EXAM 3 NUCLEIC ACIDS

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11 Terms

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Pyrimidines

  • Pyrimidines - N get the lowest number; count clockwise; 1’ usually = bottom and 4’ = top

    • Cytosine - 2’ C=O, 4’ NH2

    • Thymine - 2’ and 4’ C=O, 5’ CH3 branching off

    • Uracil = just like thymine without methyl

    • SMALLEST NUMBER CONNECTS TO RIBOSE (1)


<ul><li><p><span style="background-color: transparent;">Pyrimidines - N get the lowest number; count clockwise; 1’ usually = bottom and 4’ = top</span></p><ul><li><p><span style="background-color: transparent;">Cytosine - 2’ C=O, 4’ NH2</span></p></li><li><p><span style="background-color: transparent;">Thymine - 2’ and 4’ C=O, 5’ CH3 branching off</span></p></li><li><p><span style="background-color: transparent;">Uracil = just like thymine without methyl</span></p></li><li><p><span style="background-color: transparent;"><strong>SMALLEST NUMBER CONNECTS TO RIBOSE (1)</strong></span></p></li></ul></li></ul><p></p>
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Purines

  • Purines - bicyclic; N get lowest number; start left most N and count counter clockwise

    • Adenine = 6’ NH2

    • Guanine = 2’ NH2, 6’ C=O

    • BIGGEST NUMBER CONNECTS TO RIBOSE (9)


<ul><li><p><span style="background-color: transparent;">Purines - bicyclic; N get lowest number; start left most N and count counter clockwise</span></p><ul><li><p><span style="background-color: transparent;">Adenine = 6’ NH2</span></p></li><li><p><span style="background-color: transparent;">Guanine = 2’ NH2, 6’ C=O</span></p></li><li><p><span style="background-color: transparent;"><strong>BIGGEST NUMBER CONNECTS TO RIBOSE (9)</strong></span></p></li></ul></li></ul><p></p>
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nucleoside vs nucleotide; what does cAMP look like

nucleoside = base + sugar; connected via beta-N-glycosidic linkage

nucleotide = nucleoside + phosphate; phosphate on 3’ or 5’ end

Recognize cAMP = 3’-5’ cyclic adenosine monophosphate; 2nd messenger for signaling cascades

<p>nucleoside = base + sugar; connected via beta-N-glycosidic linkage </p><p>nucleotide = nucleoside + phosphate; phosphate on 3’ or 5’ end</p><p><span style="background-color: transparent;">Recognize cAMP = 3’-5’ cyclic adenosine monophosphate; 2nd messenger for signaling cascades</span></p>
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nucleoside analogs in medicine

Zidovudine - nucleoside analog reverse transcriptase inhibitor for HIV (NRTI)

Emtricitabine - treat HIV infection

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Xanthines; why is DNA more stable than RNA

hypoxanthine, inosine (hypoxanthine + ribose), xanthine

RNA = susceptible to base catalyzed hydrolysis (DNA = not)

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Watson and Crick; central dogma of biology

solved secondary structure of DNA; used Franklins data and Chargaff rules to solve

replication based on COMPLEMENTARITY

DNA →(transcription) RNA → (translation) protein

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B DNA (most common)

  • Double helix structure = phosphates on outside and bases on inside; antiparallel chains

    • Riboses must be on same side 

  • B DNA structure - 10 bases per 34 A so 3.4 A rise per base pair

  • MAJOR GROOVE = WIDE/DEEP

  • MINOR GROOVE = NARROW/DEEP


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Telomeres vs RNA

Telomere - g rich; quadruplex; non watson crick base pairing

RNA = A type helix; clover secondary structure (wobble); banana secondary structure

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Topoisomerase

Topoisomerase = relax super coil by breaking strand(s)

  • type 1 = break one strand 9ssDNA)

  • type 2 = break both strands (dsDNA)

Ex. drug = cipro → inhibit topisomerase → inhibit replication → cell death

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DNA packaging (eukaryotes); How is DNA damaged

  • Nucleosome = DNA is coiled around histone octamer (2x histones H2A, H2B, H3, & H4)

    • “beads on a string” 11 nm​

  • UV radiation → thymine dimer → DNA damage

  • Alkylation/HNO2 (processed meat)→ DNA mismatch → cancer


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