X-Ray Diffraction Franklin and Gosling.
Chargaff’s Rule: A:T, G:C in approximately 1:1 ratio for every organism.
Helped identify DNA as double helix.
2’ Deoxyribose sugar; has H at 2’ position instead.
-Hydrophobic bases are pushed to the center
DNA = Base + Sugar + phosphate back bone
Combined through Condensation reactions
- OH in RNA is crucial because it is used as ATP to synthesize.
Nucleoside: Base + Sugar
Nucleotide: Phosphate + Base + Sugar.
A:T = 2 H-Bonds in between
G:C = 3 H-Bonds in between
Bases interact through Van der Waals and H-Bonds.
Pyrophosphate (ppi): generated through reactions.
Neutralized into two inorganic phosphates.
Greatest Destabilizing Effect:
1.) Decrease Salt concentration because backbone is negatively charged
Neutralizes charge of DNA
2.) Cutting both strands in half because the Hydrogen bonds (2kCal each) are
easier to break this way.
Bacteria: Methylate DNA
Restriction endonuclease used to attack virus DNA
Restriction Endonuclease requires H2O. rATP: (AKA ATP):
dATP: Class 3:
DNA: Goes 5’-3’.
Nucleotides are added at the 3’ end of DNA
Free 3’OH attacks Free 5’ Phosphate yields pyrophosphate and
The bases interact through complementary base pairing through Hydrogen bonds
on opposite strands.
Planar: the DNA stacks upon each other, rigid, w/slight offset angle.
On same strand, they interact through Van Der Waals interactions.
Covalent bond between backbone
Pyrophosphate: High in E drives bonding cannot go backwards.
Antiparallel and complementary. Major groove is where all of the chemical reactions occur mostly.
Big Gap in DNA allows proteins etc to bind for transcription etc.
Transcription factors can access it.
Minor Groove: small, not enough room.
Origins of Replication: The start site of replication.
Bacteria: Contain Plasmids: small circular DNA.
mRNA: encodes for proteins
tRNA: Brings Amino Acids, Adapter
rRNA: ribosomal RNA, major component of ribosome
miRNA: Regulatory RNAs, inhibit mRNA/translation.
snoRNA: modify RNA
snRNA: small nuclear RNA splicing exons/introns. Restriction Endonucleases:
Bacteria express enzymes that cut foreign DNA and can identify foreign DNA
through methylation of their own DNA.
Sequences are usually palindromic.
Cleaves Phosphodiester Bond leaves free 3’OH and 5’ Phosphate.
Cut DNA can be put back together through ligases.
Recombinant DNA: “cloning” or cutting DNA and using the “sticky ends” to join with
other pieces of DNA.
Sticky Ends: Cut ends of DNA that tend to stick with self if cut with the same enzyme.
Electrophoresis: negative end heavier molecules, positive end lighter molecules.
These cause blunt ends. = shearing.
- overlapping bands on gel = overlapping inserts.
-Major/minor groove Major groove most information and is most accessible.
- A:T , G:C Chargaff’s Rule Equal proportions
-G:C, has three hydrogen bonds; A:T, has two hydrogen bonds.
-Anti-parallel and complementary.
-Made 5’-3’ always added to 3’ OH.
-Negatively charged phosphate backbone, and has deoxyribose.
-Bases stack on top and interact with Van Der Waals.
-pyrophosphate breaks off during synthesis; 5’ phosphate and free 3’OH.
-B helical structure.
-DNA: 2’ OH
-Uracil not thymine in RNA; missing methyl group
-A:U, G:C; but G:U can bind to each other because they are not confined.
-A Helical structure not B due to 2’ OH hindering its formation.
- Major groove inaccessible. Pseudouridylation:
Uracil change from Nitrogen to Carbon; rotation of the molecule so it binds at
carbon instead of Nitrogens.
Usually the base is modified.
2’O Methylation: aids in stability.
Ribose is commonly modified.
RNA: DNA: RNA: Short copies of genes from DNA.
Prokaryotes: Translated immediately
Eukaryotes spliced first; exit from the Nucleus and then translated.
NOT ALL ENCODE PROTEIN ONLY mRNA.
RNA can bend over on itself through Complementary anti-parallel sequence in
RNA. : Can interact with proteins and catalyze reactions.
Protein complexes or RNA itself.
Like tRNA having a loop where there are no H-Bonds and a stem where there
is complementary binding.
Every phosphodiester bond has a 3’ and 5’ side.
tRNA: Recognize mRNA
Base of stem
Bind amino acids @ top loop (CCA)
It is an adapter molecule