DNA Structure and Replication

Question 1

what are nucleic acids (e.g. DNA and RNA are both nucleic acids)?

Answer 1

- genetic material:
blueprint carrying all the information required for building proteins

Question 2

describe the structure of DNA (including structures of nucleotides)

Answer 2

DNA is made of blocks of nucleotides:

each nucleotide contains:

• deoxyribose (a pentose (five sugar carbon))
• nitrogenous base
• a phosphate group

the nitrogenous bases in the helixes can interact with each other via H bonds: double structure

these double strands of DNA twist around each other in anti-parralel direction: one runs (3’ -> 5’), the other runs (5’ -> 3’)

Question 3

what are the 5 (N containing) bases found in DNA/RNA?

what are they derived from?

Answer 3

Derived from purine:

• Adenine
• Guanine

(AG - PURE SILVER)

Derived from Pyrimidine:

• Cytosine
• Thymine (only in DNA)
• Uracil ( only in RNA)

Question 4

how many H bonds form between:

• C & G
• A & T?

Answer 4

C&G = 3

A&T= 2

Question 5

how do nucleotides join together to form polynucleotide chains?

Answer 5

phosphodiester bonds form between 5’ hydroxyl group of one nucleotide and 3’ group of 3’ hydroxyl group

Question 6

how does compaction of DNA occur?

Answer 6

1. compaction of histomes: (basic proteins that form subunit structures)

• 8 histomes form a nucleosome bead
• DNA wraps around histomes: 146 base pairs of DNA wraps around a histome

= v compact !

2. further compaction of histomes into chromatin

3. further folding of chromatin into chromosomes

-

Question 7

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Question 8

which enzyme adds bases onto DNA to allow it synthesise?

Answer 8

DNA polymerase ! :)

Question 9

what does DNA structure need to be like for DNA polymerase to synthesise DNA?

Answer 9

DNA has to be single stranded.

Therefore parental DNA double helix will unwind to give template stands

Question 10

what are origins of replication?

what are replication forks?

Answer 10

origins of replications: places in DNA where strands have opened to be single strands. here DNA synthesis starts

replication forks: DNA synthesis that occurs where the origins of replication are

Question 11

which way does DNA synthesis occur?

Answer 11

always occurs in the 5’ to 3’ direction !

Question 12

describe once origin of replication has occured, what the new splits are called?

Answer 12

parental DNA splits into:

- leading strand (5’ -> 3’)

- lagging strand (3’ -> 5’)

Question 13

describe how replication starts at the origins of replication for both:

• leading strand
• lagging strand

Answer 13

leading strand: synthesis occurs in 5’ to 3’ direction

lagging strand: synthesis cannot occur in direction continously (as would be in 3’ to 5’ direction). INSTEAD: synthesised in short segments (Okazaki fragments) of DNA in 5’ to 3’ direction. DNA ligase joins the okazaki fragments to form the second strand of DNA

Question 14

(how does DNA replication occur in bacterial DNA molcule?)

Answer 14

• only one origin of replication in bacterial DNA molecule
• synthesis occurs in 5’->3’
• topoisomerase prevents supercoiling of DNA

Question 15

what is role of topoisomerase? (enzyme found in bacterial DNA replication pathway)

Answer 15

topoisomerase = prevents supercoiling of DNA. removes knots and tangles in bacterial chromosome.

Question 16

what is the antibacterial effect of quinolones on bacteria?

Answer 16

interact with targets: topoisomerase IV and tyrase into toxic enzymes. disintegration of bacteria DNA. death

Question 17

name two types of antibodies that interfere with DNA replication in bacteria

Answer 17

1. Fluroquinolones: taret topoisomerases in resp. and urinary tract infections
2. Trimethoprim: target nucleotide synthesis

Question 18

DNA polymerase has sepeate sites for X and Y?

Answer 18

DNA polymerase has seperate sights for DNA synthesis and DNA editing

Question 19

what is the normal error rate for DNA polymerase?

Answer 19

1 in 100 000 bases

BUT: proofreading and corrections changes the error rate to 1 in 100 million bases

Question 20

what are the different types of DNA repair?

Answer 20

1. Single strand repairs

• Base Excision Repair (BER)
• Nucleotide Excision Repair (NER)

2. Double strand repairs

• Homologous recombination (HR)
• Non homologous end joing (NHEJ)

Question 22

1a) what happens if dont repair single stand defects?
1b) what are the repair mechanisms for single stand defects?

Answer 22

1a) - lead to mutations (lead to cancers)
1b) repair mechanisms: Base excision repair, nucleotide excision repair, mismatch pair
2a) leads to genetic instability
2b) repair mechanisms: non homologous end joining, homologous end-joining

Question 23

1. when does base base excision repair occur?
2. explain how base excision repair mechanism works

Answer 23

1. correction of single bases that do not sig. distort DNA helix structure
2. -single base is excised out (using an enzyme, such as uracil DNA glycosylase)
   - DNA polymerase adds correct base and DNA ligase seals the deal

Question 24

how does nucleotide excision repair occur?

Answer 24

1. pyrimidine dimer (molecular lesions formed from thymine or cytosine bases in DNA via photochemical reactions)

2. - nuclease will remove a 12 nucleotide region, where the pyrimidine dimer ison the DNA, and create a 12 nucleotide gap

• DNA helicase will unwind the DNA adjacent to the gap
• DNA polymerase will fill in correct bases

Question 25

what is DNA mismatch repair?

Answer 25

this type of repair, repairs insertion or delation mutations that occurs during DNA replication and recombination:

1. DNA strand has an error

2. A nick (break) occurs in strand of DNA that has the error in.
3. This provides signals that direct mismatch proof reading proteins to DNA strand that has nick.
4. proteins scan the strand until the nick is found
5. proteins (MutS and MutL) remove the DNA strand from the error to the nick
6. DNA repair synthesis occurs to fill in corrected DNA into strand

Question 26

• why are double strand repairs of DNA more dangerous for single strand repair?

Answer 26

there are no intact template strands to copy

Question 27

what are the two mechanisms that can repair double stranded breaks in DNA?

)whats an e.g. that could cause double stranded breaks in DNA?)

Answer 27

1. non-homologous end joining
2. homologous recombination

(ionisation radiation can cause double strands of DNA repair)

Question 28

describe the differences between non-homologous end joining and homologous recombination for double stranded DNA repair

Answer 28

non-homologous end joining:‘quick and dirty.’ get scars on DNA (regions of altered segment due to missing nucleotides). occur in non-coding regions of DNA

homologous recombination: more accurate. sister chromsome is used as a template. complete sequence is restored by copying sister chromosome.

Question 29

(examples of inherited DNA repair defects? (one for nucleotide excision repair, mismatch repair and repair by homologous recombination))

Answer 29