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26 Cards in this Set

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  • Back
What is the most common form of DNA? (What is the form that is not recognized by the cell?)
B-form is most common - clockwise
Z-form is not recognized by the cell - counterclockwise
How is formal charge calculated?
Group number - # covalent bonds - # non-bonded electrons
Bonding of which 4 atoms with H leads to H-bonding?
F, O, N, and CL
What are the molecular geometries?
Tetrahedral: bonded to 4
Trigonal Planar: bonded to 3
Linear: bonded to 2
In arrow pushing, what does an arrow ending at an atom mean? What does an arrow ending at a bond mean?
Ending at an atom - formation of covalent bond

Ending at bond - formation of double or triple bond
What is the diff. between constitutional isomers and stereoisomers?
Constitutional Isomers - different map of bonds

Stereoisomers - same map of bonds, but different molecule
How many stereoisomers are there with "n" chiral centers?
What are geometric somers?
Cis- and trans- isomers

(When groups attached to a double-bonded carbon atom are different)
Describe how cis/trans isomersisms affect our vision.
11-cis-retinal ---- lights ---- 11-trans-retinal ~ changes conformation and function of rhodopsin, intiating the signaling cascade driving vision
In order to be able to replicate, what must a molecule be able to do.
1) Resist degradation
2) Be recognized by cellular machinery
3) Contain multiple possible structures (bits) at each position
4) Possess redundancy for error correction and faithful copying
What is a nucleotide?
Phosophate, sugar, and a base
What is an example of a practical application of protonated vs. deprotonated forms?
To what carbons do the phosophate groups connect to?
5' end
To what carbon do the base pairs attach to?
1' end
What is the difference between thymidine and uracil?
Uracil lacks the methyl group on thymidine.
At what carbon is the hydroxyl group in RNA?
Is DNA parallel or anti-parallel?
Why does RNA cleave more quickly than DNA?
DNA - hydrolysis - water attacks P on phospha

RNA - OH bonds with P

Intramolecular reactions occur much more quickly than intermolecular reactions
Are there more C:G base pairs or A:T base pairs?
What is the heart of DNA polymerization?
The formation of
a covalent bond between the 3' oxygen atom of the DNA primer and the phosphate group of
the nucleotide triphosphate located closest to the ribose ring.
Why is DNA polymerization 5'-to-3'?
The newly synthesized DNA strand grows only at its 3’ end
What are the benefits of polymerization?
Increase speed of replication and proofread.
Why can't amide bonds rotate?
Amide bonds behave a
lot like ethylene in that the atoms attached to the nitrogen and carbon groups are in the same plane and rotation is restricted - resonance
How is PCR used to detect HIV?
PCR reaction contains primer
sequences that only match the sequence of the HIV genome. Therefore, PCR products can
form only if HIV RNA is present in the original blood sample. Scientists can even measure the
number of PCR cycles required to generate a given amount of PCR product to estimate the
number of copies of HIV RNA originally present in the blood, a method called quantitative PCR.
Describe the dipole in amino acids.
The electron donation from the nitrogen lone pair to the carbonyl leads to a structure in
which the nitrogen has a partial positive charge and the oxygen has a partial negative charge.
What is unique about proline?
The trans isomer is only slightly favored.