BIo 412 Genomics

• Nucleic Acids (Structures and Chemistry) is a course focusing on the structures and chemistry of nucleic acids.
• O6-methylguanine can NOT base pair with cytosine properly.
• Dimethylsulfate causes the methylation of guanine on the oxygen at the 6th position (O6).
• A repair mechanism specifically deals with this problem.
• Nucleic Acids (Structures and Chemistry) includes lectures on the introduction to nucleotides, nitrogenous bases, pentose sugar, nucleotide & nucleic acid nomenclature, nucleic acid backbone, tautomerization of uracil, properties of nitrogenous bases, levels of nucleic acid structure, DNA structure, A, B, and Z forms of DNA, nucleic acid chemistry, and nucleotide and nucleic acid transformations.
• Nucleic Acids (Structures and Chemistry) also includes suggested readings from Lehninger 7th Edition: pp. 279 - 290; 295 - 299.
• Nucleic Acids (Structures and Chemistry) includes an outline of topics such as the introduction to nucleotides, nitrogenous bases, pentose sugar, nucleotide & nucleic acid nomenclature, nucleic acid backbone, tautomerization of uracil, properties of nitrogenous bases, levels of nucleic acid structure, DNA structure, A, B, and Z forms of DNA, nucleic acid chemistry, and nucleotide and nucleic acid transformations.
• Nucleic Acids (Structures and Chemistry) includes suggested readings from Lehninger 7th Edition: pp. 279 - 290; 295 - 299.
• The Watson-Crick model of B-DNA includes a hydrophilic backbone (phosphate group and sugar groups) on the outside of the double-helix, a furanose ring in the C-2' endo conformation, base pairs perpendicular to the long (lengthwise) axis, major groove and minor grooves present along the helix, and the two strands run antiparallel to each other.
• In order for the DNA double-helix to replicate, strand separation occurs first, each strand serves as a template for the synthesis of a new strand, and newly made DNA molecules have one daughter strand and one parent strand (DNA is semi-conservative).
• Major interactions that stabilize the DNA helix include Watson and Crick confirming Chargaff's rule (Purines pair with Pyrimidines, A's pair with T's, G's pair with C's), and Watson and Crick stating that the structure of their DNA helix serves as a great model for DNA replication.
• B-DNA is "right-handed".
• DNA is flexible due to the free rotation of many of the bonds that make up the phosphodiester backbone, and C-1' of the pentose sugar also has free rotation about the N-glycosidic bond.
• Due to the fact that the N-glycosidic bond has free rotation, two stable conformations can exist: syn (nitrogenous base overshadows the pentose sugar) and anti (purines can exist in both syn and anti conformation, pyrimidines can only exist in anti conformation).
• The double-helical structure discovered by Franklin and Wilkins showed 34 Å per one turn in the DNA helix.
• The distance between vertically stacked bases in the Watson-Crick model of B-DNA is 3.4 Å, and the distance between one turn of the DNA helix is 36 Å, equating to 10.5 base pairs in one turn of the DNA helix.
• The nitrogenous base is attached to the 1’ carbon of the pentose sugar.
• The furanose ring is in the ring form and is the BETA (β) conformation.
• The furanose ring is not planar and is described as "puckered".
• Nitrogenous bases form an N-β-glycosidic bond to the pentose sugar.
• Purines consist of Adenine (A) and Guanine (G), which are present in both DNA and RNA molecules.
• Nucleic acids have a ribose sugar in the β-furanose (closed 5-membered ring form).
• Purines have the 2 and 6 position functional groups attached.
• Nitrogenous bases are made from two parent compounds: Pyrimidines, a 6-membered ring, and Purines, a 6+5-membered ring.
• Cytosine dominates in a buffered solution at pH = 2.0.
• Adenine dominates in a buffered solution at pH = 2.0.
• Nitrogenous bases are numbered in a way that recognizes the purine ring as 6+5-membered.
• Adenine pKa at N1 is 3.8, Guanine pKa at N7 is 2.4, Cytosine pKa at N3 is 4.5, and Thymine pKa at N3 is 9.5.
• Nitrogenous bases are covalently linked to the pentose sugar in nucleotides via N-1 of pyrimidines and N-9 of purines.
• Pyrimidines consist of Cytosine (C), Uracil (U), and Thymine (T), which are present in DNA and RNA molecules.
• In a fused system, numbering preferences include the ring with more nitrogens, rings with other heteroatoms, the ring that is larger, and the nitrogen atom that is closest to the ring junction.
• Every species has their own characteristic DNA t m.
• Deamination of purines can happen as well, however, the rate is lower than cytosine deamination to uracil.
• If the DNA is 100% ssDNA, it takes two steps to get the DNA back to the double-helix: the 2 ssDNA strands need to meet each other in solution via random collisions (rate determining step) and once step #1 occurs, the production of the double-helix is much easier.
• Denaturation curves are typically “S-shaped” curves.
• When G/C content is increased, there is an increase in the t m of the organism’s DNA.
• Mutations are alterations in DNA structure that produce permanent changes in the genetic information.
• When DNA is in solution and the temperature is gradually raised, a denaturation curve is produced.
• Important cellular processes like DNA replication and RNA transcription occur at these bubbles and are rich in A=T base pairs.
• Every dot (point) on the graph to the left represents the t m of different organism’s DNA.