Chem Bio test 1 Flashcards
(47 cards)
Common Chem Bio tools?
Chromophores, Assays, Microbiological Screens and Viruses
Some Small Molecules that AFfect Pathways (DNA->Proteins)
Aphidicolin, Alpha Amanitin, cyclohexamide, alendronate, platensimycins, soyasaponins
What determines bonding?
Coulomb’s law, sterics, filled vs unfilled orbital overlap
Why is nucleophilic attack on phosphate esters slow relative to carboxylic esters?
High cost to rehybridize, presence of electronegative alkoxy substituents and repellant from the negative charge.
Effect on stability of the 2’OH of RNA?
DNA less likely to undergo base promoted phosphodiester bond cleavage
but
RNA less likely to undergo SN1 acid promoted solvolysis of the nucleobase
Pros and Cons of Small molecules
Pros: Membrane permeability,
Cons: low selectivity, difficult to synthesize
PCR reagents
dNTP’s, template, primers, MgCL2, polymerase
What’s the problem with bromo-uracil?
0.1-1% of bromouracil is in the ENOL form and can base pair with Guanine (mismatch) instead of adenine
Interactions that would help something bind to DNA
+ charge, arene activity (intercalators), curved shape to fit along DNA, epoxides (ring strain)
Examples of how transcription is controlled?
Availability of DNA, Protein modification (histones, repressors, transcription factor binding), regulatory nucleic acids that make secondary structures or block binding
How is translation controlled?
Small molecule inhibition of ribosome, mRNA degradation,
The reversibility of non-bonding interactions
Kinetic Instability
Molecular oxygen is most stable in singlet form because the lone pair oxygens are paired
false
Pi stacking is strongest when the rings are right on top of each other
False
What are synthetic base pairs admitted on?
Sterics (not h-bonding - don’t need h-bonding)
What wavelength do we monitor to see unfolded vs folded DNA
260 nm (should see an increase in absorbance when unfolded
Where are the fluorophores attached for ddntps
The 3 or 8 nitrogens
Characteristics of error prone PCR?
High DMSO content, low fidelity polymerase or Mn2+
Difference between ddNTP’s and dNTP’s
dd is deoxy on 2 AND 3 so - can’t continue PCR
A pair of negatively charged functional groups and a pair of neutral atoms are initially 2 Angstroms apart and then are moved to 3 angstrom apart from each other (each unit in a pair). Describe how the energy of their interaction changes?
The negatively charged are repulsed and the change in repulsion is proportional (so tit is now 2/3’s of the original - decreased by 1/3). For the neutrals - they have a slight attraction initially from van der waal forces and this DECREASES by MORE THAN 90% - a very drastic change.
Reverse Transcript can use DNA or RNA as primer?
Both
What is on our plasmid
ORI, Promoter, operator, terminator, selectable genetic marker, info for transcribing the repressor, Multiple cloning site, any tag for affinity purification, encoding translation (RBS)
Cloning steps?
Generate recombinant vector (PCR), use restriction enzymes to introduce
Introduce to organism (take up)
Kill off those that didn’t take it up
Express protein
Purify
