DNA Structure And Function Flashcards
Central Dogma
DNA –> RNA –> Protein
Ribose
RNA sugar- has an OH on the C2
C4 is the carbon attached to the phosphate group
(C1 has base attached to it)
Deoxyribose
DNA sugar
Only an H on the C2 carbon
What form of the bases are most common?
Amino-keto form
Pauling and Corey Model (P Form)
Proposed the thin model because that way the base pairs are readily accessible –> not possible though because the DNA backbone is negative and this would be unstable (bases too close to one another)
Width of DNA
2 nm
Length of one turn of DNA
0.34 nm
Major groove
Transcription acts thru this groove
B-Form of DNA
-in wet conditions (found in vivo)
^but not necessarily b/c proteins associated with DNA can induce local hydrophobic environments
- helices are right handed
- dimensions: 10.4 bp/turn
- diameter: 2nm
- 0.34 nm helical rise
- base pairs formed across the double helix are flat, perpendicular to the helix axis and are internal to the sugar phosphate backbone
- A and C present in amino form
- G and T present in keto form
A-form of DNA
- found in low humidity environments
- dehydrated form of DNA
- bases are on the outside
- slightly wider
- grooves more equal in size
- bases are tilted with respect to the helical axis
- base pairs are closer to one another
- helix is broad
-i.e.: double stranded RNA and RNA-DNA hybrid
Z Form of DNA
Doesn’t code for anything –> used as space
Separates actively
it is the transcribing parts of the DNA
GCGCGCGC –> guarantees Z-form with this sequence
Helices are left handed due to a change in the purine: deoxyribose conformation
Helix is narrow and bases further apart
Some solvents and the presence of a methyl group on the 5 position of C favor the formation of Z form
Why is the B form impossible for RNA?
The extra hydroxyl on the RNA makes the B form impossible
Helix Handedness for 3 forms
A- right
B-right
Z-left
Base pairs per turn for 3 forms DNA
A- 11
B- 10
Z- 12
When do forms of DNA with 3-4 strands appear?
Appear at sites important for initiation or regulation of DNA metabolism such as replication and transcription –> candidates for drug design
Stabilizing factors for DNA structure
Due to hydrophobic interactions between adjacent stacked base pairs
Hydrogen bonds between base pairs –> plays major role in complementarity
More G/C base pairing
Van Der Waals interactions
Ions in the cells: K, Na, Mg, etc
Destabilizing factors for DNA
Electrostatic repulsion
–>negative charge on phosphate group at pH 7
Hyperchromicity
Increase in the absorption of UV light as more bases are exposed from denaturation
Difference between ssDNA and dsDNA in absorption?
ssDNA > dsDNA
Denaturation curve for dsDNA
Sample of ds DNA at specific salt concentration heated
1) absorption constant until DNA starts to melt
2) denatures cooperatively over a narrow temperature range
Tm
50% denaturation
Depends on % of AT and GC base pairs
I.e.: ^GC raises Tm because of increased stability
PCR and FISH
DNA can reanneal under specific conditions
Hybridization can also be achieved
Stopping HIV life cycle
1) Nucleoside reverse transcriptase inhibitors (i.e.: AZT) –> block HIV RNA being reverse transcribed into DNA
2) Non-nucleoside reverse transcriptase inhibitors (NNRTIs) –> block HIV RNA being reverse transcribed into DNA using different mechanism to NRTIs –> some also target other processes
3) Protease inhibitors- the proteins needed to create new HIV virus are cut into specific pieces
4) Entry inhibitors- Prevent HIV from entering the cell
5) HIV integrase inhibitors- prevent HIV from inserting its genetic code into the human cell’s genome
Type I topoisomerase
Act on DNA that is strained by coiling
They catalyze single strand breaks and change the supercoiling by one turn of the double helix
Helps DNA reach a more relaxed state
It DNA (-) supercoil: type 1 topo will remove one negative supercoil If DNA (+) supercoil: type 1 topo will remove one positive supercoil
No ATP used
