Nucleic Acids Flashcards
Nucleosides
Sugar + Base
Nucleotides
Sugar + Base + Phosphates
Nucleic acids
Phosphate diesters of nucleotides
Both RNA and DNA can be hydrolyzed under the proper…
Acidic conditions
RNA is susceptible to strand cleavage under…
Basic conditions
What is cleavage of RNA in basic conditions accelerated by?
Divalent cations
How does RNA have to be stored?
In buffer solutions that contain chelating agent (EDTA etc.)
What are the major disadvantages of radioactive ddNTP termination?
- Four reaction mixtures required
- Radioisotopes required (P32)
How is synthetic dye termination automated?
Capillary gel electrophoresis
In nucleic acid synthesis:
What is used as the 5’ protecting group? What is used to remove it?
Dimethoxytrityl (DMT) used to protect
* Trichloroacetic acid (TCA) used to remove
What is used as the 3’ protecting group? Is it more or less acid labile than DMT?
Linked to a polymer with a COOH group
* Less acid labile, will not be destroyed when TCA is added
What coupling reaction is required in nucleic acid synthesis?
Acid catalyzed substitution
* Phosphoramidite is oxidized into phosphate
* The amine is replaced with an alcohol (the 5’ OH of the attached monomer)
What acid is used in nucleic acid synthesis?
Tetrazole
* Must not remove DMT group or hydrolyze the ester attaching 3’ to polymer
What is the purpose of the cyanoethyl in phosphoramidite?
Prevents the phosphate O- from potentially acting as a nucleophile
What is the removal of all protecting groups and cleavage from polymer done by?
Aqueous ammonia
What are the 3 classes of UV light?
- UV-A (320-400 nm)
- UV-B (290-320 nm)
- UV-C (180-290 nm)
Rank UV light classes based on the damage they cause
- UV-A can cause some DNA damage
- UV-B is major lethal/mutagenic part of sunlight
- UV-C is deadly
What UV light classes does the ozone layer absorb?
- All UV-C
- Some UV-B
- No UV-A
Why is benzene a carcinogen?
When oxidized, it forms an epoxide that can react with DNA
Why is toluene a safer alternative to benzene?
The benzylic carbon is oxidized into COOH first
How are carcinogens made during home cooking?
Burning of fat at high temperature forms polyaromatic hydrocarbons (PAHs)
What is carcinogenic about PAHs?
- Large
- Planar
- Hydrophobic
Intercalate DNA, react with DNA
How do carcinogens form from burning meat?
Contains nitrogen from amino acids
* Forms heterocyclic aromatic amines (HAA)
What happens to carbohydrates and amino acids under high temperatures?
React together via Maillard reaction
* Can form carcinogens such as acrylamide
