lecture 1-2

Question 1

role of the immune system

Answer 1

Provides day to day protection from disease
Provides a response to vaccines which can vary from good to useless
Responds to some tumours and cancers
Responds to foreign tissue transplants
Responsible for hypersensitivities
Responsible for autoimmune diseases
(unhelpful when it leads to rejection to transplants or leads to autoimmune diseases)

It consists of a finely balanced set of interacting networks of cells and soluble mediators. These allow the immune response to be both generated and controlled

Question 2

the IS protects against what 4 types of pathogens?

Answer 2

• extracellular bacteria, parasites, fungi
• intracellular bacteria, parasites
• intracellular viruses
• extracellular parasitic worms

has to create an effect (correct type and dose)
has to be regulated
has to be memorised

TABLE IN L1 S4

Question 3

Basic features of the immune response

Answer 3

CONSISTS OF

• Innate immunity
• Adaptive immunity

Adaptive immunity DIFFERS from innate immunity:

• Has specific recognition molecules, BCR and TCR
• The TCR and BCR can recognise all the available antigens (but not self).
• Responds to 10-mer polypeptides, is sub-protein specific and peptide conformation can be essential
• Generates immunological memory

Question 4

Stimulation of the immune response

Answer 4

Initially there are only a few epitope-reactive B and T-cells

Immunogen stimulates these to divide = primary immune response
–> slow (1-2 weeks), IR low and not very protective, initiates immunological memory

The same immunogen again stimulates a secondary immune response
–> fast (2 days), higher, more protective, no time limit between first and second doses

THE IR IS ANTIGEN DRIVEN!!

Question 5

how do infectious agents activate the innate immune system

Answer 5

INFLAMMATORY RESPONSE - FIRST STEP

innate - first step
physical barriers - most infections will need to breach mucus membrane or skin or gut membrane
if breached this epithelial membrane, we have to detect by the innate IS if it is foreign
some compartments of body have millions of bacteria (in gut for example) - so we need a recognition system for foreign particles
macrophages takes in bacteria with phagocytosis, and detect the surface of it being foreign
- will release cytokines which will act locally and change the behaviour of certain cells
- will release chemokines which are like chemical attractants to attract other cells from the vasculature into that part of the tissues
the cytokines and chemokines will trigger the process of inflammation (fundatemntal to start the IR)
most org when infect us will generate an inflammatory response. the ones that dont are more dangerous because they hide

inflammatory response means that the release cytokines can lead in a change of permeability of the vasculature, which will lead to the production of an exgugate from that vasculature
so plasma can comes out of the vascular tissue fluid and accumulate to cause swelling and get heat generated
attraction of other immune cells to the area (neutrophils, T and B cells, macrophages etc)

DIAGRAM IN L1 S7

Question 6

Pattern recognition receptors (PRR)of the innate immune system

Answer 6

Pattern recognition receptors (PRR) of the innate immune system provide an initial discrimination between self and non-self

PRRs can identify if we have something dangerous
will bind to generic membrane proteins / carbohydrates / lipopolysaccharide / receptors (are invariant, dont change, non specific)

these at TLR toll like receptor
TLR2 - recognise gram +ve bacteria
TLR4 - recognise gram -ve bacteria

PRRs will recognise PAMPs (pathogen associated molecular patterns) on the surface of invading bacteria

PAMPs can be detected by different invariant pattern recognition receptors
this triggers the macrophage from secreting the cytokines and chemokines
causes the cascade that will lead to an inflammatory response

DIAGRAM IN L1 S8

Question 7

how is the Adaptive immune responses initiated

Answer 7

—–» Adaptive immune responses are initiated by antigen and antigen-presenting cells in secondary lymphoid tissues- the dendritic cell plays a central role

in inflammatory response we get cells that come to this specific area and we get the production of lymphatic tissue fluid
as this accumulates, it causes swelling and pressure
can be drained to lymphatic system (very important system)
in our tissues - we have dendritic cells and macrophages
dendritic cells - will take in by those PRRs some bacteria and antigen material. they will get washed away by the LS and are taken to lymph nodes.
in lymph nodes, if T and B cell recognises it, it will trigger the specific adaptive immune response

