Nucleic acids & Carbs Quiz 5

• Pyrimidines are always in anti position
• Purines may be in syn or anti position, but anti is preferred
• A glycosidic bond connects the ribose and nucleic base
• RNA has an extra OH group at C2 in ribose
• C3’ endo is particular to RNA while C2’ endo is particular to DNA
• Ribose Haworth

  
• Ribose Fischer

  
• Thymine - Pyrimidine


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• Cytosine - Pyrimidine


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• Adenine - purine


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• Guanine - purine


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• Uracil - pyrimidine


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• Purines show higher absorbances than pyrimidines in UV spectroscopy
• You can determine D vs L on a carbohydrate for the last chiral -OH group will be on the left (L) or right (D)
• for the number of stereoisomers, find 2^x, where x = # of chiral centers
• Ribose - aldopentose, distinctive by all D chiral centers except in L-ribose where only the distinctive carbon is L
• Glucose - aldohexose - distinctive by 3-L, 4,5-D -OH groups
• Fructose - ketohexose - 4,5 D -OH
• Furanose - 5 Carbon ring, C1-C4 bond
• Pyranose 6 Carbon ring, C1-C5 bond
• Carbohydrate rings are closed by their C1 and either C4 or C5 -OH which becomes the ester
• alpha vs beta can be determined on carb ring by looking at C1. -OH pointing down signifies alpha, and up signifies beta
• To determine whether carbon ring can reduce, hemiacetal (-OH) on carbon must be right next to ester
• Carbohydrate Helix

  • 6 residues per turn
  • compact and good for storage
  • stabilized by H-bonds on different -OH groups
• Cellulose - B-1,4-D-glucose units
• Chitin - B-1,4-N-Acetyl D-Glucosamine units
• Lectin - proteins that bind carbohydrates with high specificity and affinity

  • important for cell-cell recognition and adhesion
• Fischer left = Haworth up

  Fischer Right = Haworth down
• DNA Backbone: 5' - Phosphate⁻-C5-deoxyribose-C1-Purine/Pyrimidine-C3-OH-3'
• Ribose ring = B-D-furanose
• A nucleoside does not contain phosphate whereas a nucleotide does
• C3' endo refers to ribose puckering of RNA (A-form) where distance between phosphates is 5.9 Å
• C2' endo refers to DNA ribose puckering (B-form) where the distance between phosphates is 7.0 Å
• Keto/lactam form dominates enol/lactim form for nucleic bases
• Watson-Crick Pairing refers to the hydrogen bonds created between nucleic bases that holds together the nucleic acids.

  • A-T/U allows 2 H-bond pairings
  • G-C allows 3 H-bond pairings
• Major groove (22 Å) of nucleic acid - where proteins bind and is located on top Watson-Crick pairing
• Minor groove (12 Å) of nucleic acid - where small molecules can fit into, located on bottom Watson-Crick pairing