dna structure

Question 1

Describe basic DNA Structure & Function:

Answer 1

→DNA is the store of genetic information

→ it is made of a double helix (consists of major and minor grooves which are receptors for drugs)

→DNA bases encode genetic information

• cellular dna is supercoiled and present as chromatin

Question 2

what are the four bases and describe their composition

Answer 2

→ adenine, thymine, guanine and cytosine

→Adenine and Guanine are Purines, they have 2 benzene rings.
→Thymine and Cytosine are Pyrimidine, they have 1 benzene ring.

→Adenine and Thymine have 2 H bonds between them.
→Guanine and Cytosine have 3 H bonds between them.

Question 3

how many forms does DNA have

Answer 3

3 forms

A,B and Z

Question 4

describe A DNA

Answer 4

Right-handed helical structure 2 antiparallel polynucleotides form a RH helix)

• More densely compacted than B form DNA.
• similar to B form DNA, sugar phosphate portions are found on the outside and bases on the inside.
• 11.6 base pairs per turn
• B DNA takes this form under dehydrating conditions.
• Narrow and deep major grooves
• Wide and shallow minor grooves
• tRNA folds in an A-form helix

Question 5

Describe B DNA

Answer 5

Right-handed helical structure ( 2 antiparallel polynucleotides form a RH helix)

• Most common/predominant structure in cells and nature
• DNA prefers this form under natural physiological conditions- optimum pH and salt concentrations.
• 10 base pairs per turn,
• major groove and minor groove allows access for proteins that want to read the dna sequence.
• Major groove is wide and deep (easy to study DNA here)
• Minor groove is narrow and shallow
• the sugar phosphate portions of the chains are found on the outside of the helix and the bases are on the inside of the helix

Question 6

Describe Z DNA

Answer 6

Left-handed helical structure

• present in small amounts in the cell
• Formed by 5’…GCGCGCGCGCGC OR 5’…GTGTGTGTGTGTGT
• Nucleotide pairs are dimers
• Double helix winds in a zigzag pattern due to alternate base stacking.
• Flat major groove
• Narrow and deep minor groove
• 12bp per turn
• alternating purine and pyrimidine bases.
• can be detectd in cells favoured by high salt. Some metal ions can flip the sequence into Z-DNA . DNA supercoiling can also flip the DNA

Question 7

Give a summary of the dna helix structure.

Answer 7

2 antiparallel strands that runs from 5’-3’ and is linked by 3’5 phosphodiester bonds.
Forms a right handed helix
Bases on inside/sugar-phosphate backbone on the outside. Oxygen is linked to the 3’ carbon of deoxyribose and phosphate is linked to the 5’ carbon of the next deoxyribose. Because of the nature of the 3’5’ link, the dna strand has polarity. Dna is also an acid as phosphate groups are protonated and can give up either protons and become negatively charged. Diameter is 2nm.
One strand is complementary to the other.
The polynucleotide chains are held together by H bonds between base pairs.
DNA helix is not rigid but conformationally mobile such as a b and z

Question 8

describe bacterial DNA and how it fits inside the bacterium .

Answer 8

• dna is circular and comprises of 3 mil base pairs
• Is supercoiled – the dna ribbon is itself twisted in space
• Have plasmids that only carry certain genes, e.g those for antiobiotic resistance.
• E.coli chromosome is circular and organised into approx. 50 independetly supercoiled domains.
• a combination of loop organisation and super coiling allows the dna to be compact and fit in the bacterium .

Question 9

what is bacterial DNA supercoiled by?

Answer 9

DNA gyrase

Question 10

Describe eukaryotic DNA.

Answer 10

→ humans have 3 billion base pairs of DNA
→ DNA is complexed with histones and made into a fiber called chromatin

→ the double helix is wound around 8 histone subunits

Question 11

What are some reasons as to why mutations may occur in DNA?

Answer 11

SPONTANEOUS
→ loss of bases

→ hydrolysis of C to U

CHEMICALS
→ change of base structure
→ insert between bases (doxorubicin used as anticancer drugs)

RADIATION
→ UV light produces thymine dimers
→ ionizing radiation break DNA chromosomes to cause leukemia

Question 12

what is the importance of DNA repair

Answer 12

→ maintains the genome stability.

→ 50-100 enzymes/proteins to check that DNA is properly repaired.

Question 13

what is an example of a disease due to failed repair mechanisms?

Answer 13

→Xeroderma pigmentosum
→ defect in excision repair that deals with UV damage to DNA

→prone to skin cancer

Question 14

describe the Holliday junction and when it forms

Answer 14

• Arises naturally in living cells through DNA strand exchange between two homologous chromosomes during the process of genetic recombination
• 4 way junction when two chromosomes are brought together.
• Allows for the exchange of genetic information
• Requires an enzyme to separate

Question 15

describe how the nucleotides are arranged

Answer 15

→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 16

What are 4 main points of DNA structure?

Answer 16

Primary – sequences of bases ( DNA sequencing)
Secondary structure- Helical structure (A, B & Z) ( X ray and cyrstallography)
Tertiary structure: DNA supercoiling ( electorn microscopy)
Quaternary structure: Topologically interlocked chromosomes. Chromosomes will break if interlocked during metaphase. Requires separation enzyme. (

Question 17

When is A - form DNA found in the cell?

Answer 17

A - form occurs under dehydrating conditions​.

Question 18

What are the potential consequences of DNA repair defects?

Answer 18

→ 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.

Question 19

What are nucelosomes ?

Answer 19

Nucleosomes are basic building blocks of chromatin. 1 section of DNA wound about
8 histone proteins. There is an electrostatic attraction between positive histones and negative phosphate group (histone octane/beads on a string in EM).

Question 20

when is tRNA found in the A form and how?

Answer 20

During transcription. The hybrid helix between the DNA strand and the newly synthesised RNA is in the A form.

Question 21

describe tetraplex DNA, when it forms, what it requires and what is its function?

Answer 21

• A four stranded rna helix formed at telomeres.
• Forms when the ends of dna folds back on itself
• Requires a G-rich sequence.
• Function – protect the ends of chromosomes from degredation by nucleases

Question 22

why is the holiday junction important?

Answer 22

• Important in reparing dna damage; if one of the chromosomes are damaged, you can use the good sequence on the other chromosomes through strand invasion, use that strand to copy the proper dna sequence and repair the damage

Question 23

what is dna supercoiling?

Answer 23

• Arises when the DNA helix is coiled in space.
• In supercoiling, it has energy stored which can facilitate the unwinding of the helix at DNA replication forks.
• Supercoiling reduces the DNA in size.

Question 24

in a nucleosome, how does the dna wound around the histone octomer in a supercoiled form?

Answer 24

Electrostatic attractions between the negatively charged phosphates and the histone tails.

Question 25

why does z dna have a zigzag pattern

Answer 25

alternate base stacking.

Question 26

what bonds are formed in the sugar-phosphate backbone?

Answer 26

phosphodiester bonds

Question 27

what bonds are present between complementary base pairs ?

Answer 27

hydrogen bonds