DNA Repair, Recombination, and Rearrangement Flashcards
(42 cards)
1
Q
Things that cause damage to DNA
A
- ionizing (x/gamma rays) and UV radiation
- methylating reagants such as MNNG
- cross-linking reagents such as the anticancer drug cisplatin
- bulky hydrocarbons such as bento-a-pyrene (carcinogen from tobacco smoke)
2
Q
DNA repair mechanisms
A
- photoeactivation
- removal of alkyl guanines
- nucleotide excision repair
- base excision repair
- mismatch repair
- double-strand break repair
- daughter strand gap repair
3
Q
mutation
A
any heritable (permanent) change in the structure of an organism’s DNA or chromsomes
4
Q
loss of function mutations
A
- gene product has less or no function
- phenotypes are most often recessive
- exception: haploinsufficiency
5
Q
null allele
A
- allele that has a complete loss of function
- amorphic mutation
6
Q
haploinsufficiency
A
when the reduced dosage of a normal gene product isn’t enough for a normal phenotype
7
Q
gain of function mutation
A
- change the gene product such that it gains a new and abnormal function
- usually have dominant phenotypes
- aka neomorphic mutation
8
Q
dominant negative mutation
A
- aka antimorphic mutation
- have an altered gene product that acts antagonistically to the normal allele
- usually result in altered molecular function (often inactive)
- characterized bu a dominant or semi-dominant phenotype
9
Q
lethal mutation
A
- lead to a phenotype incapable of effective reproduction
- leads to death
10
Q
whole chromosome or genome level mutation
A
- fragment deletions/insertions (gene aberrations)
- inversions
- ploidy changes
11
Q
molecular or base-pair level mutation
A
- deletions
- insertions
- substitutions (point mutations)
12
Q
origins of mutations
A
- errors during DNA replication
- errors in chromosome alignments & separation during mitosis and meiosis
- spontaneous chemical changes in base structure
- induced chemical changes in base structure
13
Q
polymerase I & III function
A
- exonuclease proof-reading
- corrects mistakes
14
Q
tautomeric shifts
A
- spontaneous mutations
- the spontaneous isomerization of a nitrogenous base to/from keno and enroll forms or to/from amino and amino forms
- cause transition mutations
- replacement occurs in second generation of replication
15
Q
transition mutation
A
one purine/pyrimidine base pair is replaced with the other purine/pyrimidine base pair
16
Q
transversion mutation
A
replacement of a purine//pyrimidine with a pyrimidine/purine pair
17
Q
Sickle Cell Anemia
A
- effect of a single missense mutation
- B-hemoglobin
- mutation in hemoglobin causes Hb^s phenotype
- glutamic acid is instead mutated to valine (hydrophilic to hydrophobic amino acid)
- hydrophobic nature causes the hemoglobin to oligomerize
18
Q
principal cause of cancer
A
genomic instability resulting from defective repair of DNA damage
19
Q
Endogenous DNA-damaging reactions
A
- depurination of adenine
- deamination of cytosine
- oxidation of guanine
- methylation of guanine
- oxidation of thymine
20
Q
depurination
A
removes purine from backbone of nucleotide
21
Q
deamination
A
removes amine from part of the base and turn it into a different base
22
Q
oxidation
A
occurs most often
-why you should eat antioxidants!!!
23
Q
photolyases
A
- repair DNA damage
- use light energy to break bonds linking pyrimidine rings
- mammals and frogs don’t have this repair mechanism
- uses FADH to break pyrimidine-pyrimidine bonds
- 1 of 2 enzymes that uses direct repair
24
Q
alkyltransferases
A
- repair DNA damage
- 1 of 2 enzymes that uses direct repair
- methylating agents yield modified bases (that could induce mutagenesis or death if not repaired)
- some used in cancer therapy bc of ability to block replication
- most common product of alkylation = O6 methyl guanine (can lead to AT mutations if not repaired)
- alkyltransferase can only function once, but alkylated form can activate the transcription of the gene encoding alkyltransferase
25
nucleotide excision repair
- indirect mechanism
- used to repair thymine dimers and bulky adducts
- involves bending DNA and endonuclease cleavage on either side of the dimer on the single DNA strand
- helicase, polymerase, and ligase complete the repair
26
bulky adducts
- aka polycyclic aromatic hydrocarbons
| - environment-damaging agents that only interact with DNA when they are activated in our bodies
27
removal of uracil from DNA
- one of the best understood base excision repair systems
- uracil can arise from incorrect incorporation or deamination of cytosine
- UNG removes dUMP resides in DNA
- enzyme that removes the ribose-phosphate is called deoxyribose-5'-phosphatase
- has to happen so GC doesn't transition to AT
28
structure of the uracil-binding pocket of human UNG
- uracil-DNA N-glycosylase
- acts by flipping the uracil base out of the DNA duplex and into a pocket where cleavage occurs
- pocket is small enough to exclude purine bases & prevents thymine from binding between C5 methyl group of thymine and Tyr-147
- doesn't discriminate between U's paired with A's or G's
29
BER (base excision repair) of oxidative damage
- 8-oxoguanine is an abundant ROS (reactive oxygen species) oxidation product
- C-oxoG base pair becomes A-oxoG in a second round of replication & A-T after a 3rd round
- both bacteria and humans have BER enzyme system to recognize and repair oxoG bases
- in humans, OGG1 DNA glycosylase recognizes and cleaves oxoG base
- transversion mutation
30
methyl-directed mismatch repair in E. coli
- mismatch repair enzymes identify the newly replicated strand by its lack of methylation at -GATC- sites by MutS
- MutHLS complex scans the DNA for the nearest 5'-GATC sequence, cleaving to the 5' of G in the unmethylated strand and excising the DNA back past the mismatch
- DNA pol III and ligase complete the repair
31
double strand break (DSB) repair through homologous recombination
- genetic defects involving DSB in the BRCA1 and BRCA2 genes are risk factors for breast/ovarian cancer
- DSBs are the most lethal form of DNA damage bc it destroys the physical integrity of the chromosome
- repaired bu homologous recombination or non-homologous (end joining NHEJ)
- NHEJ more efficient if ends can be rejoined precisely at sites of damage
- HR can only occur in S or G2 when a sister chromatid is available
- begin with phosphorylation of a variant histone
32
daughter strand gap repair
- the replicated portion of an incompletely replicated chromosome is used as a repair template
- process depends on the multifunctional protein, RecA
- damaged site (thymine dimer) isn't repaired
- allows replication to continue and an excision system comes in later to repair damage
33
holliday model for homologous recombination
1. DNA is nicked at the same site on 2 paired chromosomes
2. next partial unwinding of the DNA allows strand invasion
3. Enzymatic ligation generates a crossed-strand intermediate (Holliday junction)
4. cross-strand structure can move along the duplex
5. holiday junction isomerizes
6. strand breakage generates a recombinant or non recombinant heteroduplex
34
RecA
-uses ATP to promote the pairing of homologous DNA sequences
35
RuvA
- DNA binding protein
| - recognizes the Holliday junction
36
RuvB
- ATP-driven motor protein
| - rotates arms of bench in opposite directions to drive branch migration
37
RuvC
nicks the two strands
38
gene rearrangements
generates antibody diversity
39
v-joining
- RAG1 & RAG2 catalyze double strand breaks, initiating recombination
- cutting and splicing may occur anywhere within the terminal trinucleotide, and can generate 4 different recombinant forms
40
transposon
-bacterial transposable element flanked by short repeated sequences
41
transposase
catalyzes the reactions involved in transposition
42
retroviruses
use long terminal repeats (LTRS) for integration into the host chromosome
