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1

What is a mutation?

A mutation is a change in the normal base pair sequence

2

If left unrepaired, mutations in the genetic code or in regulatory regions that impact gene expression, what can happen?

Cell cycle arrest, cell death (apoptosis), genomic instability and disease (like cancer)

3

Most instances of inherited syndromes with defects in DNA repair involve ___ mutant alleles.

Recessive

4

What are the three classes of small-scale mutations (point mutations)? Describe them.

1. Base substitutions and modifications (replacement or modification of a single base; transitions (Pu/Pu or Py/Py) and transversions (Pu/Py); methylation; unnatural bases)
2. Deletions (one or more nucleotide is eliminated, leading to frameshift)
3. Insertions: copy/duplicative transposition (duplicated copy moved to another location); non-copy transposition (movement to a new location), leads to frameshifts)

5

What are the four major types of large scale mutations/changes that occur at the chromosomal level?

1. Amplification (gene duplications)
2. Deletions
3. Translocations (fusions or inversion)
4. Loss of heterozygosity

6

What are allelic sequence variations?

Allelic sequence variations are polymorphisms arising with a frequency >1%.

7

What is the average heterozygosity for human genomic DNA?

1:250-1:1000 bases are different between allelic sequences

8

What can be used to distinguish between individuals?

SNPs (single nucleotide polymorphisms)

9

Mutations that change alleles can produce new genetic traits; some are good, leading to ___, and some are deleterious, leading to ___.

Adaptation; Disease susceptibility

10

What are de novo mutations and where can they occur?

Naturally occurring mutations; they can occur in both somatic cells and germline cells

11

Are somatic mutations heritable? Why or why not?

No, they only affect those cells that result from mitotic division; mutations can accumulate in these cells, leading to disease

12

Are germline mutations heritable? Why or why not?

Yes, they affect all cells, thus increasing the susceptibility to disease

13

What are the sources of de novo mutations?

Copying errors, spontaneous chemical attack, environmental exposure

14

Describe how spontaneous DNA alterations occur.

Bases within DNA are altered through several types of endogenous attack, including oxidative damage, hydrolytic attack, or modifications.

15

What are the most frequent types of chemical attack?

1. Depurination of AG (hydrolytic cleavage of the bases from the sugar backbone)
2. Deamination (typically the removal of amino group from C, leading to conversion to U)

16

Replication and environmental factors can result in DNA mutations. Different types of damage can result in the activation of ___, which usually remove the mutagenic lesion.

Specific removal pathways

17

How do cells deal with mutated DNA that is not repaired?

If the rate of DNA damage = the rate of repair, the cell remains healthy. If the rate of DNA damage > the rate of repair, damage accumulates, which can lead to excessive proliferation (cancer), senescence (halted growth), or apoptosis (cell death)

18

What are the three general classes of DNA repair mechanisms?

1. Direct repair (damage reversal)
2. Excision repair (remove and replace - BER, NER, TCR, MMR)
3. Double-stranded break repair (HEJ, NHEJ)

19

What are the four types of excision repair?

1. Base excision repair (BER)
2. Nucleotide excision repair (NER)
3. Transcription coupled repair (TCR)
4. Mismatch repair (MMR)

20

True or False: Most lesions can be repaired by more than one mechanism.

True

21

What does direct repair do?

Direct repair reverses base damage in a quick, though energetically costly manner.

22

Describe the direct repair mechanism.

O6-meG, an abnormal base, can base pair to C or T. O6-meG can block polymerase. MGMT (O6-meg methyl transferase) removes the methyl group and reverses the base damage.

23

What does base excision repair (BER) do?

Uses specific glycosylase enzymes to recognize and remove abnormal bases and generate AP (abasic) sites. AP endonuclease and phosphodiesterase cut the backbone, fill the gap, and seal.

24

BER dysfunction has been linked to disease progression in ___.

Alzheimer's disease

25

What does nucleotide excision repair (NER) do?

Removes bulky lesions that distort the helix. The gap is repaired.

26

What are the two types of NER?

General/global NER and transcription coupled repair (TCR)

27

What is the difference between general NER and TCR?

TCR is specifically associated with active transcription.

28

What does mismatch repair (MMR) do?

Repairs mistakes AFTER DNA replciation and before mitosis

29

What are the four common steps of DNA excision repair?

1. Recognition of damage
2. Cleavage by endonuclease
3. Removal by nuclease or helicase activity
4. Replacement by polymerase and ligase activity

30

Describe the process of base excision repair.

1. Specific glycosylases recognize specific altered bases and generate abasic (AP) sites by cleaving the glycosidic bond between a base and the sugar.
2. An AP endonuclease and phosphodiesterase remove the sugar phosphate.
3. DNA polymerase adds new nucleotides.
4. DNA ligase seals the nick.