Chapter 28 Flashcards
DNA Helicases
Enzymes responsible for forcibly separating the DNA strands and unwinding the parental duplex
Single Stranded DNA Binding Proteins (SSB)
Prevents the strands from reassociating and protect the strands from enzymatic cleavage
DNA Topoisomerases
Enzymes that are responsible for removing positive and negative supercoils that form as a result of overwinding by transiently cleaving one or both strands of DNA
Ciprofloxacin
MOA: Inhibits bacterial DNA gyrase (type II DNA topoisomerase)
Results: Inhibition of bacterial DNA synthesis, eukaryotes do not have DNA gyrase therefore does not interfere with the patient’s own cells
RNA Primer
DNA polymerase cannot initiate synthesis without it, the free 3’-OH primer acts as the 1st acceptor of a dNTP from the polymerase. Only one needed for the leading strand and multiple needed for the lagging (Okazaki fragments)
Types of Polymerase (E. coli)
Pol I, II, and V function primarily in DNA repair. DNA Pol III is involved in elongation
DNA Gyrase (E. coli)
Unwinds DNA
DnaA Prokaryotes
Initiation factor; origin-binding protein
DnaB
5’ to 3’ helicase
DnaC
DnaB chaperone; loading DnaB on DNA
Primase (DnaG) Prokaryotes
Synthesis of RNA primer
DNA ligase
Covalently links Okazaki fragments
Tus
Termination
Polymerase alpha (Eukaryotes)
Contains primase, initiates DNA synthesis
Polymerase beta (Eukaryotes)
Repair
Polymerase gamma (Eukaryotes)
Replicates mitochondrial DNA
Polymerase delta (Eukaryotes)
Elongates Okazaki fragments of the lagging strand
Polymerase epsilon (Eukaryotes)
Elongates the leading strand
RNA primers are removed by what enzymes?
Rnase H and flap endonuclease-1 (FEN1)
Telomeres
Complex of noncoding DNA plus proteins located at the end of linear eukaryotic chromosomes that form protective caps
Telomerase
Maintains telomeric length in germ, stem, and cancer cells
How does telomerase work?
Elongates the already longer 3’ end of the DNA with a “AAGGTT” sequence, then adds the reverse compliment RNA primer, then DNA pol alpha goes to work to fill in the gaps of the 5’ end
North to South Cleavage
Splice recombinant heteroduplex
East to West
Patch Recombinant heteroduplex
RecBCD enzyme complex
Intiaties recombination
RecA protein
Binds ssDNA
RuvA, RuvB, RuvC proteins
Drive branch migration and process Holliday junction
BRCA1 protein
Functions in the regulation of the cell cycle response to DNA damage
BRCA2 protein
Participates in pathway for DNA repair by HR
Transposable Elements
A repetitive DNA sequence that can enzymatically change its position within in the genome
Class I TEs
Retrotransposons (copy and paste)
Class II TEs
DNA Transposons (cut and paste)
Melanomas
Develop from exposure from the sun, causes pyrimidine dimers to form in the DNA (Thymine Dimers). Mutations may result from non- repair of dimers.
Benzo[a]pyrene
A carcinogen, binds to the P53 gene segment of DNA leading to lung cancer. Upon oxidation, it covalently binds to guanine residues in DNA, interrupting G-C pairs and producing distortions
3 Common Steps of DNA Repair
- Excision
- Repair
- Ligation
Nucleotide Excision Repair (NER)
Identifies pyrimidine dimer or an adduct, specific endonucleases nick both sides of the damaged strand, and the gap is filled with polymerase and ligated.
Base Excision Repair (BER)
Removes abnormal bases by using specific glycosylases that cleave the faulty base from the backbone. AP endonuclease recognizes the site of the missing base and nicking the 5’ side of the backbone. Deoxyribose phosphate lyase finishes the job by removing the nicked backbone, allowing for DNA polymerase and ligase to repair.
Mismatch Repair
Used when base pairs are mismatched. Mut proteins are used to identify the parent strand via methylation. The daughter strand is then nicked by an endonuclease, and repaired by DNA polymerase and ligase
Homologous Recombination
Used when there is a double stranded break. Holliday junction
Non-Homologous Recombination
Ku protein is used to ligate the two broken ends together, loss of DNA can lead to mutations.
Transcription-Coupled Repair
This pathway is used when RNA polymerase discovers an error in the DNA. The same repair system as NER is used.
Xeroderma pigmentosum
A deficiency in the NER pathway, leading to extreme consequences when an individual is exposed to UV radiation. Cannot be exposed.
Cockayne Syndrome
An autosomal recessive disorder that is linked to defects in NER and TCR. Results in the inability to repair mutated DNA which can lead to symptoms like premature aging, impaired development of the nervous system, and sensitivity to UV irradiation.
Burkitt’s Lymphoma
A lymphoma cancer that is characterized by the translocation and deregulation of the c-myc on chromosome 8. Ultimately leads to deregulation of cell cycle control. One of the fastest growing malignancies in humans.
Origin of Replication Difference in Prokaryotes vs Eukaryotes
Eukaryotes have multiple origins while prokaryotes only have one
