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Sugars to Nucleotides. Last lecture, the role of sugar nucleotides in carbohydrate biosynthesis was described. Also, the role of ATP in energy metabolism has been emphasized. Various cofactors have nucleotide character Later, we see a role for them in cell signaling pathways

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sugars to nucleotides
Sugars to Nucleotides
  • Last lecture, the role of sugar nucleotides in carbohydrate biosynthesis was described.
  • Also, the role of ATP in energy metabolism has been emphasized.
  • Various cofactors have nucleotide character
  • Later, we see a role for them in cell signaling pathways
  • Now, we will look primarily at their role in information processing and storage as RNA and DNA
slide3

RNA, a multi-functional molecule

  • mRNA (messenger RNA) codes for

proteins

  • rRNA (ribosomal RNA) performs peptide

bond catalysis in protein synthesis

  • tRNA (transfer RNA) specify incorporation

of amino acids into a protein

  • additional catalytic and functional RNA

molecules (anti-sense, Rnase P, etc.)

Although single stranded, RNA can adopt

various structures that are important to function

nucleotides have three components
Nucleotides have three components
  • Nitrogenous base
  • Pentose (ribose or deoxyribose)
  • Phosphate
    • The molecule without the phosphate is called a nucleoside
other bases can be found in rna and dna
Other bases can be found in RNA and DNA
  • Pseudouridine
  • Methylcytidine
    • Methylation of DNA nucleotides (most notably C) is a key aspect of eukaryotic gene expression patterns and adds to the information content of genomic DNA

Etc.

nucleotides are linked via phosphodiester linkages
Nucleotides are linked via phosphodiester linkages
  • Bridges the 5’ hydroxyl

group of one sugar and 3’

hydroxyl of the next

Phosphate groups are

completely ionized at pH

7, thus negatively charged

(complexed with metals, etc.)

phosphate groups do not only appear at 3 and 5 positions of sugars
Phosphate groups do not only appear at 3’ and 5’ positions of sugars
  • 3’, 5’ cAMP is a key intra- and extracellular signal for many biological processes
pyrimidines and purines have chemical properties that affect structure and function
Pyrimidines and Purines have chemical properties that affect structure and function
  • Planar, or nearly planar
  • Resonance leads all nucleotide bases to maximum absorption at 260 nm (contrast with 280 nm for protein); Beer’s Law
continued
Continued.
  • Hydrophobic characteristics leads to hydrophobic stacking interactions between bases
  • Functional groups such as ring nitrogens, carbonyl groups and exocyclic amino groups allow for H-bonding
dna has distinctive non random base composition
DNA has distinctive, non-random base composition
  • In all DNA, regardless of species, the number of A’s equals # of T’s, and # G’s = # C’s, such that A + G = T + C
  • DNA specimens from different tissues of same organism have same base composition
  • Base composition of DNA can vary wildly among organisms (25% GC vs. 80% GC)
  • Non-randomness generates signals
dna structure
DNA structure
  • The hydrophilic backbones of deoxyribose and phosphates are on the outside of the double helix, facing water
  • The bases are stacked inside the double helix
  • The glycosidic bonds holding the bases in each basepair are not directly across from one another, hence the sugar-phosphate backbones are not equally spaced yielding a major and minor groove
dna has three different forms
DNA has three different forms
  • B-form DNA: Watson-Crick structure- most stable under physiological conditions; one turn per 3.4 angstroms
  • A-Form DNA – unclear if a physiological form, only observed in test tube
  • Z-form DNA – Left-handed helical rotation; Alternating C, G bases can adopt this form in the cell, barely any major groove, minor groove is narrow and deep
enzymes modulate dna supercoiling
Enzymes modulate DNA supercoiling
  • Topoisomerases (gyrase)
slide22

Nucleic acid structure can be disrupted

  • Similar to proteins, by heating, or change in pH, one can denature nucleic acid structures
  • Hydrogen bonds are broken, loss of base-stacking interactions cause strands of DNA double helix to separate
  • The strands can anneal once temperature or pH is returned to an appropriate temperature
    • dsDNA and ssDNA have distinct absorbance properties
slide25

Understanding the significance of DNA sequences provides valuable insight into biology

  • Reactions

terminated by

dideoxy NTP’s

infer metabolism from genomes
Infer Metabolism from Genomes
  • http://www.genome.jp/kegg/
  • Click on KEGG gene universe
  • Click on PATHWAY
  • Click on Glycolysis/Gluconeogenesis
  • Reactants/Products/Enzymes/Pathways
rna structure
RNA structure
  • RNA does not have simple secondary structure such as DNA’s double helix
  • G:U base pairs are prevalent in RNA in addition to one’s found in DNA
  • Like proteins, RNA 3-D structure is a complex network of various interactions, most prominently base-stacking