DENDRITIC CELLS BRIDGE THE INNATE TO ADAPTIVE SYSTEM

Question 8

The cells of the immune system derive from precursors in the bone marrow

Answer 8

all cells in our IS and hematopoietic (blood) system generate from stem cells in the bone marrow
we have the pluripotent hematopoietic stem cells
pluripotency - can change to different types of cells. can divide to a common lymphoid progenitor cell (CLP) or a common myeloid progenitor cell (CMP)
progenitor cell - quite narrow differentiation options, more committed stem cell
CMP - will generate all our erythrocytes (red blood cells) and some leukocytes (white blood cells)

so it generates our erythrocytes and platelets
it is also from our granulocyte macrophage progenitor cells
this will create our granulocytes
granulocytes - have granules in their cells
leukocytes- have individual specific functions
also called polymorphonuclesr - because their nuclei are quite lobbed

precursors for our mast cells are full of histamine and are hypersensitive
monocytes are attracted by chemokines and they push their way through the vasculature into the tissue to become macrophages (macrophages are not found in the blood only in tissues)

our common lymphoid progenitor generates into our two types of lymphocytes which are the T cells and B cells
they create a very specific responses because on the surface they have receptors
natural killer cells are a bit more generic which allows it to target unhealthy infected cells (like cancer cells)

dendritic cells are predominantly generated via the myeloid line
when they mature they circulate in the blood
because they recognise antigens they become more mature

Question 9

The myeloid lineage includes which cells?

Answer 9

The myeloid lineage includes most of the cells of the innate immune system

• macrophages (phagocytosis and antigen presentation)
• dendritic cell (antigen uptake, and antigen presentation)
• neutrophil (phagocytosis)
• eosinophil (killing of antibody coated parasites
• basophil (promotion of allergic responses)
• mast cell (release of granules containing histamine and active antigens)

Question 10

natural killer cell lymphocytes

Answer 10

NK is large compared to the WBC
really good at killing cells that are signalling that they are distressed
this cell are lymphocytes (some lymphocytes are T and B lymphocytes)
most of them are found in our lymph nodes in our tissues
some circulate in the blood

when in the blood, they are resting and relaxed cells (not active)
they have very little cytoplasm and very large and round nuclei
(may find the antigens they are specific for in the blood)
difficult to differentiate between T and B cells (similar staining)

Question 11

Properties of the lymphocytes of adaptive immunity

Answer 11

(most of them are T cell, less are B cells
most of T cells are found in tissues, less in blood
when in blood, it will try and navigate towards the lymph nodes)

About 5 x 1011 in total

20% are B cells; 80% are T cells

49% in tissues, 49% in the Lymph nodes and spleen

Only 2% circulates in the blood (about 1010 ); 10% B-cells

Only inactive cells circulate

Activated cells home to lymphatic tissues, mainly the lymph nodes and spleen

Question 12

lymphoid tissues throughout the body

Answer 12

DIAGRAM IN L1 S14

Question 13

clones of antigen-specific effector cells

Answer 13

Lymphocytes activated by antigen give rise to clones of antigen-specific effector cells that mediate adaptive immunity

both B and T cells are made in bone marrow
B cells stay in bone marrow
T cells go to the thymus

B and T cells will divide to make an army with each having unique receptors (generated by complex recombination events in the germ line of these precursor cells) - random event
need to make sure they dont act against the self antigens (and we need to destroy the ones that do)
we now have a pool of lymphocytes that we know for sure don’t recognise our own cells antigens
if they recognise foreign antigens, they will increase by clonal expansion - army specific to the same antigen

Question 14

Clonal selection of lymphocytes is the central principle of adaptive immunity and has 4 basic principles

