immune functions

discuss Helper 1 CD4 T cells

macrophage phagocytizes antigen, chops it up, and presents to CD4 T cell. will recognize and activate T cell producing cytokines to get the macrophage activated to increase immune response

discuss Helper 2 CD4 T cells

BCR recognizes pathogen bringing it into cell chopping into pieces, process antigen picked up by MHC and presents to helper T cells. CD4 co receptor and TCR will activate T cells making cytokines to act on B cells to become a plasma cell that will secrete antibodies

what is the CD8 cytotoxic T cell

a co-receptor made of 2 chains, alpha and beta. found next to every CD8 receptor and is responsible for killing intracellular pathogens or infected cells.

describe CD8 T cells

pathogen is processed in cytoplasm, presented to CD8 T cell. then will activate the. CD8 T cell to kill virus infected cell. secretes toxins on infected cell

what are the two different types of MHC molecules used to present a pathogen, and when are they used

MHC1 partners with CD8 to fights intracellular antigens. MHC2 partners with CD4 to fight extracellular antigens

what cells can present MHC1 to CD8 T cells

all nucleated cells in body

what cells can present CD4 T cells

only specialized immune cells such as B cells, macrophages, or dendritic cells. these cells are referred to as professional antigen presenting cells (Pro APC)

MHC1 structure

works with CD8. made up of alpha chain with three domains, alpha 1, 2, and 3. will interact with antigen peptide forming antigen binding site in between alpha 1 and 2. have beta chains that make flood of binding groove. the binding groove has alpha helixes that make up the walls of the groove. has small protein chain, beta 2 macroglobulin which is important to structure but doesnt bind to alpha chain. also has 1 transmembrane domain associated with alpha chain.

MHC2 structure

works with CD4. made of two protein chains, and each has 2 domains. alpha 1 and 2, and beta 1 and 2. alpha 1 and beta 1 domain make up the peptide binding groove. have beta sheets. have alpha helixes in binding grooves, making the walls of the groove hold the peptide in place. also has 2 transmembrane domains.

what happens when CD8 co receptor presents antigen to TCR

TCR has to specifically recognize that antigen peptide and recognize MHC molecule. CD8 coreceptor has affinity for binding to alpha 3 chain of MHC1

what does CD4 recognize

beta 2 domain of MHC2

since MHC protein is expressed from a traditional gene, what is there none of?

recombination, splicing, mutations, etc

what does it mean for an antigen peptide to bind to MHC in a degenerate way?

MHC molecule can bind to the COVID peptide, but can also bind to FLU, etc

what is MHC1 restricted by

size. can only bind to very small antigen peptides. it also requires a C terminus at the end of the protein for the amino acid to be hydrophobic or basic

does MHC1 or MHC2 have a bigger binding groove

MHC2. can accommodate larger antigen peptides

how are intracellular peptide antigens processed

processing is done in the cytosol. will degrade protein into peptide that will go into ER

\n how are extracellular peptide antigens processed

taken up by phagocytosis and endocytosis. degradation of pathogen is phagolysosome generating antigen peptides

what is the proteosome

a large protein complex that degrades viral proteins in cytosol. always present in every cell of the body regardless of pathogen present. degrades old/defective self protein if no pathogen present

when cell is infected/not infected, what subunits is the proteosome changed to

infected= immunoproteosome

not= constitutive proteosome

what happens to intracellular antigens when cell is infected

when cell is infected, it recognizes virus present and activates a signaling cascade turning on interferon alpha and beta, and interferon gamma is present. it then switches to a 19S cap, and PA28 speeds up release of peptides as they’re degraded. the beta subunits on immune proteosomes change by cutting protein, making sure C terminus has basic or hydrophobic end.

what is the TAP? what is its use?

Transporter associated with Antigen Processing. used to look for antigen peptides that fit MHC1 binding groove and transport them to ER

once transported to ER, what happens?

translated at ribosome of rough ER and then sent to ER to be folded and protein chains come together.

what is needed to help protein chains fold and come together? discuss

proteins. on the alpha chain it is the chaperone Calnexin which makes sure proper structure is made. on the beta 2 macroglobulin it comes and binds to the alpha chain which releases Calnexin. then chaperone protein Calreticulin comes after beta 2 is bound making sure correct structure is there for MHC1

what is the peptide loading complex

a protein complex including Calreticulin. helps load antigen peptides into

what are some components of the peptide loading complex? what are their functions?

calreticulin- chaperone

tapasin- keeps MHC molecule near the TAP transporter. also makes sure it is optimizing MHC1 ability to bind to antigen peptides. also helps stretch out alpha 2 domain to keep binding groove big to bring peptides in and out

ERp57- ingteracts with peptide binding groove to help keep it open, allowing for peptide to come in and then leave if they dont match

discuss binding affinity

very important. MHC1 and antigen peptide need to establish noncovalent bonding. if there is a high affinity, it will stay. if there is low affinity, it will leave. once the peptide binds, the peptide loading complex is released

what enzyme comes and removes/cuts amino acids that are hanging over the peptide binding group

ERAP

once MHC1 has correct antigen peptide bound, what happens

MHC1 will leave ER in a vesicle to be transported to the surface of cell/plasma membrane to present antigen peptide to CD8 T cells

describe extracellular antigen processing

professional antigen cells (B cells, macrophages, dendritic cells) present antigen peptide. the antigen is brought into 1 of 3 cells by macrophage or cell mediated endocytosis by B cell or dendritic cells. the pathogen ends in a vesicle that will fuse with lysosome causing processing/degradation of antigen. eventually MHC2 will be in vesicle that fuses with vesicle antigen peptide

how is MHC2 synthesized

translated in the rough ER and protein chains are transported into the rough ER. alpha and beta chain come together in ER brought with third chain, invariant chain. invariant chain blocks peptide binding group from binding to MHC2 in rough ER. all 3 chains leave ER in vesicle. Vesicle will then fuse with phagolysosome (contains antigen peptide) where sampling of antigen peptide occurs

what must happen regarding extracellular antigens before sampling takes place

CLIP protein must be removed and binding groove opened. protein HLA-DM will open the alpha 1 and beta 1 domains of MHC2 causing CLIP to pop out allowing binding groove to sample peptides. once right size and binding affinity, vesicle will go to surface where MHC2 will present.

MHC2 is only presented at what concentration?

high concentration when infection is present in tissue/body

what does HLA-DO do

also in the vesicle. counteracts HLA-DM to inhibit binding groove opening.