Secondary Structure of Nucleic Acids Flashcards by heather wade

Q

ssDNA folds back on itself to create

A

+ Single-stranded loop

+ Base-paired stem

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Q

Hairpin structures

A

+ Loop: size varies

+ Stem: homologous bases paired

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Q

Cruciform structures

A

Form if inverted repeats base pair with the complementary sequence on strand

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Q

Inverted repeats cause

A

Stem

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Q

Base separating inverted repeats cause

A

Loop

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Q

T or F: Cruciform DNA probably does not form in vivo.

A

False

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Q

Holiday structures

A

+ Junction of 4 loops

+ Permit crossing over during meiosis

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Q

Lacks free ends

A

Closed DNA

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Q

Circular genomes

A

Closed DNA

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Q

Bacteria form nucleoids

A

Closed DNA

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Q

Where are circular genomes found?

A

+ Viruses
+ Chloroplast
+ Mitochondria

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Q

Twist in DNA duplex along axis in space

A

Supercoiled DNA

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Q

DNA placed under tension

A

Supercoiled DNA

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Q

Only occurs in closed molecule

A

Supercoiled DNA

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Q

Single nick releases tension and supercoiling

A

Supercoiled DNA

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Q

1 twist

A

1 superhelical turn

Q

No supercoils

A

Relaxed DNA

Q

Applies to open or closed DNA

A

Relaxed DNA

Q

Twist DNA opposite to the duplex

A

Negative supercoils

Q

Relieves torsional stress by unwinding helix

A

Negative supercoils

Q

If sufficient stress, strand separation occurs

A

Negative supercoils

Q

Twist DNA in same direction as duplex

A

Positive supercoils

Q

Winds duplex tighter

A

Positive supercoils

Q

Never occurs in vivo

A

Positive supercoils

Superhelical density =

Number of superhelical turns of helix per 10 bp

Linking number =

Number of times that the duplex crosses itself (deltaW =deltaT)

W =

writhe (turning of double helix in space)

T =

twist (rotation of strands around each other)

Writhe is increased | Twist unchanged

Negative supercoil

Twist decreased | Writhe unchanged

Underwound

Higher L means

Higher negative supercoiling or unwinding

Lower L means

Lower negative supercoiling or overwinding

Toposiomers

A topologically distinct isomer

Topoisomerases (Topo)

+ Change L | + Break 1 or both strands

Helicases

+ Separate strands | + Do not change L

DNA gyrase

Facilitates supercoiling