Answer 14

each lymphocyte bears a single type of receptor with a unique specificity

interaction between a foreign molecule and a lymphocyte receptor capable of binding that molecule with high affinity leads to lymphocytes activation

the differentiated effector cells derived from an activated lymphocyte will bear receptors of identical specificity to those of the parental cell from which that lymphocyte was derived

lymphocytes bearing receptors specific for ubiquitous self molecules are deleted at an early stage in lymphoid cell development and are therefore absent from the repertoire of mature lymphocytes

Question 15

structure of B and T cell receptors

Answer 15

STRUCTURE IN L1 S17

Each developing lymphocyte generates a unique antigen receptor by rearranging its receptor gene segments

membrane of T and B cells will express their receptors B cell receptor → membrane bound molecule with specific parts that recognise foreign antigens. when B cell is activated and matured, it will secrete these receptors as antibodies
T cell → looks similar to a variable region of B cells, but has a beta and an alpha chain

Question 16

B cell receptors binding to antigen

Answer 16

STRUCTURE IN L1 S18

Antigens are the molecules recognised by the immune response, but receptors bind to epitopes

B cell can only recognise 3 dimensional antigens
antigenic because it stimulates an immune response
epitopes - small part of antigen that the B cell receptor binds to
2 populations of b cells that recognise the same antigen, but through different epitopes

Question 17

T cell receptors binding to antigen

Answer 17

DIAGRAM IN L1 S19

variable region will recognise short polypeptides (10-18 aa) which sits in a little groove of a major histocompatibility complex
cannot see the antigen unless it is being presented to it by MHC molecule
so T cells are less effective than B cells

Question 18

Circulating lymphocytes encounter antigen in peripheral lymphoid organs

Answer 18

LEADS TO INFLAMMATION
find their way to the lymph nodes
at the same time, T and B cells are in the blood until they are caught up in a lymph nodes
then they can start to sample what is being brought ot it
so they identify and recognise a protein or lipopolysaccharide epitope brought by the MHC molecules
this will trigger an immune response

will trigger an IR which means the B and T cells have to mature and differentiate into something a bit more specific
so we get a journey back from lymph node the the heart and tissues to target that infection
has to be initiated by inflammation in that part of the body

Question 19

structure of a lymph node

Answer 19

DIAGRAM OF LYMPH NODE IN L1 S21

lymphatics coming out through efferent lymphatic vessel
has vasculature
compartments are specific zones of T cells and B cells
blue zones - T cells // faded yellow zones - B cells // dark yellow spheres - germinal center where the B cells crank up their activity

afferent lymphatic vessels will lead the drained lymphatic tissue fluid for its dendritic cells to pass through the T cells FIRST, then the B cells get to interact
main overarching role of lymph nodes is that they filter the lymphatic and trap the material that was brought in there (traps the lymphocytes and antigenic material)
forces them all to interact and if the lymphocytes recognise the antigenic material, then it starts the process of an immune response

Question 20

structure of the spleen

Answer 20

secondary lymph node tissue
degrade red blood cells (each survives for 120 says)
complement cascade can lead to antigen complexes that bind to our red blood cells (to reach the spleen and get destroyed)

maldivian bodies - are lymph nodes

Question 21

architecture of the spleen

Answer 21

DIAGRAM IN L1 S23

resemble structure of lymph nodes but they don’t have any lymph circulatory system, only have vasculature circulatory system (only bring in things from the blood)
also forces things to go through separate T and B cell zones

Question 22

Gut associated lymphoid organs, GALT

Answer 22

DIAGRAM IN L1 S24

peyer’s patches are
covered by an epithelial layer containing specialised cells called M cells which have characteristic membrane ruffles

gut associated lymphoid tissues - GALT - very specialised areas
gut needs to be impenetrable (to prevents unnecessary materials crossing it)
not leaky epithelial layers
pathogens in our gut are detected
M cells - microfolds - allows it to sample whatever is in the gut
dendritic cells use their PRRs to detect pathogens and hold them to T cells
triggers immune response in gut
they drain through the lymphatic system

Question 23

antigen presenting cells (3 types)

Answer 23

dendritic cells, macrophages and B lymphocytes present antigens
dendritic cells are the most important because they can move from the infection to the diff types of lymphatic tissues (like spleen)

they connect the innate and adaptive immune responses
B cells are antigen presenting cells too - they have receptors that bind their 3D antigens, it will take it in through receptor mediated endocytosis, and present it on its surface so that the T cell helps it become a plasma cell to help it start secreting these antibodies

Question 24

what does Lymphocyte activation require?

