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Oncology > Chapter 2: DNA structure and stability: mutations vs. repair (Lecture 1) > Flashcards

Chapter 2: DNA structure and stability: mutations vs. repair (Lecture 1) Flashcards

1
Q

What will be discussed in the lecture? (you obv don’t have to know this, just so you know what you can expect)

A

1) DNA maintenance and cancer.
2) Type of DNA aberrations.
3) Causes of DNA aberrations: exogenous & endogenous.
4) DNA Repair mechanisms: cancer-predisposition syndromes.
5) Cancer therapeutics.

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2
Q

How does a DNA molecule look? (you should be able to identify all structures, but because I deem this basic knowledge, there is only one card about it)

A
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3
Q

Explain the process of genetic stability and genetic instability

A
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4
Q

Cancer can result from (epi)genetic alterations in human Cancer Genes. What are the three categories for this?

A
  1. Stability genes (e.g. repair)
  2. Oncogenes (eg growth factors)
  3. Tumor suppressor genes

note: tumors can also be caused by DNA tumor viruses

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5
Q

Explain for each category of (epi)genetic alterations whether there is activation or inactivation so that cancer can ‘occur’. (1. stability genes, 2. oncogenes, 3. tumor suppressor genes)

A
  • Activation: oncogenes
  • Inactivation: stability genes and tumor suppressor genes
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6
Q

Changes in the DNA can be divided into small and larges changes. What are some examples for each group?

A
  • Small changes: Base pair substitutions, deletions or insertions, single- and double-strand breaks.
  • Large changes: Changes in DNA content per nucleus, chromosome rearrangements, gene amplifications.
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7
Q

Are all DNA changes oncogenic?

A

No

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8
Q

What can base pair substitutions (also called point mutation) lead to? (3 answers)

A

A point mutation may cause a silent mutation if the mRNA codon codes for the same amino acid, a missense mutation if the mRNA codon codes for a different amino acid, or a nonsense mutation if the mRNA codon becomes a stop codon.

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9
Q

What are examples of frameshift mutations?

A

Insertions and deletions

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10
Q

What can frameshift mutations (insertions/deletions) cause?

A

A change in the reading frame and/or a premature stop codon

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11
Q

What is more dangerous and why; single strand breaks or double strand breaks?

A

Double strand breaks because there is a risk for deletions and large chromosome rearrangements. It is also extremely toxic

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12
Q

DNA aberrations can be exogenous or endogenous. What are risk factors for exogenous DNA aberrations?

A
  • smoking: polycyclic aromatic hydrocarbons (PAHs)
  • drinking: alcohol
  • sun: UV - radiation
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13
Q

DNA aberrations can be exogenous or endogenous. What are risk factors for endogenous DNA aberrations?

A
  • DNA replication mistakes
  • reactive oxygen species (ROS)
    • Oxidative phosphorylation in the mitochondria produces reactive oxygen species
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14
Q

What type of genetic alteration (by a DNA-damaging agent) is depicted in this figure? What is it caused by?

A

A pyrimidine dimer caused by UV

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15
Q

What type of genetic alteration (by a DNA-damaging agent) is depicted in this figure? What is it caused by?

A

Strand break by X-rays

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16
Q

What type of genetic alteration (by a DNA-damaging agent) is depicted in this figure? What is it caused by? add fig

A

Bulky adduct by PAH

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17
Q

What can cause base loss?

A

Spontaneous hydrolysis

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18
Q

What type of genetic alteration (by a DNA-damaging agent) is depicted in this figure? What is it caused by?

A

6-4 photoproduct by UV

(note the difference between a pyrimidine dimer by UV where there’s a double bond between the thymines)

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19
Q

What type of genetic alteration (by a DNA-damaging agent) is depicted in this figure? What is it caused by?

A

Interstrand crosslink by nitrogen mustard, cisplatin and MMC

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20
Q

What type of genetic alteration (by a DNA-damaging agent) is depicted in this figure? What is it caused by?

A

Intrastrand adduct by cisplatin

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21
Q

What can a modified base be caused by?

A

Alkylating agents, such as reactive oxygen

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22
Q

For overview purposes, what are the different genetic alterations induced by DNA-damaging agents?

A
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23
Q

Oxidative stress can cause 8-oxoguanine. How does this look different from a normal guanine?

A

As indicated by the red circle and green arrow, an O and N is added

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24
Q

What can 8-oxoguanine be caused by?

A

Ionizing radiation or normal cellular metabolism (aging)

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25
Q

Why is 8-oxoguanine potentially mutagenic?

