DNA repair

DNA repair Damaged DNA must be repaired If the damage is passed on to subsequent generations, then we use the evolutionary term - mutation. It must take place in the germ cells - the gametes - eggs and sperm If damage is to somatic cells (all other cells of the body bar germ cells) then just that one individual is affected.

Damage from where? Consequences of DNA replication errors Chemical agents acting on the DNA UV light imparting energy into DNA molecule Spontaneous changes to the DNA

Why repair DNA? DNA pol does a great job, but not good enough Introduces errors in about 1 in 10E7 nucleotides added, which it does not correct Other mechanisms exist (as we will see) to correct many of the errors left by the replication system Most mistakes and damage corrected (99% -leaving just a few - only 1 in 10E9 errors are left) Mutations are permanent changes left in the DNA

Why repair DNA? Repair of non-replication related damage to the DNA must also be a priority for the cell. These defects also will prevent translation and duplication of the DNA Cell will die. Again, any errors or changes to the DNA become Mutations - which are permanent changes left in the DNA

Sickle Cell Disease This is a very good illustration of the devastating effects of even tiny changes to the DNA Red Blood Cells Hemoglobin - Has a large protein component 2 beta globin chains A single base change -substitution causes the disease

06_19_sickle_cell.jpg 06_19_sickle_cell.jpg

Spontaneous Mutations Involves thermal energy Due to random molecular collisions between molecules and DNA in the cell Cannot be prevented Parts of the DNA molecule are stripped off and alterations introduced Many outcomes…

Direct DNA Damage Some agents damage DNA directly Chemicals and light Chemicals - alkylating agents Methy and ethyl groups added to DNA bases This type of damage can be repaired by direct reversal involving special enzymes They remove the offending atoms and restore the base

DNA Damage Just a few types of damage is repaired via simple reversal of the chemical change - UV light induced dimers Methylation of bases Ethylation of bases Large chemical groups added to the DNA Most other damage require other systems…

Random photons of ultraviolet (UV) light induce aberrant bonding between neighbouring pyrimidines (thymine & cytosine) bases on the same strand of DNA. The will prevent the replication machine from duplicating the DNA. The cell will die! 06_24_radiation.jpg 06_24_radiation.jpg This type of defect can be readily reversed by a process called photoreactivation. Visible light energy is used to reverse the defect (in bacteria, yeasts, protists, some plants, and some animals but NOT in humans)

Other forms of DNA damage Deamination - An amino group of Cytosine is removed and the base becomes Uracil Deamination - An amino group of Adenine is removed and the base becomes Hypoxanthine Deamination - An amino group of Guanine is removed and the base becomes Hypoxanthine

And… Depurination - the base is simply ripped out of the DNA molecule leaving a gap (like a missing tooth)…

06_23_Depurination.jpg Molecular level view- Remember these are random events 06_23_Depurination.jpg 06_23_Depurination.jpg

DNA level view of the same two events as last slide 06_25_mutations.jpg 06_25_mutations.jpg

Which is which? The cell has a big problem to overcome… How does it tell which strand carried the correct information? We think we know…

06_21_Errors corrected.jpg The cell has to pick the right strand to fix or else… 06_21_Errors corrected.jpg 06_21_Errors corrected.jpg

The cell has a mechanism of identifying new strand synthesis by leaving nicks that DNA. There are enzymes which scan these new regions looking for errors 06_22_DNA mismatch.jpg 06_22_DNA mismatch.jpg

Correction mechanisms Direct reversal of damage - Photoreactivation (bacteria, yeast, some vertebrates - not humans) Two thymines connected together by UV light. Excision Repair - removal of defective DNA. There are three distinct types 1) base-excision 2) nucleotide-excision 3) mismatch repair

base-excision Presence of the Uracil in DNA is a great example of this type Special enzymes replace just the defective base 1 snip out the defective base 2 cut the DNA strand 3 Add fresh nucleotide 4 Ligate gap

nucleotide-excision Same as previous except that It recognizes more varieties of damage Remove larger segments of DNA (10 -100s of bases)

mismatch repair Special enzymes scan the DNA for bulky alterations in the DNA double helix These are normally caused by mismatched bases AG AC CT These are excised and the DNA repaired

06_26_three steps.jpg Basic mechanism is the same for all three types Remove damaged region Resynthesis DNA Ligate 06_26_three steps.jpg

Consider… Sunlight - sunbathing or daily exposure Impact of ozone depletion Impact on different skin tones Environmental degradation

Evolution acts on mutations If we did not have mutation then we would all be the same! Any changes in the environment would be deleterious to all members of the population equally = There would be no evolution!!!! But mutation does exist and it is supported by comparison of related organisms…

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Mutations of Genes Mutation – change in the nucleotide base sequence of a genome; rare Almost always deleterious Rarely lead to a protein having a novel property that improves ability of organism and its descendents to survive and reproduce

Mutations of Genes Types Point mutations (most common) – one base pair is affected Insertions, deletions, and substitutions Frameshift mutations – nucleotide triplets after the mutation displaced Insertions and deletions

Effects of Mutation Figure 7.21a-c

Effects of Mutation Figure 7.21d-e

An English Example THEBOYANDTHEDOGRANFAR THE BOY AND THE DOG RAN FAR Missense: THE BOY AND THE HOG RAN FAR Nonsense: THE BOY AND .

English Example-Frameshift THEBOYANDTHEDOGRANFAR THE BOY AND THE DOG RAN FAR DEletion: THE BOY ADT HED OGR ANF AR Insertion: THE EBO YAN DTH EDO GRA NFA R

Mutagens Radiation Chemical mutagens Ionizing radiation – induces breaks in chromosomes Nonionizing radiation – induces pyrimidine dimers Chemical mutagens Nucleotide analogs – disrupt DNA and RNA replication and cause point mutations Nucleotide-altering chemicals – result in base-pair substitution mutations and missense mutations Frameshift mutagens – result in nonsense mutations

DNA Repair Figure 7.25a-b

DNA Repair Figure 7.25c-d