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Chem Bio > Chem Bio test 1 > Flashcards

Chem Bio test 1 Flashcards

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1
Q

Common Chem Bio tools?

A

Chromophores, Assays, Microbiological Screens and Viruses

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2
Q

Some Small Molecules that AFfect Pathways (DNA->Proteins)

A

Aphidicolin, Alpha Amanitin, cyclohexamide, alendronate, platensimycins, soyasaponins

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3
Q

What determines bonding?

A

Coulomb’s law, sterics, filled vs unfilled orbital overlap

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4
Q

Why is nucleophilic attack on phosphate esters slow relative to carboxylic esters?

A

High cost to rehybridize, presence of electronegative alkoxy substituents and repellant from the negative charge.

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5
Q

Effect on stability of the 2’OH of RNA?

A

DNA less likely to undergo base promoted phosphodiester bond cleavage
but
RNA less likely to undergo SN1 acid promoted solvolysis of the nucleobase

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6
Q

Pros and Cons of Small molecules

A

Pros: Membrane permeability,
Cons: low selectivity, difficult to synthesize

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7
Q

PCR reagents

A

dNTP’s, template, primers, MgCL2, polymerase

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8
Q

What’s the problem with bromo-uracil?

A

0.1-1% of bromouracil is in the ENOL form and can base pair with Guanine (mismatch) instead of adenine

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9
Q

Interactions that would help something bind to DNA

A

+ charge, arene activity (intercalators), curved shape to fit along DNA, epoxides (ring strain)

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10
Q

Examples of how transcription is controlled?

A

Availability of DNA, Protein modification (histones, repressors, transcription factor binding), regulatory nucleic acids that make secondary structures or block binding

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11
Q

How is translation controlled?

A

Small molecule inhibition of ribosome, mRNA degradation,

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12
Q

The reversibility of non-bonding interactions

A

Kinetic Instability

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13
Q

Molecular oxygen is most stable in singlet form because the lone pair oxygens are paired

A

false

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14
Q

Pi stacking is strongest when the rings are right on top of each other

A

False

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15
Q
A
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16
Q

What are synthetic base pairs admitted on?

A

Sterics (not h-bonding - don’t need h-bonding)

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17
Q

What wavelength do we monitor to see unfolded vs folded DNA

A

260 nm (should see an increase in absorbance when unfolded

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18
Q

Where are the fluorophores attached for ddntps

A

The 3 or 8 nitrogens

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19
Q

Characteristics of error prone PCR?

A

High DMSO content, low fidelity polymerase or Mn2+

20
Q

Difference between ddNTP’s and dNTP’s

A

dd is deoxy on 2 AND 3 so - can’t continue PCR

21
Q

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?

A

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.

22
Q

Reverse Transcript can use DNA or RNA as primer?

A

Both

23
Q

What is on our plasmid

A

ORI, Promoter, operator, terminator, selectable genetic marker, info for transcribing the repressor, Multiple cloning site, any tag for affinity purification, encoding translation (RBS)

24
Q

Cloning steps?

A

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

25
Q

Major RNA structural motifs

A

Coordinating divalent cations (diffuse and site dependant), HOOGSTEIN triple base pairing, deep major groove, shallow minor groove, short herlices, base pairing in lines with the helix (as opposed to through the center), long distance BP

26
Q

Difference between acid catalyzed and base catalyzed phosphodiester cleavage in RNA

A

In Acid - The phosphate is protonated and more stabilized - allows for the rearrangement to make it a 2’ OH, - in Base - not the case - just end up cleaving the 5’ bond on the next nucleobase

27
Q

Common targets in Thymine synthesis

A

Step 1 - Removal of 2’OH and Step 3 - Removal of Methyl

28
Q

Most nucleophilic Nitrogens across DNA base pairs

A

G (N7), A(N3), A(N1), C(N3)

29
Q

Cation pi interactions are destabilziing

A

False

30
Q

Becaose of the SP3 hybridization of water - 109.5 degrees is the strongest H bonds

A

False

31
Q

Amides are more stable than esters because of resonance

A

True!

32
Q

Key Reaction in translation

A

Aminolysis of ester bond to amide (catalyzed by weak bases)

33
Q

Which nucleotide performs the key step of translation

A

N3 of Adenine

34
Q

Interaction types to look out for?

A

Coulombic, Van Der Waals, Dipole, Hydrophobic, Pi stacking (arene activity). Positive charge ( for negative charge for DNA)

35
Q

Where does Hoogstein base pairing occur in DNA

A

Major groove (DOES OCCUR!)

36
Q

Order of DNA transcription events

A

Transcription begins RNA POLII binds - once 5’ mRNA is out - it gets capped - then splicing occurs at splcie points then finally when done - poly A tail at 3’ end

37
Q

How does tRNA synthase recognize the right tRNA

A

Global conformation and induced fit

38
Q

What causes the color change in 4-nitrophenol?

A

Loss of aromaticity through resonance

39
Q

Describe how DNA replication begins with RNA primers

A

DNA primase lays down RNA primers because DNA polymerase can only extend. It extends and eventually RNA-ase comes back and chews it up and it’s replaced by DNA polymerase and DNA ligase to connect the two

40
Q

Steps in DNA polymerase error correction

A

If the wrong base pair is present and the reaction proceeds - due to poor fit - it will occur at a much slower rate and causes a different pathway where an exonuclease to cut it out

41
Q

What are common checkpoint failure that can lead to apoptosis

A

Not enough DNA or too much DNA repair

42
Q

common RNA 2ndary structures

A

Hairpins and stem loops

43
Q

What makes up energy of bonding

A

Charge, reuplusion attraction (Charge is R^-1), repulsion is R^-6) and attraction is R ^-12)

44
Q

Longevity of DNA , RNA ,peptides lipids

A

That order

45
Q

pka of phosphodiester

A

1-2

46
Q

Why does RNA undergo phosphodiester rearrangement under acidic conditions

A

Under acidic conditions - the phosphate can be protonated - make it more neutral -

47
Q

What are the 3 amino acids important in RNA degradation

A

His 119 (protonated - acts as acid - stabilizes)), His 12 (deprotonated acts as base - removes H from OH)) and Lys 41

Chem Bio (17 decks)

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