A

Because DNA polymerase reads it as a thymine, (wrong nucleotide -> wrong amino acid -> harmful for the protein)

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26
Q

There are many DNA repair mechanisms. How are all the mechanisms called from each of the following DNA aberrations?

  1. Damaged base
  2. Bulky adducts
  3. Replication errors
  4. Strand break
  5. Cross-links (we are going to discuss this step by step, but you really ought to know this!)
A
  1. Damaged base: base excision repair
  2. Bulky adducts: nucleotide excision repair
  3. Replication errors: mismatch repair
  4. Strand break: homologous recombination repair or non-homologous end joining
  5. Cross-links: complex repair (coordinated by the FA pathway)
27
Q

What does it mean when a gene/allele is recessive?

A

Both alleles have to be mutated for abnormalities to occur

28
Q

What does it mean when a gene/allele is dominant?

A

Only one allele has to be mutated for abnormalities to occur

29
Q

As we all know, mutations in DNA repair genes are cancer-predisposition syndromes. What are some recessive examples of that? (this will be discussed in greater detail, but you should really know this!)

A
  • Ataxia telangiectasia (leukaemia, lymphoma)
  • Fanconi anemia (leukaemia, squamous cell carcinoma)
  • Xeroderma pigmentosum (skin cancer)
  • Nijmegen breakage syndrome (lymphoma)
  • Bloom’s syndrome (all types)
30
Q

As we all know, mutations in DNA repair genes are cancer-predisposition syndromes. What are some dominant examples of that? (this will be discussed in greater detail, but you should really know this!)

A
  • HNPCC (colon)
  • BRCA1/BRCA2 (breast, ovary, pancreas)
31
Q

DNA repair is a complex multi-step process where multiple proteins are involved. However the mechanism for this is similar for all the repair mechanisms. What are the steps for the repair mechanisms?

A
  1. Signaling damage
  2. Recognition damage
  3. Removal
  4. Repair
32
Q

What type of repair is the Fanconi/BRCA pathway involved in?

A

DNA breaks and cross-links

33
Q

Why are double-stranded breaks (that occurs in e.g. BRCA pathway) so dangerous?

A

They are lethal if they are not repaired and can give rise to large deletions. They are the cause of many chromosomal abnormalities (aberrations, translocations)

34
Q

Which cancer predisposition syndromes are linked to homologous recombination (that ‘fixes’ double-strand break repair)

A
  • Ataxia telangiectasia (ATM)
  • Fanconi anemia (BRCA/FA pathway)
    • BRCA1 and BRCA2
35
Q

What are the different steps of the repair homologous recombination for double-strand break repair? (also mention the proteins involved)

A
  1. ATM (ataxia telangiectasia mutated) is activated, this is a tumour-supressor gene that transduces a double-strand break repair signal to downstream effector machinery when activated
  2. 5’-3’ exonuclease activity of RAD50/MRE11/NBS1 complex digests damaged strands to expose single stranded regions
  3. RAD proteins promote sensing of homologies
  4. RAD proteins facilitate strand exchange (RAD51)
  5. DNA polymerase, ligases and resolvases restore the four strands
36
Q

Can you explain how the homologous recombination double-strand break repair looks like?

A
37
Q

Patients with Fanconi anemia (BRCA / FA pathway) should not drink or smoke. Why?

A

They have a 700x higher chance of mutations and moreover the cancer treatment is harder than non-FA patients

38
Q

What are two examples of intracellular processes causing damaged nucleotides?

A
  • Free radical oxidations (8-oxoguanine)
  • Deaminations (cytosine to uracil)
39
Q

How is the type of repair called that removes damaged nucleotides?

A

Base excision repair

40
Q

Which enzyme recognizes a damaged base (in the process of base excision repair)?

A

DNA glycosylase

41
Q

The DNA glycosylase recognizes and removes the damaged base. How is this site called that has no base?

A

AP (apurinic/apyrimidinic) site (also called an abasic site)

42
Q

What does an abasic (AP) site look like?

A
43
Q

When happens in the base excision repair after DNA glycosylase has removed the damaged base?

A

An AP endonucelase cleaves the deoxyribosephosphate chain 5’ to the damaged base to create a 3’ hydroxyl group

44
Q

In the process of bas excision repair, an abasic site and a 3’ hydroxyl group is formed. In the last step, a base is replaced. By which enzyme?

A

DNA polymerase II

45
Q

For overview purposes, what are the different steps of base excision repair?

A
  1. A DNA glycosylase recognizes and removes a damaged base
  2. An AP/abasic site is formed
  3. An AP endonuclease cleaves the deoxyribosephosphate chain 5’ to the damaged base to create a 3’ hydroxyl group
  4. The 3’ hydroxyl group is used by DNA polymerase II to replace one base
46
Q

How does the process of base excision repair look?

