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Dan Chase

Class 2: 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. Deoxyribonuclec Acid:  2’ Deoxyribose sugar; has H at 2’ position instead.  5’ Phosphate -Hydrophobic bases are pushed to the center Bases: -Adenine -Cytosine -Guanine -Thymine 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  Backbone interaction  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 phosphodiester bond. 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. EcoR1 PVuII  These cause blunt ends. = shearing. - overlapping bands on gel = overlapping inserts. DNA: -Double helix -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. RNA: -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 --At lea
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