Nucleic acids Flashcards by Mikayla Hume

What does each colour represent in a ball and stick model?

Red- oxygen
Blue- Nitrogen
Grey/black - Carbon
White- Hydrogen
Yellow- Sulfur

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Are these Pyrimidines or Purines? And what base is each?

They are pyrimidines, the left is cytosine and the right is thymine

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Are these Pyrimidines or Purines? And what base is each?

They are Purines, the left is adenine and the right is guanine

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What is this the common structure of?

A pyrimidine

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What is this the common structure of?

A purine

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What structure is this?

Uracil

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What structure is this?

Deoxyribose

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What structure is this?

Ribose

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What is the numbering order of this base

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what is the numbering of this base?

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what did Avery-Macleod-McCarty discover when the mouse was injected with the rough strain?

the mouse lived

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what did Avery-Macleod-McCarty discover when the mouse was injected with the smooth strain?

the mouse died

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what did Avery-Macleod-McCarty discover when the mouse was injected with the heat killed smooth strain?

the mouse lived

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what did Avery-Macleod-McCarty discover when the mouse was injected with the rough strain and heat killed smooth strain?

the mouse died

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what is T2

a virulent virus that infects E.coli
-protein coat high in S and DNA high in P

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what experiment proved to scientists that DNA is the genetic material and not protein?

Hershey-chase experiment showed that DNA is responsible for genetic transduction

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what are nucleotides comprised of?

Phosphate, sugar and base

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what determines the structure of nucleic acids?

the strucuture of nucleotides incorporated into nucleic acids

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what is the structural difference between uracil and thymine?

thymine has a methyl group at C5

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what is a nucleoside?

a base and a sugar (no phosphate group)

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what N of the base is the 5C sugar linked to in pyrimidines vs purines?

N1 in pyrimidines
N9 in Purines

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what is the suffix when naming purine nucleosides? what is adenine and guanine called when attatched to a ribose? and deoxyribose?

“osine”

adenosine and guanosine
deoxyadenosine and deoxyguanosine
-depends on the sugar attached

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what is the suffix when naming pyrimidine nucleosides? what are cytosine, thymine and uracil called when attatched to a ribose? and deoxyribose?

“idine”

cytidine, thymidine, uridine

deoxycytidine, deoxythymidine, deoxyuridine

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what is the difference between a phospho ester and a phosphodiester?

phospho diester is attatched to 2 R groups while a phospho ester is only attatched to one

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what bond links a carbon group to a phosphate group?

phosphoesters

what bond links TWO different CARBONS to one phosphate group?

phosphodiester

what bond links TWO PHOSPHATES to each other?

phosphoanhydride

what is the conventional nucleotide structure sequence?

5' to 3'

is DNA or RNA more readily hydrolyzed?

RNA is more readily hydrolyzed due to the prescence of a 2' OH

is DNA or RNA more stable under basic conditions?

DNA is more stable due to abscence of 2' OH

how can uracil be formed from cytosine?

-spontaneous uncatalyzed reactions that convert C to U -Uncorrected DNA mutation

what products can form fromhydrolysis of phosphodiester bonds?

https://youtu.be/HO0B3j7HBuA?si=JO8xxZ_dj7DEJBYu

are the bases polar or non-polar?

they are poorly soluble in water as they are largly hydrophobic

is the sugar phosphate backbone polar or non-polar?

it is polar

are pyrimidines numbered clockwise or counterclockwise?

clockwise

are purines numbered clockwise or counterclockwise?

counterclockwise

what kind of light do bases absorb? why?

they absorb UV light due to their electron delocalization of the ring

what can UV absorption of DNA be used to determine?

purity -1.95 is pure

what wavelength is protein maximally absorbed at?

280nm

will impure DNA have a higher or lower A260/A280 ratio?

lower

what is A260nm used to measure?

the [nucleic acids] in a solution

what carbons are joined together in phosphodiester bonds that link adjacent nucleotides?

carbon 3' to the adjacent 5' nucleotide carbon

what is the prominent form of DNA in the body?

B form -right handed twist

what is the primary stabilising force in DNA?

base stacking forces -van der waals (primary) -hydrophobic

why are bases in DNA largely excluded from H2O?

to stabalize H-bonds

what part of DNA is exposed to H2O?

ribose / deoxyribose and phosphates due to their higher polarity

how many base pair are there per turn of DNA?

~10 bp per turn

what is found in the core of DNA?

the hydrophobic bases

why is DNA more stable in high [salt]?

salt reduces electrostatic repulsion among phosphodiester groups -low [salt] will destabalize H-bonds

will absorption increase or decreases after denaturation?

increase in absorption will be seen at 260nm as strands separate

what is Tm?

the midpoint of melting and is characteristic of the base composition

does single stranded DNA or double stranded DNA have higher absorbance?

single stranded

what is hyperchromicity?

high absorbance -SS DNA

what is hypochromicity?

low absorbance -DS DNA

what is the difference between nucleation and zippering?

they are both renaturation (reformation of DS DNA) to regain native conformation -nucleation is slow -zippering is fast

why is Tm lower for AT in comparison to GC?

there are stronger base stacking interactions in GC than in AT

what does Tm depend on?

primary structure, solvent environment and base pairing

how can you tell this spot is AT rich?

there is more denaturation indicating high [AT]; Tm is lower so it requires less energy to unwind

how does pH affect Tm?

it affects protonation state of DNA

what does changing [salt] do to Tm?

decreased [salt] decreases Tm; destabilizes the double helix -ions shield negative charges on phosphate backbone

does increased hybridization following renaturation show an increase or decrease in Tm?

high Tm -used to identify similar sequences in different species

what kind of base pairing does DNA have?

interstrand

what forces stabalize RNA?

same as DNA -hydrogen bonds (base pairs) -base stacking

why can RNA form complex structures better than SS DNA?

the abscence of OH in DNA limits it from forming structures as complex as RNA

can DNA and complimetary RNA forma a DS helix?

yes this is common in trancription

what is the absorption 260nm/280nm ratio for pure RNA?

~2.1

can RNA for DS helices?

yes, even though it is SS, it will still form some SS or DS helical structures in which G may pair with U

why does the absorption melting curve for RNA begin higher than DNA?

due to the mixture of DS and SS strutcures