RNA and DNA Structures Flashcards
What is the function of Gyrase?
Gyrase is a Type II Topoisomerase that relieves positive supercoiling generated upstream of polymerases by introducing negative supercoils at the expense of ATP.
What does the non-template or coding strand refer to in terms of DNA transcription or replication?
The DNA strand.
What is positive supercoiling?
When DNA strands are “overwound” or have fewer than 10.5 bases per turn.
What is negative supercoiling?
When DNA strands are “underwound” or have more than 10.5 bases per turn.
What are topoisomeases? What is the difference between Topoisomerase I and II?
Topoisomerases are cellular enzymes that catalyze the removal or addition of supercoils. Type I cuts one strand and removes supercoils one link at a time. Type II cuts 2 strands and removes supercoils 2 links at a time.
What causes supercoiling?
DNA can become positively supercoiled as a polymerase moves through it forcing the strands in front of the opened region to become tightly wound.
NOTE: Prokaryotic DNA is slightly negatively supercoiled to allow proteins to access the DNA with less energy expenditure.
What are Quinolones? What are a few examples of this type of drug?
Quinolones are antibacterial drugs that inhibit bacterial gyrase (Type II topoisomerase found in gram negative bacteria; Type IV in gram positive bacteria). Inhibition of gyrase interferes with proper supercoiling and ultimately leads to arrest in DNA replication and bacterial cell death.
Example drugs: Nalidixic Acid and Ciprofloxacin)
NOTE: Quinolones have been useful against intracellular bacteria (Legionalle , Mycoplasm) because they are taken up through porin channels.
What are Aminocoumarins? Example drug?
An antibiotic that inhibits bacterial gyrase. Polycyclic ring structures are characteristic of these drugs.
Example: Novobiocin
What is Daunorubicin and Doxorubicin?
A chemotherapuetic drug that intercalates between DNA (bases) and interferes with eukaryotic topoisomerase activity.
What is Cisplatin?
A chemotherapuetic drug that binds to bases, primarily guanine, and causes distortion, which interferes with replication and transcription.
What is Etoposide?
A chemotherapuetic drug that targets mammalian topoisomerase II.
How does radiation therapy work?
The direct energy transfer causes double stranded breaks in DNA.
What is the structural difference between RNA and DNA?
The main difference in the the C2 hydroxyl group of the pentose that is found only in RNA (ribose- 2 pentose hydroxyl groups) and not in DNA (deoxyribose- only 1 pentose hydroxyl group)
What is the main structural difference between Uracil and Thymidine?
Both are pyrimidines and have very similar structures, except Uracil lacks the methyl group on the 2’ carbon of the cyclic ring.
What is strand hybridization? At what temperature is it optimally performed?
Hybridization (or annealing) is the process in which 2 strands of DNA, RNA or both rejoin. The temperature at which hybridization occurs most efficiently is typically 5 degC bellow the Tm (or temperature at which 50% of the molecules are denatured).
