What are the components of a nucleotide
- sugar
- phosphate
- nitrogen bases
Draw and label the donor and accpetor in the nitrogen bases
Draw Uracil and compare it to thymine
where are the nitrogenbases attached to the sugar?
- N1 in pyrimidines
- N9 in purines
How to differinatiate DNA and RNA by the sugar base
- OH group on C2
Draw a sugar and label the carbons
label chirality
How to name nucelosides (base + sugar)
- pruines uses osine as a suffix
- pyrimidines become idine as a suffix
label the differnces of phosphodiester, phosphoester and phosphanhyride bonds within a dinucleotide structure
What is the overall net charge of the nucleotide, is the back bone polar or non-polar? and compare the backbone of RNA and DNA, which is more polar?
- net charger = more negative largely consistent within the strucutre (cause of phosphate groups)
- sugar is polar and the phosphate is more polar
- backbone in RNA vs DNA = RNA is more polar
explain spontanous, alkaline hydrolysis of phosphodiester bonds in RNA
- 2 products are fromed:
- a free nucleotide
- and a nucleotide with phosphate group attachment
- in DNA the absense of the OH group prevents this reaction, making it more stable than RNA in alkaline conditions
Explain the deamination of cytosine to uracil
- spontaneous (uncatalyzed) reaction
- uncorrected in DNA can cause a mutation
- DNA repair mechanisma will reocgnize U and remove it
what is a dideoxynucleotide
Explain the properties of the bases
- heterocyclic
- aromatic with elctron delocalization
- basically planar
- poorly soluble
- largely hydrophobic with some polar groups (abilit to form H-bonds)
Explain absorbance
how to measure pure DNA, what is used to measure concentration
- A260nm/280nm = 1.95 for pure DNA
- contamination lowers the ratio
- protein abs maxi at 280nm
- DNA abs is about 50% at 280 nm
- A260nm is used to meaure the concentration of nucleic acids in solution
Draw the hydrogen bonding between the nucleotides in DNA
What is DNA (B-form) and describe the characteristics
- stablized by base stacking interactions and H-bond but base stacking is the primary force
- base stacking: primarily van der wasl forces and hydrophobic forces
- has an overall right handed twist
- ~10bp per turn
Explain the denaturation of DNA
- separation of the two paried stranded ds -> ss
- disruption of non-covalent forces (H-bonds and base stacking)
- essential for some cellular processes
- changes in absorption properties; increase at 260nm as the strands separate
What does DNA melting (denaturating) look like on a graph
Label Tm
- Absorbance increases as temp increases
- Tm = midpoint of melting with comprise of dsDNA and ssDNA 50;50
Define hyperchromicity and hypochromicity
- hyper = is a relatively high abosrbance
- hypo = is a low absorbance
Explain DNA zippering
- theres a fast zippering
- slow rate depends on the complexity of the necleic acid = nucleatio; eg. its like the slow step of alinging the zipper before it zips properly
Explain the relationship b/w Tm and the GC content of a DNA
- as GC content increases so does Tm
- GC bairs have stronger base stackng interactions than AT pairs
What can affect Tm?
- changing PH: affects protonation state of DNA; but a bell curve
- changing slat concentrations; increase causes more stabilization as there are less repulsions on the phosphate backbone; increase salt -> increase Tm; decrease salth -> decrease in Tm
- Tm of hybridization; more identical = an increase in Tm
What is the differnce in DNA and RNA structures
define : inter and intrastrand base pairing
- RNA has intrastrand base pairing; DNA has interstrand
- strucutre of RNA is much more dependent on nucleotide sequecence thn double-stranded DNA
