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Biochem > Lecture 7: Nucleic Acid Structure I > Flashcards

Lecture 7: Nucleic Acid Structure I Flashcards

1
Q

Primary DNA structure

A

single strand of bases

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2
Q

Secondary DNA structure

A

-helix
-stem loop
-pseudoknot

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3
Q

Tertiary DNA structure

A

-A, B, Z forms
-stem loop and psuedoknot

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4
Q

Quaternary DNA structure

A

-DNA around a histone
-RNA with monomers

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5
Q

purine bases

A

-adenine
-guanine

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6
Q

pyrimidine bases

A

-cytosine
-thymine
-uracil

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7
Q

Non B-form DNA structures

A

-form transiently during replication, recombination, or transcription
-ex: triplex DNA/H-DNA
-can cause DNA polymerase to stall = nicks, breaks, possible malfunction

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8
Q

triplex DNA/H-DNA

A

-G-quadruplex structures in guanine-rich regions of DNA
-i-motif in cytosine-rich region of DNA
-expanded triplex sequences

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9
Q

Expanded triplex sequences

A

can cause certain hereditary neurological diseases

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10
Q

G-quadruplex and i-motif structures

A

-essential roles in regulating transcription and genome stability
-disruption can lead to cancer and aging

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11
Q

Topoisomerases

A

-maintain DNA supercoiling
-target of anticancer drugs

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12
Q

B-DNA structure

A

-base pairing
-base stacking
-most stable under physiological conditions
-elongated and narrower than A
-larger degree of twist

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13
Q

A-DNA structure

A

-observed under dehydrating conditions and high salt
-compatible with RNA
-compressed and wider

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14
Q

B-DNA major binding groove

A

-wider and shallower than A
-highly accessible for proteins to bind

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15
Q

Major and minor grooves

A

SLIDE 8 adn SLIDE 9

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16
Q

Double stranded DNA

A

-conformationally flexible

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17
Q

Helix features A vs B

A

SLIDE 10

18
Q

A-form DNA

A

-less solvent exposure
-under dehydrating conditions
-protects it under desiccating conditions
-often occurs in formation of DNA-RNA hybrid helix

19
Q

SIRV2 virus protein

A

-certain protein that dehydrates DNA upon binding = A-form
-infects hyperthermophilic acidophile sulfolobus islandicus

20
Q

DNA deformability

A

-structure can deviate locally (around a few bps) when bound to small molecules while still maintaining base pairing
-intercalators
-groove binders

21
Q

Intercalators

A

-hydrophobic
-heterocyclic
-insert between bases through ring stacking
-Ex: TOTO

22
Q

TOTO

A

-intercalator
-fluorescent label used to detect dsDNA in gels

23
Q

Minor-groove binders

A

-outnumber major-groove binders
-ex: Netropsin
-some groove binders change twist

24
Q

Netropsin

A

-antibiotic and antiviral
-interacts with sugars and an edge of the bases giving sequence-specific binding

25
Q

DNA intercalating agents

A

-interfere with DNA replication, transcription and repair
-distortions to DNA structure also lead to mutations = mutagens
-Actinomycin D

26
Q

Actinomycin D

A

-chemotherapeutic agent
-treats Wilms’ tumor
-pediatric kidney tumors

27
Q

Superhelical (supercoiling)

A

-created by underwinding (negative) or overwinding (positive) DNA to lowest energy helical state (thermo favored B-form)
-circularized DNA after loss of bp
-compacts DNA
-tend to disrupt H bonding that may lead to repair and replication

28
Q

DNA activity in replication and transcription

A

-topologically supercoiled form has greater activity than relaxed B-form
-supercoiling disrupts H bonding which may lead to repair and replication

29
Q

Negative supercoiling

A

-underwinding
-form right-handed superhelix
-easier to unwind
- = repair, replication, recombination

30
Q

Positive Supercoiling

A

-overwinding
-form left handed superhelix
-hard to unwind
-stabilizes DNA under extreme conditions

31
Q

Supercoiling equation

A

Lk = Tw + Wr

-sum of Tw and Wr constant = one to one change

32
Q

Lk

A

-linking number
-does not change once both ends are fixed (anchored to protein or circular DNA)

33
Q

Tw

A

-twist
-turns in DNA chain
-one every ~10 bp for relaxed DNA

34
Q

Wr

A

-writhe
-superhelical coild

35
Q

SLIDE 19 MELTED DNA

A

SLIDE 19

36
Q

For double stranded DNA with 110 base pairs, what is the relative length of the helical structure in A-form and B-form

A

B-form is longer than A-form

37
Q

Linear DNA in eukaryotes

A

-supercoiled
-anchoring by nuclear proteins created topological domains

38
Q

Linear DNA supercoiling

A

-induced by transcription and replication
-number of twists is constant while bps is decreased

39
Q

Supercoiled DNA vs relaxed DNA

A

-more compact
-chromatin for packaging in nucleus

40
Q

DNA of most organisms

A

negatively supercoiled

41
Q

DNA replication and transcription winding

A

-overwound ahead of replication fork (positive)

Biochem (30 decks)

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