lec19 Flashcards
dna/rna levels of structure and examples
rimary structure: The nucleotide sequence (e.g., 5’-GCGGCAATCGTA-3’).
Secondary structure: Stable base-paired structures, like the DNA double helix or RNA hairpins.
Tertiary structure: 3D folding, such as supercoiled bacterial nucleoids, eukaryotic chromatin, or folded RNA (e.g., tRNA).
pentose sugar in dna vs rna
2’-OH group (Hydroxyl group at the 2’ carbon)
Has 5’ and 3’ ends, carbons numbered with primes (’)
Important in RNA splicing reactions
DNA: Deoxyribose
2’-H group (Hydrogen at the 2’ carbon, hence “deoxy”)
Has 5’ and 3’ ends, carbons numbered with primes (’)
Common Features:
Pentose sugar attached to nitrogenous base via 1’ carbon
Phosphate attached to 5’ carbon of the pentose (5’-PO4)
3’-OH linked to 5’-PO4 of adjacent nucleotide, forming the sugar-phosphate backbone.
pentose forms a covalent bond with ba\se via b-glycoside
purine vs pyrimadine shape
purine has 2 loops
pyr has one benz type thing
highly conjugated and aromatic, bases cuz n on ring can be protonated
DNA & RNA Primary Structures
Backbone: Pentose sugars linked by phosphodiester bonds
Polarity:
5’ end → Free 5’-phosphate (5’-PO₄)
3’ end → Free 3’-hydroxyl (3’-OH)
Charge:
Phosphate groups are acidic and deprotonated at physiological pH → Net negative charge
Terminology:
Despite nitrogenous bases, DNA & RNA are nucleic acids due to the acidic phosphate groups.
dna secondary structure
double helix
strands run antiparallel:
5’ → 3’
3’ →5’
whats the distance between bases and other things in dna
The distance between the deoxyribose C-1’ atoms is almost C-1’ atoms on pentose
identical for A-T and for G-C pairs, ~11 Å.
The G-C interaction, with 3 H-bonds, is stronger than the A-T
interaction, with 2 H-bonds
base stacking
Definition: Base stacking minimizes water contact and stabilizes the DNA double helix.
Forces Involved: Van der Waals interactions between stacked bases.
Offset Stacking: Bases are slightly tilted rather than perfectly aligned.
Orientation: Bases lie almost perpendicular to the helix axis.
Function: Enhances DNA stability and maintains its helical structure.
major and minor grooves dna
Backbone Exposure: Hydrophilic sugar-phosphate backbone faces water; hydrophobic bases are stacked inside.
Groove Formation:
Major Groove (deep)
Minor Groove (shallow)
Cause: Offset base pairing creates these grooves.
Arrangement: Grooves are on opposite sides and twist around the helix.
Protein Interaction: Major groove is more exposed, making it the primary site for protein binding (e.g., transcription factors)
kid ex:
Okay! Imagine DNA is like a twisted ladder.
The sides of the ladder (the backbone) love water, so they stay on the outside.
The steps of the ladder (the bases) don’t like water, so they hide inside.
But! The steps aren’t lined up perfectly—they’re a little tilted. This makes:
A big gap (major groove)
A small gap (minor groove)
These grooves go around the DNA like a spiral.
The big groove is where proteins like to grab on to help control DNA!
Forms of the DNA Double Helix
A-form:
Found in dsRNA & DNA:RNA hybrids
Right-handed helix
10.7 bp/turn
Forms when DNA is at 75% humidity
B-form:
Most common in dsDNA
Right-handed helix
10.5 bp/turn
Watson & Crick’s DNA model (found at 92% humidity)
Z-form:
Found in alternating purine-pyrimidine sequences
Left-handed helix
12 bp/turn
Has a zigzag-shaped backbone (hence “Z-DNA”)
Discovered by Alexander Rich (1979)
DNA Melting & UV Absorption
A260 Measures DNA Structure:
dsDNA absorbs less UV (bases are stacked).
ssDNA absorbs more UV (bases unstacked).
Melting (Denaturation):
Heat disrupts base-pairing & stacking → dsDNA → ssDNA.
Occurs at a specific melting temperature (Tm), depending on the sequence.
Annealing (Renaturation):
Cooling allows strands to rejoin → ssDNA → dsDNA.
UV Absorbance Change:
Higher A260 = More ssDNA (melted).
Lower A260 = More dsDNA (annealed).
what can removing salt do to dna
Salts stabilize the DNA double helix by neutralizing the negative charges on the phosphate backbone. removing can strands become less stable and are more likely to separate (denature). This helps melt the DNA apart.
how can u melt dna
DNA strands can be melted apart by raising the temperature or by adding chaotropic (denaturing) agents like urea, and by removing salt.
both the formation and disruption of the DNA double helix are highly cooperative - the strands hold fast until the melting point, Tm, and then rapidly let go
DNA Denaturation & Renaturation - Flashcard
Denaturation (Melting):
DNA strands separate due to increased temperature, adding chaotropic agents (like urea), or removing salt.
Cooperative process: Strands stay together until the melting temperature (Tm) is reached, then they rapidly separate.
Hyperchromic Shift:
The increase in UV absorbance at 260 nm during denaturation (from dsDNA to ssDNA).
When DNA melts, ssDNA absorbs more UV because the bases become unstacked.
Renaturation:
Cooling allows DNA strands to rejoin (dsDNA).
UV absorbance decreases as DNA re-anneals.
Tm (Melting Temperature):
The temperature at which 50% of DNA is in the double-stranded (dsDNA) form, and the other 50% is in the single-stranded (ssDNA) form.
which base pair has higher Tm and why
Melting occurs at a specific Tm depending on the nucleotide sequence,
length, and concentration of salt in the solution
The stacking energy is more negative (more stable) for GC pairs, so Tm is higher.
The AT-rich regions melt first.
**all the girlies in the gc are actually mentally stable and are so hot
Tm & Salt Concentration
Tm (Melting Temperature):
Proportional to salt concentration and sequence length.
High salt and longer DNA sequences stabilize the double-stranded structure and increase Tm.
How Salt Affects Tm:
Salt ions shield the negatively charged phosphates on the DNA backbone.
This reduces the repulsion between phosphates, stabilizing the duplex.
As salt concentration increases, the DNA strands are more stable and the Tm increases.
difference between nucleoside and nucleotide
side=ribose + base
tide=phosphate+ribose+base
ribose of rna vs dna
rna has 2’oh and 3’oh (this whoRe has 2 bfs)
dna has one 3’oh (dna is monogamous)
