study guide

what does antiboidy look like

what are antibodies

seceretd form of B-cell receptr

clears extracellular pathogens + toxins

what are immunoglobulins

cell surface b-cell antigen receptor and secreted antibody

what do antibodies do

bind pathogens

, which leads to inactivate or destory them

humoral immune response

immune response using antibodies

antibodies secreted by B cells

what are effector cells

short-lived activated immune cells that carry out the response

fights infection

effector cell examples

monocyte

lymphocytes

neutrophils

eosinopihls

basophils

macrophaes

erhtocytes

plaeltles

what are antigens

any substance recogniced by b or t lymphocytes

what is immunity

protection agsint foreign pathogens or substances

what are common types of antigens

proteins

glyocporteins

polysachs

nickel

drugs

chemicals

what cells recognize antigens

b and t cells

b cell function

make antibodies

t cell function

interact with other cells, maybe add more

antibody structure basic

2 heavy chains+ 2 light chains

quatnery protein

heavy vs light chain

heavy: n-term + c-term

light: kappa or lambda

both have variable and constant regions

variable domains

vh heavy

Vl (varibalelight

what do variable regions do

form antigen-bindign site

determine speciificty

Hypervariable regions (CDRs)

• 3 regions: HV1, HV2, HV3

• Also called CDR1, CDR2, CDR3

• Directly bind antigen

antigen-binding site

• Formed by VH + VL

• Each antibody has 2 identical binding sites

• Can bind to pockets, grooves, surfaces

vary in shpe and physcial poreoties

constant region function

determiens effector function

control interaction with immune cells

Fab fragment function

• “Fragment antigen binding”

• Binds directly to antigen

• has variable regions

Fc fragment function

• “Fragment crystallizable”

• Interacts with immune cells

• Triggers immune response

• determins effector function

disulfide bonds

• Hold chains together

• Stabilize antibody structure

2 heavy + 2 light → variable binds antigen (CDRs)

constant= immune action then fab binds and FC signals

primary portien

amino acid seqeunce (peptide bonds)

secondary

alpha /beta sheet folding local

tertiary

3d shape of one chain (functional shape)

quat

multiple chain (final protein)

IgG

monomer

most abunodna in antibodies

blood lymph intestine

crosses placenta,

neutralied toxins

triggers compleet+ phag

protects the fetus

IgM

penatmer (5 mono units+ a J chain)

6% of antiboides

stays in blood

first eposnse in infection

short lived

causes clump (aggulutination)

IgD

monomer

0.02

b cells and blood

activates b cells, assists in immune reposne

IgA

monomer for blood, and dimer for secretions

13

mucus, saliva, tears, breast milk

protects mucuols surfaces which prevents pathogen attachment

IgE

monomer

0.002

mast cells and basophils

causes histomaine release

fights worms

how do immungolgobls differ

different heavy chains

which antibidy neturlizes pathogens

igG

why is igG special

its the most abudnanct

inly one thst crosses placenta

provides long-term immunity

protects fetus

what are monoclonal antiboides

from one clone of b cels

all the same same speicifcity identicl

how are monoclonala tnbodies made

fusion b cells + myeloma cells

peg gell

forms hyrbdioma

hyrbidoma

b cell and myleoma cell

makes antiboidei and lives forever

HAT medium

selection media made to select hybdrioma cells

use of monoclonal antibodies

treat cancer

arhtitis

and target specific atngiens

what are immunogloilbins

b cell receptors + seceretd antibodies

10^11 types

what creates antiboidy diveristy

vdj recomib

juncitnal diversty

somatic hypermutation

junctional diversity

• Addition/removal of nucleotides

• Happens during gene rearrangement

• Increases variability

Somatic hypermutation

• Mutations in mature B cells

• Affects variable (V) regions only

• Improves antigen binding

Germline configuration

• Ig genes exist as separate segments before rearrangement

• Not yet functional

Gene basics

• Gene = DNA → protein/RNA

• Exons = coding

• Introns = noncoding

Central dogma

• DNA → (transcription) → pre-mRNA

• pre-mRNA → (splicing) → mRNA

• Introns removed, exons joined

locus

Physical location of a gene on a chromosome

TP53 gene

• Controls damaged DNA (repair, stop, death)

• 11 exons + 10 introns

Order of Ig gene segments

Heavy chain:
V → D → J → C

Light chain:
V → J → C (no D segment)

Front: Where are Ig genes located?

• Heavy chain → chromosome 14

• Light chains → chromosome 2 (κ) & chromosome 22 (λ)

germline organization

• Ig genes exist as separate segments in order on chromosome

• Called germline configuration

what is vdj recom

• Rearrangement of gene segments in B cells

• Creates antibody diversity

What controls V(D)J recombination?

