Exam 2: Mutations (contd) and DNA Repair

Question 1

mutations are potentially cause by a number of different factors (4 in this lecture)

Answer 1

1. spontaneous replication errors
2. spontaneous chemical changes
3. chemically induced mutations
4. radiation

Question 2

types of spontaneous replication errors (4)

Answer 2

1. tautomeric shifts
2. mispairing due to other structures
3. incorporation errors and replication errors
4. deletions and insertions

Question 3

what is a tautomeric shift

Answer 3

proton position shifts allowing mispairing

Question 4

causes of deletion and insertions

Answer 4

strand slippage and unequal crossing over

Question 5

when mispairing is due to altered protonation the result is _

Answer 5

a changed nucleotide that does not get corrected in the next round of replication (transition mutation)

Question 6

strand slippage results in

Answer 6

the loss or gain of 1 nucleotide

Question 7

why is strand slippage serious if it happens in a coding sequence

Answer 7

either newly synthesized strand loops out (insertion) or template strand loops out (deletion) cause a frame shift mutation

Question 8

origin of InDels:

Answer 8

unequal crossing over produces insertions and deletions

Question 9

depurination and results in?

Answer 9

loss of purine (A or G) results in a nucleotide that can’t pair

Question 10

deamination and results in?

Answer 10

nitrous acid; loss of an amino group results in biochemical change resulting in a different nucleotide replacing the original (alters DNA bases)

Question 11

relevance of 5mC

Answer 11

a lot of 5mC in our genome which are hotspots for mutations (in promoters) deamination into a thymine

Question 12

what is a base analogue

Answer 12

chemicals with structures similar to normal bases ex 5-bromouracil (resembles thymine) treats neoplasms/research by causing mispairing and replication errors

Question 13

alkylating agent

Answer 13

donate alkyl group (methyl and ethyl groups)

*changes charge, arrangement of atoms, interact with dna/rna/proteins)

Question 14

examples of alkylating agents (2 in this lecture)

Answer 14

1. EMS (ethylmethylsulfonate)

2. mustard gas

Question 15

hydroxylamine

Answer 15

add hydroxyl group

Question 16

oxidative reaction

Answer 16

superoxide radicals ex hydrogen peroxide

Question 17

intercalating agents

Answer 17

proflavin, acridine orange, and ethidium bromide

insert themselves btwn adjacent bases in DNA, distorting the 3D structure of the helix; difficult to replicate

Question 18

some sources of oxidative stress

Answer 18

diet, smoking, fast foods, stress, excessive exercise, alcohol, contaminants

Question 19

t/f: radiation greatly increases mutation rates in all organisms

Answer 19

true

Question 20

ionizing radiation

Answer 20

ex x-rays; dislodges e-s in tissue causing free radicals which often damages dna

Question 21

UV light induces

Answer 21

the formation of pyrimidine dimer, 2 thymine bases covalently bonded that blocks replication; covalent bond makes repair ineffective (if dimer is repaired, if often leads to errors ie mutations)

Question 22

SOS system in bacteria

Answer 22

SOS system allows bacteria cells to bypass the replication block with a mutation-prone pathway

Question 23

detecting mutagens with the ames test:

Answer 23

• bacteria cannot synthesis histidine due to frameshift/point mutation
• placed in histidine deficient media w/ potential mutagen
• if colonies grow, number reflects mutagenicity/carcinogenicity of the substance due to reverse mutation

Question 24

many incorrectly inserted nucleotides that escape proofreading are corrected by _

Answer 24

mismatch repair

Question 25

mismatch repair in proks

Answer 25

new strand is not methylated (until stabilized), parent strand is, and bacterial can recognize the mismatched nucleotide and replace it with the correct seq

Question 26

mismatch repair in euks

Answer 26

euks also have mismatch repair but the parent dna strand is identified by a currently unknown mech

Question 27

inherited defects in mismatch repair

Answer 27

mutations in MLH1 and MSH2 (tumor suppressor genes get turned off my methylation)

Question 28

cologuared cancer screening test works by identifying

Answer 28

highly methylated dna in the promoter of tumor suppressor genes to detect colon cancer (MLH1 and MSH2)

Question 29

how does methyltransferase work

Answer 29

gets rid of extra methyl groups where inappropriate (direct repair of pyrimidine alkylation)

Question 30

base-excision repair

Answer 30

excises modified bases and then replaces one or more nucleotides with the correct original seq

Question 31

nucleotide-excision repair

Answer 31

removes bulky DNA lesions, like pyrimidine dimers, that distort the double helix; distortion is cut out and polymerase and ligase restore the original seq
found in all organisms examined to date

Question 32

thymine dimer repair

Answer 32

(NER) dimer is repaired by enzymes that cut out the surrounding nucleotides and fill the space back in

Question 33

the repair process can be damaged by _

Answer 33

mutation to the genes encoding the repair enzymes; these enzymes lose efficiency w/ age

Question 34

repair of double stranded breaks

Answer 34

homologous recombination or nonhomologous end joining in mammals repair dna double stranded breaks
homologous recombination is more accurate than NHEJ bc of the template (homologous section of dna to act as template for repair)

Question 35

translesion dna polymerases

Answer 35

allow polymerases to skip over distorsions/dimers but often results in mutations (last resort for repairing dna results in predictable types of mutations)

Question 36

type of damage repaired: mismatch

Answer 36

replication errors, including mispaired bases and strand slippage

Question 37

type of damage repaired: base excision

Answer 37

abnormal bases, modified bases, and pyrimidine dimers

Question 38

type of damage repaired: nucleotide excision

Answer 38

dna damage that distorts the double helix, including abnormal bases, modified bases, and pyrimidine dimers

Question 39

defects in NER leads to what types of diseases (3)

Answer 39

1. xeroderma pigmentosum (frecklelike spots on skin, sensitivity to sunlight, predisposition to cancer)
2. cockayne syndrome (dwarfism, sensitivity to sunlight, premature aging; developmental and neurological)
3. trichothiodystrophy (brittle hair, skin abnormalities, short stature; developmental and neurological)

Question 40

defect in mismatch repair leads to

Answer 40

hereditary nonpolyposis colon cancer (predisposition to colon cancer)

Question 41

defect in homologous recombination leads to

Answer 41

werner syndrome (premature aging, predisposition to cancer)

Question 42

bloom syndrome:

Answer 42

mutations in gene encoding dna helicase results in flaws in sister chromatid exchange (autosomal recessive)

Question 43

base analogs are mutagenic bc:

Answer 43

they are similar in structure to the normal bases and can replace them causing errors in replication

Question 44

websites curated by NIH

Answer 44

-predicting deleterious mutations