The origins of mutations and DNA replication/repair

Question 1

What is depurination?

Answer 1

bond between base and deoxyribose of DNA spontaneously hydrolyzes; approximately 5000 purine bases (adenine or guanine) are lost ever yday

Question 2

Approximately 5000 purine bases are lost every day due to what process?

Answer 2

depurination

Question 3

What is deamination?

Answer 3

spontaneous conversion of cytosine to uracil

Question 4

What are pyrimidine dimers?

Answer 4

UV light from the sun or elsewhere can cause dimerization of adjacent thymine bases on the same DNA strand..

thymine –> thymine dimer

Question 5

Explain a somatic mutation (3 concepts)

Answer 5

1. affects only the cell where the mutation occurred and the progeny of that cell
2. can be problematic if affects proliferation
3. if mutation occurs in early embryogenesis then the affected individual will harbor a significant amount of mutant cells referred to as mosaicism

Question 6

Explain the concept of a germline mutation?

Answer 6

Will be passed on to offspring

Question 7

What are the 4 types of mutations (based on levels)?

Answer 7

1. gene mutations
2. Chromosomal mutations
3. Genomic mutations
4. mutations impacting chromatin

Question 8

What will a miss-segregation of chromosomes during meiosis or mitosis cause?

Answer 8

genome mutation

Question 9

What is the frequency of a genome mutation?

Answer 9

10^-2

Question 10

What results from rearrangements of chromosomes following DNA double stand breaks or faulty recombination?

Answer 10

Chromosome mutation

Question 11

Freq of a chromosome mutation?

Answer 11

6 x10^-4

Question 12

What results from a nucleotide exchange, insertion, or deletion?

Answer 12

10^-10

Question 13

What are the two main ways in which a mutation can alter the nucleotide sequence of a gene?

Answer 13

1. point mutation

2. small insertions and deletions

Question 14

What is a silent mutation?

Answer 14

change in nucleotide sequence does NOT result in a change in AA sequence

Question 15

What type of point mutation causes a change in nucleotide sequence that does result in a change in the AA sequence?

Answer 15

missense

Question 16

What is a nonsense mutation?

Answer 16

change in nucleotide

Question 17

What is a missense mutation?

Answer 17

change in nucleotide does result in a change in AA sequence

Question 18

What type of point mutation causes a change in a nucleotide sequence that does not result in a change in the AA sequence of the encoded protein?

Answer 18

silent mutation

Question 19

What causes a change in nucleotide sequence destroys an RNA splicing site or generates a novel splicing site?

Answer 19

RNA mutant

Question 20

Small insertions or deletions result by 3 distinct mechanisms. What are they?

Answer 20

1. incorrect recombination
2. strand slippage during replication
3. intercalating agents

Question 21

What occurs during incorrect recombination?

Answer 21

unequal crossing over, which results in loss or addition of genetic material

Question 22

Where is incorrect recombination most likely to occur?

Answer 22

at loci that contain repetitive DNA

Question 23

Explain strand slippage?

Answer 23

in areas of repetitive sequences, the strand may loop out and slip; causing the DNA replication machinery to copy the strand twice! AH!

Question 24

What do intercalating agents result in?

Answer 24

insertions or deletions of one or more nucleotides during DNA replication

Question 25

Insertion or deletion of a number of nucleotides that is not a multiple of three will result in what?

Answer 25

frameshift mutation

Question 26

Frameshift mutations account for what % of human genetic diseases?

Answer 26

25%

Question 27

In anaphase, what can occur to homologous chromosomes that is bad?

Answer 27

Nonjud\sjunction: less to germ cells with surplus or missing chromosomes

Question 28

At the completion of anaphase, the cell divides, giving rise to how many cells with how many chromosomes?

Answer 28

2 haploids; 23 chrom

Question 29

What are the 4 types of DNA repair mechanisms?

Answer 29

1. DNA polymerase proofreading 2. Strand-directed mismatch repair 3. Base excision repair 4. Nucleotide excision repair

Question 30

Explain the concept of DNA poly proofreading.

Answer 30

3-5 exonuclease activity, re-reads the base pairing and will fix any mistakes

Question 31

Explain strand-directed mismatch repair.

Answer 31

A newly synthesized strand contains gaps and nicks which identify the strand and DNA repair mech recognize the distortion in the helix. Enzymes recognize the error and chew it back to the nearest nick, and gap is filled in by DNA poly.

Question 32

What disease is related to stand-directed mismatch repair?

Answer 32

Lynch Syndrome/HNPCC: hereditary nonpolyposis colorectal carcinoma; defects in mismatch repair and have a high risk of developing colon cancer

Question 33

Explain base excision repair.

Answer 33

DNA glycosylases recognize specific types of altered bases in DNA and catalyze hydrolytic removal

Question 34

Common example of base excision repair.

Answer 34

1. cystosine gets deaminated to uracil. 2. uracil DNA glycosylase removes the bad base. 3. The sugar-phosphate backbone remains intact. 4. AP endonucleases then recognize that a base is missing and cut the sugar phosphate backbone 5. DNA phosphodiesterase removes the deoxyribose phosphate group and gap is filled in by DNA ploly

Question 35

Explain nucleotide excision repair.

Answer 35

repairs damage caused by agents that result in large changes in the structure of DNA. AKA pyrimidine dimers. Repair things recognize distortions; helicase unwraps it; and nucleases cut out the defective strand.

Question 36

Clinical correlation to nucleotide excision repair?

Answer 36

xeroderma pigmentosum

Question 37

Describe non-homoglous end joining vs homologous end joining.

Answer 37

DNA damaging agents can cause double stranded breaks. NHEJ: the ends of the double stranded break are cut, resulting in the loss of a nucleotides or nucleotides and put back together HEJ: recombination processes are used to repair broken DNA; it uses info from one strand to fix the break without losing info

Question 38

What is xeroderma pigmentosum?

Answer 38

mutations in nucleotide excision repair; leads to extreme sensitivity of skin to sunglight, pigmentation changes, etc

Question 39

What are 3 inhibitors of DNA replication in chemotherapy?

Answer 39

Cytarabine: analouge of cytidine that contains arabinose; competes for binding to DNA poly Cyclophosphamide; bi-functional alkylating agent; works in the liver and converted to phosphoramide mustard; and inter-intra strands formed with DNA; blocks replication Doxorubicin: inhibits top II; causing double-stranded breaks to accumulate; strand cant be re-ligated