Lecture 6 Flashcards by Adwoa B

Which base does RNA tend to have?

Uracil as opposed to thymine

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What is the most important difference between DNA and RNA?

DNA lacks the 2’ -OH group

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What are the similarities between DNA and RNA?

•Both have a 5’ and 3’ end
•Both carry a strong negative charge
•

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What is the charge of each part of the nucleotide?

Bases don’t carry a charge
Sugars don’t carry a charge
Phosphate groups have a negative charge

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What is the backbone of nucleic acids?

The sugar phosphate structure

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What is the polarity of the backbone of nucleic acids?

It is polar

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What kind of bonds can the phosphates of nucleotides form?

Hydrogen bonds and ionic interactions

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Which backbone is more polar? RNA or DNA?

RNA is more polar because of the hydroxyl group

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How many potential hydrogen bonds can RNA form?

Three

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What is the polarity of the bases themselves?

They are relatively non-polar but can form H-bonds

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What is the solubility of bases in aqueous environments?

The bases are relatively low solubility

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What order are the primary structure of Nucleic acids written?

5’ to 3’ Ex. 5’-ATGCAATG-3’

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What is the Primary Structure?

The sequence of monomers within a polymeric structures. In nucleic acids its the sequence of nucleotides within the larger polymeric nucleic acid structure

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What is a Mononucleotide?

A single nucleotide

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What is a Dinucleotide?

Two nucleotides bonded by a phosphodiester bond

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What is a Dinucleotide?

Two nucleotides bonded by a phosphodiester bond

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What are examples of Mononucleotides?

ATP, ADP, FMN

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What are examples of Dinucleotides?

FAD, NAD+, dCdG

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What is a Oligonucleotide?

Relatively short nucleotide chain?

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What is a Polynucleotide?

A large number of nucleotides in a polymer

When are mono-/di-/tri- prefixes used?

When phosphates attached to a single carbon/OH group

When are bis- or tris- (ex, Adenosine 2’,5’ bisphosphate) prefixes used?

When phosphates are attached to multiple carbon/OH groups

What would be a situation where Phosphodiester bonds need to be broken?

If one were to ingest nucleic acids in order to free the nucleotides

What would the products of Hydrolysis of a Phosphodiester bond?

A hydroxyl
Phosphate group that is no longer attached
And a free hydrogen

What happens in RNA when the pH is > 10?

Spontaneous Hydrolysis of Phosphodiester bonds occur

What does Spontaneous Hydrolysis of Phosphodiester bonds start with?

A hydroxyl acting as a base

What is the first product of Spontaneous Hydrolysis of Phosphodiester bonds?

A 5' OH attached to the 5' C

What is the second product of Spontaneous Hydrolysis of Phosphodiester bonds?

Either a 2' or a 3' phosphoester attached

Why is the Spontaneous Hydrolysis of Phosphodiester bonds important?

Because it doesn't happen in DNA

Why is DNA more stable than RNA in alkaline conditions?

Because DNA doesn't undergo Spontaneous Hydrolysis of Phosphodiester bonds because it doesn't have the 2' OH group

What does the spontaneous deamination of cytosine form?

Uracil and an Ammonia

What could occur if the spontaneous deamination of cytosine into uracil goes uncorrected?

It can cause DNA mutation

What changes in cytosine when it converts to uracil?

The NH2 on cytosine is replaced with a carbonyl and the nitrogen at position 3 gains a hydrogen

What happens if Uracil is found in DNA?

Specific DNA repair mechanisms will recognize the lack of methyl group on U and remove it

What is dideoxynucleotide used for?

In lab scenarios where they don't want a DNA chain to extend indefinitely so it has H at both 2' and 3' instead of one hydroxyl

What does a Phosphodiester have to contain?

Two carbons attached to an phosphate

What is a Phosphoanhydride?

To phosphates attached to an oxygen

What are the properties of the bases in nucleic acid structures?

* Heterocyclic * Aromatic, electron delocalization * Basically planar, slight pucker in purine base * Poorly soluble * Largely hydrophobic with some polar groups

What is always seen with electron delocalization in aromatic structures?

UV absorbance

How do nucleic acids tend to organize themselves since the bases are hydrophobic and the backbone is polar?

The sugar phosphate backbones are usually on the outside where they can interact with water

What kind of light do Nucleic acids absorb?

UV light

At what wavelengths does DNA absorb the most?

280nm and approx half that at 260nm

Where do proteins tend to absorb more strongly?

At 280nm

What does comparing the absorbance at 260 and 280nm do?

Tells us the purity of a DNA sample. 1.95 for pure DNA and will decrease if there is protein present

What kind of relationship is seen with absorbance and concentration of DNA?

As DNA concentration goes up, so does absorption at a constant wavelength

What does the Beer-Lambert Law do?

Relates concentration to absorbance

What is the absorbance related to?

The concentration of DNA

What is each chain in the double helix associated by?

Non covalent interactions with each other