DNA I and II

Question 1

Purines

Answer 1

Adenine, Guanine. Contain 2 rings

Question 2

Pyrimidines

Answer 2

Thymine, Cytosine. Contain 1 ring

Question 3

Nucleosides

Answer 3

Nucleotide without the phosphate group

Question 4

Ribose

Answer 4

One of the three base components of RNA. Has a hydroxyl group at the 2’ carbon (how differs from deoxyribose)

Question 5

Deoxyribose

Answer 5

One of the three base components of DNA. Does not have a hydroxyl group off the 2’ carbon differing it from a ribose sugar.

Question 6

What are the relative solubilities between purines, pyrimidines, bases, nucleotides and nucleosides

Answer 6

• Pyrimidine nucleotide > Purine Nucleotide > nucleoside > bases
• Purines are less soluble that pyrimidines because they are larger nonpolar molecules. Bases are less soluble than nucleosides because they do not contain the polar pentose sugar. Nucelosides are less soluble than nucleotides because they don’t contain the charged phosphate groups.

Question 7

Gout and Lesch-Nyhan disease

Answer 7

gout and Lesch-Nyhan disease are caused by improper accumulation of purines of low solubility in tissues.

Question 8

Avery, McCloud, McCarty

Answer 8

Dudes tested two serotypes of pneumococcus (S and R). They discovered that if they injected the R serotype into mice, the mice lived, but if they injected S, the mouse died. They than found that killing the S cells with heat made them non lethal. However, if they had the heat killed S and R both injected into mice the mice still died. Than, they isolated the DNA from S cells, injected that into the mouse along with R cells, and the mouse still died. Made them believe DNA was what transformed the pneumococcus

Question 9

Chargaff’s rules

Answer 9

The ratio of purines to pyrimidines and more specifically, A to G, is 1:1. Because this rule was so specific, it provided strong evidence for base pairing. In addition, this base pairing theory than provided evidence for a copying mechanism.

Question 10

Watson Crick three dimensional model

Answer 10

Two strands oriented in a R handed helix. Phosphodiester backbone on the outside, bases in the middle. Strand backbones oriented antiparallel. Minor and major groove.

Question 11

Describe the chemical basis for the stability of the double helix DNA in solution

Answer 11

Salt concentration. Positive ions surround the negatively charged phosphodiester backbone reducing its charge and stabilizing the molecule (negatively charged backbones don’t want to be in close proximity to each other).

Stability also provided by H-bonding of bases and base stacking (hydrophobic ineractions).

Question 12

Methylation

Answer 12

Occurs at the 5 carbon of the cytosine base at CpG sequences (cytosine next to guanine). It does not disrupt base pairing between cytosine and guanine but it is recognized by endogenous proteins and shuts off transcription of the region. Normally irreversible. Drugable as therapy

Question 13

Deamination

Answer 13

Spontaneous slow process by which water reacts with amino groups on bases to remove them creating ammonia. Replaces NH2 with oxygen. When methylcytosine is deaminated it turns into thymine. It is difficult for DNA repair mechanisms to detect this and can be mutagenic. Nitrous acid and its precursors (preservatives) and nitrosamine (cigarette smoke) speed up this process.

Question 14

Depurination

Answer 14

removal of base. Makes phosphate backbone prone to breaking.

Question 15

Oxidative damage

Answer 15

Hydroxyl radicals bind and oxidize bases.

Question 16

Thymine Dimerization

Answer 16

UV light dimerizes pyrimidines (thymine) Forms a kink in the helical structure

Question 17

Alkylation

Answer 17

Nucleophilic nitrogen in bases are prone to targeting alkylating agents

Question 18

Intercalation

Answer 18

These are molecules that can insert themselves within the bases of DNA preventing transcription and replication.

Question 19

Explain the chemistry of DNA polymerization

Answer 19

Nucleotides are joined together by a condensation reaction that occurs between a 5’ phosphate group and 3’ hydroxyl group releasing a pyrophosphate. When pyrophosphate is cleaved by the addition of water, a great deal of free energy is released ensuring that the reverse rxn is very unlikely to occur.

Question 20

Explain how nucleoside analogues are used as drugs

Answer 20

Nucleoside analogues are used as drugs to prevent elongation of DNA in replication. These analogues are similar enough to nucleosides that they are taken up by the replicative machinery but are missing a 3’ hydroxyl group. This ensures elongation doesn’t occur.

Question 21

Describe how DNA melting temperature/annealing to complementary sequence is negatively affected if there is a mismatch and how this can be taken advantage of in diagnostic techniques to distinguish the presence of a particular unique sequence using a “probe” that is completely complementary to that sequence.

Answer 21

DNA is destabilized by the repulsion of the highly negative phosphate backbones. To overcome this, it relies on the attractive forces of base pairing and hydrogen bonding.

With northern and southern blots, people place a small known sequence of ss DNA on a piece of paper, than melt an unknown strand and see if there is annealing between the two. If there is a mismatch, the DNA will bond very weakly and dissociate quickly. If a strong binding occurs, one can say that the “probe” sequence is also in the unknown DNA sequence.