Class 22: DNA Repair/Transposons

Induced mutations: what are the 3 different types of radiation mutations

X rays, Gama rays, and UV

Moderate level of radiaition can lead to mutations, extreme can lead to DNA/cell death

What is ionizing radation? what does it create? What are the 2 types of radiation that fall under it.

Ionizing radiation: Interacts with DNA (direct or indirect) to generate reactive ions and free radicals, which can modify bases leading to breakage of DNA. Double stranded breaks and DNA become fragments.

Free radicals: chemicals that have unpaired electrons and are very reactive with biological molecules

What does ultraviolet radiation cause

Pyrimidine dimerrs: somewhere in sequence that is exposed to UV light, thymines that are close together (in the same strand) will form covalent bonds. It creates a structure kink or legion in the DNA

Causing porblems during replication

What does Nucelotide excision repair system solve 

DNA damage that distorists the double helix, including abnormal bases, modified bases, and pyrimidine dimers 

What does the homology directed repair fix 

Double stranded breaks. Homologous recombination 

What does nonhomologous end joining fix 

Double stranded breaks. Teo fragments of DNA and ends get joined and stuck toether. Sometimes it can fix things, sometimes it can make things worse 

Describe miss match repair

Mismatch nucleotides occasionally get incorporates - causing kinks in DNA. Miss match repairs enzymes recognize these kinks and replace local stretch of DNA including the mismathces nucleotide. The exonucleases remove the nucleotides on the new strand and DNA pol rep;aced the nucleotides, correcting the mismatch. Then DNA ligase seals the nick in the sugar phosphate backbone 

Describe the direct repair mechanism. What are the two major enzymes in direct repair?

Enzymatic fixing of altered nucleotides back to original nucleotide

Photolysae: cleaves the covalent bonds that link pyrimidine dimers

Methyltransferase: Demethylates methyl guanosine 

Base excision repair

1. there is some damage base. Enzyme called DNA glycolase removes just the damaged base. THe sugar phosphate bond is still intact

2. Enzume called endonuclease remvoed the sugar and phosphas, so now the backbone is cut There is a nic in the backbone 

3. DNA polymerase fills the approprist base, but there is still a nick in the back bone 

4. DNA ligase seals the nick in the sugar phosphate backbone 

Describe Nucleotide Excision repair

Repair mechanism that deals with bigger distortions that a singal base

1. some damage distors the DNA causing a lesion

2. Recognized by reoaur enzume complex

3. It seperates the strands of the damged segments

4. Cleaves the damage strand so the whole chunk

5. DNA Pol and DNA ligase create new DNA and seal nick, respectively

What is a transposon?

Genes that are able to move locations. aka called jumping genes

How were transposons divovered

First identified because of vairation in pigmentation of corn kernels. Determined that transposon caused variations. Enzyme catalysed insetion at new site can lead to mutation or chromsoma rearrangement. Transposons are present in some form in all genomes

Are genes always part of the moving DNA

No, they odten occur in the spon where the stransporon gets inserted in

How much of human DNA is transposable element

45%

Describe the typical structure of a transposon 

The transposable element is a portion of the DNA itself and terminal inverten repeat. Next to the terminal invert repeat are flanking direct repeats 

erminal inverted repeats: INverted relative to each other, terminal in the sense that they mark the end of the trnasposon. Inverted in the sense that they run in the opposite direction 

Flanking direct repeat: flanking the inverted repeats and run in the same direction 

What are the types of transposons/ WHat are the genes encoded. How does the transposition occur. In prokaryotes, eukaryotes, or both? 

DNA transposons (class II): moveable component of DNA, what is being moved and being inserted in the DNA sequence. Genes encoded are transposase genes (sometiem others). Transposistion through DNA replicatiove or non replicative. found in prokaryotes and eukaryotes 

Retrotransposons (class I): transpose through an RNA intermiedate. DNA copied th RNA which is then reverse transcribed to DNA. Encode for reverse transcriptae (which is a type of primase) gene. Only in eularyote 

Describe replicative transposition

Repliative is copy and paste. Generates copies = each new copy is inserted at a newsite. Increases the numver of transposons 

Describe nonreplicative transposition 

A given transposon is cut and moved to a new site. No increase in the number of transposons 

Descrube the general mechanism of transposition

1. staggered breaks are generated in target site by transpoase 

2. Transposon is jpined to single stranded ends of target DNA 

3. DNA in single stranded gaps is replicated and filled in 

4. The replication and filled parts are the flanking direct repeats 

What does transposition rely on? WHat is requried for the process

Relies on enzymes encoded by the transposon (transposase) and components of cell’s own machienry

Terminal inerted repeats are recognied by ezymes that catayse transpotition (requried for the process