• purines
  • adenine
  • guanine
• pyrimidines
  • cytosine
  • uracil
  • thymine

N glycosidic bonds cannot be easily broken, making DNA more stable.

base

sugar

information

high energy

molecular flag/signal (binding cleft for enzymes)

• antiparallel double helix
• A binds to T with 2 H bonds
• G binds to C with 3 H bonds
• base stacking
• major groove- see bases H bonded together
• minor groove- see phosphodiester backbone
• 3.4 A per turn
• 10 bp's for each turn
• highly hydrated

• major groove- proteins attempt to bind to see if they match the primary sequence (ex: TATA box)
• minor groove- proteins attempt to see if they fit the general structure (ex: modifications)

• Allows for resonance stabilization of structure via pi orbitals of double bonds in N base
• it pushes out water to ensure water will not bind to the nitrogenous base

5'-3' phosphodiester bond

1. 3' OH group is attracted to the phosphate on any molecule such as GTP or ATP
2. via nucleophilic attach, H leaves and is bound to one phosphate and the nitrogenous base
3. pyrophosphate leaves and combines with water to become two inorganic phosphate molecules

H bonding

base stacking interaction

backbone geometry

• saw that heavy N and light N distribute in a quantal fashion upon gradient centrifugation
• this proved that DNA replicates in a semiconservative fashion

ATP

FAD

NAD

cAMP

CoA

• rigid
• inflexible
• weak
• contains AT rich regions
• found in promotor regions of DNA, aiding in gene expression activation

• left handed zig zag
• function- block expression
• usually seen in DNA that is GC rich

• areas rich in A and T
• but they tend to fall apart very easily (TATA box promotor sequence), so it allows for gene expression

telomeres to seal off end of chromosomes

• DNA- flexible, structurally conserved
• RNA- not flexible (only A form), structurally diverse (complementary sequence can fold back on self)

structure and function relationship of hammer head ribozyme

• structure- 2'OH interacts with ribose naturally in rRNA
• function- autocatalytic
  • cleave phosphodiester bond in processing rRNA

ribosome scaffold

catalytic surface

Explain what makes RNA so structurally rigid

• 2'OH hinders flexibility by protruding into the minor groove and:
  • sterically clashing with neighboring ribose
  • coordinating semi-crystalline water spine in the minor groove

• contains binding pocket looking to bind to end product of entire pathway
• it will then shut down gene expression

Ex: purine and thiamine pyrophosphate

• temperature
• pH effects (tautomers)
• chemical solvents (dimethylformamide)
• chemical modification (formaldehyde)

base stacking

H bonds

• DNA will absorb optimally at about 260
• however, single strands and double strands absorb differently
• single strands have significantly higher absorbance

How does formaldehyde denature DNA?:

1. denature DNA
2. put probe at segment of DNA we want to label (fluorescent tag)
3. reanneal (aka hybridize)

Effect of DNA not havin an OH at the 2' position