Answer 24

DIAGRAM IN L1 S26

Lymphocyte activation requires additional signals beyond those relayed from the antigen receptor when antigen binds

t cell will differentiate
needs signals - more than 1 to activate a t cell response
B cells are presenting - T cell helps it become a plasma cell that presents antigens on its surface
left - stimulates cellular immune response // right - stimulates the humoral immune response
needs more than 1 signal because it s a fail safe mechanism - makes sure we have the right number of signals and actually need that specific response

Question 25

T cells recognize peptides bound to what type of molecules?

Answer 25

T cells recognize peptides bound to two different classes of MHC molecules

T cell will only recognise antigens presented out to them
MHC1 (all cells in our body express MHC1 and can signal to T cells)

• CD8 positive T cells (cytotoxic T cells, will see antigen presenting via our MHC1 signalling)
• CD4 positive T cells (helper T cells, 2 transmembrane anchors in MHC2, will show antigenic peptides to CD4+ T cells)

Question 26

role of Tc cells during viral intracellular infections

Answer 26

TC cells orchestrate cell-mediated immunity during intracellular virus infections

cytotoxic T cells important in viral infected cells
virus is intracellular, broken down, shown on MHC1, cytotoxic T cell will see it and will kill the cell
all cells can show its viral infection via MHC1

Question 27

role of Th cells with intracellular bacteria

Answer 27

only certain cells express the MHC2 and they tend to be the antigen presenting cells (which have to be able to go through phagocytosis or receptor mediated endocytosis)

because T helper cell can only see the exterior of an infected cell
macrophage - takes in mycobacterium, breaks it down, shows it via MHC2, CD4+ T helper cells binds to it

Question 28

The structure of a B cell receptor - antibody molecule

Answer 28

LEARN THIS STRUCTURE IN L2 S2

antigen binds to the B cell receptors
once the B cell is sure of what antigen it is, it is activated and will secrete receptors as immunoglobulin/antibody
a domain is a functional part of the protein and it is usually conserved. they independently fold to give their independent functions
so the domain of the polypeptide chain have different roles
→ so we have heavy chains and light chains / each have variable domains and constant domains

disulfide bond forms a hinge, so it’s flexible

Question 29

Immunoglobulin heavy and light chains

Answer 29

Both chains have constant and variable domains with a characteristic folded structure – 7-10 β strands linked via disulphide bond (Immunoglobulin fold)

Question 30

Heavy and light chains have regions of hypervariability

Answer 30

we stretched out the polypeptide chain and number the residues of the primary sequence up to 120
look at many variations of these polypeptide chains
look at the variations of these amino acids
we find that at specific locations of this chain we get a real increase in diversity of these amino acids

this gives us a unique pattern to the one specific immuno B cell receptor (like a fingerprint)
these are called complementarity determining regions - CDRs
OR
hypovariable regions HR

Question 31

Is the antigen a certain shape?

Answer 31

Ag -can bind in pockets, grooves or extended surfaces in the binding site of the BCR and antibodies, but recognition is always of 3D shape

Question 32

DRAW THE DIAGRAM OF A B CELL RECEPTOR

Answer 32

DIAGRAMS IN L2 S7

Question 33

The TCR and BCR, are there similarities?

Answer 33

• T cell receptor resembles a membrane bound Fab fragment. Also has regions of hypervariablility (CDRs)
• But is encoded by a completely different set of gene segments

T cell receptor similar to FAB fragments of B cell receptors
also part of the immunoglobulin super family so has immunoglobulin folds within the domains
they are heterodimers because they have an alpha chain and a beta chain
they have a constant region and variable region
have 3 regions of each of the variable domains that allow for specificity and diversity

similar so genes are similar but are still on different chromosomes

Question 34

T cell structure

Answer 34

The T cell receptor is a heterodimeric membrane bound receptor
have carbohydrates - help stabilise the molecule

they have very short cytoplasmic tails which means it is not very good at signalling so will need help

Question 35

BCR and TCR see different epitopes from the same antigen.

