Nucleic Acids

Question 1

How many rings do purines have?

Answer 1

Two! (two syllables, two rings)

Question 2

Draw a nucleic acid chain..

Answer 2

Do it!

Question 3

What are the relative solubilities of Purines, pyrimidines

Answer 3

Nucleotide > nucleoside > bases (Pyrimidine > Purine) Pyrim > purine because it only has one ring

Question 4

Polarity of the DNA nucleotide / growing DNA strand

Answer 4

5’ end has the PO4 group, 3’ has the -OH. The 3’ OH gets replaced with PO4 as the chain grows

Question 5

Genetic material experiment?

Answer 5

Smooth strain killed mice, rough strain did not.

DNA from heat-killed S + live R then killed mice

Question 6

Chargaff’s Rules

Answer 6

%G = %C and %A = %T Values vary from organism to organism, but all total 1

Question 7

DNA is a _____-handed double helix. Every ___ base pairs completes one full turn.

Answer 7

right; 10.

Question 8

How does salt concentration affect Tm of DNA?

Answer 8

As salt conc. goes down, so does Tm because the PO4 groups are no longer neutralized by the Na or Mg cations. The exposed negative charges tend to force the strands apart, thereby lowering Tm.

Question 9

How does pH impact the Tm of DNA?

Answer 9

Alters the ionisation states of the groups on the bases which provide/accept H-bonds

Question 10

What 3 factors stabilize DNA helical structure?

Answer 10

1. PO4 groups are stabilized by salt
2. Base pair linkages
3. Stacking of adjacent base pairs

Question 11

Describe relaxed vs super-coiled DNA

Answer 11

Relaxed = normal state
Super-coiled = increased torsional strain leading to figure-8 structures (think phone cord).  This is also called writhe.

Question 12

What are the four chemical modifications that can be made to DNA?

Answer 12

Methylation, Deamination, Depurination, Dimerization

Question 13

Describe methylation of DNA

Answer 13

Occurs on 5’ cytosine ends of CpG sequences (cytosine –> 5-methylcytosine). This decreases gene activity and is epigenetically inherited.

Question 14

Describe deamination of DNA

Answer 14

Cytosine - NH2 = Uracil (repaired by BER; not a big deal)
Me-Cytosine - NH2 = Thymine (big problem, more subtle). If not fixed before replication, you’ll get AT instead of GC at that point.

Question 15

Describe depurination of DNA

Answer 15

Hydrolysis of the purine base off the ribose sugar. Afterwards, the phosphate backbone is sensitive to breakage.

Question 16

What are the implications of UV damage?

Answer 16

Creation of thymine dimers. This distorts the DNA and can block replication (fixed by NER)

Question 17

Define the different classes of RNA in a cell

Answer 17

Structural: rRNA, snRNA/snoRNA = splicosome
Regulatory: siRNA, miRNA = downreg gene exp.
Information-containing: mRNA

Question 18

How does puromycin work?

Answer 18

Translational inhibitor that mimicks a tRNA and enters a bacterial ribosome causing premature chain termination.