1. Nucleotides and DNA Structure
C483 Spring 2013

2. 1. Purine(s) which are found mainly in both deoxyribonucleotides and ribonucleotides are
A) thymine and cytosine.
B) cytosine and uracil.
C) cytosine.
D) guanine and cytosine.
E) adenine and guanine.
2. The abbreviation dGp indicates
A) 5' deoxyguanylate.
B) 3' deoxyguanylate.
C) 3', 5' deoxyguanylate.
D) 5', 3'deoxyguanylate.
E) dGMP
3. Much of the stability of the double stranded helical DNA structure is the result of
A) hydrogen bonding between purines.
B) the phosphodiester backbone.
C) Ionic nucleobase attraction.
D) the stacking interactions between base pairs.

3. All five histones are rich in ________ amino acid residues whose positive charges allow binding to the sugar-phosphate backbone of DNA.
A) lysine and alanine
B) lysine and arginine
C) leucine and alanine
D) leucine and arginine
Which does not apply to most bacterial DNA?
A) Circular.
B) Relaxed.
C) Not packed into nucleosomes.
D) Supercoiled.
Which best describes the structure of a nucleosome core particle?
A) A histone octamer with DNA threaded through its center.
B) About 50 bp of DNA associated with one histone H1 molecule.
C) One nucleosome plus one histone H1 and linker DNA.
D) A histone octamer wrapped approximately two times around with DNA.

4. Nucleic Acid Structure
Nucleobase
Nucleoside
Nucleotide
Nucleic acid
Chromatin
Chromosome

5. Base Structure
Purines and pyrimidines
Aromatic
Tautomers
H-bonding

6. Nucleosides Ribonucleosides and deoxyribonucleoside
Purine = osine; pyrimidine = idine (watch cytosine)

7. Nucleotides Phosphorylated on 2’, 3’, or 5’ 5’ unless noted
Draw these: dA
ADP
ppAp
ApAp
pA is normally called _______ or _______________

9. Polynucleotides Phosphate diesters polyanion directionality 5’  3’
Abbreviation is pdApdGpdTpdC
tetranucleotide

10. Double Stranded DNA Chargaff’ Rule: %A =%T and %G = %C
(C + G) not necessarily equal to (A + T)

11. Complementary Base Pairs
Mismatching may occur with tautomers

12. Antiparallel
Inaccuracy of two-dimensional drawing: bases are perpendicular to the paper
“ladder”
H-bonding

13. Helix Maximization of base pair stacking More compact
Major and minor groove
How do we explain major/minor grooves?

14. Major/Minor Groove Many pictures show ladder with backbone at 180o
Actually a distorted ladder with poles closer to each other, on one side

15. Weak Forces Stabilize Double Helix
Stacking interactions (vdW forces)
Hydrogen bonding
Hydrophobic effect
Charge-charge

16. Denaturation
Melting point
Melting curve
UV-absorption
cooperative

17. A/T Rich and G/C Rich strands
GC rich strands harder to denature due to STACKING (not H-bonds)
Cooperativity due to initial unstacking, which exposes bases to water, which destabilizes H-bonds, which leads to further denaturation

18. Supercoiling Bacterial DNA Closed, circular DNA
Topology and topoisomerases

19. Eukaryotic DNA Chromatin 8000x packing ratio Nucleosomes (10x)
30nm chromatin fiber (4x)
RNA/Protein scaffold holds loops (200x condensation of DNA length

20. Nucleosomes
Beads on string
Histones form octamer
Core particle

21. Unpacking Histones serve as negative supercoiling
Histone acyltransferases (HATS)
Necessary for expression

22. Chromosome Scaffold of RNA and protein
30nm fibers are looped many times
Picture of histone-depleted chromosome: DNA strands have fallen off of scaffold

23. Answers E B D