Class 8: DNA damage, repair, and cancer

Question 1

10 hall marks of cancer

Answer 1

• evading growth suppressors
• avoiding immune destruction
• enabling replicative immortality
• tumor promoting inflammation
• activating invasion and metastasis
• inducing angiogenesis
• genome instability and mutation
• resisting cell death
• deregulating. cellular energetics
• sustaining proliferative signaling

Question 2

endogenous damage types

Answer 2

replication errors –> mismatches
Spontaneous loss of nucleosides –> base altercation
chemical exposure –> base alteration

Question 3

exogenous damage types

Answer 3

chemical exposure –> base alteration
UV Light exposure –> Thymine dimer
double strand break –> Ionizing radiation

Question 4

it is estimated that each cell undergoes ____ DNA damaging events and. ____ replication errors per cell per day

Answer 4

> 20,000
10,000

Question 5

Mutation types

Answer 5

chromosomal (segment) + point

Question 6

chromosomal mutations

Answer 6

are mutations that involve changes to the entire chromosome or sections of it
- chronic myeloid leukemia

Question 7

Point Mutations

Answer 7

are changes to one or a few base-pairs in the DNA in the for of substitution, deletion, or insertion

Question 8

substitution point mutation

Answer 8

change of a nucleotide or a few from one type to another

Question 9

insertion point mutation

Answer 9

an insertion of one or a few in the DNA sequence

Question 10

deletion point mutation

Answer 10

a deletion of one or a few nucleotides in the DNA sequence

Question 11

Substitution
pyrimidine –> pyrimidine
purine –> purine

Answer 11

transition

Question 12

Substitution
purine –> pyrimidine
pyrimidine –> purine

Answer 12

transversion

Question 13

Know the substitutions between AGCT

Answer 13

Question 14

what could happen when there’s a disincorporated nucleotide in a mismatch

Answer 14

a) DNA polymerase delta moves backward and degrades recently synthesized strand, then polymerase moves forward again and undertakes once again to synthesize proper sequence

b) misincorporated nucleotide stays

Question 15

oxidative deamination

Answer 15

GC to AT
-adenine deaminase

Question 16

transition mutations

Answer 16

replace a purine with a purine or a pyrimidine with a pyrimidine

Question 17

GC –> CG

Answer 17

transversion
-guanine deaminase

Question 18

CG –>TA

Answer 18

transition
-cytosine deaminase
-most common point mutation in cancer cells

Question 19

Oxidation: ROS such a hydroxyl radical

Answer 19

• Guanine, the base component of dGMP in DNA, can be oxidized
  to 8-oxo-deoxyguanine.
• 8-Oxo-deoxyguanine can base-pair with deoxyadenosine, rather than deoxycytidine

GC –> TA transversion

Question 20

alkylation

Answer 20

the addition of a hydrocarbon molecule

Question 21

methylation

Answer 21

most common type of alkylation
transfer of methyl group of CH3

Question 22

depurination

Answer 22

cleavage of the glycosidic bond connecting purines to the backbone (2,000~10,000 purines/24 h/per cell)

• destabilize the covalent bond to deoxyribose, resulting in the loss of the purine or pyrimidine base from DNA (AP sites, apurinic or apyrimidinic, abasic sites)
• Triggered by endogenous metabolites undergoing chemical reactions
• misread by the DNA polymerase

Question 23

thymine dimer

Answer 23

Ultraviolet radiation (sunlight or tanning lamps) leads to cross-linking of adjacent pyrimidines (thymine) along one strand of DNA

UV

Question 24

double strand break

Answer 24

Ionizing radiations, including X-rays and radioactive decays, and free radical products of oxidative metabolism.

-radiation

Question 25

Cellular response to DNA Damage

Answer 25

Cell Cycle Check Point activation Damage Tolerance DNA Repair Apoptosis

Question 26

checkpoint activation

Answer 26

pauses the cell cycle and gives the cell time to repair the damage before continuing to divide

Question 27

In G0 and early G1

Answer 27

Rb physically associates with E2F factors and blocks their transactivation domain.

Question 28

In late G1

Answer 28

Rb-p releases E2F, allowing the expression of genes that encode products necessary for S-phase progression.

Question 29

cyclin D1

Answer 29

the product of bel-1 gene`

Question 30

direct reversal repair

Answer 30

Cells are known to eliminate damage to their DNA by chemically reversing it. These mechanisms do not require a template, since the types of damage they counteract can only occur in one of the four bases. Such direct reversal mechanisms are specific to the type of damage incurred and do not involve breakage of the phosphodiester backbone.

Question 31

Methylation of guanine bases, is directly reversed by the protein ...?

