Lecture 3 Flashcards
What is Chargaff’s rule
OF purines =. # of pyrimides
so #A=#T and #C=#G
but A+T doesnt necessarily = C+G
What did theyknow in early 50s (Crck and Watson)
-phosphodiester bond between oh group at c3 and phosphate bound to c5 in next sugar
B DNA
Right handed: meaning that from bottom to top , the strands 5’3 twist in a clickwise direction
Major and Minor Groove significicane
1) binding site for regulatory factors each regulatory factor recognizes spcific nucleotide sequences
Major grooves are the ones where the two strands are further apart, whereas minor grooves are where the two strands are closer together on the bumbs
Because the major groove is further apart it allows more room for the bidning of important proteins such as transcripatse
These areas have specific H bond DONOR and ACCEPTORS, unique to each
Impoernr things to keep in mind
-bases are what hdrogen bond to eachother, the are on the inner part whereas the sugar phosphates are on the outer ends (backbone)
What are the forces that helpt o formt the dna double helix
1) Rigid phosphate backbone
-has overall negative charge to molecule
2)Stacking interactions: Vanderwaals interactions between the bases (these are weak but thereis alot of them so ebd up having an effect)
3) Hydrophobic interactions : Highly negative phosphate backbone OUTSIDE, where the hydrophobic, nonpolar bases inside
(hydrophobic meansthat these are hiding from water, leaving them more susceptible to vanderwhaals)
4) Ionic Interactions: Salts (+ve ions) stabilize phosphate backbone (DNA shielding)
5) Hydrogen Bonding: this is responsible for complimentary base pairing BUT IS NOT THE MOST ENERGETICAL SIGNIFICANT COMPONENT
What force is responsible for complimentary base pairing
Hydrogen bonding of the bases
What are other forms of dna
A:
Right handed
Major groove: deep and narrow
Minor: Shallow and broad
bases :11
Conditions: Low humidity (75%), high salt
B: DNA
Right handed
Major: Moderate depth and width
Minor: Moderate depth and naroow
Bases; 10.5
Conditions: High Humidty, low salt
Z:
Left handed
Major: Very shallow, viturally nonexisisent, sometimes called a single groove
Minor: Very deep and narror
Bases: 12
High Mg, or ehtanol
What aresome unusua forms of DNA
Triple Helix Dna:
Formed when purines make up one strand, and pyrimidines make up the other, then a third strand can be accomodated
-usually done in test tube, and likely in vivo during DNA recom or repair
-gene therapy posibilities (because it binds to certain regions, potentially promoter, preventing the enzymes for transcription from bidning, preventing transcriptipm
third strand typically forms h bonds with the purines in one of the exisitng strands of the double helix
What is the mean base pairs/ turn for B form dna helix
10 +/- 1.2 (10)
its 10
What is the rise/base pair along helix axis (A)
0.34 nm
What is the diameter in nm
2
Will two sequences that are not complimentary base pairs hybridize?
NO
DNA hybridization refers to the process by which two complementary strands of DNA (or RNA) come together to form a double-stranded structure through base pairing. This process involves the alignment of nucleotide sequences from different sources,
What factors denature DNA
1) Heat
2) Low ionic Strength : promotes repulsion between negative phosphate bacbones (low salt)
3) high pH: strips of H+ shared between electronegative centers (NaOH)
4) Agents that influence H bonds (Competitions nad Covalent modificatorys)
5) Enhance solubility of hydrophobic substances (organix solvents, temperature, pH)
What are agents that influence H-bonds?
1) Competition: Have functional groups that can form H bonds with the electronegative centers (NH2 and O) urea, formaide
What are electronegative centers? the phosphate backbone and the bases are considered this becauae they have high negative atoms
2) Covalent modifications: modify electronegative centers and block the formation of H bonds (formaldehyde, glyoxal)