Answer 35

overall response first
T cell receptor has to recognise linear peptide of antigen
B cell receptor will recognise 3D shapes

if we want a b cell response, the t cells have to recognise it first to give the b cells a helping hand, to then produce its antibodies and immunoglobulins
have to recognise the same source of pathogen, but in diff ways

b-cell epitopes have different parts of the protein
t-cell receptor has the fragments of that peptide chain

the B cells can internalize it and present it to the T cell

Question 36

when can TCR see its cognate antigen?

Answer 36

TCR can only see its cognate AG if it is presented by a specific MHC molecule
KNOW THE STRUCTURES AND ORDERS OF ALPHA DOMAINS

MHC1 has 1 transmembrane domain which is composed of alpha 1 2 and 3
we also have a separate molecule because it is a different polypeptide chain called beta 2 microglobulin
when b2 binds it provides stability
looking at it from above we can see a binding groove formed by the alpha helix at the top and the Beta sheets at the bottom

MHC2 has two transmembrane domains composed of alpha 1 and 2 and beta 1 and 2
so mhc1 and mhc2 are different and show different peptides to different types of T cells

MHC1 - CYTOTOXIC T CELLS - CD8+
MHC2 - HELPER T CELLS - CD4+

Question 37

T cells will express either CD4 or CD8 surface proteins

Answer 37

These proteins stabilise the binding of TCR to the MHC:peptide complex.

CD4 – a single molecule.
CD8 either a heterodimer or homodimer.

CD - cluster differentiation - a way to describe a protocol to look at expression on the surface
CD4 - presented on a T helper cell. it has four domains on one polypeptide chain
CD8 - presented on a T cytotoxic cell, is a heterodimer or a homodimer (so can have alpha alpha or beta beta). have a longer cytoplasmic tail to penetrate into the cytoplasm

stabilise the interaction between T cell receptor and MHC
play a role in signalling
long cytoplasmic tail

Question 38

The relationship between CD4 and -8 and MHC II and -I

Answer 38

The binding sites for CD4 and CD8 on the MHC II and MHCI respectively are on the immunoglobulin domains.

close association of all proteins
CD8+ cell - closely associated to the domains of our MHC1 molecules
signals allow us to regulate and make sure we reached a threshold to get a good response from the activation of our T cells

Question 39

MHC binds peptides tightly within the cleft

Answer 39

MHC1 - binding groove will hold the polypeptide chain at both ends by ionic forces, hydrogen bonds
peptide is a smaller
the peptide needs to buldge out
this there is some interaction between the side chain of the peptide chain and the side chain of the amino acid alpha helix and underneath on the Beta sheet
groove closed off at the ends

MHC2 - groove is more open so we can have a longer peptide chain

mhc molecules are highly variable
similarities in siblings, but not identical
highly polygenic and polymorphic (variations across populations and between cells)

Question 40

The T Cell Receptor binds to the complex of MHC and peptide

Answer 40

T cell receptors come down from the top
interacts with the MHC molecule itself (grey) and the peptide (yellow)
important to the T cell to recognise all of the potential repertoire of all the antigenic peptides and recognise the mhc molecules themselves to create strong interactions

1a and 2a focus on the carboxyl end of the mhc groove
2B and 1B focus on the amino end
3rd hypervariable region on both the alpha and beta chains js in close association with the peptide
3rd hypervariable region has to be the one that is the most diverse because it is the region that will recognise the antigen

