Biophysical Chemistry

Biophysical Chemistry
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1. DNA and RNA are both polymers of ___, a ____.: Nucleotides, monomers
2. Look up pka of protein functional groups:
3. Nucleotides are composed of: -phosphate group (outside)
-sugar (center)
-nitrogenous base/aromatic pentagon+hexagon w/ nitrogens (inside)

Or
-phosphate group
-nucleoside
4. Nucleoside: sugar + base (no phosphate)
(Guanidine)




5. A:
Base and Nucleoside name: Adenine
(deoxy)Adenosine
6. G:
Base and Nucleoside name: Guanine
(deoxy)Guanidine
7. C:
Base and Nucleoside name: Cytosine
(deoxy)Cytidine
8. T:
Base and Nucleoside name: Thymine
(deoxy)Thymidine
9. U:
Base and Nucleoside name: Uracil
Uridine
10. The sugar in nucleotides contains ___ carbon atoms: 5
11. The sugar in nucleotides is a cyclic form of ___: Pentose
12. ___ of the 5 carbon atoms in the sugar form a ___-member ring with ___: 4,
5, oxygen
13. The carbons in the sugar ring are labeled _____ and the oxygen is labeled
___: C1' to C4'
O4'




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14. The fifth carbon in the nucleotide sugar is labeled ___ and is atttached to
___: C5'
C4'
15. The phosphate group in nucleotides uses ___ atom to attach to ___: a
single bond oxygen
C5' (the sugar)
16. The nitrogenous base in nucleotides uses ___ atom to attach to ___: A
nitrogen
C1' (the sugar)
17. Aromatic hexagon and pentagon
9 positions
5 Nitrogens
Nitrogens on positions 1,3 and 7 are in a C=N-C bond AND are H-bond
ACCEPTORS
Nitrogen at position 9 is C-N(H)-C bond
NH2 attached at POSITION 6 CARBON:
18. Purine: double ring structure (Aromatic hexagon and pentagon)
at least 4 nitrogens attached at positions 1,3,7,9
A and G




19. Pyrimidine: Aromatic hexagon
at least 2 nitrogens attached at positions 1,3
U, T, C




20. Guanine: Purine or Pyrimidine?: purine






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21. Guanine: ___ attached at POSITION 6 CARBON: =O
(H-bond acceptor)
(WC)




22. Guanine: ___ attached at POSITION 2 CARBON: NH2
(either H used in H-bond donating)
(one closer to O is WC)




23. Adenine: Purine or Pyrimidine?: purine




24. Adenine: ___ attached at POSITION 6 CARBON: NH2
Either Hydrogen can be an Hbond donor




25. Adenine: Nitrogen at position ___ is C-N(H)-C bond: 9
(does NOT participate in H-bonds)
(Glycosidic bond formed and H2O is released)