Exam 2 Notes

Exam 2 Notes - 1. NUCLE IC ACIDS 1. Nucleotides have a...

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1. NUCLEIC ACIDS 1. Nucleotides have a covalently-linked sugar and base and a phosphate group 1. Phosphoric acid esterifies to hydroxyl group (OH) of sugar 2. Phosphate can linked to 3’ or 5’ hydroxyl group of sugar 1. But more commonly linked to 5’ 3. Additional phosphate groups form “anhydride linkages ” to first phosphate 4. Polymerization of nucleotides gives rise to nucleic acids 2. Nucleosides have sugar plus base, but lack a phosphate group 1. Sugar is linked to base via N-glycosidic bond 1. RNA ( -D-ribose β ) – has OH group at 2’ Carbon of the sugar
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1. Total: 2-OH groups on the sugar 2. DNA ( -D- β deoxy ribose) – does not have OH group at 2’ Carbon 1. Total: 1-OH group on the sugar at 3’ 3. Nucleic acid bases ( nucleobases ) 1. Linkage between nucleic acids form 2 ester bonds by phosphoric acid 1. Resulting repeated linkage: 3’,5’-phosphodiester bond 2. Pyrimidines ( one-ring ) - C-1’ carbon is linked to N-1 nitrogen 1. Cytosine – has one keto group 2. Thymine – has two keto groups 3. Uracil – has two keto groups but no carbon branching 3. Purines ( two-ring) – C-1’ is linked to N-9 nitrogen 1. Adenine – has no keto group 2. Guanine – has a keto group 4. Nomenclature (____ 5’-monophosphate) 1. RNA 1. Purine 1. Adenine Adenosine
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2. Guanine Guanosine 2. Pyrimidine 1. Cytosine Cytidine 2. Uracil Uridine 2. DNA 1. Purine 1. Adenine Deoxy adenosine 2. Guanine Deoxy guanosine 2. Pyrimidine 1. Cytosine Deoxy cytidine 2. Thymine Deoxyt hymidine 2. DNA 2˚ STRUCTURE 1. Chains run “anti-parallel”
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2. At neutral physiological pH, each phosphate carries at negative charge 3. Complementary base pairing is mediated via hydrogen bonding 1. In B-form each base pair is rotated 32 ˚ 4. Hydrophobic bonding via pi-orbital e- is referred to as base stacking 1. Propeller-twist – optimize base-stacking 5. Base stacking uses more energy than hydrogen bonding 6. Three Conformations of DNA 1. Both A-DNA and B-DNA are right-handed helices 2. B-DNA is the major form, has 10 base pairs, and perpendicular to helical axis 3. A-DNA has 11 base pairs, not perpendicular to helical axis, lie at 20 ˚ 1. DNA:RNA hybrids can adopt A formation 2. Base pairs marked propeller-twist 4. Z-DNA is left handed 1. Occurs in long stretches of alternating purine-pyrimidine sequences (CGCGCGCGCG) dCpG islands – may play role in regulation f gene expression 3. DNA 3 STRUCTURE ˚ 1. Supercoiling – DNA twists and coils back on itself to aid compaction 1. In Eukaryotes 1. Chromatin – higher order protein-DNA complexes 1. Euchromatin - genes turned on 2. Heterochromatin - genes switched off
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2. Histone – principal proteins in chromatin that DNA wraps around (H1, H2A, H2B, H3, H4) 1. Abundant in Lysine + Arginine 2. Responsible for extensive post-translational modification - epigenetics 3. Nucleosomes – DNA wrapped around histone octamer, which 2. Negative supercoiled – when unwinding, right-handed double helix
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Exam 2 Notes - 1. NUCLE IC ACIDS 1. Nucleotides have a...

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