A
47
Q

Which cancer-predisposition syndrome is associated with the base excision repair? Also explain a little about the genes involved.

A

Colerectal cancer is associated with base excision repair. Here, there’s inherited deficiencies in DNA glycosylase MUTYH linked to familial adenomatous polyposis (FAP) MUYTYH is involved in the repair of 8-oxoguanine damage.

48
Q

Thus far, we have discussed double-strand break repair and base excision repair. Now we will discuss nucleotide excision repair. What does this look like and how is it induced?

A

Nucleotide excision repair removes both small oxidative DNA damages and gross DNA distortions. It is induced by UV-induced pyrimidine dimers and large chemical adducts

49
Q

True/false: the process of nucleotide excision repair is similar to the base excision repair in that only one base/nucleotide is removed and replaced.

A

False, although only one base is removed and replaced in base excision repair, in nucleotide excision repair a stretch of 25-30 nucleotides are removed

50
Q

Which cancer-predisposition syndrome is associated with the nucleotide excision repair? What are the clinical symptoms of this genetic disorder?

A

Xeroderma Pigmentosum, the clinical symptoms are extreme sun sensitivity, sun-exposed skin freckled and up to 1000x increased skin cancer

51
Q

Thus far we discussed base excision repair, nucleotide excision repair, strand break repair. Now we will discuss mismatch repair. Is this repair a pre- or post replication repair?

A

Post-replication repair (of the newly synthesized daughter strand)

52
Q

Which cancer-predisposition syndrome is associated with the mismatch repair? In what gene is a mutation?

A

Hereditary non-polyposis colerctal cancer (HNPCC, aka Lynch syndrome). There is a mutation in MSH2 or in MLH1

Note: this is distinct from FAP (she doesn’t explain how in the lecture unfortunately)

53
Q

We now move on to the fifth subject of this deck: cancer therapeutics. I would like to say beforehand that this lady did not explain anything on how they work, so if you feel that the information is limited and you do not understand… first of all: same, second of all: I really put in everything that was discussed in the lecture so I assume that this is all you need to know

A

:) (this also applies to the previous flashcards)

54
Q

Why is knowledge on DNA repair important?

A

So that we can develop personalized medicine

55
Q

True/false: Only hereditary tumors have specific DNA repair defects

A

False, also non-hereditary tumors can have specific DNA repair defects

56
Q

A medicine, called cisplatin inhibits cancer (cytostatica). Can you explain for which type (gene) of cancer this works?

A

In BRCA1 carriers (=one allele is mutated). Here, there’s BRCA1 loss which causes a defect in homologous recombination of cancer cells (this is not the case for normal cells). These cancer cells are sensitive to DNA cross-linkers like cisplatin (which causes apoptosis of cancer cells) and can therefore be used as a treatment.

57
Q

Why are the normal cells of a BRCA1-carrier not affected by cisplatin?

A

Because the normal cells do not have an HR defect.

58
Q

Why can cisplatin not be used in patients with biallelic mutations (=two alleles are mutated) in the homologous recombination gene (BRCA)?

A

Because tumors, as well as normal cells are sensitive to cisplatin. All cells will then be killed.

59
Q

So can a fanconi patient get a cisplatin treatment?

A

No, because it has a biallelic mutation! This will have an adverse effect and will lead to hospitalization and death

60
Q

What does synthethic lethality mean?

A

Synthethic lethality arises when a combination of deficiencies in the expression of two or more genes leads to cell death, whereas a deficiency in only one of these genes does not.

61
Q

How can synthetic lethality be used as a cancer therapeutic (explain with a gene mutation)?

A

For example, BRCA1 carries have a defect in the BRCA1-gene. By mutating another gene (using a PARP inhibitor), this will result in cell death only in those cells that have a mutation (thanks to synthetic lethality)

62
Q

What are the highlights of this chapter? (you obv don’t have to know this)

A
  • DNA damage in relation to DNA repair mechanisms.
  • When DNA repair goes wrong:
    • consequences for the individual (cancer predisposition syndromes; non-hereditary cancer).
    • consequences for the treatment of cancer.
63
Q

Which of the four figures is the right one?

1) A
2) B
3) C
4) D

A

B

see the figure for explanation

64
Q

The shown situation is a step in the following DNA repair mechanism:

  1. Base-excision repair
  2. Nucleotide-excision repair
  3. Mismatch DNA repair
  4. Cross-link repair by the FA network
A
  1. Base-excision repair

Note: she did not give the answer in the lecture, I am quite sure this is the correct answer, but feel free to correct me!

Oncology (18 decks)

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