Chapter 3 Flashcards
Properties of Nitrogenous Bases
- heterocyclic
- aromatic
- planar rings
- hydrophobic with varying polar groups
- synthesized in cells from amino acids
Base to Sugar
Reaction
Linkage
C1’ linked to base
Pyr - N1
Pur - N9
Condensation Reaction
N-glycosidic bond
Purpose of Nucleotides in cell
- energy currency
- nucleic acid building blocks
- coenzymes (NAD - nicotinamide adenine dinucleotide)
- ADP - glucose
- cAMP
Phosphodiester bond
links phosphate to sugar
3’ OH linked to phosphate of next nucleotide
Phosphoanhydride
links phosphate to phosphate
ADP and ATP
best known nucleotides
adenosine diphospate and adenosine triphosphate
large, negative delta G of hydration
high phosphoryl transfer potential
ATP = 5mM in cell (fairly high)
Nucleotide Derivative: ADP - glucose
Ends of DNA
5’ End - phosphate off of 5’ C of sugar
3’ End - OH off of 3’C of sugar
RNA Polynucleotide
because of angles (from extra -OH group), RNA has a little twist, so the bases kinda stack on top of each other.
Thymine and Guanine
have keto and enol form
keto form preferred
makes an H-bond acceptor instead of donor
Chargaff’s Rules
A=T
G=C
(purine-pyrimidine pairs)
each pair takes up exactly the same amount of space (keeps backbone regular distance along chain)
B-Form DNA
Handedness
Diameter
Base pairs per helicle turn
Helix pitch (rise per turn)
Right
~20Ang.
10
36 degrees
B-Form DNA
Interior Base pairs
Helix rise per base pair
Interior base pairs are stacked - this causes the exclusion of water and makes it very stable. Sugars are slightly tilted, but the helix axis is near parallel. Base stacking is the primary stabilizing force of helix structure.
3.4 Ang. (Van der Waals distance)
B-Form DNA
Polar Exterior
Sugar-phosphate backbone
Associated with Mg2+ ion because phosphate groups are ionized at physiological conditions.
Exposed to solven
H-Bonding allows
dynamic structural changes induced by proteins/cellular conditions
-> replication and repair
B-DNA
Base tilt normal to helix axis
Major groove
Minor groove
Sugar Pucker
Glycosidic bond conformation
6 degrees
wide&deep
narrow&deep
C2’ ends
anti
DNA-RNA Helix
Hybrid helices exist primarily for shorter periods to complete task inolved
->replication and repair
protein expression
RNA Structure
- mostly single-stranded and variable
- Ribose sugar 2’ OH alters nucleotide conformation due to sugar pucker
- often highly folded with some base-pairing, but less stacking
- bases “tilt” more stacking
- more base-pairing variation
- dynamic structure built for function and carrying info
- contains modified and varied base derivatives other than A, U, C, and G.
Alkaline Hydrolysis of RNA
basis of limit RNA half-life
catlytic RNA’s hydrolize phosphodiester bonds
DNA Denaturation and Renaturation
Hydrogen bonds
Stacking interactions
Ionic Interactions
related to helix stability
stacking provides majority of helix stability
PCR; spectroscopy
Hydrogen bonds: necessary for specificity, but interchangeable between bases and water - no real contribution to DNA helix stability
Stacking interactions: from hydrophobic forces (not like amino acids) van der waals -> nonpolar solvent destabilized DNA
Ionic interactions: cations shield negative phosphates; monovalent - nonspecific binding - specific binding to phosphates
Hyperchromic effect
double-stranded DNA (pH 7.0), max abs @ 260nm
absorbance increases 12-40% with denaturation
because of stacking energies (GC greatest)
Tm
Melting temperature
sequence-dependent
cooperative (all or nothing)
solution: ions present, solvent, pH - affects (lower pH destabilizes h-bodning, causes Tm to go down)
G-C DNA has higher Tm than AT DNA due to increased stacking, 3 vs. 2 h-bonds
Renaturation
single-strands reanneal when temp decreased slowly
heat or chaotropic agents (like urea, act to dehydrate DNA) can denature DNA
DNA Replication
Central Dogma of Molecular Biology
DNA -> transcription mRNA ->RNA -> translation tRNA -> protein
