DNA Structure

Question 1

What is the central dogma of biology?

Answer 1

• it deals with the detailed residue-by-residue transfer of sequential information
• it states that such information cannot be transferred back from protein to either protein or nucleic acid

Question 2

Draw out the DNA to RNA to protein flow chart?

Answer 2

DNA - DNA - replication
DNA - RNA - transcription
RNA - DNA - reverse transcription
RNA - RNA - replication
RNA - protein - translation

Question 3

What are the three components of nucleic acids/DNA?

Answer 3

• base pairs
• phosphodiester / Phosphate Group
• (deoxy)ribose / Sugar

Question 4

What is DNA?

Answer 4

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

Question 5

What are the two forms of nucleobases?

Answer 5

• pyrimidine
• purine

Question 6

What are the five base pairs?

Which ones are based from pyrimidines and which ones are based from purines?

Answer 6

pyrimidine:
- cytosine
- uracil
- thymine

purine:
- adenine
- guanine

Question 7

Which base pairs pair up?

How many hydrogen bonds between each?

Answer 7

AT - adenine and thymine
- 2 hydrogen bonds DA/AD

CG - cytosine and guanine
- 3 hydrogen bonds ADD/DAA

Question 8

What is ribose?

Answer 8

• a sugar and has standard structure of sugar
• it goes between planar and cyclic structure - there is an equilibrium which exists between the two
• it is metabolically produced from glucose (reduction of glucose)

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
• nucleobase replaces the OH on the RHS

Question 10

What is the main link between two nucleotides?

Answer 10

• phosphodiester links 5’ to 3’
• this asymmetric linkage gives DNA strands direction (gives it curved structure)

Question 11

Define nucleobases, nucleoside and nucleotide?

Answer 11

• nucleobase = base pairs
• nucleoside = base pair + sugar
• nucleotide = base pair + sugar + phosphate

Question 12

What are the five nucleosides called and therefore what are the five nucleotides?

Answer 12

• adenosine
• cytidine
• guanosine
• thymidine
• uridine
• adenosine 5’-phosphate
• cytidine 5’-phosphate
• guanosine 5’-phosphate
• thymidine 5’-phosphate
• uridine 5’-phosphate

Question 13

What is the antiparallel duplex?

Answer 13

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

Question 14

What is the primary structure of DNA?

Answer 14

• sequence of nucleotides

Question 15

How is DNA duplex formed?

Answer 15

• with strand of complementary sequence (complementary bases in opposite order)

Question 16

What can be said about link between stability and G-C contetnt?

Answer 16

• longer duplex with higher G-C content = more stable
• more hydrogen bonds so more stable

Question 17

How do you find complementary sequence?

Answer 17

• split strand into three base pairs
• write down complementary bases
• reverse the order to give strand in 5’ to 3’ format?

Question 18

What are main features of DNA double helix? (handed, turn, width, nucleotides per turn, grooves, base stacking distance)

Answer 18

• right handed
• 1 turn = 33A
• width = 20A
• 10.5 nucleotides per turn
• major and minor groove
• base stacking distance = 3.3A

Question 19

Why is DNA in a double helix?

Answer 19

• negatively charged phosphate groups repel each other so when they are separated there is a reduced electrostatic repulsion
• stacking of nucleobases through hydrophobic/van der Waals interactions compact duplex vertically - removal of water (as water would disrupt hydrogen bonding if bases closely packed) causing hydrophobic collapse and pi stacking
• base pairs hydrogen bond

Question 20

What are three forms of double helix forms?

When do these usually occur

Answer 20

• A-DNA - right handed - occurs under dehydrated conditions or in hybrid DNA-RNA
• B-DNA (most common) - right-handed - found in cells under physiological conditions
• Z-DNA - left-handed - after DNA has undergone methylation - common in some diseases (Alzheimer’s)

Question 21

What is triplex DNA?

Answer 21

• where 3rd strand binds in major groove

Question 22

What is quadruplex DNA?

Answer 22

• 4 strands of DNA around a metal ion
• G-Quadruplex found in telomeres (end of chromosomes)
• protects DNA ends and stop DNA repair systems from treating them as damaged
• allows copying of ends which wouldn’t be possible with 3’ end

Question 23

What are some examples of tertiary structures of DNA?

Answer 23

• hairpin (small loop)
• stem-loop (large loop)
• Holliday junction

Question 24

What are some differences between DNA and RNA structures? (sugar, base paid, single or double stranded, use, location)

Answer 24

• DNA contains 2-deoxyribose
• RNA contains ribose
• DNA uses thymine
• RNA uses uracil
• DNA is usually double stranded
• RNA is usually single stranded
• DNA - stores genetic information
• RNA - protein synthesis and gene regulation
• DNA located in nucleus
• RNA located in cytoplasm

Question 25

Why is ribose more easily hydrolysed than 2-deoxyribose

Answer 25

- further possible hydrogen bonds patterns from extra OH so phosphodiester more easily hydrolysed

Question 26

What are some RNA structures?

Answer 26

- hairpin - bulge - stem-loop - bubble/interior loop

Question 27

What is a nucleosome?

Answer 27

- DNA coiled around proteins called histones to produce nucleosomes - 8 protein units required for each nucleosome

Question 28

What is a chromosome?

Answer 28

- DNA coiled around proteins called histones to produce nucleosomes which are further packed to produce chromosomes

Question 29

How is nanotechnology used with DNA?

Answer 29

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

Question 30

What are the functions of DNA?

Answer 30

- DNA directs machinery of a cell to make specific proteins - stores the hereditary information of an individual - has the ability to mutate - allows for new characteristics (evolution)