Answer 31

methyl guanine methyl transferase

Question 32

types of DNA repair

Answer 32

mismatch base excision nucleotide excision repair

Question 33

base excision repair (BER)

Answer 33

1. Apurinic/apyrimidinic (AP) endonuclease is an enzyme that is involved in the DNA base excision repair pathway (BER). 2. in the repair of damaged (deamination, alkylation) DNA. (8-oxo deoxyguanine, 3-methyladenine, deaminated bases) 3. create a nick in the phosphodiester backbone of the AP site which is created when DNA glycosylase removes the damaged base.

Question 34

nucleotide excision repair

Answer 34

1. Identification of the mismatched or mutated DNA strand 2. Nick the mismatched DNA or mutated strand by endonuclease. Remove the mismatch or mutated DNA strand by exonuclease to create a gap. 3. 5’-3’ DNA polymerase fill the gap 4. DNA ligase forms the phosphodiester linkage

Question 35

nucleotide excision repair

Answer 35

1. Identification of the mismatched or mutated DNA strand 2. Nick the mismatched DNA or mutated strand by endonuclease. Remove the mismatch or mutated DNA strand by exonuclease to create a gap. 3. 5’-3’ DNA polymerase fill the gap 4. DNA ligase forms the phosphodiester linkage

Question 36

DNA Repair of UV-induced Thymine Dimer

Answer 36

-Exposure to ultraviolet light causes adjacent thymines to become cross-linked, forming a thymine dimer and disrupting their normal base pairing. 1. Identification of the mismatched or mutated DNA strand 2. An enzyme cut out and remove the damaged DNA. (Excision endonuclease, also called Excinuclease or UV-specific Endonuclease) 3. 5’-3’ DNA polymerase fill the gap 4. DNA ligase forms the phosphodiester linkage

Question 37

Double-Strand Break Repair

Answer 37

a) non-homologous end joining b)homologous recombination repair

Question 38

LigIV

Answer 38

DNA Ligase IV, a specialized DNA ligase that forms a complex with the cofactor XRCC4, directly joins the two ends.

Question 39

slide 28

Answer 39

name - cancer - what kind of repair

Question 40

xeroderma

Answer 40

write facts

Question 41

carcinogens

Answer 41

agents that cause cancer directly

Question 42

procarcinogen

Answer 42

precursor of carcinogen. Turn into carcinogen in the body -80% of cancer caused by environmental & food carcinogens

Question 43

salmonella his-strain

Answer 43

must be grown in the presence of Histidine, and the mutant allele is susceptible to back-mutation to a wild-type allele.

Question 44

ames test assys

Answer 44

many non-carcinogens are converted to carcinogens in the liver small amount of rat liver is added to Ames test to mimic mammalian metabolism

Question 45

Conversion of procarcinogens to carcinogensby Cytochrome P450

Answer 45

Question 46

Intercalating Agents

Answer 46

Several hydrophobic molecules containing flat aromatic and fused heterocyclic rings can insert between the stacked base pairs of DNA. different from alkylating reagents Ethidium bromide, Acridine orange, Actinomycin D

Question 47

oncogenes

Answer 47

cancer-causing genes porto-oncogenes are the corresponding normal cellular genes that are responsible for normal cell growth and division conversion of a proton oncogene to an oncogene can lead to abnormal stimulation of the cell type (gain of functions)

Question 48

proto oncogen abilities

Answer 48

Question 49

tumor suppressor genes

Answer 49

help prevent uncontrolled cell growth mutations that decrease protein functions of tumor-suppressor genes may contribute to cancer onset (loss-of function, defect on two copies) tuomr-suppresor routines : repair damaged DNA, control cell adhesion, inhibit the cell cycle in the cell-signaling pathway

Question 50

tumor suppressor genes pathways

Answer 50

inhibit cell division promote apoptosis inhibit immortality inhibit angiogenesis inhibit metastasis all to inhibit malignant tumor progression

Question 51

multistep model for cancer development

Answer 51

- Multiple mutations (5-7) are generally needed for full-fledged cancer; thus the incidence increases with age - At the DNA level, a cancerous cell is usually characterized by at least one active oncogene and the mutation of several tumor-suppressor genes

Question 52

inference with normal cell signaling pathways

Answer 52

Mutations in the ras gene can lead to production of a hyperactive Ras protein and increased cell division, Ras: oncogene, GTP-bound state of Ras is the "on" state, and the GDP-bound state is the "off" state. mutations in the p53 gene prevent suppression of the cell cycle

Question 53

HNPCC - name of gene - cancer phenotype - enzymes or process affected

Answer 53

4-5 genes colonic polyposis mismatch repair enzymes

Question 54

XP - name of gene - cancer phenotype - enzymes or process affected

Answer 54

8 genes UV-induced skin cancer nucleotide-excision repair

Question 55

AT - name of gene - cancer phenotype - enzymes or process affected

Answer 55

ATM leukemia, lymphoma response to dsDNA breaks