Nucleic Acids & Modulating Enzymes Flashcards
What structural forms can nucleic acids take?
A-form, B-form and Z-form.
B-form is the most common.
What is “puckering”
Sugar puckering is the conformation sugar rings take since flat rings are sterically unfavourable. 2’-endo and 3’endo rings are the two structures that arise from this ring puckering.
Describe the groves of A-form DNA.
The A-form has a narrow but deep major groove and a wide but shallow minor groove.
Describe the grooves of B-form DNA.
The B-form has a wide but shallow major groove and a narrow minor groove.
Describe “Epi-genomics”
Epi-genomics = DNA methylation
It can be spontaneous or done by enzymes.
Eukaryotes use it to regulate gene expression by turning on or off the methylated gene via it’s interaction with transcription factors.
What is special about 7-methyl-guanine?
It induces the loop structure in tRNA by binding to guanine and the phosphate backbone to stabilise the twisted tRNA.
What is RNA modification for?
It can be to stabilise or otherwise influence the 2D and/or 3D structure, which can impact binding partner interaction. It’s like the fine tuning of translation.
Describe the mechanism of DNA polymerase.
The 3’OH of the template is activated by Mg2+ and AA in the active site.
The activated Nu- attacks the P of the incoming dNTP.
The beta and gamma P act as LGs and the dNTP has been added.
Why does extension go in the 5’ to 3’ direction?
Because if it were to go in the 3’ to 5’ direction the LG would have to be OH which is a very poor LG in comparison to P2.
DNA polymerase requires a primer while RNA polymerase doesn’t, why?
It is theorised that because DNA polymerase has proof reading ability it binds less tightly to the dNTPs so could not start synthesis without the base stacking effect provided by the primer.
What are the 4 steps in modern DNA synthesis?
- Detritylation or Deprotection of the 5’OH
- Addition of the E+ to the 5’OH
- Capping of any unreacted 5’OH with acetyl group
- Oxidation of the phosphite linkage to a phosphate linkage.
After you rinse with ammonia and then cleave from the solid support. Because the phosphoamidite binds to the 3’ position synthesis proceeds in opposite polarity from 3’ to 5’.
Why might we alter RNA post-translation synthetically?
To add labels for use in further research.
To alter their reactivity.
To alter their structure and modulate interactions.
To alter the stability of the products.
Explain the four key elements of DNA polymerase.
Fidelity: How accurate the enzyme is at matching base pairs.
Thermal stability: How stable the enzyme is at certain operating temperatures.
Extension rate: How fast the enzyme adds bases.
Processivity: How many bases the enzyme can add before falling off the template strand.
What are obligatory and non-obligatory chain terminators?
Obligatory chain terminators: Do NOT have a 3’OH group so have no Nu- to react.
Non-obligatory chain terminators: Possess a 3’OH but it is conformationally constrained or sterically hindered so can not react.
What is ASO and how does it work?
ASO = Anti Sense Oligonucleotide
They are small segments of RNA that interfere with gene expression.
They stop the 5’-capping of mRNA or they sterically block the entry point for translation, alternatively they can activate RNAse H to chop up the duplex RNA.
