Nucleic Acid Structure

Question 1

How many strands does RNA typically have?

Answer 1

1

Question 2

What is an oligonucleotide of RNA?

Answer 2

Tetra-nucleotide with 4 nucleotides joined together.

Question 3

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

Answer 3

Deoxy-ribose in DNA. RIbose in RNA.

Question 4

How are the sugars in the RNA backbone joined?

Answer 4

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

Question 5

How many carbons are in the sugar?

Answer 5

5 - pentosugar

Question 6

How are the carbons in the sugar numbered?

Answer 6

1’ to 5’ - (physical card 1)

Question 7

Where is the base attached to the sugar?

Answer 7

1’ carbon using an N-glycosidic bond

Question 8

Which part of the sugar structure is removed in DNA?

Answer 8

The 2’ OH group.

Question 9

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

Answer 9

3’ OH.

Question 10

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

Answer 10

The 5’ OH.

Question 11

Are bases covalently bonded?

Answer 11

No.

Question 12

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

Answer 12

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

Question 13

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

Answer 13

No.

Question 14

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

Answer 14

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

Question 15

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

Answer 15

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.

Question 16

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

Answer 16

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

Question 17

Bases have proton_____ and _____.

Answer 17

Donors and receivers. (Card 2)

Question 18

What is the direction of DNA and RNA molecules?

Answer 18

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

Question 19

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

Answer 19

Adenine and Guanine. Two.

Question 20

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

Answer 20

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

Question 21

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

Answer 21

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

Question 22

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

Answer 22

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

Question 23

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

Answer 23

Cytosine and Uracil. One.

Question 24

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

Answer 24

Uracil. Thymine.

Question 25

What are the main structural differences between DNA and RNA?

Answer 25

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.

Question 26

DNA takes the form of a _____.

Answer 26

Double helix.

Question 27

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

Answer 27

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

Question 28

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

Answer 28

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

Question 29

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

Answer 29

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.

Question 30

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

Answer 30

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

Question 31

Why do pyrimidines and purines bond the way they do?

Answer 31

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.

Question 32

What creates the twisted form of the DNA structure?

Answer 32

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.

Question 33

Why does the stability of DNA vs RNA change?

Answer 33

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...

Question 34

Why is RNA less stable than DNA?

Answer 34

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

Question 35

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

Answer 35

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

Question 36

What happens if a base spontaneously changes to another base?

Answer 36

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.

Question 37

Why does thymine replace uracil in DNA?

Answer 37

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.