dna genomics l

Question 1

structure of basic nucleotide

Answer 1

1. has a pentose sugar
2. nitrogenous base attached covalently to carbon 1
3. phosphate group attached to carbon 5
4. hydroxyl group attached to carbon 3

Question 2

how to differentiate between the 2 pentose sugar

Answer 2

1. if H attached to C2 = deoxyribose
2. if OH attached to C2 = ribose

Question 3

what are the type of nitrogenous bases

Answer 3

1. purines: 2 ring structure - guanine and adenine
2. pyrimidines: 1 ring structure = cytosine, uracil and thymine

Question 4

complementary base pairing occurs between

Answer 4

adenine and uracil (2 hydrogen bonds)
adenine and thymine (2 hydrogen bonds)
cytosine and guanine (3 hydrogen bonds)

Question 5

how are phosphodiester bonds formed

Answer 5

: OH group on carbon 3 of pentose sugar of 1 nucleotide joined to phosphate group on carbon 5 of adjacent nucleotide with 2 phosphate groups being removed as inorganic phospate

Question 6

how are nucleic acids formed

Answer 6

1. polymerase catalyses formation of phosphodiester bond between 2 adjacent nucleotides
2. addition of further nucleotides forms a long polynucleotide chain with sugar-phosphate backbone
3. nucleotides are added in 5-3 direction with 3’ free hydroxyl group at the end of chain

Question 7

structure of DNA

Answer 7

1. ratio of nitrogenous bases:
   A:T = 1:1, C:G = 1:1 so (A+G) = (C:T)
2. since a purine always complementary base pairs with a pyrimidine, there is a constant width of 2 nm between sugar phosphate backbone
3. 1 dna molecule is made up of 2 strands of DNA
4. the 2 strands are anti-parallel: one strand runs in 5-3 direction, the other runs in 3-5 direction
5. DNA has directionality
6. 1 complete turn of the double helix has 10 base pairs and spans a distance of 3.4nm
7. basic unit is deoxyribonucleotide

Question 8

structure of RNA

Answer 8

1. single stranded
2. no fixed ratio (within the single strand) of A/U/C/G
3. basic unit is ribonucleotide

Question 9

what is semi conservative DNA replication

Answer 9

1. double stranded parental DNA unwinds and separates by breakage of hydrogen bonds
2. each strand acts as a template to synthesise 1 new DNA strand by complementary base pairing
3. each daughter DNA molecule is made up one parental strand and one synthesised strand

Question 10

what are the prerequisites of dna synthesis

Answer 10

1. requires DNA polymerase to add nucleotides in a 5-3 direction to a preexisting chain
2. DNA polymerase can only work in presence of RNA primer and template in form of parental DNA strand present
3. RNA primer: pre-existing chain that provides free 3’-OH group

Question 11

what occurs before replication

Answer 11

free deoxyribonucleoside triphosphates (dNTPs) are manufactured in the cytoplasm and transported into cytoplasm via nuclear pores

Question 12

what are the main events in dna replication

Answer 12

unzipping of parental strand
addition of primer
synthesis of leading strand
synthesis of lagging strand
end of replication

Question 13

unzipping of parental strand

Answer 13

1. replication begins at origin of replication (ori)
2. helicase binds to ori = disrupts hydrogen bonds between complementary base pairs, requiring ATP = parental strands unzip and separate
3. single stranded binding proteins bind to separated DNA strands = keep strands apart and prevent them from reannealing = allow them to serve as templates for synthesis of new strands
4. at where unzipping occurs, replication forks form and spread in both directions to create a replication bubble
5. topoisomerase relieves overwinding strain ahead of replication forks - break, swivel and rejoin DNA strands

Question 14

addition of primer

Answer 14

primase adds short RNA primer to each parental DNA strand where the end of RNA primer provides free 3’-OH end for DNA polynerase to catalyse elongation

Question 15

synthesis of leading strand

Answer 15

1. DNA polymerase uses parental strand as a template and aligns the free activated dNTPs in a sequence complementary to the parental strand
2. adenine base pairs with thymine, cytosine base pairs with guanine
3. DNA polymerase catalyses formation of phosphodiester bond between adjacent daughter DNA nucleotides of the newly synthesised strand
4. as DNA polymerase moves along the template, it proof reads the previous region for proper base paring
5. any wrongly added deoxyribonucleotide is removed and replaced by the correct one
6. leading strand is synthesied continuouisly in 5-3 direction

Question 16

synthesis of lagging strand

Answer 16

1. lagging strand is syntheised in fragments known as Okazaki fragments
2. each fragment is initiated by an RNA primer before addition of DNA nucleotides
3. when the Okazaki fragments join up, a different DNA polymerase removes the RNA primer adn replaces it with deoxyribonucleotides
4. DNA ligase seals the nicks by forming phosphodiester bonds between adjacent nucleotides of each of the DNA fragments on the new strand

Question 17

end of replication

Answer 17

complementary parental and daughter strands rewind into a double helix
resultant helix consists of one parental strand and one daughter strand

Question 18

why cant a strand be synthesised continuously in 3-5 direction

Answer 18

1. DNA polymerase’s active site is complementary to 3’ OH groups attached to end of growing DNA strand
2. DNA polymerase does not interact with phosphate attached to end of growing DNA strand

Question 19

what are the feature of DNA that make it a suitable store of information

Answer 19

1. weak hydrogen bonding between the 2 strands allows them to separate and act as a template for new strand synthesis = it can be replicated accurately leading to daughter cells having identical copies of DNA as the parent cell
2. numerous hydrogen bonds holds the 2 strands of DNA together and adjacent nucleotides in each strand are joined by strong phosphodiester bonds = makes DNA a stable molecule to be passed on to the next generation without loss of thecoded information
3. DNA is double stranded so one strand can serve as a template for repair of the other if a mutation occurs in the other = backup of code available
4. weak hydrogen bonding allows template strand to separate and allow transcription to take place + complementary base pairing allows the faithful transfer of info from DNA to RNA in transcription = coded information can be readily accessed

Question 20

what are the advantages of DNA being double stranded

Answer 20

1. it is a stable molecule
2. backup code available