Lecture 7: Nucleotides Flashcards
What is a nucleotide
Nitrogenous base
Pentose
Phosphate
What is a nucleoside
Nitrogenous base
Pentose
What is the numbering convention for pyrimidine and purines
What does the number in front of adenosine 5’-monophosphate mean?
Indicated where on the ribose sugar it is attached
What is the formula for aldehyde and the sugar it forms?
Sugared rings form different puckered conformations. What are they?
What is the structure for the Purines?
What is the structure for the Pyrimidines
What is the nomenclature for deoxyribonucleotides?
What are is the nomenclature for ribonucleotides?
What is the bond between the pentose ring and the nitrogenous base
N-glycosidic bond
The glycosidic bonds have free rotation what angles can they forms
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
What is the tautomerization of Uracil called and structures?
What DNA modification can Eukaryotes and bacteria do?
Both: 5-methylcytosine
Bac: N6-methyladenosine
What is inosine?
Sometimes found in the “wobble position” of the anticodon in tRNA
- made by de-aminating adenosine
What is
S-RNase
RNase P
Dicer
- S-RNase: prevent interbreeding in plants
- RNase P: is a ribozyme that processes tRNA precursors
- Dicer: an enzyme that cleaves double stranded RNA into oligonucleotides (protects from viruses)
What makes RNA less stable than DNA
Where to do AT and GC pair?
What does base stacking do?
The primary contributor to DNA stability and they are caused by the hydrophobicity of the bases and the pi-bond cloud
What is the following for A, B, Z form
- Diameter
- Base/turn
- Pucker
Where can DNA only be read?
From the Major groove, minor groover is inaccessible
Is DNA right handed or left handed
Right handd
What type of sequences on RNA can form hairpins and cruciforms
Palindromes
Complex structure are stabilized by Non-Watson Crick Base-Pair interactions (T/F)
True
If base stacking is lost what happens to UV absorbance?
It increases
What is Tm and what does it depend on?
The midpoint of melting depends on base compoistion
- High GC increases Tm
- Longer DNA has higher Tm
- High salt increases Tm
What is mutagenesis Deamination?
Deamination is spontaneous and very slow.
What is mutagenesis Depurination
N-glycosidic bond is hydrolyzed
10,000 purines lost per day
What does UV light do to DNA
Dimerizes pyrimidine
What does ionizing radiation (x-rays and skin cancers)
Causes ring opening and strand breaking
