mbb 20 topic 6 replication and repair

DNA replication \ the process by which a copy of DNA is made ;

Replication origins\ where dna replicationg begins, opened up by initiator proteins;

replication forks \ y shaped junctions formed at the replication origin, Dna replication is bidirectional - each fork moves in opposite directions, the replication fork location is dynamic, changing as replication progresses;

DNA helicase \ pries the doble stranded helix apart at the fron of the fork, requires ATP hydrolysis;

what keeps the newly opened up DNA single stranded? \ Single stranded DNA binding proteins, bind to single stranded DNA, prevents them from reforming base pairs;

what keeps DNA polymerase firmly attached to the template? \ sliding clamp forms a ring around DNA attaches to DNA polymerase and keeps it from falling off,;

whatsa clamp loader\ it locks the clamp onto the DNA;

DNA topoisomerases\ relieve tension that builds up in front of a replication fork, creates transient single stranded nicks in the DNA which they then reseal;

materials neede for DNA replication \ 1.DNA template 2.deoxyribonucleoside triphosphates (dNTPs) 3. a protein complex involving the DNA polymerase enzyme 4.a primer (rna primer here) 5 mg2+ as a cofactor;

which way is dna replicated \ always 5’ to 3’ direction;

why is the replication fork asymmetrical \ bc the two strands run anti parallel to one another and the fact that DNA is replicated in a 5 to 3 direction, only one newly synthesized strand can be made continuously and is know as the leading strand, one strand is made discontinuously in short okazaki fragments its called the lagging strand;

DNA polymerase \ -synthesises and proof reads by catalyzing addition of nucleotides to the 3’ end of a growing nuclei acid, has a separate exonuclease site for error correcting;

primase\ an rna polymerase that creates RNA primers using the DNA template, primer is eventualy remvoed ;

repair polymerase \ creates a continuous new dna strand from separate okazaki fragments, ahs a proofreading function ;

DNA ligase \ sealse the nick gaps between tow okazaki fragments during replication, catalyzes the formation of the phosphodiester bond between the 3’ -OH end of one fragment and the 5’ phosphate end of the next, requries ATP;

whats the end replication problem\ gap remains at end of lagging strand, rna primers are prelaced by dna and gaps sealed by ligase, except leading strand;

solution to end replication problem \ telomeres are caps, theyre recognized by telomerase which extend the length of telomeres using an internal RNA template , a short strand of single stradned DNA remains at the end of chromosomes, eventually enough DNA islost that DNA containing important info gets lsot and cells can no longer replicate, telomerase activity is elevated in stem cells and some tumor cells which is neede for their unlimited proliferation;

fwhat are mutations \ alteration in the DNA structure that can produce permanent changes in the genetic info encode if theyre not repaired, most mutations are neutral, rarely do they have an advantage ;

where does DNA damage come from \ spontaneous mutations, errors during repliation, chemical mutagens, ionizing radiation;

deamination \ can lead to alterations in the DNA sequence when it replicates ;

depurination \ could lead to a deletion of one or more nucleotides when DNA replicates;

mismathc repair mechanism MMR, base excision repair (BER) and necleotide exision repair (NER), \ indirect repair, fix mistake byreplacing a stretch of nucleotides. shaer similar mechansim: 1. use endonuclease to creat a nick in the DNA near the damage 2. remove a section of the damages DNA with an exonuclease 3. fill in the gap with a polymerase and seal it with DNA ligase;

steps of MMR \ 1.a complex of proteisn binds to the mismatched bp and an endo nuclease cuts the damaged strand 2. an exonuclease degrades the DNA from the cut sit to the mismatch 3. DNA polymerase fills in the mising nucleotides and the DNA ligase seals the gap;

base exision repair BER \ repairs DNa when th single bases are altered ex: deamination of sytosine to uracil, genreally follows same steps as MMR;

BER steps \ 1.cytosine can easily lsoe an amino group forming a base called uracil 2.uracil cant forma base pair with guanine 3. an enxyme removes the offending bas 4.endonucleases cut the DNA to help remove the incorrect base from the DNA strand 5. DNA polymerase fills in the gap and the DNA strand is seald by dna ligase ;

NER \ cuta nd patch mechanism that removes DNA damage that is bulky such as made up of changes that alter several nucleotides, this DNA damage can occur by thngslike UV irradiation that causes thymines to covalently bind together stpes : 1. damage is recognized and 2 DNA strands are unwound 2. DNA is cut on oth sides of the lesion 3. pice of DNA isremoved 4. specilaized DNA polymerase synthesizes new DNA;

danger of double strand break \ -chromosome fragmentation and subequent lsos of genes, dysfunctional genes;

homologous recombination \ capable of repairing ds dna breaks w/o mutations , often occurs shortly after DNA replication, info on undamaged strand of the intact double helix is used to repair the compleetary broken strand in the other ;

homologous recombination steps \ 1.double stranded dna break occurs 2.exonuclease degrades 5’ ends of DNA 3. strand invasion of unbroken homologous chromosome 4. invading strand is extended by DNA polymerase 5. invading strand is released 6. DNA polymerase fills in gap 7.DNA ligase seals the gaps;