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Molecular Biology > Nucleic Acid Structure > Flashcards

Nucleic Acid Structure Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

How many strands does RNA typically have?

A

1

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2
Q

What is an oligonucleotide of RNA?

A

Tetra-nucleotide with 4 nucleotides joined together.

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3
Q

What form does Ribose take in DNA and where is it in the form of simple ribose?

A

Deoxy-ribose in DNA. RIbose in RNA.

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4
Q

How are the sugars in the RNA backbone joined?

A

A phosphodiester link - everything is attached to the sugar. (Physical palm card 1.)

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5
Q

How many carbons are in the sugar?

A

5 - pentosugar

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6
Q

How are the carbons in the sugar numbered?

A

1’ to 5’ - (physical card 1)

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7
Q

Where is the base attached to the sugar?

A

1’ carbon using an N-glycosidic bond

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8
Q

Which part of the sugar structure is removed in DNA?

A

The 2’ OH group.

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9
Q

Which part of the sugar structure does the next nucleotide attach to?

A

3’ OH.

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10
Q

The 5’ phosphate is added where on the sugar structure?

A

The 5’ OH.

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11
Q

Are bases covalently bonded?

A

No.

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12
Q

What are the bases bonded to and what is the covalent bond?

A

The sugar-phosphate backbone. The phosphodiester bonds are covalent.

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13
Q

Does the sugar-phosphate backbone change if the bases change?

A

No.

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14
Q

What causes DNA and RNA to behave in certain ways? What properties cause this?

A

The sugar backbone. It has a negative charge and is hydrophilic and easy to dissolve in water.

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15
Q

What can the properties of the sugar-phosphate backbone be used for?

A

Electrophoresis - uses neg charge - molecules in the electric field will move towards the positive terminal.
Ethanol Precipitation - uses backbones hydrophilic nature - easy to dissolve in water - dehydrate the backbone and make molecules fall out of the solution and precipitate.

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16
Q

What is considered the ‘information face’ of the RNA?

A

All the information is held on the side where the bases are.

17
Q

Bases have proton_____ and _____.

A

Donors and receivers. (Card 2)

18
Q

What is the direction of DNA and RNA molecules?

A

Phosphate group 5’ to 3’ hydroxyl (OH) group. (Card 2).

19
Q

What are the purines? How many rings do they have that bond to their pyrimidine?

A

Adenine and Guanine. Two.

20
Q

At physiological pH, which group acts as a proton donor and acceptor in adenine?

A

NH2 group donor. Ring N acceptor. (card 3)

21
Q

At physiological pH, which group acts as a proton donor and acceptor in guanine.

A

O group acceptor.
Ring N donor.
Amino group donor. (card 3)

22
Q

What about a base contributes to its ability to absorb UV light and what is the max wavelength?

A

The conjugated ring structure - aromatic nature - pi-electron clouds above and below. 260nm.

23
Q

What are the pyrimidines (in RNA) and how many rings do they have?

A

Cytosine and Uracil. One.

24
Q

_____ takes the form of _____ in DNA due to methylation.

A

Uracil. Thymine.

25
Q

What are the main structural differences between DNA and RNA?

A

DNA:
5’ carbon added to uracil to make thymine.
No hydroxyl (OH) in DNA at the 2’ sugar.

RNA
There is no CH3 group in the uracil.

26
Q

DNA takes the form of a _____.

A

Double helix.

27
Q

Proteins mainly access which part of the DNA form and why?

A

The major groove. It is the window into the sequence and so it is easier to read.

28
Q

What are the strong bonds that hold the double helix together?

A

Covalent bonds - nucleotides joined by a phosphodiester bond where the 5’ phosphate joins to 3’ OH and holds the strands together.

29
Q

What are the weak bonds that hold the double helix together?

A

Hydrogen bonding between bases.
The planar structure of bases means that sit flat on top of each other.
Hydrophobic interactions means bases want to sit internally - internal base stacking.
Ionic interactions
Van der Walls forces - the attraction between stacked bases interacting hydrophobically inside of the interior double helix.

30
Q

A-T bases form how many hydrogen bonds? G-C? Which bond is stronger and how does the affect the way they stack?

A

2, 3. G-C stronger and so they stack slightly better. (Physical card 4).

31
Q

Why do pyrimidines and purines bond the way they do?

A

The two bases that bond must physically fit inside the structure of DNA. In order to do this, a smaller pyrimidine with a single ring must bond to the purine with 2 rings in order to fit. 2 purines too large, 2 pyrimidines fall out/too small.

32
Q

What creates the twisted form of the DNA structure?

A

Electrostatic interactions - phosphate in each residue is negatively charged at physiological pH and repel each other. Bases want to associate together but are being pulled apart by phosphates - pull gives twisted shape so the phosphates can be as far away from each other at all times as possible.

33
Q

Why does the stability of DNA vs RNA change?

A

DNA want to hold onto that information for many years - the sugar-phosphate backbone is stable to chemical attack - two strands do that there is more information for copy and a template for repair - all info inside so that safe from free-radicals etc…

34
Q

Why is RNA less stable than DNA?

A

We want to transcribe for a while but don’t want it to continue making protein for a long time.

35
Q

What is the mechanism behind RNA’s lack of stability?

A

2’OH on RNA makes it susceptible. (Physical card 5)

36
Q

What happens if a base spontaneously changes to another base?

A

The bases are chemically stable except for when cytosine is deaminated into uracil. About 100 cytosines in each cell per day. These need to be removed and replaced.

37
Q

Why does thymine replace uracil in DNA?

A

Due to the reaction where cytosine changes to uracil. How would we know which base to fix if uracil was meant to be in DNA. If it is only meant to be thymine in the DNA, we know that any uracil in the DNA must have come from cytosine and must be replaced.

Molecular Biology (14 decks)

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