Nucleic Acids Flashcards
Distinguish purines and pyrimidines bases
purines have two rings: PURe As Gold (adenine, guanine)
pyrimidines have one ring: CUT PYe. (Cytosine, Urasil, Thymine)
Distinguish ribose and deoxyribose
deoxyribose does not have a OH group at the 2’ carbon on the ring.
distinguish nucleotides, nucleosides di and tri phosphates
nucleotide- base, sugar, phosphate
nucleoside- base, sugar
discuss solubility of components of nucleotides and related diseases
solubility- pyrimidines > purines. Nucleotides>nucleosides>bases.
Gout and Lesch-Nyhan disease are caused by accumulation of purines.
Discuss chemistry in phosphodiester linkage of DNA and RNA polynucleotide strands.
phosphodiester linkage between 5’ phosphate of one nucleotide to 3’OH of another. enzymes add nucleotide 5-3
What drug fights HIV by lacking a 3’OH and acts like a nucleotide, preventing polymerization of virus?
DDI
Chargaffs rules
Molar amts of Pur and Pyr was always equal in any cellular DNA sample. Led to base-pairing idea
Describe Watson-Crick Model model
Double Helix- 2strands intertwined in right-handed turn
Anti-Parralel stands- stand 1 is 5-3 and other is 3-5
Phosphate Backbone- outside of the helix with one (-) per phosphate. Geometry only allows for AT and GC pairing.
Base Pairing- through H-bonds in the center of the helix and stacking (hyrdophobic interactions).
Melting Temp- when 50% of molecules are separated. GC has 3 H-bonds, AT has 2. So more GC is more stablility.
Describe basis for stability of double helix in solution
higher salt concentration helps stability by neutralizing phosphate (-).
extremes of pH- alter base ionization states
increase in DNA length increases melting temp.
Discuss DNA melting/annealing is weakened by a mismatch. This is diagnosed by a complementary ‘probe’.
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DNA and RNA similarities and differences
Ribose has 2’OH, which makes it more susceptible to hydrolysis. Allows cell to regulate [RNA] thus gene expression. RNA has Uracil instead of thymine.
Usually is single stranded
3 classes of RNA in humans
Informational- mRNA (translated into protiens)
Structural- tRNA, rRNA, snRNA.
Regulatory- microRNA, small interfering RNA, long noncoding RNA.
How does puromycin mimic amino-acyl tRNA to terminate translation?
it mimics, the ‘acceptor’ 3’end in tRNA, and it binds in the ribosome during translation and terminates it. Streptomuces makes puromycin and also an inhibitor for it.
DNA damage-Base Alkylation:
caused by benzene from coal and cig smoke, forms large covalent adducts to DNA. Not easily repaired and blocks replication and transcription. used against cancer.
DNA damage- De-purination
low pH can break bond between base and sugar
DNA damage- oxidative damage
oxygen free radicals from mitochondria can disrupt DNA stx, by adding OH groups
DNA damage- Thymine Dimers
UV light causes covalent bonding of adjacent thymines on same strand.
DNA damage- Deamination of bases-
nitrous acid from nitrosamine in cigarrete smoke, cleave the amines. If a nromally methylated C loses amine group, it becomes T. causes mismatch and point mutation. Mismatch is fixed, but eh point is often missed.
DNA damage- Methylation of Adenine-
in bacteria helps repair enzymes identify older strands.
DNA damage- Methylation of Cytosine-
in eukaryotes C’s adjacent to G’s (CpG) are methylated in the 5’ position, silencing transcription.
Drugs-Cisplatin
base akylating agent
Drugs- Actinomycin D
natural antibiotic. “intercalates” (inserts ring stx into DNA sirupting stx.) prevents replication and transcription.
Drugs- Doxorubicin
similar to Actinomycin
Drugs- Etoposide and Camptothecin
chemotherapuetics that target topoisomerases (prevent supercoiling). Leaves breaks in DNA that aren’t repaired.
