Quiz 3 Part 2

Question 1

Explain the difference between a linear epitope and a discontinuous epitope

Answer 1

A linear epitope usually only occurs on peptides because they are not 3 dimensional. when an epitope is linear, each stalk on the antibody can bind to THREE linear epitopes each

A discontinuous epitope happens on PROTEINS (or even 2 polypeptides) because they are three dimensional. Usually 3 epitopes cannot be bound at the same time as in the case of continuous

Question 2

What cells contain fragmented Ig genes??

Answer 2

ALL CELLS EXCEPT B CELLS

only the B cell can form a functional Ig gene, but every cell possesses inactive Ig genes that cannot be transcribed

Question 3

The assembly of functional Ig genes only occurs in…..

Answer 3

B CELLS

Question 4

What is the term for inherited gene segments

Answer 4

germline form (inactive and can only be activated by B cells)

Question 5

Are heavy chains and light chains assembled together or individually?

Answer 5

heavy chains and light chains are assembled in the same B cell, but are done independently of each other.

Question 6

What happens after the heavy chains and light chains are assembled in the same B cell?

Answer 6

they associated with each other and are expressed on the B cell surface

Question 7

Do V, D, and J segments rearrange?

Answer 7

yes

Question 8

Do C (constant) regions and L segments rearrange?

Answer 8

no

Question 9

What do V D and J stand for
What do C and L stand for

Answer 9

V=variable segments
D=diversity segments
J=joining segments

C=constant segments
L=leader segments

Question 10

Which is longer — heavy chain or light chain?

Answer 10

heavy chain

Question 11

What is the purpose of the leader peptide and where is it located

Answer 11

to bring the antibody to the correct location.
They are next to every variable segment

Question 12

What is the term for the joining of the V,D, and J segments

Answer 12

SOMATIC RECOMBINATION

Question 13

Is somatic recombination random

Answer 13

yes

Question 14

How many recombinations does the light chain have?

Answer 14

only one — VJ joining

Question 15

How many recombination events exist for the heavy chain

Answer 15

2———
D and J segments form first
then V segment joins DJ to form VDJ

Question 16

the light chain can either be…..

Answer 16

kappa or lambda

Question 17

how many possible heavy chain combinations are there

Answer 17

5520

Question 18

How many possible light chain combinations are there

Answer 18

Lkappa=175
Llambda=120

Question 19

How many possible variations are there of association of the heavy chain with the light chain and what is the term for this

Answer 19

1.6 million variations
COMBINATORIAL DIVERSIFICATION

Question 20

What else can cause more diversity (besides association of heavy chain with light chain)

Answer 20

JUNCTIONAL diversity

Question 21

What event takes place after recombination?

Answer 21

splicing to get rid of the RSS’s (recombination signal sequences) between segments

Question 22

The selection of gene fragments depends on…..

Answer 22

RSS’s (recombination signal sequences)

–sequences found between the fragments

Question 23

What actually cuts the RSS’s and splices the fragments together?

Answer 23

DNA recombinases

Question 24

where are DNA recombinases made?

Answer 24

in the B cell and NOWHERE ELSE

Question 25

What are RAG1 and RAG2 and where are they expressed?

Answer 25

RAG1 and RAG2 are recombination-activating genes that are ONLY expressed by small lymphocytes

Question 26

What exactly do RAG1 and RAG2 do? (RAG complex)

Answer 26

the RAG complex promotes recombination between segments which creates a CODING JOINT

Question 27

What is a coding joint?

Answer 27

the ultimate goal: VDJ/DJ

Question 28

How many nucleotides are directly next to every “V” “D” or “J”?

Answer 28

7

Question 29

describe the structure of heavy chain genes

Answer 29

“V”, 7 nucleotides, 23 nucloetides, 9 nucleotides, RSS, 9, 12 ,7, D, 7, 12, 9, RSS, 9, 23 ,7, J

there cannot be 2 “12’s” or 2 “23’s” in the same module

Question 30

What is the name of the specific DNA recombinase that brings VDJ/VJ together (creating a coding joint)

Answer 30

RAG1 and RAG2

Question 31

Where is the spacer located

Answer 31

between 7 and 9
spacer is either 12 or 23

Question 32

What forms a signal joint?

Answer 32

a signal joint is formed from everything that gets spliced out of the gene

Question 33

Are DNA recombinases present in all cells?

Answer 33

DNA recombinases are present in all nucleated cells, however, only small lymphocytes express RAG1 and RAG2 to initiate the process of cutting and splicing RSS’S (recombination signal sequences). Nothing can happen without RAG1 and RAG2

Question 34

When the RAG complex promotes recombination between segments, what does this form?

Answer 34

a coding joint (ie: VJ, VDJ)

Question 35

Where does the RAG complex cut?

Answer 35

the RAG complex makes a clean cut across the heptamer (7mer)

Question 36

What happens after RAG makes a clean cut across the heptamer?

Answer 36

Repair genes come in and paste the coding joint together, and repairs the signal joint to form a circle that diffuses away

Question 37

The RAG complex introduces ______ diversity

Answer 37

junctional

Question 38

HOW does the RAG complex introduce junctional diversity

Answer 38

through the addition of new nucleotides that were not in the original germline DNA sequence

Question 39

What is the term for the new nucleotides that the RAG complex adds?

Answer 39

P and N nucleotides

Question 40

Where in particular does the RAG complex promote junctional diversity

Answer 40

HV3

Question 41

Which enzyme actually adds the random bases?

Answer 41

TdT (terminal deoxynucleotide transferase)

Question 42

Explain the entire process of JUNCTIONAL DIVERSITY

Answer 42

RAG makes a blunt cut across the heptamer to yield “DNA hairpins”. (still double stranded at this point)

then, the RAG complex opens the hairpins by nicking one strand of the DNA which generates P nucleotides

TdT comes in and adds random N-nucleotides.

These random bases search for base pairing

they pair and the UNPAIRED bases are removed by an EXONUCLEASE

The gaps are then filled in by DNA synthesis and ligation to form the CODING JOINT

Question 43

Explain the difference between P nucleotides and N nucleotides

Answer 43

P nucleotides are the ones that were generated when RAG cut the heptamer, and opened the “DNA hairpin” by nicking a strand of DNA

N nucleotides are the random ones that were added by TdT (terminal deoxynucleotide transferase)

Question 44

What can occur if the net amount of bases added is NOT a multiple of 3?

Answer 44

frameshift mutations

Question 45

Between which segments is RAG creating this junctional diversity?

Answer 45

D and J segments (variable region)

Question 46

What id Combinatorial Diversity?

Answer 46

different light chains can associate with the same heavy chain

Question 47

What are naive B cells?

Answer 47

those that have not yet encountered an antigen