Question 41

how are peptides bound to MHC1 molecules

Answer 41

The MHC molecule interacts with the peptide backbone via hydrogen bonds and ionic interactions (blue dots).
Peptide ~8-10 aa in length

alpha helices are creating the grooves and the Beta sheets are creating the floor of that binding groove
specific anchor residues will incur the peptide chain into that binding group
on the sides we find tyrosine residues which will bind to the amino side of the peptide chain, and some on the other side that will bind to the carboxyl side of the peptide chain
have anchors residues on each side so peptide can buldge out and be a bit bigger
COMMON TO ALL MHC1

if I take mhc-1 from all different types, and flush out the peptides there will be similarities

Question 42

how are peptides bound to MHC2 molecules

Answer 42

The MHC molecule interacts with the peptide backbone via hydrogen bonds and ionic interactions (blue dots)
Peptide size is less constrained ~13-17 aa.

this also happens in our mhc II molecules
anchor residues are seen as the hydrogen bonds in blue

diff MHC2 compared to MHC1 - not bound on the ends, just along the peptide chain, ends are hanging out a bit
they are harder to identify anchor residues

Question 43

The two classes of MHC molecule are differentially expressed

Answer 43

TABLE IN L2 S21

Question 44

The diversity of the immunoglobulin repertoire is generated by four main processes

Answer 44

1. Combinatorial diversity during segment recombination.
   [ when you look at the gene that codes for the B line receptor it is segmented (split into segments). so you get a random assortment of those segments so every B cell receptor will be different ]
2. Junctional diversity during segment joining.
   [ when you join these different segments together you adding new nucleotides at the junction of those segments which gives us junctional diversity. both give us difference amino acid primary sequences and so different diversities in that b-cell repertoire ]
3. Combinatorial diversity driven by different combinations of heavy and light chain.
4. Somatic hypermutation

Question 45

how are variable region genes constructed IN B CELL RECEPTORS

Answer 45

Variable region genes are constructed from somatic recombination of separate gene segments

in L chain - we have one recombination event
in H chain - we have two recombination event

gene segments:
V - variable gene segment
J - joining 
C - constant gene segment
L - leader sequence

so the diversity of the variable region of a light chain is a result of one type of V region binding to one type of J region.
you can get shuffling of the gene segments from V and J regions - RANDOM

this also happens in the heavy chain but twice because they have an extra gene segment called the diversity segment
they have the variable, diverse and joining segments
they start off with the shuffling of the segments for the heavy chain
the first recombination event occurs when a D and a J join together
the second recombination event is one of the types of V regents binding to one type of DJ combination
this generates the order of the gene segment for the variable region of the heavy chain

Question 46

Rearrangement of V, D, and J gene segments is guided by ?

Answer 46

Rearrangement of V, D, and J gene segments is guided by flanking DNA sequences called RSS sequences

it has a very specific mechanism to ensure that one V will bind to one J which will bind to one D
this is created by the process shown which has directionality of our gene segments

we have caps on the end of our segments called base pair spacers, which either have 23 base pairs in the middle or 12 - called RSS
this is to ensure that the correct segments binds together
this is because a 23 spacer can only bind to a 12 spacer → 23-12 space rule
so the joining of different segments is not completely random and has some directionality

Question 47

V region gene sections joining by recombination

Answer 47

PROCESS IN L2 S27 TO 32

Question 48

how are gene segments arranged in T CELL RECEPTORS

Answer 48

The T-cell receptor gene segments are arranged in a similar pattern to immunoglobulin gene segments and are rearranged by the same enzymes

instead we have an alpha chain and a beta chain
which are also located on different chromosomes and have variable regions joining regions and and constant regions

the similarity is that the Beta chain is similar to the heavy chain since it has diversity segments as well
so the alpha chain will also have 1 recombination events like the light chain
and the Beta chain will have have 2 recombination events like the heavy chain

Question 49

where do T-cell receptors concentrate diversity

Answer 49

T-cell receptors concentrate diversity in the third hypervariable region which contacts peptide

the third complementarity determining hypervariable region of both the alpha and beta chain that really has to recognise the peptides (which is what will differ between diff pathogens)
and so the hypervariable region 3 tends to have more diversity than region 1 and 2 of both a and B chains