Molecular Biology of Cells Chapter 5 (Second Half)

DNA Repair

Organism should maintain the genetic stability for its survival. DNA repair is correction of spontaneous changes in DNA by a set of processes that are collectively. The importance of DNA repair is evident from cells make in DNA repair enzymes. For example, human disease named Xeroderma pigmentosum (XP), the afflicted individuals have an extreme sensitivity to ultraviolet radiation because they are unable to repair certain DNA photoproducts.

Without DNA repair, spontaneous DNA damage would rapidly change DNA sequence. For example, the DNA of each human cell loses about 5000 purine bases (adenine and guanine) every day because their N-glycosyl linkages to deoxyribose hydrolyze, a spontaneous reaction called depurination. If left uncorrected when the DNA is replicated, most of these changes would be expected to lead either to the deletion of one or more base pairs or to a base-pair substitution in the daughter DNA chain.

The DNA double helix is readily repaired. Thus, when one strand is damaged, the complementary strand retains an intact copy of the same information, and this copy is generally used to restore the correct nucleotide sequences to the damaged strand.

DNA damage can be removed by 2 pathways:

1.     Base excision repair -> the altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate.

2.     Nucleotide excision repair -> a small section of the DNA strand surrounding the damage is removed from the DNA double helix as an oligonucleotide

Other critical repair systems-based on either non-homologous end-joining or homologous recombination-reseal the accidental double-strand breaks that occur in the DNA helix.

Homologous Recombination

Nucleotide sequences are exchanged between two similar or identical molecules of DNA. The used of homologous recombination are:

1.     Accurately repairing double-strand break

2.     Exchange bits of genetic information between two different chromosomes to create new combinations of DNA sequences in each chromosome during meiosis

3.     Used in horizontal gene transfer to exchange genetic material between different strains and species of bacteria and viruses

Term: hybridization -> single-stranded DNA or RNA molecules anneal (pair by hydrogen bonds to form a double-stranded polynucleotide) to complementary DNA or RNA.

Transposition and Conservative Site-Specific Recombination

These two types of recombination (collectively termed mobile genetic elements) can alter gene order along a chromosome, and cause unusual types of mutations that add new information to genomes. It often considered to be molecular parasites that persist because cells cannot get rid of them; they certainly have come close to overrunning our own genome. However, it can provide benefits to the cell, in the case of antibiotics resistance in bacterial cells.

1.     Transposition is the movement of genetic material between unicellular and/or multicellular organisms by horizontal transmission of DNA from parent to offspring. This is the primary mechanism for the spread of antibiotic resistance in bacteria.

On the basis of their structure and mechanism, transposition can be grouped into: DNA-only transposons, retroviral-like retrotransposons, and nonretroviral retrotransposons.

Term: transposons or transposable elements -> a specific enzyme called transpoase, acts on a specific DNA sequence at each end of transposon, causing insert into a new target DNA site.

2.     Conservative site-specific recombination can distinguish from transposition. First, it requires specialized DNA sequences on both the donor and recipient DNA. Second, the reaction mechanisms are fundamentally different.

This recombination can be used to turn genes on or off. It was discovered in bacteriophage lambda.

Discussion

Is it possible to make the desired sequence by utilizing transposition?

The idea: 

- transposons can move everywhere on the genome.

- we can imagine where the transposons will be move on the genome.

Application of Transposons

1. Control HIV virus to become less active. There are 2 ways: 1) copy and paste, 2) cut and paste. With cutting the HIV sequence, it can decrease the spread of HIV virus. Cut and paste way can make the desired sequence by using transposons.
2. Cure danger sequence in human (possibly).
3. Transposons can be used to randomly disrupt gene. So, we can select good result from it.
4. To introduce new sequence.