L. Sci. - Exam 1 Quest.

Front 1

What is the most common form of DNA? (What is the form that is not recognized by the cell?)

Back 1

B-form is most common - clockwise
Z-form is not recognized by the cell - counterclockwise

Front 2

How is formal charge calculated?

Back 2

Group number - # covalent bonds - # non-bonded electrons

Front 3

Bonding of which 4 atoms with H leads to H-bonding?

Back 3

F, O, N, and CL

Front 4

What are the molecular geometries?

Back 4

Tetrahedral: bonded to 4
Trigonal Planar: bonded to 3
Linear: bonded to 2

Front 5

In arrow pushing, what does an arrow ending at an atom mean? What does an arrow ending at a bond mean?

Back 5

Ending at an atom - formation of covalent bond

Ending at bond - formation of double or triple bond

Front 6

What is the diff. between constitutional isomers and stereoisomers?

Back 6

Constitutional Isomers - different map of bonds

Stereoisomers - same map of bonds, but different molecule

Front 7

How many stereoisomers are there with "n" chiral centers?

Back 7

2^n

Front 8

What are geometric somers?

Back 8

Cis- and trans- isomers

(When groups attached to a double-bonded carbon atom are different)

Front 9

Describe how cis/trans isomersisms affect our vision.

Back 9

11-cis-retinal ---- lights ---- 11-trans-retinal ~ changes conformation and function of rhodopsin, intiating the signaling cascade driving vision

Front 10

In order to be able to replicate, what must a molecule be able to do.

Back 10

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

Front 11

What is a nucleotide?

Back 11

Phosophate, sugar, and a base

Front 12

What is an example of a practical application of protonated vs. deprotonated forms?

Back 12

Prilosec

Front 13

To what carbons do the phosophate groups connect to?

Back 13

5' end

Front 14

To what carbon do the base pairs attach to?

Back 14

1' end

Front 15

What is the difference between thymidine and uracil?

Back 15

Uracil lacks the methyl group on thymidine.

Front 16

At what carbon is the hydroxyl group in RNA?

Back 16

2'

Front 17

Is DNA parallel or anti-parallel?

Back 17

Anti-parallel

Front 18

Why does RNA cleave more quickly than DNA?

Back 18

DNA - hydrolysis - water attacks P on phospha

RNA - OH bonds with P

Intramolecular reactions occur much more quickly than intermolecular reactions

Front 19

Are there more C:G base pairs or A:T base pairs?

Back 19

C:G

Front 20

What is the heart of DNA polymerization?

Back 20

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.

Front 21

Why is DNA polymerization 5'-to-3'?

Back 21

The newly synthesized DNA strand grows only at its 3’ end

Front 22

What are the benefits of polymerization?

Back 22

Increase speed of replication and proofread.

Front 23

Why can't amide bonds rotate?

Back 23

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

Front 24

How is PCR used to detect HIV?

Back 24

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.

Front 25

Describe the dipole in amino acids.

Back 25

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.

Front 26

What is unique about proline?

Back 26

The trans isomer is only slightly favored.