origins of mutations and DNA repair

Question 1

somatic vs germline mutation

Answer 1

germline is passed on, inherited

somatic can cause cancer

Question 2

gene mutations vs chromosome and genome

Answer 2

gene mutations affect only one gene, only one base
chromosomal mutations affect many genes
genome mutations affect entire chromosomes

Question 3

point mutation types, causes, effects

Answer 3

silent: no change in codon, no effect on protein
missense: change in codon, decrease in function
nonsense: codon changed to stop, truncation
RNA processing: affects splice site, addition or deletion

Question 4

small insertions and deletions

Answer 4

type of gene mutation

include strand slippage/triplet repeat expansion and frameshift mutation

Question 5

strand slippage/triplet repeat expansion

Answer 5

CAG/CTG repeats can result in single strand loops during replication because strand can be displaced or slipped
new DNA will carry extra triplets

Question 6

frameshift mutation

Answer 6

caused by intercalating agents (acridine dyes, ethidium bromide, doxorubicin)
insertion or deletion of one or more nucleotides
results in “frameshift” where codons downstream of mutation are altered
nonfunctional protein or shortened

Question 7

incorrect recombination

Answer 7

incorrect alignment during recombination may cause unequal crossover
nonhomologous regions are exchanged, leading to gain/loss of gene

Question 8

clinical correlation of unequal crossover

Answer 8

alpha thalassemia

cri-du-chat

Question 9

miss-segregation/nondisjunction

Answer 9

incomplete separation of chromosomes during anaphase I or II
germ cells end up with more or fewer chromosomes than normal
frequency of nondisjunction increases with maternal age
trisomy, monosomy, triploidy, or tetraploidy

Question 10

depurination

Answer 10

purine (A or G) can be cleaved off, forming an abasic site where deoxyribose lacks a base
can cause mutations

Question 11

deamination

Answer 11

cytosine can be converted to uracil via spontaneous deamination
U pairs with A in next replication, producing GC to AT transition mutation
repaired via base excision repair

Question 12

DNA polymerase

Answer 12

elongates DNA during replication

also aids in repair, has proofreading activity

Question 13

DNA helicase

Answer 13

unwinds DNA double helix for replication

uses ATP

Question 14

DNA ligase

Answer 14

connects Okazaki fragments at end of replication

Question 15

exonuclease

Answer 15

a

Question 16

primase

Answer 16

synthesizes RNA primer necessary for replication of lagging strand

Question 17

strand-directed mismatch repair

Answer 17

corrects replication errors during G2 phase
MSH2 recognizes mismatch near single-strand nick, signals need for repair
MLH1 coordinates excision of incorrect BP
gap is filled by DNA polymerase
backup plan to polymerase delta

Question 18

clinical correlation of strand-directed mismatch repair

Answer 18

hereditary nonpolyposis colorectal carcinoma (HNPCC)

Question 19

base excision repair

Answer 19

repairs damage due to deamination
C that has been converted to U is recognized and removed by uracil DNA glycosylase
glycosylase hydrolyzes U, leaves bond intact
AP endonuclease recognizes missing base, cuts strand on one side of missing base
DNA phosphodiesterase removes deoxyribose phosphate
DNA polymerase and ligase fill and seal gap

Question 20

nucleotide excision repair

Answer 20

repairs thymine dimers that form as a result of UV light
distortion in helix identified, then helicase separates strands
excision endonuclease cuts at either side of lesion
polymerase and ligase re-synthesize damaged strand

Question 21

clinical correlation of nucleotide excision repair

Answer 21

xeroderma pigmentosum

extreme sensitivity to light, excessive freckling, carcinoma/melanoma

Question 22

nonhomologous end joining

Answer 22

fixes DS breaks
repair proteins bring together ends of broken strands, but nucleotides are lost at breakpoint
usually used to repair noncoding DNA regions, therefore does not result in nonfunctional proteins

Question 23

homologous end joining

Answer 23

uses recombination to fix broken DNA
undamaged homologous chromosome is used as template for repair of damaged chromosome
allows repair of DS breaks WITHOUT LOSS of information

Question 24

proofreading activity of polymerase

Answer 24

polymerase delta has 3’-5’ exonuclease activity
edits 3’ end of growing strand during S phase
rereads strand and if base pairing is wrong, hydrolyzes phosphodiester bond and starts over until correct

Question 25

cytarabine

Answer 25

analogue of cytidine competes with dNTPs for binding of DNA polymerase, blocking DNA replication S phase inhibitor used in AML and non-Hodgkin's

Question 26

cyclophosphamide

Answer 26

``` forms DNA crosslinks, blocking DNA uncoiling blocks replication triggers apoptosis bi-functional alkylating agent used in Hodgkin's, breast, lung, etc. ```

Question 27

doxorubicin

Answer 27

targets topo II, topo poisoning by trapping at replication sites can cause frameshift mutation by intercalating during replication

Question 28

radiation

Answer 28

causes cross-linking of pyrimidines, usually thymine, producing dimers thymine dimers can block replication in next round

Question 29

oxidative damage

Answer 29

commonly occurs at guanine residues due to high oxidation potential ROS oxidizes guanine to 8-hydroxyguanine 8H can pair with adenine, resulting in GC to AT transition mutation

Question 30

clinical correlation of triplet repeat expansion

Answer 30

Huntington disease | fragile X and myotonic dystrophy

Question 31

gene polymorphism

Answer 31

genes may have more than two sequence variants that are slightly different from one another equally acceptable variants, called polymorphic sequence variants

Question 32

Huntington disease

Answer 32

triplet expansion in coding region | abnormal protein contains > 30 adjacent glutamines

Question 33

fragile X and myotonic dystrophy

Answer 33

tandem repeats of nucleotides in untranslated region of FMR1 or DMPK

Question 34

trisomy 13

Answer 34

Patau syndrome

Question 35

trisomy 18

Answer 35

Edward syndrome

Question 36

trisomy 21

Answer 36

Down syndrome

Question 37

monosomy

Answer 37

missing copy of chromosome dur to nondisjunction | always lethal in autosomes

Question 38

mosaicism

Answer 38

embryonic cell loses third chromosome in setting of trisomy, forming a normal cell other embryonic cells still trisomic --> mosaic nature of phenotype

Question 39

chromatin mutations

Answer 39

type of genome mutation | caused by changes in DNA methylation or histone protein modification

Question 40

DNA repair mechanisms

Answer 40

``` base excision repair nucleotide excision repair non-homologous end joining homologous end joining strand-directed mismatch repair proofreading by DNA polymerase ```