1. DNA damage, cellular sensing/responding and repair

2. 2

4. DNA Damage
DNA damage, due to environmental factors and normal metabolic processes inside the cell, occurs at a rate of 1,000 to 1,000,000 molecular lesions per cell per day.
While this constitutes only % of the human genome's approximately 6 billion bases (3 billion base pairs), unrepaired lesions in critical genes (such as tumor suppressor genes) can impede a cell's ability to carry out its function and appreciably increase the likelihood of tumor formation. 4

5. Failure to repair DNA lesions may result in blockages of transcription and replication, mutagenesis, and/or cellular cytotoxicity.
In humans, DNA damage has been shown to be involved in a variety of genetically inherited disorders, in aging, and in carcinogenesis. 5

6. Sources of DNA Damage
DNA damage can be subdivided into two main types:
1. endogenous damage such as attack by reactive oxygen species produced from normal metabolic byproducts (spontaneous mutation), especially the process of oxidative deamination;
also includes replication errors
5. ^ Roulston A, Marcellus RC, Branton PE (1999). "Viruses and apoptosis". Annu. Rev. Microbiol. 53: 577ñ628. doi: /annurev.micro PMID Retrieved on 6

7. 2.exogenous damage caused by external agents such as
ultraviolet [UV nm] radiation from the sun
other radiation frequencies, including x-rays and gamma rays
human-made mutagenic chemicals, especially aromatic compounds that act as DNA intercalating agents
cancer chemotherapy and radiotherapy
5. ^ Roulston A, Marcellus RC, Branton PE (1999). "Viruses and apoptosis". Annu. Rev. Microbiol. 53: 577ñ628. doi: /annurev.micro PMID Retrieved on 7

9. Types of Damage
The main types of damage to DNA due to endogenous cellular processes:
1. oxidation of bases [e.g. 8-oxo-7,8-dihydroguanine (8-oxoG)] and generation of DNA strand interruptions from reactive oxygen species.
2. alkylation of bases (usually methylation), such as formation of 7-methylguanine, 1-methyladenine, O6 methylguanine
3. hydrolysis of bases, such as deamination, depurination and depyrimidination.

10. 4. "bulky adduct formation" (i. e
4. "bulky adduct formation" (i.e. benzo[a]pyrene diol epoxide-dG adduct).
5. mismatch of bases, due to errors in DNA replication, in which the wrong DNA base is stitched into place in a newly forming DNA strand, or a DNA base is skipped over or mistakenly inserted.

11. DNA damage and mutation
It is important to distinguish between DNA damage and mutation, the two major types of error in DNA.
DNA damage and mutation are fundamentally different.
Damage is a physical abnormalitie in the DNA, such as single and double strand breaks, 8-hydroxydeoxyguanosine residues and polycyclic aromatic hydrocarbon adducts.

12. In contrast to DNA damage, a mutation is a change in the base sequence of the DNA. A mutation cannot be recognized by enzymes once the base change is present in both DNA strands, and thus a mutation cannot be repaired.
At the cellular level, mutations can cause alterations in protein function and regulation.
Mutations are replicated when the cell replicates. In a population of cells, mutant cells will increase or decrease in frequency according to the effects of the mutation on the ability of the cell to survive and reproduce.

13. Types of DNA damage 1. Base loss
The glycosyl bond linking DNA bases with deoxyribose is labile under physiological conditions.
Within a typical mammalian cell, several thousand purines and several hundred pyrimidines are spontaneously lost per diploid genome per day. Loss of a purine or pyrimidine base creates an apurinic/apyrimidinic (AP) site (also called an abasic site):

15. 2. Base modification
2a. Deamination
The primary amino groups of nucleic acid bases are somewhat unstable. The amino group is removed from the amino acid and converted to ammonia.
In a typical mammalian cell, about 100 uracils are generated per haploid genome per day in this fashion.
Other deamination reactions include conversion of adenine to hypoxanthine, guanine to xanthine, and 5-methyl cytosine to thymine.

16. Example: cytosine deamination
Spontaneous deamination is the hydrolysis reaction of cytosine into uracil, releasing ammonia in the process.

17. 2b. Chemical modification
The nucleic acid bases are susceptible to numerous modifications by a wide variety of chemical agents.
For example, several types of hyper-reactive oxygen (singlet oxygen, peroxide radicals, hydrogen peroxide and hydroxyl radicals) are generated as byproducts during normal oxidative metabolism and also by ionizing radiation (X-rays, gamma rays).
These are frequently called Reactive Oxygen Species (ROS). ROS can modify DNA bases. A common product of thymine oxidation is thymine glycol:

19. Another type of chemical modification: Methylation/alkylation
Many environmental chemicals, including "natural" ones (frequently in the food we eat) can also modify DNA bases, frequently by addition of a methyl or other alkyl group (alkylation).