• Recombination signal sequences (RSS)

• Recognized by RAG1 & RAG

role of rag1 and rag2

• Cut DNA at RSS

• Bring segments together

• Enable joining of V, D, J

Heavy chain recombination steps

1. D + J gene segments join

2. V gene segments joins DJ sequence → forms VH exon

3. heavy chain C region enocded by exons, the c region exons are joined to VH exon by spolicing of heavy chain RNA

4. c lleader peptide directs protien inot the cell’s secretor pathways and is then cleaved

maybe make better

heavy chain srtucture

• V region = V + D + J

• C region = multiple exons

• Leader (L) → directs secretion

light chain recomb

• v and j gene segment in genomic dna formed to compelte variable light chain exon

• light chain C is enocded into seperate exons and is joined to Vl by splicing of light chain RRNA

• leader peptide directs portien onto the cells seceteaory pathway and cleaved

What creates diversity in Ig genes?

• Random recombination of V, D, J

• Different numbers of segments (polymorphism)

isotype switching

• Changes C region only

• Keeps same antigen specificity

t cell receptor

membrane bound has v and c domains

recognzied peptides and mhc complex not the antigen alone

can t cells recgonzie free antigens

no, only antigens bound to mhc

what is MHC

cell surface glycoprotein

displays antigen peptides

where does the peptide on MHC come from

from pathogens

mhc classes

1: most cells

2: only APC, antigen rpesentiv cells

whats are apc

• Cells that process + present antigen to T cells

• Include: dendritic cells, macrophages, B cells, Langerhans cells

denditic cells

macorphage

b cells

mhc.1 func

• Presents intracellular (inside cell) antigens

• Recognized by CD8 T cells

MHC II function

• Presents extracellular antigens

• Recognized by CD4 T cells

peptide binding site on MHC

Peptide-binding cleft (groove)

Steps of MHC I antigen presentation

1. Protein in cytosol → broken into peptides (proteasome)

2. Peptides transported into ER (TAP)

3. MHC I assembled + loaded with peptide

4. Goes to surface → recognized by CD8

proteasome function

Breaks intracellular proteins → peptides

What helps MHC I assembly?

• Calnexin, calreticulin, ERp57, tapasin

• Form peptide-loading complex

MHC II antigen processing

• Extracellular proteins → taken into vesicles

• Broken down in acidic vesicles

• Loaded onto MHC II

• Presented to CD4

eptiope

part of antigen that antiboidy binds

multivalent antigen

• Has multiple epitopes

• Or repeated copies of same epitope

types of epitopes

• Linear: continuous amino acids

• Discontinuous: brought together by protein folding

plasma b cell function

secrets antibodies

highyl specifilaied effector B cells

b cell devlops where

bone marrow

order of iG geen rearrngment

heavy chain first then light chain

Early B-cell development steps

occurs in bone marrow

stem cells differinaite into pro-b cell

d and g gene segment come together , then v segents joins DJ

a u heavy chain is then made

pre-b cell receptor forms

light chain then rearranges

IgM is expressed and diffeirnates into an immature B cell

can you check

pre b cell receptor

wuality contorl checkpoint

checks is u heavy chain works

imature b cell

expression of IgM on surface

negatuve selection

removes B cells that binds self-antigens

prevents automminuty

positive selection

b cells compete for suvival

in seocndary kympohid irgans

where do t cells develop

thymus

immature= thymocytes

Structure of thymus

• Cortex (outer): immature T cells desne

• Medulla (inner): mature T cells, less dense

• Supported by thymic stroma (epithelial cells)

thymus involution

thymus shrisk with age

What do macrophages do in thymus?

Remove dead/self-reactive T cells (cleanup)

Pre-T cell receptor function

• Tests TCR formation

• Ensures proper development (quality control)

T cell stages (CD markers)

• Double negative: no CD4/CD8

• Double positive: CD4 + CD8

• Single positive: either CD4 OR CD8

postiive selection

in cortext

keeps t cells that recognize self -mhc

negative selection

• Removes T cells that bind self-antigens

• Prevents autoimmunity

t cells become

cd4 helper

cd8 cytotoxic

Central vs Peripheral tolerance

• Central: in thymus/bone marrow (development stage)

• Peripheral: outside (after development)

Which MHC do APCs express

• MHC II (main) → activates CD4 T cells

• Also have MHC I

Why are dendritic cells important?

• Main activators of naïve T cells

• Link innate → adaptive immunity

Immature vs mature dendritic cells

• Immature: in tissues, capture antigen

• Mature: in lymph nodes, activate T cells

Where do naïve T cells encounter antigen?

• Lymph nodes (secondary lymphoid organs)

• Enter via HEV (high endothelial venules)

Signals required to activate naïve T cells

1. Signal 1: TCR + CD4/CD8 binds peptide-MHC

2. Signal 2: CD28 binds B7 (co-stimulation)

BOTH required