Nucleic Acid Flashcards
Describe the phosphodiester bond between bases in DNA and RNA chains
Links successive nucleotides, polar backbone, occurs between 3’ OH group of one nucleotide and 5’ phosphate group of another nucleotide
RNA is more labile (more easily altered) than DNA. Describe the process of RNA hydrolysis and what is explains about DNA vs. RNA.
A base deprotonates the 2’ OH group on RNA nucleotide, allows nucleophilic attack on adjacent phosphate group, results in catalysis of RNA. DNA is resistant to this due to lack of 2’ OH so this supports its likelihood of being the carrier of genetic information compared to RNA. This process partially explains why RNA’s half life is not terribly long.
What is the major force holding DNA together?
Major force holding DNA together is base stacking - hydrophobic interactions between hydrophobic bases want to be close together in an aqueous solution so they condense and stack on top of each other stabilizing the DNA double helix. Driven by enthalpy.
What are the 3 known variants of DNA secondary structure?
A - DNA
- Right handed helix, wider, flatter, occurs under dehydrating conditions
- When RNA is in double stranded form it is A-structure
- When RNA and DNA complex it is A-structure
B - DNA
- The DNA we all know and love, right handed helix
Z- DNA
- Left handed helix, seen in conditions of high salt concentration, found when there are a lot of GCGC or ATAT repeats in a sequence
What is snRNA?
Small nuclear RNA
It is involved in processing of mRNA in nucleus
What is miRNA? (Name, function, location)
Micro RNA
It inhibits translation of mRNA
Located in cytoplasm
What is siRNA? (Name, function, location)
Small Interfering RNA
Triggers degradation of other RNA molecules
Cytoplasm
What is chargaff’s rule?
The amount of A in sample of DNA = amount of T
Amount of G =amount of C
What is the diameter of DNA?
2nm or 20 Angstroms
Where are the bases in DNA? Where are the sugars? Where are the phosphates?
Bases: interior of helix
Sugars: Backbone
Phosphates: Backbone
Which bases are purines? Pyrimidines?
Purines: PURE As Gold (A, G)
Pyrimidines: CUT the PYE (C,U,T)
How many base pairs per turn of DNA?
What is the width of one turn?
~10
3.4nm = 34A
Why does UV absorbance increase the more DNA is denatured? (Hyperchromic shift)
As DNA is denatured, the bases in the middle of the helix become more exposed to UV light, these bases are aromatic, so they are able to absorb more light. This is due to distruption of their aromatic electron configurations as they are exposed to more UV light.
What is Tm?
What does it depend on?
The denaturation tempterature or melting temperature of DNA. It is the temperature at the midpoint of the denaturation curve.
Solvent, concentrations/types of ions, pH, fraction of GC base pairs
How is the denaturation of DNA cooperative?
The collapse of one part of the DNA will lead to the collapse of the rest of the structure near it, which leads to a domino effect of instability and cooperative destabilization.
What is annealing?
DNA that has been denatured is maintained at 25º C below the Tm which leads to complete renaturation of DNA (base pairs bind again correctly)
Blots:
- Northern
- Southern
- Eastern
- Western
- RNA
- DNA
- Immunoblot
- Protein
Compare and contrast the pre- and post-encode features of the human genome and how the new data influences genetics.
Pre-encode: thought that the part of the genome that wasn’t transcribed was just junk DNA
Post-encode: most diseases don’t lie within the transcribed regions of DNA but the non-coding regions of DNA, parts of the genome that don’t code still have functions (bind to transcription factors, histones, cis-acting elements, 5’ and 3’ UTR, etc.)
