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Biochem > Lecture 8: Nucleic Acid Structure II > Flashcards

Lecture 8: Nucleic Acid Structure II Flashcards

1
Q

Topoisomerases

A

-catalyze concerted breakage and rejoining of DNA strands
-control formation of superhelical DNA

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2
Q

Topoisomerase enzyme function

A

-break and rejoin DNA strands
-need to alter topological status of DNA by changing the linking number and therefore the number of supercoils

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3
Q

Topoisomerase biological role

A

-control formation of superhelical DNA
-resolve winding problem from replication and transcription = altered DNA topology

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4
Q

Topology control

A

-cells need for survival
-DNA topology altered during replication and translation

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5
Q

No topology control

A

-accumulation of supercoils
-hinders melting of DNA duplex
-hinders movement of protein machinery along DNA

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6
Q

Human topoisomerases

A

Top1 and Top2
-targets for anticancer drugs

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7
Q

Eukaryotic topoisomerases

A

-do not introduce supercoils
-only relaxes them

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8
Q

prokaryotic topoisomerase

A

can introduce negative supercoils

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9
Q

Top1

A

-cuts only ONE strand of DNA
-cut strand rotates around intact
-no energy needed
-removes +/- supercoiling
-bacterial and eukaryotic enzymes

-change LK by 1 ?

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10
Q

Top2

A

-cuts both strands of DNA
-requires ATP
-moves another dsDNA segment through opening in cut strand
-changes linking number by 2
-bacterial and eukaryotic enzymes
-gyrase

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11
Q

Gyrase

A

-Top2
-only bacteria
-adds negative supercoils

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12
Q

Supercoiling of linear DNA

A

-generated by protein complexes translocating along DNA
-anchoring nuclear proteins create closed topological domains

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13
Q

Where is DNA overwound

A

-supercoiling ahead of replication fork
-jumprope

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14
Q

Where is DNA underwound

A

-DNA before replication fork

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15
Q

Top1 mechanism

A
  1. Cleaves one DNA strand
  2. Forms a transient covalent bond between tyrosine residue and phosphoryl group at cleavage site
  3. DNA relaxes by controlled rotation of the free end
  4. Seal gap by re-ligating cleaved strand

-slide 7 pic nvm its wrong

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16
Q

Top1 tyrosine residue phosphoryl group bond

A

-different top1 enzymes form enzyme link as either 3’ or 5’ -phosphotyrosine

17
Q

Controlled rotation of free end

A

-relaxes DNA
-free end swivels around intact strand
-add or subtract turns depending on substrate DNA

18
Q

Underwound

A

Top1 adds turns

19
Q

Overwound

A

Top1 removes turns

20
Q

Top2 mechanism

A

-needs ATP hydrolysis
1. breaks 2 strands of DNA
2. passes duplex DNA through gap and reseal gap

-eukaryotic relaxes supercoil
-prokaryotic add supercoil

21
Q

Topoisomerase inhibitors

A

-Antineoplastic and anitmicrobial agents
-anticancer targeting
-trap intermediate complex of enzyme and DNA
-degradation of DNA, addition of mutations, or inhibition of transcription replication and repair

22
Q

TOP1 drugs (Camptothecin Class)

A

-irinotecan and topotecan
-derivatives of camptothecin (tree bark)
-inhibit re-ligation step
-traps Top1-DNA complex
-replication fork hits complex = ds break = apoptosis

23
Q

Topotecan

A

ovarian and cervical cancer

24
Q

SLIDE 8 is remove turn

A

idk why
minus one
negative supercoiling
underwound

25
Q

irinotecan

A

-prodrug converted to active DN-38
-combo therapy for colon or rectum carcinomas

26
Q

indenoisoquinoline

A

-another Top1 drug class
-shamless Dr Cushman plug i think

27
Q

Drug action of Top1 drugs

A

-binds covalent intermediate and stops religation
-crystal structures define interactions
-camp vs indeno interactions and residence time

28
Q

G-quadraplex structure

A

-4 guanines in plane with central cation
-sequence variation in structure
-top structure same
-different sequences have alternative strand directions (bottom)

28
Q

Topology of promoter regions

A

-changed by singlestranded structures generated from DNA transcription

29
Q

G-Quadraplex function

A

-telomer extension
-genome stability
-regulation of expression/replication/translation
-sensor of oxidative DNA damage

30
Q

G-Quadraplex

A

-found in human promoter regions (esp of highly transcribed genes like oncogene MYC)
-formation and stabilization should stall transcription machinery = inhibit transcription

31
Q

TmPyP4 porphyrin

A

-binds to G-quadraplex of MYC promoter
-inhibits MYC transcription
-suppression of gene expression
-anticancer activity

Biochem (30 decks)

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