DNA I, DNA II & RNA Flashcards
Which nucleic acids are purines?
Adenine & Guanine
- Heterocyclic aromatic compounds
- Other important purines: ATP, GTP, cyclicAMP, NADH, coenzyme A
Which nucleic acids are pyrimidines?
Cytosine, Thymine & Uracil
-Heterocyclic aromatic compound; 6 membered w/ 2 N in ring
In which direction is RNA transcribed?
5’ to 3’
What is the relative solubility of purines v. pyrimidines?
solubility: pyrimidines > purines
What are the relative solubilities of nucleosides, bases and nucleitides?
solubility: nucleotides> nucleosides> bases
Describe Gout
genetic deficiency of one or another enzymes of purine metabolism which decreases their solubility.
a. build up of uric acid in blood and tissues -> inflamed and painful joints (abnormal sodium urate crystal deposits
b. excess uric acid in kidney tubules
c. more common in males
d. treated by decreasing intake of nucleic acid rich food (liver, glands)
e. allopurinol-> inhibits conversion of purines into uric acid -> xanthine and hypoxanthine (more water soluble than uric acid)
Describe Lesch-Nyhan Disease
– geneic lack of hypoxanthine-guanine phosphoribosyltransferase activity
a. Almost exclusively male, manifests by age 2
b. Sometimes results in poor coordination, mental retardation, compulsive self-destructive behaviors (bit off fingers, toes, lips)
c. Deficit of pathway-> purines over produced -> gout like damage to tissue
d. Brain is dependent on salvage pathway (nucleotides synthesized from intermediates in degradative pathway for nucleotides) -> does not get purine products -> CNS deficits?
What experiment did Griffith perform?
- 2 forms of pneumonia : with capsule lethal, w/o capsule non-lethal
- Mix dead capsule form with live non-capsule form -> lethal
What experiment did Avery, MacLeod & McCarty perform?
a. Virulent (encapsulated, lethal) and non-virulent (non-encapsulated, non-lethal) strains of bacteria
b. DNA (treated with protease) from encapsulated mixed with live non-encapsulated, injected in to mouse -> LETHAL
c. Protein (treated with deoxyribonuclease) from encapsulated mixed with non-encapsulated, injected into mouse -> non-lethal (disproving theory that had been popular up till that point that protein carried genetic information)
What is Chargaff’s rule?
“In all DNA, molar ratios of total purines to total pyrimidiens (Adenine to thymine and Guanint to Cytosine were not far from one”
-Purines (G+A) = Pyrimidines (T+C)
-This introduces the concept of base pairing; there must be some type of precise matching or alignment going on in order for this ratio to occur
-Important to know that the G+C/ A+T ratios are different in DNA from different organisms (they do not have the exact same code!) but:
%G=%C & %A = %T in every cellular organism
(not necessarily viruses b/c they can have only single stranded RNA)
What is the Tm?
temperature at which 50% if DNA separates
What factors affect the Tm of DNA?
-In solution, - backbone attracts + ions to help neutralize
[salt] – as this decreases, phosphate no longer stabilized by Mg and Na ions -> lower Tm
-pH extremes – alter ionization of groups on bases that provide/ accept H-bonds
-Increased chain length = increased Tm
-Increasing G-C content increases Tm (G-C have 3 bonds, A-T have 2 bonds)
How many bonds are there between A-T?
2 hydrogen bonds
How many bonds are there between G-C?
3 hydrogen bonds
What is methylation?
major covalent modification of human DNA is methylation of C at CpG (site with cytosine next to guanine) sequences SYMMETRICALLY => consequences for gene regulation and mutagenesis
- A & C more often than G & T
- In some cases distinguishes self from foreign (bacteria/ virus)
- 5% of Cytidine residues are methylated -> turns off/ silences gene regulation
- As new strand is templated, parent strand induces/ propagates methylation
What is deamination?
enzymatic removal of amino groups from biomolecules such as amino acids or nucleotides: spontaneous loss of exocyclic amino groups -> major casue of mutations, sped up by nitrous acid
Ex) deamination of cytosine -> uracil ~100x / day / cell -> intrinsic mechanism of repair for DNA b/c uracil is foreign – should not be present in DNA
Ex) 5-methylcytosine -> Thymine hard to fix b/c naturally occurring
What is depurination?
water cleaves base -> weakens phosphate backbone => double DNA break
-much more common in purines
What is UV cross linking?
covalent linking bwtween stacked base pairs
-Changes DNA metabolism, especially Thymine (T-T bond)
What are the 3 classes of RNA?
Structural
Regulatory
Information containing
What is structural RNA and what does it do?
- Ribosomal – rRNA
- Transfer RNA – tRNA – works with ribosome
- Small nuclear RNA – snRNA
- Small nucleolar RNA - snoRNA – works to build RNA
What is Regulatory RNA and what does it do?
regulate RNA after transcription through translational repression or degredation
- Micro RNA – miRNA – natural
- Small interfering RNA – siRNA – synthetic biologic tools – mRNA cleavage -> cessation of translation-> loss of protein
What is informational RNA and what does it do?
- Messenger RNA – mRNA – code for translation of protein
- Go to ribosomes
How does puromycin mimic amino-acyl tRNA to terminate translation?
-Puromycin is nucleotide analogue
-Mimic tRNA acceptor region -> allows peptide transfer -> termination of translation
-All about mimicry-> looks like 3’ end of aminoacyl tRNA-> binds at ribosomal A site -> participates in peptide bond formation => peptidyl-puromycin
B/c only has 3’ mimicry -> does not participate in translocation -> dissociates from ribosome shortly after linke to carboxyl terminus of peptide
=> PREMATURE TERMINATION
