1' Biochemistry: an Evolving Science

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DNA, RNA, AND FLOW OF GENETIC INFORMATION
1. Nucleic acids 1) polymer of nucleotide -
base - nucleoside base ribose (deoxyribose)
linked by ß-glycosidic linkage - nucleotide
nucleoside phosphate - phosphodiester bond
riboses linked by phosphate groups - polarity
base sequence in the 5'? 3' direction 2) bases
- purine base adenine, guanine - pyrimidine
base cytosine, uracil, thymine 3) nucleosides
adenosine, guanosine, cytidine, uridine,
thymidine 4) nucleotides adenylate, guanylate,
cytidylate, uridylate, thymidylate

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• 2. DNA structure
• 1) DNA double helix
• - James Watson, Francis Crick (1953)
• - two helical chains
• 2) structure
• - base ? inside phosphate and deoxyribose units
  ? outside
• - diameter of the helix 20Å
• - separation by adjacent bases 3.4Å
• - rotation of adjacent base 36 degree
• - hydrogen bonds between pairs of bases
• - base stacking van der Waals interaction,
  hydrophobic effect
• - sugar (five-membered ring) rigidity

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• 3. Semiconservative replication of DNA
• 1) complementary chain
• 2) Matthew Meselson, Franklin Stahl (1958)
• - 15N ? 14N
• - density gradient centrifugation
• - semiconservative replication
• 4. Melting of DNA
• 1) melting curve
• - melting
• - hyperchromism
• - highly cooperative structure
• - GC contents
• - renaturation annealing
• 2) hybridization

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• 5. Other structures of nucleic acid
• 1) superhelix
• - supercoiling more compact
• - supercoiled DNA vs. relaxed DNA
• - negative supercoiling ? unwound states
• 2) single-stranded nucleic acids
• - stem-loop structure
• - nonWatson-Crick base pairs
• - higher-order folding

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• 6. Replication of genetic materials
• 1) DNA polymerase
• - monomers dATP, dGTP, dCTP, TTP, Mg2
• - template-directed enzyme
• - primer a free 3'-OH
• - proofreading high fidelity lt 10-8
• 2) RNA polymerase
• - tobacco mosaic virus (6,390 nt)
• - RNA-directed RNA polymerase
• 3) reverse transcriptase
• - RNA tumor viruses or retroviruses
• - reverse transcriptase RNA-directed DNA
  polymerase 

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• 7. Flow of genetic information
• 1) DNA ? RNA ? protein
• - transcription
• - translation
• 2) RNA molecules
• - ribosomal RNA (rRNA) 80 in E. coli
•   3700 nt (23S), 1700 nt (16S), 120 nt (5S)
• - transfer RNA (tRNA) 15, 75 nt
• - messenger RNA (mRNA) 5
• - snRNAs small nuclear RNAs, RNA splicing in
  eukaryotes
• - miRNA micro RNA 
• - telomerase RNA
• - ncRNA noncoding RNA

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• 8. Transcription
• 1) RNA polymerase
• - template DNA
• - activated precursors ATP, CTP, GTP, UTP
• - single RNA polymerase in E. coli
• - three RNA polymerases in eucaryotes
• 2) template DNA
• - coding strand
• - noncoding strand
• - template strand

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• 3) transcription unit
• - promoter
• - terminator
• 4) promoter RNA polymerase binding,
  transcription start
• - procaryotes -35 region, -10 region (Pribnow
  box)
• - eucaryotes TATA box, upstream sequence (CAAT
  box)
• 5) terminator termination signal (procaryotes)
• - terminator hairpin and 3' U-rich sequence
• - rho-factor dependent terminator (?-dependent
  terminator)
• 6) eukaryotic mRNA

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• 9. Transfer RNA (tRNA)
• 1) adaptor molecules
• 2) amino acid attachment site
• - 3'- or 2'-hydroxyl group at the 3' end of the
  tRNA chain
• - the carboxyl group of the amino acid
• 3) template recognition site
• - three base
• - anticodon

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• 10. Genetic code
• 1) the relation
• - between the base sequence in RNA and the amino
  acid sequence in protein
• 2) a group of three bases codon
• - 44464
• 3) nonoverlapping
• 4) sequential
• - deletion, insertion ? frame shift mutation
• 5) degeneracy
• - more than one triplet for one amino acid
• - synonyms XYC, XYU XYG, XYA
• - minimizing the deleterious effects of mutations
  
• - variation of DNA base composition for one amino
  acid

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• 6) start signal
• - Met formylmethionine (fMet) in bacteria
• - AUG (internal Met), GUG (internal Leu)
• - stop codons UAA, UAG, UGA
• - translation initiation signal purine rich in
  bacteria
• - the first AUG closest to the 5' end of mRNA in
  eukaryotes
• - polycistronic vs monocistronic
• 7) nearly universal
• - exception human mitochondria, ciliated
  protozoa (UGA, stop signal)
• - mitochondria in the direction of a simpler
  code

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• 11. Introns and exons
• 1) mRNA-DNA hybrid
• - introns intervening sequence
• - exons protein domain
• 2) splicing
• - 5' splice site
• - 3' splice site
• 3) expansion of genetic repertoire with exons
• - exon shuffling 

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