Genomics I

Question 1

How does nucleotides synthesize?

Answer 1

Two condensation reaction takes place between the pentose sugar , phosphoric acid and nitrogenous base. The nitrogenous base is added to the carbon 1 atom and the phosphoric acid is added to the carbon 5th atom. Two molecules of water is removed.

Question 2

How is a polynucleotide synthezised?

Answer 2

Two nucleotides are joined to form a dinucleotide by a condensation reaction between the phosphoric acid of one nucleotide and part of a sugar on the other. Phosphodiester bonds are formed between a dinucleotide. Further addition of nucleotides forms a polynucleotide.

Question 3

Why is there a 5’ and 3’ end of a polynucleotide?

Answer 3

The 5’ end contains a phosphate group attached to the 5th carbon atom of a pentose sugar. The 3’ contains a -OH group attached to the 3rd carbon atom of a pentose sugar.

Question 4

Describe the structure of DNA.

Answer 4

Nucleotides
* Each nucleotide consists of a pentose sugar/deoxyribose, a phosphate group and one of the four nitrogenous bases (adenine, guanine, cytosine or thymine).
* The phosphate group is joined to carbon atom number 5 of the pentose sugar/deoxyribose while the nitrogenous base is joined to carbon atom number 1 of the pentose sugar/
deoxyribose.

Polynucleotide
* One polynucleotide consists of many nucleotides joined together by phosphodiester bonds.
* The polynucleotide backbone consists of alternating sugar and phosphate groups
* with the nitrogenous bases projecting sideways from the sugars.
* The 5’ end of a polynucleotide ends with a phosphate group attached to carbon atom 5 of
deoxyribose.
* The 3’ end of a polynucleotide ends with the -OH group on carbon atom 3 of deoxyribose.

Double Helix
* Two strands of polynucleotides are held together by hydrogen bonds
* Complementary base pairing between the nitrogenous bases of opposite strands.
* The two strands/chains run in opposite directions/are antiparallel.
* One strand runs in the 5’ to 3’ direction while the other strand runs in the 3’ to 5’ direction.
* Adenine pairs with thymine forming two hydrogen bonds
* while cytosine pairs with guanine forming three hydrogen bonds.
* The distance between the two strands of polynucleotides is approximately 2.0nm and every
10 base pairs that constitute one turn of the double helix are approximately 3.4nm long.

Question 5

What are the roles of DNA and why they are suitable.

Answer 5

Roles: Store genetic information and serves as a template to be read for synthesis of protein.

Reasons: DNA is able to store large amounts of genetic information as linear sequences of nitrogenous base within the cell as it is able to
coil up to fit within the cell.

Ability to replicate accurately. Each strand of DNA acts as a template where a complementary set of deoxyribonucleotides will attach by complementary base pairing via hydrogen bonds. The newly synthesized DNA will have identical structure and sequences.’

Repair of damage: Due to the double helical structure of DNA , the intact strand can be used to guide the repair of the damaged strand via complementary base pairing.

Question 6

What is the first level of DNA packing.

Answer 6

Formation of 10nm nucleosomes. Linear DNA will bind to histone proteins to form a nucleosome. The positively charged lysine and arginine allows histone protein to bind tightly onto the negatively charge phosphate group on the DNA backbone via ionic bonds.

Question 7

What is the second level of DNA packing.

Answer 7

The formation of 30nm solenoid. Chromatin fibres will wrap around itself to form a solenoid , each turn of the helix contains 6 nucleosomes.

Question 8

What is the third level of DNA packing?

Answer 8

Formation of 300 nm chromatin fibres where 30nm solenoids attaches to non-histone proteins to form a series of looped domains to form 300 nm chromatin fibres.

Question 9

What is the fourth level of DNA packing?

Answer 9

Formation of chromosomes. The 300nm chromatin fibre will coil and fold , further compacting all the chromatin to form a chromosome with each chromatid being 700nm long during metaphase.

Question 10

What happens during the packing of DNA in prokaryotes?

Answer 10

It undergoes folding and supercoiling.

Question 11

What is the function of mRNA?

Answer 11

Carries information from the DNA on the sequence of amino acids for protein synthesis.

Question 12

What is the function rRNA?

Answer 12

Catalytic and structural roles in ribosomes.

Question 13

What is the function of tRNA?

Answer 13

It is an adaptor molecule that carries the right amino acids to the ribosome and its anti-codon base pair with its complementary mRNA codons.

