Nucleic Acids

Question 1

Nucleoside

Answer 1

Lacking phosphate group.
Sugar + base
Can be mono, di, tri-phosphate
A nucleoside monophosphate = a nucleotide.

Question 2

What’s soluble?

Answer 2

Nucleotide > nucleoside > bases

pyrimidine > purine

Question 3

Where is the OH group on ribose sugar?

Answer 3

At the 2’C

Question 4

dNTP

Answer 4

deoxynucleotide-triphosphate

Question 5

Lesch-Nyhan

Answer 5

an accumulation in tissues of purines. This forms uric acid in kidneys and other body tissues.

Question 6

Purine

Answer 6

Pure as gold. A and G.

Question 7

Gout

Answer 7

Defect in phosphoribosyl synthetase, accumulation in tissues of purines. Low solubility. Uric acid in joints.

Question 8

Why the 5’-3’ polarity?

Answer 8

This is because the 3’ end has a spare OH group.

5’ end has spare phosphate group.

Question 9

Phosphodiester linkage

Answer 9

Strong covalent bonds. OR (R is akyl group). Between phosphate group and 2 5-C ring carbs.
Link between 3’ carbon of one sugar and the 5’ C of another.
Pyrophosphate breaks away (can be 1 or 2 P’s) to provide the catalyzing energy for the bond formation.

Question 10

Where is the P?

Answer 10

On the 5’ C because it is the most partially positive.

Question 11

Avery, McCloud, and McCarty

Answer 11

They transformed pneumococcus serotype R to S, showed that DNA causes bacterial transformation. Before they thought it was protein.
Living R + heat-killed S –> dead mouse.

Question 12

Chargaff’s rules

Answer 12

In DNA there is always equality in quantity between bases A and T, C and G. (every organism has diff G+C/A+T)

Question 13

Watson-Crick

Answer 13

Discovered definitive double-helical structure and that DNA semi-conservatively replicates

Question 14

B form DNA

Answer 14

2 strands in a right-handed helix
Strands backbones are oriented anti-parallel
Sugar phosphate backbone is on OUTSIDE of helix (hydrophilic)….

Question 15

Chemical basis for stability of double helix DNA

Answer 15

Hydrophobic interactions b/w adjacent base pairs
H bonding between complementary bases in a base pair are imp for DNA stability (to compensate for the neg charged P which want to repel).
In sol’n: Mg (cations in sol’n) stabilize negative P. Base pair linkages & adjacent base pairs stack via hydrophobic interactions.

Backbone is phosphodiester, it binds with water, negative.

Question 16

Increased salt concentration

Answer 16

Increases the Tm.

Salt stabilizes the P groups with na and Mg. Exposed negatives would force strands apart.

Question 17

Extremes of pH

Answer 17

alter ionization of groups on bases that provide and accept the H bonds.
Really acidic, really positive.

Question 18

Increased chain length

Answer 18

Increased length stabilizes the molecule, and increases the Tm

Question 19

Increased GC content?

Answer 19

Increases the Tm. 3 bonds b/w G and C.

Question 20

Linear DNA

Answer 20

Can be relaxed or supercoiled.
Relaxed is the NORMAL, straight ribbon of proper twisting.
Supercoiled: torsional strain that becomes contorted into shapes like a Figure 8.
Important for DNA packaging in eukaryotes.

Question 21

Circular DNA

Answer 21

is in prokaryotes

Question 22

Methylation

Answer 22

Occurs at CpG sites. 5’ end on cytosine. Converts cytosine to 5-methyl-cytosine. DNA methyltransferase facilitates this.
Human DNA has 80-90% methylated CpG sites… often associated with promoters of 56% of genes.
CpG can often be seen around genes that DO get transcribed (bizarre thought).
Can be epigenetically inherited.

Question 23

Deamination

Answer 23

C can lose an amine to become U (results in mutated DNA).
MAJOR cause of mutated DNA. Repair enzymes should catch this.
5’ methylcytosine can be deaminated to THYMINE (so this becomes A-T and is harder to catch).
Nitrous acid, tobacco, speeds this up.

Question 24

Depurination

Answer 24

A or G is removed by hydrolysis of the beta-N-glycosidic link (b/w base and first sugar)… leaves HYDROXIDE in its place
Lower pH promotes the hydrolysis of this.
The phosphate backbone is now prone to breakage.

Base excision repair??

Question 25

Oxidative damage

Answer 25

Reactive O2 free radicals generated in mitochondria can damage DNA.
Leads to OH groups on bases.

Question 26

UV light

Answer 26

covalently bonds thymines (distorts DNA helix) and can block replication enzymes.
Occurs between thymines (get cyclobutane thymine dimers). PYRIMIDINE DIMERS.
Transcription factor IIH human (repair)… nucleotide excision repair.

Question 27

Alkylating agents and chemo

Answer 27

Alkylating agents are used as chemo to damage the DNA of cancer cells (prevents proper DNA replication/transcription and thus cell growth).