DNA Structure

Question 1

What are the three molecules that make up the DNA?

Answer 1

Phosphoric acid (H3PO4)

2. Pentose sugar, there are two types ; ribose (C5H10O3) and deoxyribose (C5H10O4) the extra oxygen in the deoxyribose gives it stability as opposed to the ribose.
3. Organic bases ; there are two groups of organic bases

Question 2

What is the difference between pyrimidines and purines and which bases belong to which?

Answer 2

Pyrimidines - single rings with 6 sides such as cytosine, thymine and uracil.

b) Purines - these are double rings comprising a six-sided and a five-sided ring, such adenine and guanine.

Question 3

How many hydrogen bonds form between AT and CG?

Answer 3

There is a double hydrogen bond between A and T and a triple bond between C and G which means CG pairing is more stable.

Question 4

How is there uniformity and smoothness of the DNA helix?

Answer 4

The distance between the bases are roughly the same

Question 5

Why does DNA have more than one form?

Answer 5

DNA has conformational ability

Question 6

Describe the structure pf B-DNA(6)

Answer 6

1. The B-form DNA is the most common form of DNA found in cells (at a neutral pH) and has a right hand helix like A DNA.
2. The minor groove is 120 degrees
3. Associated with the A-T sequences and is an excellent binding site for minor-groove binding drugs
4. The preference to the A-T regions is due to the greater negative electrostatic potential at the bottom of the minor groove.
5. The major groove is 240 degrees, these grooves are formed due to the antiparallel arrangement of the two backbone strands.
6. In B DNA there are 10 bases per turn which are all perpendicular to the helical axis.

Question 7

Describe the structure of A-DNA(6)

Answer 7

1. The A form DNA is more tightly coiled and there are no differences in the grooves,
2. they are identical in width.
3. There are 11 base pairs per turn in the A form,
4. the base pairs are not perpendicular to the helical axis like in the B form.
5. DNA is driven to take the A form when under dehydrating conditions, which protects the DNA in conditions such as the extreme desiccation of bacteria A
6. DNA is also 20-25% shorter than B DNA. tRNA is configured in the A DNA form.

Question 8

Describe the structure of Z-DNA(4)

Answer 8

1. Has a left-handed configuration with
2. 12 base pairs per turn
3. Formed when you have alternating purine and pyrimidine bases, or when there is negative supercoiling or high salt.
4. Z-DNA structure is difficult to study because it is only present for brief amounts of time. 4. 5GCGC or 5GTGT

Question 9

Describe the structure of C-DNA

Answer 9

C DNA can be observed in low humidity and in the presence of Li + and Mg 2+

Question 10

Describe the structure of tetraplex/G quadruplex and why are they needed?(2)

Answer 10

1. 4-stranded DNA helix formed at telomeres Involves Guanine-rich DNA sequences.
2. a signaling mechanism is needed at the end of the chromosomes so they would not be picked up as being linear DNA

Question 11

Describe the structure of Holliday junction(3)

Answer 11

“1. DNA strand exchange between two homologous chromosomes

2. Important role in DNA repair.
3. They play an important role in DNA repair and transmission of genetic information “

Question 12

Recall the levels of DNA Structure

Answer 12

Primary -sequence of bases (DNA sequencing)

Secondary- helical structure (X-ray and chemistry)

Tertiary- DNA supercoiling (Electron microscopy) Quaternary- interlocked chromosomes

Question 13

How can DNA be visualised by Snager sequencing?(3)

Answer 13

1. A DNA strand is copied with a DNA polymerase in the presence of inhibitors that arrest DNA synthesis specifically at A, C, G or T.
2. The DNA strands are separated by length on a polyacrylamide gel.
3. If the DNA or incorporated inhibitor is radioactive or fluorescent, the DNA bands can be visualized and the sequence read. 700-1000 bases per read.

Question 14

Describe the structure of bacterial DNA(4)

Answer 14

1. Circular structure and comprises of 3x106 base pairs.
2. The chromosome is organized into 50 supercoil groups.
3. These are independent domains and by this further level of super coiling tertiary structure, the DNA can fit into the cell.
4. Bacterial cells also have plasmids that only carry certain genes. eg: those for antibiotic resistance.

Question 15

Decsribe DNA gyrase(3)

Answer 15

1. An enzyme that uses ATP hydrolysis as an energy source. A Type II Topoisomerase 2. They travel ahead of the replication fork removing positive supercoils 3. Competition between coiling an uncoiling by Topo 1,4 and gyrase sets an intermediate.

Question 16

Describe eukaryotic DNA(5)

Answer 16

1. 3 billion base pairs.
2. DNA double helix organized into chromatin and into 8 histone subunits
3. These come together and result in 3D coiling of DNA.
4. Multiple nucleosomes stack together which forms a fiber of packed nucleosomes called a solenoid fiber.
5. . The fiber is then looped and coiled again using scaffolding proteins that become chromatin and condense even more to form chromosomes.

Question 17

Summarise the three ways damages can occur to a DNA molecule

Answer 17

Chemically, Spontaneous, Radiation

Question 18

Describe how chemicals cause damage to DNA molecules.(3)

Answer 18

1. change base structure by inserting between bases- (intercalators such as doxorubicin widely used as anticancer drugs).
2. Oxidative metabolism can generate free radicals like superoxide of hydroxyl radicals and they damage the bases in DNA.
3. They can convert guanine into 8oxoguanine which is a lethal or mutagenic base

Question 19

Describe how spontaneous reactions can damage DNA molecules(4)

Answer 19

1. Simple mutations- switching from one base to another.
2. Loss of bases- cleavage of the N-glycosidic bond between purine and sugar causes loss of the purine.
3. Hydrolysis- Sugars can become hydrolysed to give a basic side which is problematic during DNA replication. eg. Cytosine can also become hydrolysed to uracil which has different base pairing and is found in RNA.
4. The phosphodiester bonds can also become hydrolysed to give breaks in the DNA which is caused by various chemicals like peroxides and enzymes like DNAsess.

