Notes
DNA Damage and Repair
Sections
DNA DAMAGE MECHANISMS
Endogenous Agents
• Spontaneous chemical reactions
- Deamination: nucleotides lose amine groups
• Cytosine --> uracil
• Adenine --> hypoxanthine - Depurination: purine (adenine or guanine) released from DNA
• Bond between deoxyribose and purine base spontaneously cleaves
• Produces AP site (apurinic site)
Exogenous Agents
- Exposure to mutagens (chemicals or radiation)
- Pyrimidine dimers: induced by UV light exposure
• Cyclobutane ring forms between adjacent pyrimidines (often thymines)
• Distorts the DNA double helix - Alkylation: addition of methyl/ethyl groups to nucleotides
• -CH3 or –CH2CH3 add to nitrogenous bases at numerous positions - Bulky group addition: exposure to carcinogens
• i.e. benzo(a)pyrene: aromatic, polycyclic structure can react with purines/pyrimidines at numerous positions
• Cause distortions in DNA helix
Carcinogen
• Cancer-causing mutagen
CONSEQUENCES OF DNA DAMAGE
• Can increase frequency of mutations
• Mutations: nucleotide substitutions, deletions and insertions
CLINICAL CORRELATIONS
Skin melanomas
• Pyrimidine dimers produce helical distortions that result in skin cancers
Cigarette smoking
• Carcinogens in smoke form covalent bonds with DNA
• Disrupts H-bonding between nucleotides: causes frameshift
• Frameshift changes subsequent codons in DNA strand
• Constant exposure to carcinogens --> lung cancer
REPAIR MECHANISMS
• Mismatch-repair: fixes replication errors missed by DNA Pol proofreading (cannot repair damage)
• Base excision repair: deamination, depurination and alkylation
• Nucleotide excision repair: pyrimidine dimers and bulky group addition
Full-Length Text
- Here we will learn about DNA damage and repair.
- To begin, start a table to learn some key mechanisms of DNA damage.
- Denote that endogenous or exogenous agents can induce DNA damage.
- For endogenous damage, denote that spontaneous chemical reactions can damage a nucleotide or nucleotides.
- For exogenous denote that damage can be initiated by exposure to mutagens (chemicals or radiation).
- Denote that spontaneous DNA damage is most frequently in the form of:
- Deamination, in which adenine and/or cytosine nucleotides lose amine groups.
- Depurination, in which a purine (adenine or guanine) is released from DNA.
- Denote that mutagens can cause damage in the following ways:
- Formation of pyrimidine dimers, which is induced by UV light exposure.
- Alkylation, the addition of methyl or ethyl groups to nucleotides.
- Addition of a bulky group, which often occurs upon exposure to carcinogens (cancer-causing mutagens).
Let's illustrate these forms of damage, now.
We will start with endogenous DNA damage: deamination and depurination. First, deamination.
- Draw a purine base as a hexagonal ring and specifically label one carbon.
- Show it bound to an amino group.
- Label this base cytosine. We will not worry about the rest of its Lewis structure.
- Next, draw the purine adenine as a hexagon bound to a pentagonal structure.
- Again, label one carbon in the hexagonal portion bound to an amino group.
- Now, redraw both cytosine and adenine without their amino groups.
- Instead, replace them with a carbonyl oxygen.
- Show that the deamination of cytosine produces uracil, and that the deamination of adenine produces a molecule called hypoxanthine.
- Now draw the sugar-phosphate backbone bound to all four bases; deamination only affects the nitrogenous base of each nucleotide, not the backbone.
- Write that deamination can affect DNA replication and gene expression if not repaired; a single nucleotide change can alter the codon and corresponding amino acid.
Now, depurination.
- Draw a double-ringed purine and label it adenine/guanine; it represents both purine nucleotides.
- This time, show it attached to the deoxyribose of the sugar-phosphate backbone, a five-membered ring bound to a phosphate group.
- Next, illustrate that the bond between the deoxyribose and purine spontaneously cleaves.
- Redraw the deoxyribose without a purine bound.
- Label it an apurinic site.
- Indicate that this monosaccharide is now a deoxyadenosine monophosphate (dAMP) or deoxyguanosine monophosphate (dGMP), depending on the lost purine.
- Write that like deamination, depurination does not break the sugar-phosphate backbone.
Finally, let's learn exogenous damage: pyrimidine dimers, alkylation and bulky group addition.
We'll start with pyrimidine dimers.
- First, write that they are caused by exposure to UV radiation.
- Now, draw a DNA strand with a six-membered pyrimidine ring and label carbon five and six.
- Show that carbon 5 and 6 form a double bond.
- Indicate that carbon 5 is bound to an R group, which is just a hydrogen in cytosine and a methyl group in thymine.
- Indicate that carbon 6 is bound to a hydrogen in both pyrimidines.
- Next, draw another pyrimidine adjacent to this one, labeling the same atoms.
- Now, indicate that the carbon 5 and 6 of one pyrimidine bind the carbon 5 and 6 of the second pyrimidine.
- Indicate that the resulting structure forms a cyclobutane ring.
- Write that these cyclobutane pyrimidine dimers occur only between adjacent pyrmidines (most often thymines).
- Write that they distort the DNA double helix.
- As a clinical correlation, write that these distortions can produce skin melanomas.
Now for alkylation.
- Draw a methyl group, CH3, and an ethyl group, CH2CH3.
- Indicate that these groups can add to DNA bases (both purines and pyrimidines) at numerous positions.
Finally, bulky group addition.
- Write that this mostly occurs upon exposure to carcinogens, which are mutagens that make cells cancerous.
- Draw the bulky group benzo(a)pyrene, an aromatic, polycyclic structure.
- Write that this structure can react with both purines and pyrimidines at numerous positions.
- Write that these bulky groups also cause distortions in the DNA double helix.
- As a clinical correlation, write that carcinogens in cigarette smoke form covalent bonds with DNA and disrupt hydrogen bonding between nucleotides.
- This distorts the helix and causes a frame-shift that changes the character of all the subsequent codons in the DNA strand. Constant exposure to carcinogens can lead to lung cancer.
To emphasize this point, return to our table and denote that DNA damage can increase the frequency of mutations, which include nucleotide substitutions, deletions and insertions.
Now that we know the most common types of DNA damage, let's add the major repair pathways to our diagram.
- First, write that mismatch-repair fixes the replication errors that are missed by DNA polymerase's proofreading and exonuclease activity.
- Write that it cannot repair damaged DNA nucleotides.
- Now, indicate that the base excision repair pathway can repair deamination, depurination and alkylation.
- Finally, indicate that the nucleotide excision repair pathway can address pyrimidine dimers and bulky group addition.