DNA Structure

Question 1

What are the 3 components of nucleic acids?

Answer 1

• Base Pair
• Phosphodiester/Phosphate Group
• (Deoxy)ribose/sugar

Question 2

What is DNA?

Answer 2

DNA is a polymer composed of two polynucleotide chains that coil around each other

Question 3

What are the two forms of nucelobases?

Answer 3

1. Pyrimidine
2. Purine

Question 4

What are the 5 base pairs?

Answer 4

1. Cytosine
2. Thymine
3. Uracil
4. Adenine
5. Guanine

Question 5

What are the base pairs that are based from pyrimidine?

Answer 5

1. Cytosine
2. Thymine
3. Uracil

Question 6

What are the base pairs that are based from purine?

Answer 6

1. Adenine
2. Guanine

Question 7

How many hydrogen bonds are between adenine and thymine?

Answer 7

2 - DA/AD

Question 8

How many hydrogen bonds are between guanine and cytosine?

Answer 8

3 - ADD/DAA

Question 9

How is deoxyribose produced?

Answer 9

It is generated from ribose 5-phosphate by enzymes called ribonucleotide reductases which catalyse the deoxygenation process

Question 10

What is the main link between two nucleotides?

Answer 10

Phosphodiester link 5’ to 3’

Question 11

What are the base pairs called?

Answer 11

Nucleobases

Question 12

What is a base and a sugar called?

Answer 12

Nucleoside

Question 13

What is a base, sugar and phosphate called?

Answer 13

Nucleotide

Question 14

What are the 5 nucleosides called?

Answer 14

1. Adenosine
2. Cytidine
3. Guanosine
4. Thymidine
5. Uridine

Question 15

What are teh 5 nucleotides called?

Answer 15

1. Adenosine 5’-phosphate
2. Cytidine 5’-phosphate
3. Guanosine 5’-phosphate
4. Thymidine 5’-phosphate
5. Uridine 5’-phosphate

Question 16

What is the anti-parallel duplex?

Answer 16

One side of the DNA strand going from 5’-3’ down and the other side 5’-3’ up

Question 17

What is the primary structure of DNA?

Answer 17

The sequence of nucleotides

Question 18

How is the duplex formed?

Answer 18

Strand of complementary sequence (complementary bases in opposite order)

Question 19

How do you find the complementary sequence?

Answer 19

1. Split the strand into three-base units for clarity
2. Write down the complementary bases
3. Reverse order to give strand in 5’ to 3’ format

Question 20

What are the main features of a DNA strand?

Lengths/heights and grooves

Answer 20

• 1 turn = 33 Å
• Width = 20 Å
• 10.5 nucleotides per turn
• Major groove and minor groove
• 3.3 Å base stacking distance
• Right handed

Question 21

Why is DNA in a double helix?

Answer 21

• Negatively charged phosphates repel each other - when they are separated there is a reduced electrostatic repulsion
• Stacking of nucleobases through hydrophobic / Van der Waals interactions compacts duplex vertically - removal of water (water would disrupt the hydrogen bonding), hydrophobic collapse, pi-stacking

Question 22

What are the alternate forms of the double helix?

Answer 22

• B-DNA: right handed
• A-DNA: right handed
• Z-DNA: left handed

Question 23

What is the main form of the double helix?

Answer 23

B-DNA

Question 24

Where are B-DNA ususally found?

Answer 24

Found in cells under physiological conditions

Question 25

Where does A-DNA usually occur?

Answer 25

Under dehydrated conditions or in a hybrid DNA-RNA

Question 26

How is Z-DNA formed?

Answer 26

After DNA has undergone methylation - common in some diseases (Alzheimers)

Question 27

What is triplex DNA?

Answer 27

3 strand binded together with the 3rd strand binded in the major groove

Question 28

What is quadruplex DNA?

Answer 28

* 4 strands of DNA around a metal ion * Found in telomeres (end of chromosomes) * Protects DNA ends and stop DNA repair systems from treating them as damaged * Allows coping of ends which wouldn't be possible with 3' end

Question 29

What are some examples of tertiary structures of DNA?

Answer 29

* Hairpin (small loop) * Stem-loop (large loop) * Holliday junction

Question 30

What are the differences between DNA and RNA structures?

Answer 30

DNA: * 2-Deoxyribose * Thymine * Usually double stranded * Stores genetic information * Located in the nucleus RNA * Ribose * Uracil * Usually single stranded * Protein synethesis and gene regulation * Located in the cytoplasm

Question 31

Why is ribose more easily hydrolysed than 2-deoxyribose?

Answer 31

Further possible H-bonding patterns from an extra OH, phosphodiester more easily hydrolysed

Question 32

What is a nucelosome?

Answer 32

* DNA colled around proteins

Question 33

How are chromosomes produced?

Answer 33

DNA is coiled around proteins called histones to produce nucleosomes, whihc are futher packed to produce chromosome

Question 34

How is nanotechnology used with DNA?

Answer 34

Predictable sequence-specific hybridisation can be used to create 3D nanostructures for a wide variety of nanotechnological applications

Question 35

What are the functions of DNA?

Answer 35

1. DNA directs the machinery of a cell to make specific proteins 2. Stores the hereditary information of an indivdual 3. Has the ability to mutate - allows for new characteristics (evolution)