20. Photodamage
Ultraviolet light is absorbed by the nucleic acid bases, and the resulting influx of energy can induce chemical changes.
The most frequent photoproducts are the consequences of bond formation between adjacent pyrimidines within one strand, and, of these, the most frequent are cyclobutane pyrimidine dimers (CPDs).

21. Ultraviolet light induces the formation of covalent linkages by reactions localized on the C=C double bonds
T-T CPDs are formed most readily, followed by T-C or C-T; C-C dimers are least abundant. One can obtain an idea of the extent of distortion of DNA chain structure caused by CPDs by noting that, in the diagram of a T-T CPD below, the cyclobutane ring, shaded in light blue, should have sides of approximately equal length. Thus the two adjacent pyrimidines must be pulled closer to each other than in normal DNA.
Dimers can also be produced by formation of a single covalent bond between the 6 position of one pyrimidine and the 4 position of the adjacent pyrimidine on the 3' side. The order of abundance of such pyrimidine (6-4) pyrimidone photoproducts (6-4PPs) is T-C>>C-C>T-T>C-T. Although only one bond attaches the adjacent pyrimidines, there is nevertheless extensive distortion of the normal DNA structure. In the diagram below of the T-C 6-4PP, notice that the amino group, originally from the 4 position of the cytosine, ends up at the 5 position of the thymine. Although it is not evident from this crude diagram, the structural distortion generated by 6-4PPs (a DNA bend of 44°) is greater than that produced by CPDs (bend of 30°).

22. Inter-strand crosslinks
By attaching to bases on both strands, bifunctional alkylating agents such as the psoralens can cross-link both strands.
Cross-links can also be generated by UV and ionizing radiation.

24. Strand breaks
Single-strand and double-strand breaks are produced at low frequency during normal DNA metabolism by topoisomerases, nucleases, replication fork "collapse", and repair processes.
Breaks are also produced by ionizing radiation.

26. What can the cell do to protect itself?

27. DNA damage recognition
DNA damage is recognized by sensor proteins that then initiate a network of signal transduction pathways.
This ultimately results in the activation of effector proteins that execute the functions of the DNA damage response, including recruitment of DNA repair proteins, cell cycle arrest, damage induced transcription, or the induction of apopotosis. 27

29. An option: DNA damage checkpoints
After DNA damage, cell cycle checkpoints are activated.
Checkpoint activation pauses the cell cycle and gives the cell time to repair the damage before continuing to divide.

30. The cell cycle of eukaryotic cells can be divided into four successive phases:
M phase (mitosis), in which the nucleus and the cytoplasm divide;
S phase (DNA synthesis), in which the DNA in the nucleus is replicated,
two gap phases, G1 and G2.
The G1 phase is a critical stage, allowing responses to extracellular cues that induce either commitment to a further round of cell division or withdrawal from the cell cycle (G0) to embark on a differentiation pathway.

31. The G1 phase is also involved in the control of DNA integrity before the onset of DNA replication.
Between S and M phases is the G2 phase during which the cell checks the completion of DNA replication and the genomic integrity before cell division starts.
The transition from one phase of the cell cycle to the next is controlled by cyclin–CDK (cyclin-dependent kinase) complexes which ensure that all phases of the cell cycle are executed in the correct order.

33. DNA damage checkpoints occur at the G1/S and G2/M boundaries
DNA damage checkpoints occur at the G1/S and G2/M boundaries. An intra-S checkpoint also exists.
Checkpoint activation is controlled by two master kinases, ATM and ATR.
ATM responds to DNA double-strand breaks and disruptions in chromatin structure, whereas ATR primarily responds to stalled replication forks.
These kinases phosphorylate downstream targets in a signal transduction cascade, eventually leading to cell cycle arrest.

35. What happens if we have defective ATM??
ataxia telangiectasia mutated

36. Disease: Ataxia-telangiectasia
Ataxia-telangiectasia is a rare, childhood neurological disorder that causes degeneration in the part of the brain that controls motor movements and speech.
Its most unusual symptom is an acute sensitivity to ionizing radiation, such as X-rays or gamma-rays. The first signs of the disease, which include delayed development of motor skills, poor balance, and slurred speech, usually occur during the first decade of life.

37. Telangiectasias (tiny, red "spider" veins), which appear in the corners of the eyes or on the surface of the ears and cheeks, are characteristic of the disease, but are not always present and generally do not appear in the first years of life.

38. About 20% of those with A-T develop cancer, most frequently acute lymphocytic leukemia or lymphoma.
Many individuals with A-T have a weakened immune system, making them susceptible to recurrent respiratory infections.

39. ATM mutations are associated with breast cancer
Researchers have found that having a mutation in one copy of the ATM gene in each cell (particularly in people who have at least one family member with ataxia-telangiectasia) is associated with an increased risk of developing breast cancer.
About 1 percent of the United States population carries one mutated copy of the ATM gene in each cell. These genetic changes prevent many of the body's cells from correctly repairing damaged DNA.

