Lecture 7: Nucleotides

Question 1

What is a nucleotide

Answer 1

Nitrogenous base

Pentose

Phosphate

Question 2

What is a nucleoside

Answer 2

Nitrogenous base

Pentose

Question 3

What is the numbering convention for pyrimidine and purines

Answer 3

Question 4

What does the number in front of adenosine 5’-monophosphate mean?

Answer 4

Indicated where on the ribose sugar it is attached

Question 5

What is the formula for aldehyde and the sugar it forms?

Answer 5

Question 6

Sugared rings form different puckered conformations. What are they?

Answer 6

Question 7

What is the structure for the Purines?

Answer 7

Question 8

What is the structure for the Pyrimidines

Answer 8

Question 9

What is the nomenclature for deoxyribonucleotides?

Answer 9

Question 10

What are is the nomenclature for ribonucleotides?

Answer 10

Question 11

What is the bond between the pentose ring and the nitrogenous base

Answer 11

N-glycosidic bond

Question 12

The glycosidic bonds have free rotation what angles can they forms

Answer 12

The sequence of atoms chosen to define this angle is O4-C1-N9-C4 for purines, and O4-C1-N1-C2 for pyrimidines

• Angle near 0 corresponds to syn conformation
• Angle near 180 corresponds to anti-conformation

Question 13

What is the tautomerization of Uracil called and structures?

Answer 13

Question 14

What DNA modification can Eukaryotes and bacteria do?

Answer 14

Both: 5-methylcytosine

Bac: N6-methyladenosine

Question 15

What is inosine?

Answer 15

Sometimes found in the “wobble position” of the anticodon in tRNA

• made by de-aminating adenosine

Question 16

What is

S-RNase

RNase P

Dicer

Answer 16

1. S-RNase: prevent interbreeding in plants
2. RNase P: is a ribozyme that processes tRNA precursors
3. Dicer: an enzyme that cleaves double stranded RNA into oligonucleotides (protects from viruses)

Question 17

What makes RNA less stable than DNA

Answer 17

Question 18

Where to do AT and GC pair?

Answer 18

Question 19

What does base stacking do?

Answer 19

The primary contributor to DNA stability and they are caused by the hydrophobicity of the bases and the pi-bond cloud

Question 20

What is the following for A, B, Z form

1. Diameter
2. Base/turn
3. Pucker

Answer 20

Question 21

Where can DNA only be read?

Answer 21

From the Major groove, minor groover is inaccessible

Question 22

Is DNA right handed or left handed

Answer 22

Right handd

Question 23

What type of sequences on RNA can form hairpins and cruciforms

Answer 23

Palindromes

Question 24

Complex structure are stabilized by Non-Watson Crick Base-Pair interactions (T/F)

Answer 24

True

Question 25

If base stacking is lost what happens to UV absorbance?

Answer 25

It increases

Question 26

What is T_m and what does it depend on?

Answer 26

The midpoint of melting depends on base compoistion

• High GC increases T_m
• Longer DNA has higher T_m
• High salt increases T_m

Question 27

What is mutagenesis Deamination?

Answer 27

Deamination is spontaneous and very slow.

Question 28

What is mutagenesis Depurination

Answer 28

N-glycosidic bond is hydrolyzed

10,000 purines lost per day

Question 29

What does UV light do to DNA

Answer 29

Dimerizes pyrimidine

Question 30

What does ionizing radiation (x-rays and skin cancers)

Answer 30

Causes ring opening and strand breaking