Question 20

How can radiation cause damage to DNA molecules?(2)

Answer 20

Radiation -UV light produces thymine dimers -Ionising radiation (X-rays, gamma rays) break DNA chromosomes to cause leukaemia.

Two adjacent thymine in the same polynucleotide chain can be cross-linked together making a thymine dimer, leading to a bulky lesion making it difficult for DNA polymerase to copy the strand.

Question 21

How can ionising radiation cause damage to DNA molecules?(2)

Answer 21

1. ionizing radiation such as alpha and beta they can break the backbone and knock off electrons which disrupt the hydrogen bonding
2. it can ionize water molecules which produce oxygen free radicals and cause oxidative stress as a result.

Question 22

What is translesion DNA?

Answer 22

Translesion synthesis is a DNA damage tolerance process that allows the DNA replication machinery to replicate past DNA lesions such as thymine dimers or AP sites.

Question 23

How do cosmic rays cause DNA damage?(3)

Answer 23

They cause the breakage of the chromosomes.

Translocation can also occur where phosphodiester bonds break and two different pieces of from two different chromosomes are released and they can be linked together.

Genes at the junction of these aberrant chromosomes cam be switched on leading to cancers

Question 24

Why are repair enzymes needed?

Answer 24

DNA is not inert it is chemically unstable over a long period of time so DNA repair maintains the genomes stability.

Question 25

Sumarise the different repair mechanisms

Answer 25

Excision, Mismatch, Direct, Recombination

Question 26

Describe direct repair of DNA damage(2)

Answer 26

The damage is reversed by photoreactivation which involves an enzyme called DNA photolyase, 2. it uses energy from the photons from sunlight to cleave the C-C bond of the cyclobutyl ring of the thymine dimers so they are monomerized.

Question 27

Describe excision repair of DNA damage(3)

Answer 27

An endonuclease cleaves the DNA backbone on the 5’ side of the abnormal base 2. then DNA polymerase removes the abnormal base and replaces it with the correct base 3. DNA ligase reseals the nucleotide. The endonuclease enzymes involved are UvrA,UvrB, which recognize the damage and UvrC makes the incision and UvrD removes the base. They deal with the thymine dimers that are produced when ultraviolet light attacks DNA

Question 28

What is xeroderma pigmentosum?

Answer 28

Xeroderma pigmentosum is a defect in excision repair that deals with UV damage to DNA. This leads to being prone to skin cancer

Question 29

How does mismatch repair DNA damage?

Answer 29

The wrong bases are incorporated into the daughter strand only so the adenine bases of the template are labeled or tagged by methyl groups so the newly replicated DNA is demimethylated, the excision of wrong bases occurs in the daughter strand.

Question 30

How does recombination repair DNA damage?

Answer 30

In thymine dimerization the DNA replication cannot work properly so a gap is left and is repaired by a retrieval mechanism called sister strand exchange.

Question 31

What does experimental evidence suggest about e.coli chromsome?

Answer 31

The chromosome is actually organised into 50 supercoil groups. These are independent domains and by this further level of super coiling of tertiary structure, the DNA is able to fit into the cell.

Question 32

What are intercalators?

Answer 32

Insert between bases- (intercalators such as doxorubicin widely used as anticancer drugs)

Question 33

How do UV light and thymine result in damage to DNA?

Answer 33

Two adjacent thymines in the same polynucleotide chain can be cross-linked together making a thymine dimer, leading to a bulky lesion making it difficult for DNA polymerase to copy the strand.

Question 34

How does Histone 1 enable more coiling?

Answer 34

Histone 1 sits at the entry point and the exit point of DNA and they are present on adjacent nucleosomes. These come together and result in 3D coiling of DNA

Question 35

What sets the supercoiling in bacteria at an intermediate level?

Answer 35

Competition between coiling an uncoiling by Topo 1,4 and gyrase

Question 36

What is a linker DNA?

Answer 36

Linker DNA interconnects nucleosomes. It is double strandedAssociated with the H1

Question 37

What is the difference between transition and transversion chemical changes to DNA?

Answer 37

In transition, one pyrimidine switches to one pyrimidine. In transversion one purine switches to a pyrimidine

Question 38

What are histones and how do they increase fold compaction?

Answer 38

Histones: basic proteins that interact with negative charges in the phosphates of DNA. 4. Core of the nucleosome is called the optima containing 2A, 2B, 3, Using histones, 6-fold compaction is enabled. Histone 1 sits at the entry point and the exit point of DNA and they are present on adjacent nucleosomes

Question 39

describe how the nucleotides are arranged

Answer 39

linked by 3' 5' phosphodiester bonds → DNA runs from 5' to 3' → the two strands of DNA that are bonded together by H bonds run antiparallel to each other

Question 40

What are the potential consequences of DNA repair defects?

Answer 40

→ DNA repair defects = cancer likely. → Hereditary DNA repair defects, due to mutations, so unable to repair DNA properly. → Mutations in DNA lead to formation of tumours.