Question 14

What is the semi-conservative mechanism in

Answer 14

Each DNA strand unwinds and is separated, breaking the hydrogen bonds between the complementary base pairs. They are used as a template for complementary base pairing , leading to the synthesis of two new daughter strands. Hydrogen bonds are formed between the new strand and the old strand to form a complete DNA molecule. Each daughter cell inherits a hybrid DNA molecule , containing one new strand and one old one.

Question 15

State the importance of hydrogen bonds in DNA structure?

Answer 15

*Hydrogen bonds allow for the formation of double stranded DNA / a double helix
* Hydrogen bonds hold the complementary bases together
* Many hydrogen bonds give stability to DNA molecule

Question 16

What is initiation of replication.

Answer 16

Helicase unwinds and unzips the DNA , hydrolysing the hydrogen bonds between the nitrogenous base break , separating the DNA strand. DNA unwinds over a short span of nucleotide residues , forming a replication bubble with replication forks at each end. Single -stranded DNA binding protein will stabilize the single stranded DNA so that it will not wind back into the double helix structure and to allow the unwound region to be used as a template. The untwisting of the double helix causes a tight twist and strain ahead of the replication fork. Topoisomerase relieves that strain by breaking , swiveling and joining the DNA strands back together. Since DNA synthesis is bidirectional , the replication bubble will expand laterally and many of them will bind together and the synthesis of the daughter strand is completed.

Question 17

What happens during priming?

Answer 17

Primases catalyses the synthesis of RNA primer which is complementary to the DNA template strand. RNA primer provides a 3’-OH for DNA polymerase III to extend for elongation.

Question 18

Why is priming needed?

Answer 18

Due to the limited function of DNA polymerase of adding deoxyribonucleotides onto existing 3’-OH ends of a nucleotide.
DNA polymerase cannot initiate the synthesis of a polynucleotide.

Question 19

What happens during elongation?

Answer 19

DNA polymerase III recognizes and selects free deoxyribonucleotides that are complementary to the ones that are found on the parental DNA strand. DNA polymerase III catalyses the formation of phosphodiester bonds between the nucleotides. DNA polymerase III performs proof-reading function to correct mistakes. It can remove mismatched deoxyribonucleotides on the primer end and replace it with the correct ones before proceeding for polymerization.

Question 20

Why are the leading and lagging strands synthesized differently along each replication fork?

Answer 20

1. DNA polymerase III can only add on deoxyribonucleotides to a pre-existing 3’-OH end of a nucleotide.
2. The DNA strands are anti-parallel.

Question 21

What is the similarity between leading and lagging strand?

Answer 21

They are both synthesized by DNA polymerase in a 5’-3’ direction.

Question 22

What are the difference between leading and lagging strand?

Answer 22

Leading strand: DNA polymerase moves towards the replication fork.
Leading strand synthesis is continuous from 5’-3’
direction.
Lagging strand: DNA polymerase moves away from replication fork.
Lagging strand synthesis is discontinuous as short
Okazaki fragments from 5’ - 3’ direction. => each
Okazaki fragment is synthesis begins with the
synthesis of RNA primer and is elongated by DNA
polymerase III.

Question 23

What are the functions of DNA polymerase I?

Answer 23

-hydrolyses the RNA primer on both leading and lagging strand and fills the gaps with complementary deoxyribonucleotides.

Question 24

What are the functions of DNA ligase?

Answer 24

-to complete the synthesis of intact daughter strands on both leading and lagging strands.
-catalyzes the formation of phosphodiester bonds between adjacent Okazaki fragments on the lagging strand.
-joins the 3’ end of the DNA strand that replaces the primer of the leading strand to the rest of the strand.

Question 25

How does the lagging strand elongate?

Answer 25

1. Synthesis of primer from primase
   2.Synthesis of first Okazaki fragment: DNA polymerase III adds deoxyribonucleotides from 5’-3; direction.
   3.DNA polymerase III detaches after reaching previous primer.
   4.Synthesis of 2nd Okazaki fragment.
   5.DNA polymerase I removed the primer and replaces them with complementary deoxyribonucleotides.
   6.DNA ligase catalyzes phosphodiester bonds between the new DNA and preceding Okazaki fragment .

Question 26

What happens during Rewinding?

Answer 26

Both parental and daughter strands rewind into a double helix.
The process is semi-conservative as the resultant daughter strand consists of one parental strand and one newly synthesized daughter strand.