BCHM 3050 1st Edition Lecture 14 Outline of Last Lecture I. Nucleic AcidsII. Components of NucleotidesIII. Nitrogenous BasesIV. NucleosidesV. NucleotidesVI. Role of ATP in Energy MetabolismVII. Significance of ΔGVIII. Cyclic NucleotidesOutline of Current Lecture I. Levels of Structure in DNAII. Formation of Phosphodiester BondsIII. B-DNA Spatial DimensionsIV. Stabilizing Forces in DNAV. Functions of Major GroovesVI. Functions of Minor GroovesVII. DNA Structural VariationsCurrent LectureI. Levels of Structure in DNAa. Nucleic acids is the polymer form made up of nucleotide monomers (A, G, C, T)These notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.b. Primary – sequences of basesc. Secondary – double helix coild. Tertiary – super-coiled DNAII. Formation of Phosphodiester Bondsa. This is deoxyribonucleotideb. Cannot have ribonucleotides in DNAc. Sugar should not have OH in the second position if part of DNAd. Sugar in the second position indicates an RNA componente. Bonds connecting the different phosphate groups = phosphoanhydridef. Bond connecting different nucleotides in DNA= phosphodiester g. Bond connecting phosphate group to OH = phosphoesterh. Nucleotide attaches by breaking off two phosphate group and adding to the single phosphate lefi. 3rd carbon atom will always have a free OH group at the end of the chainj. The first nucleotide of the chain will have free phosphate group at the 5’ carbonk. Nucleotides in the middle are all involved in phosphodiester bondsl. Free phosphate group at 5’ endm. Last nucleotide has a free 3’ OH groupn. Start with a triphosphate because they are more abundant, but you loose two of these phosphate groups as the DNA chain growso. Uracil = RNAp. Thymine = DNAq. If one strand runs 5’-3’ in one direction, the opposite strand runs 3’-5’r. A and T bond using a double bond, but G and C bond using a triple bond (stronger)s. In DNA, start with 5’ and end with 3’ (anti-parallel to each other)t. Purine always bond with pyrimadine III. B-DNA Spatial Dimensionsa. B-form of DNA is the form characterized by Watson & Crick. It was originally isolated from aqueous solutions as the partly hydrated “sodium salt”. It is thought that this form represents most native DNA in the cell.b. Another form (the A-form) is observed when DNA is extracted/purified from ethanol, which tends to dehydrate the molecule and make it more compact than the B-form. Also, the angle of the base plane with the ribose plane in no longer perpendicular (as in B-form), but tilted 20 degrees away from perpendicular.c. Major groove is about 2 nm across & 1 nm deep. This can easily accommodate a 0.5 nm alpha helix of protein.d. B-form of DNA is the most common forme. Anything with a diameter of more than 2nm can fit a protein through it à DNA can fit a protein through its nucleotidesf. Big gap – major grove g. Small gap – minor groveh. Major and minor alternatei. The distance between 2 turns in 3.4 nm – within a turn you have one major groveand one minor grove and can fit about 10 basesj. One base pair occupies about 0.34nmIV. Stabilizing Forces in DNAa. Hydrogen bondsb. Hydrophobic interactionsc. Van der Waals Forcesd. Electrostatic interactionse. Phosphate groups on the backbone of DNA are negatively charged so the entire backbone (phosphate and sugar) is highly negative f. DNA dissolves in water because of the opposite charges interactV. Functions of Major Groovesa. The major grove attracts a protein and gives it a home; it can spread out over many grovesb. Transcription factors – proteins that commonly interact with major grovesc. Motif – combine a bunch of secondary structures togetherd. Helix-turn-helix protein motife. Leucine-zipper motif VI. Functions of Minor Groovesa. Minor grove accommodates smaller things than proteins like vitamins, co-factors,drugsVII. DNA Structural Variationsa. Other forms of DNA are the A-form and the Z-form but they are transient and notinvolved in transition of genetic informationb. A-DNA in dehydrated cellsc. Z-form is lef handed; DNA can adopt the Z–form during transcription but can then revert back to the B-formd. A and T have very similar percentages because they bond together, same with G and Ce. More A and T than G and C in
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