chapter 11 part 2 Flashcards
induced mutations
produced by mutagens in an experimental setting to study types of damage caused, the mutation process itself, or repair responses to damage
what are the types of chemical mutagens
- nucleotide base analogs
- deaminating agents
- alkylating agents
- oxidizing agents
- hydoxylating agents
6, intercalating agents
mutagens
agents that cause DNA damage leading to mutations
can some molecules fit between base pairs?
yes! these are intercalating agents
what are intercalating agents?
they distort the DNA duplex, some can also form bulky adducts that contribute to DNA distortion
this distortion leads to DNA nicking that is not efficiently repaired which results in added or lost nucelotides
examples of intercalating agents
ethidium bromide
acridine orange
what are photoproducts
aberrant structures with additional bonds involving nucleotides, caused by UV irradiation
what are photoproducts caused by?
UV irradiation
what is one common photoproduct?
a thymine dimer which is formed between 5 & 6 carbons of adjacent thymines
what is another common photoproduct?
6-4 photoproduct formed by a bond between carbon 6 on one thymine & carbon 4 in the other (inter-strand cross links)
what are some radiations higher than UV?
X-rays, gamma rays, & radioactive materials
how does radiation cause damage?
in multiple ways, but the most serious are single-stranded or double stranded breaks in DNA
what do single stranded or double stranded blocks in DNA do?
block DNA replication & are dealth with by specializer repair systems
how do organisms preserve the fidelity of DNA?
by using multiple repair systems which directly repair DNA damage or allow organism to circumvent the problems caused by unrepaired damage
what is the most direct way to repair DNA lesions?
to identify & then reverse the DNA damage
what is a way to fix DNA errors immediately?
the proofreading ability of DNA polymerase
-5’ to 3’ exonuclease activity
how can pyrimidine dimers be directly repaired?
by photoreactice repair which is when the enzyme photolyase uses energy from visible light to break the bonds between pyrimidine dimers
what is photolyase encoded by?
E.coli phr gene (photoreactive repair)
what organisms can photoreactive repair occur in?
bacteria, eukaryotes, plants, some animals, not humans
what is DNA damage by alkylating agents repaired by?
enzymes that remove the added chemical groups, restoring the nucleotide to its normal form which is performed by a class of enzymes called alkyltransferases
what do alkyltransferases do?
they remove an alkyl group & reverse the effects of EMS & NG
-it is permanently inactivated after one reaction repair… its a suicide enzyme
what is nucleotide base excision repair (BER)?
a multistep process that may repair damage to a nitrogenous base or replace an incorrect base
what is DNA glycosylases?
a series of enzymes that recognize specifically modified or incorrect bases & remove modified purine bases, leaving an AP site
-apurinic/apryrimidic = no base
what do AP endonucleases do?
creates a single-stranded “nick” near the AP site
when does nick translation occur?
where DNA polymerases initiate removal & replacement of nucleotides, including the AP site; DNA ligase seals the sugar-phosphate backbone
what is nucleotide excision repair (NER) often used to repair?
UV-induced damage to DNA so it is also known as ultraviolet (UV) repair
nucleotide excision repair process (not detailed)
- enzymes recognize to the damaged region
- a segment of nucleotides is removed from damaged strand
- DNA polymerase fills in the gap & DNA ligase seals the sugar-phosphate backbone
what is nucleotide excision repair (NER) also called
ultraviolet (UV) repair
UV Repair (NER example) detailed
-UV-damage repair uses proteins encoded by the genes uvrA, uvrB, uvrC, and uvrB
-UVR A & UVR B proteins bind to the DNA strand opposite of the photoproduct, then UVR A dissociates
-UVR C joins UVR B, forming the UVR BC Complex
-UVR C then cleaves the damaged DNA strand
-UVRD (a helicase) helps remove the DNA fragments that contains the photoproduct
-then DNA polymerase fills the gap & DNA ligase selas the sugar-phosphate backbone
what is an example of a human hereditary cancer-prone condition that is caused by a mutation of any of seven different genes involved in what?
Xeroderma Pigmentosa
-NER (nucleotide excision repair)
mechanism of mismatch repair
-the e.coli protein MutH binds to the hemimethylated DNA region
-MutS located & binds to the DNA mismatch & then forms a complex with MutL
-MutS/MutL compex binds to MutH
-MutH protein breaks a phosphodiester bond on the 5’ side of the guanine of a GATC sequence on the unmethylated daughter strand
-exonuclease enzymes digest nucleotides from the ‘nick’ through the mismatched nucleotide
-DNA polymerase fills the gap in the daughter strand
-DNA ligase completes the repair
-Dam methylase methylates the adenine of the GATC sequence on the daughter strand
biochemical mechanisms to recognize the presence of DNA lesions & initiate a repair response consist of what?
a lightly regulated genetic process
what consists of a lightly regulated genetic process?
biochemical mechanisms that recognize the presence of DNA lesions & initiate a repair response
what acts as a genomic sentry to identify damage in both humans & animals
a multiprotein complex
-this process is in action throughout the cell cycle
what does ATM do?
it plays a big role in communicating cells damage which activates transcription of the p53 gene (p53 repair pathway)
what does the p53 repair pathway do?
controls the cell responses to mutation by deciding to either pause the cell cycle at the G1 to Gs transition to allow time to repair OR initiate apoptosis
are p53 levels high or low in healthy cells?
they are low but increase as the ATM levels increase
what does p53 initiate?
G1 arrest by inducing synthesis of p21, that inhibits formation of cyclin-CDK complexes
-this allows for time to repair damaged DNA
-completed repair reduces p53 levels & allows the cell cycle to proceed
what does p53 also activate?
transcription of the BAX gene which encodes a slowly acting inhibitor BCL2
-BCL2 represses apoptosis; in helathy clles BCL2 protein maintains repression
-in damaged cells, if the p53-induced pause of the cell cycle persists too long, the apoptotic pathway is induced when BCL2 is inhibited
what does the BAX gene encode?
a slowly acting inhibitor called BCL2
what do mutations in genes that participate in DNA damage repair cause?
an organism to be highly sensitive to chemical mutagens & radiation
-greatly increase the organisms susceptibility to cancers caused by exposure to mutagens
what is Li-fraumet syndrome caused by?
mutation in p53
when is SOS repair activated
in response to heavily damaged DNA in E.Coli cells
what is SOS repair accomplished by?
translesion of DNA polymerase or bypass polymerase (Pol V) <– 5
about Pol V
error-prone polymerases that have no proofreading ability & can replicate across lesions that would stall Pol III
SOS repair in e. coli
-when pol iii stalls at damaged DNA, RecA proteins cot the template strand ahead of the lesion (already bound by SSB protein); this forms a DNA-RecA-SSB complex
-RecA also activates transcription of pol V
-Pol V displaces pol iii, synthesizes a short stretch of a new DNA across the lesion, & is then replaced by pol iii, which resumes normal replication
if both strands of DNA are broken, then what?
neither strand is able to act as a template for repair
what can double-stranded breaks occur from?
damage from exposure to X-rays & certain types of oxygen radicals
what is it called when both strands of DNA are broken?
double-stranded breaks (DSBs)
what can DSBs cause?
chromosome instability & incomplete replication, possibly leading to cell death; they also increase the risk of cancer & chromosome structural mutations
what are the two mechanisms that are in place to carry out DSB repair?
non-homologous end joining
synthesis-dependent strand annealing