40. So thank goodness for DNA Repair

41. DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome.
In human cells, both normal metabolic activities and environmental factors such as UV light and Radiation can cause DNA damage, resulting in as many as 1 million individual molecular lesions per cell per day.
Many of these lesions cause structural damage to the DNA molecule and can alter or eliminate the cell's ability to transcribe the gene that the affected DNA encodes.

42. DNA repair mechanisms
Cells cannot function if DNA damage corrupts the integrity and accessibility of essential information in the genome (but cells remain superficially functional when so-called "non-essential" genes are missing or damaged).
Depending on the type of damage inflicted on the DNA's double helical structure, a variety of repair strategies have evolved to restore lost information.

44. Direct reversal
Cells are known to eliminate damage to their DNA by chemically reversing it.
These mechanisms do not require a template, since the types of damage they counteract can only occur in one of the four bases.
Such direct reversal mechanisms are specific to the type of damage incurred and do not involve breakage of the phosphodiester backbone.
10.^ Sancar A. (2003). Structure and function of DNA photolyase and cryptochrome blue-light photoreceptors. Chem Rev 103(6):2203ñ37. PMID
11.^ Volkert MR. (1988). Adaptive response of Escherichia coli to alkylation damageEnviron Mol Mutagen 11(2):

45. An example:
Methylation of guanine bases, is directly reversed by the protein methyl guanine methyl transferase (MGMT), the bacterial equivalent of which is called as ogt.
This is an expensive process because each MGMT molecule can only be used once; that is, the reaction is stoichiometric rather than catalytic.
A generalized response to methylating agents in bacteria is known as the adaptive response and confers a level of resistance to alkylating agents upon sustained exposure by upregulation of alkylation repair enzymes.

47. How do we end up with methylated Guanine???

48. Exposure to alkylating agents!
Damage induced mimics
some chemotherapeutics
guanine X
cytosine
Damage induced mimics
environmental exposures
thymine
O6-meG can mispair with thymine
G/C to A/T transitions
Can be cytotoxic or mutagenic lesion

50. Base excision repair (BER), which repairs damage to a single base caused by oxidation, alkylation, hydrolysis, or deamination.
The damaged base is removed by a DNA glycosylase, resynthesized by a DNA polymerase, and a DNA ligase performs the final nick-sealing step.

53. 2. Nucleotide excision repair (NER), which recognizes bulky, helix-distorting lesions such as pyrimidine dimers and 6,4 photoproducts.
A specialized form of NER known as transcription-coupled repair deploys NER enzymes to genes that are being actively transcribed.

55. What happens if we have defective NER??

56. Xeroderma pigmentosum (XP)
Xeroderma pigmentosum (XP) was first described in 1874 by Hebra and Kaposi.
In 1882, Kaposi coined the term xeroderma pigmentosum for the condition, referring to its characteristic dry, pigmented skin.

57. Xeroderma pigmentosa, or XP, is an autosommal ressessive genetic disorder of DNA repair in which the ability to repair damage caused by ultraviolet (UV) light is deficient (NER deficiency).
This disorder leads to multiple basal cell carcinomas (basaliomas) and other skin malignancies at a young age.

58. 3. Mismatch repair (MMR), which corrects errors of DNA replication and recombination that result in mispaired (but undamaged) nucleotides.

59. Are there health effects from MMR deficiency?

61. Double-strand breaks
Double-strand breaks (DSBs), in which both strands in the double helix are severed, are particularly hazardous to the cell because they can lead to genome rearrangements.
Various mechanisms exist to repair DSBs:
1) non-homologous end joining (NHEJ),
2) recombinational repair (also known as template-assisted repair or homologous recombination repair)
13.^ a b c Watson JD, Baker TA, Bell SP, Gann A, Levine M, Losick R. (2004). Molecular Biology of the Gene, ch. 9 and 10. Peason Benjamin Cummings; CSHL Press. 5th ed.

63. In NHEJ
DNA Ligase IV, a specialized DNA Ligase that forms a complex with the cofactor XRCC4, directly joins the two ends.

64. DNA ligase, shown above repairing chromosomal damage, is an enzyme that joins broken nucleotides together by catalyzing the formation of an internucleotide ester bond between the phosphate backbone and the deoxyribose nucleotides.

65. Recombinational Repair
Recombinational repair requires the presence of an identical or nearly identical sequence to be used as a template for repair of the break.
The enzymatic machinery responsible for this repair process is nearly identical to the machinery responsible for chromosomal crossover during meiosis.
This pathway allows a damaged chromosome to be repaired using a sister chromatid (available in G2 after DNA replication) or a homologous chromosome as a template.

67. Clear association of DNA repair and cancer
Inherited mutations that affect DNA repair genes are strongly associated with high cancer risks in humans.
Hereditary nonpolyposis colorectal cancer (HNPCC) is strongly associated with specific mutations in the DNA mismatch repair pathway.
BRCA1 and BRCA2, two famous mutations conferring a hugely increased risk of breast cancer on carriers, are both associated with a large number of DNA repair pathways, especially NHEJ and homologous recombination.