LO1-3
What is the pentose sugar in DNA? What about in RNA?
DNA: deoxyribose
RNA: ribose
What bond type bonds nucleotides in DNA and RNA?
3',5'- phosphodiester bonds
How many base pairs per helical term is B-DNA, A-DNA, and Z-DNA?
B: 10.5
A: 11
Z: 12 (can't be involved in regular DNA)
What cleaves DNA from the inside?
endonuclease
Many antiviral drugs in HIV treatment are analogs of? Why are they effective?
dNTPs, they lack 3' OH group for addition of next dNTP and thus there is no replication for viral DNA
Polymers of repeating subunits are called ____. They provide chemical energy via ___ and ___
BONUS: what 3 parts are they made up of?
Nucleotides (they provide chemical energy via ATP and GTP)
1st: nitrogenous base
2nd: pentose sugar
3rd: phosphate group
Why cannot cAMP and cGMP be incorporated in growing chain oligonucleotides?
there is no open phosphate or hydroxyl group for nucleic acids
This type of DNA has a 3 stranded DNA structure, and when it is apparent in the gene, leads to diseases
H DNA (triple helix DNA)
Tm= melting temperature
How do nucleoside analogs act as antimetabolites?
Act as natural nucleosides. They transport inside via nucleoside transporters where they are phosphorylated via nucleoside kinase, nucleoside monophosphate kinase, and diphosphate kinase before being incorporated in nucleic acids
Purines: Adenine and Guanine
Pyrimidine: Cytosine, Thymine, Uracil
Explain strand complementarity and Chargaff's rule
A pairs with T (2H bonds), G pairs with C (3H bonds). The specificity of base pairing gives rise to strand complementarity. Chargaff's rule tell us that DNA from any cell of an organism has A=T and G=C. (n (A+G) = n (T+C))
Explain the difference between exonuclease and endonuclease
Exonucleases: cleaver phosphodiester bonds at the last nucleotide at either terminus
Endonucleases: cleaves phosphodiester bonds between nucleotides at the interior of a chain
Which base pairing has higher Tm?
GC
These are repeated or inverted DNA sequences that may make chromatin unstable and disrupt replication
What makes up an ester bond?
1 or more phosphate groups attached to sugar
How are DNA bases stabilized?
What is the difference between denaturation and renaturation?
denaturation: strands of double helix separate when hydrogen bonds between bases are disrupted
renaturation: complimentary strands reform a double helix (aka annealing) after denaturation if treated properly
What happens to DNA when pH>11.3 (alkaline)? What about RNA?
DNA denatures but strands stay intact. RNA degrades to nucleotides in alkali solution
Define Tm
Temperature at which half of the double helical structure is lost
__ consists of a base bound to either ribose or deoxyribose via N-B-glycosyl bond. This bond is formed between __ of sugar and __ of pyrimidines or __ of purines
Nucleosides; C1; N1; N9
Where do proteins bind to DNA?
Bonus: why is DNA negative?
on the major groove
Bonus: Phosphate groups give a net negative charge
What happens to absorbance when DNA is heated?
absorbance increases at 260 nm
What is an example of a reaction that increases in alkaline solutions?
trans-esterification (nucleophilic attack by 2-OH of ribose breaks phosphodiester backbone)
In an alkali solution, what does RNA do
Degrade to nucleotides