Question

Make up YOUR OWN strand of dsDNA having five codons (15 nucleotides). You only have to show the sequence of bases and not the sugar phosphate backbone. Replicate your DNA giving me all the proteins discussed in the course for replication to take place. Include the function of all proteins. Indicate the new and old strands (semi-conservative replication). Show the 5’ and 3’ ends of all strands. Tell me how many hydrogen bonds are between the bases holding the double helices together.

Answer 1

1- Make up YOUR OWN strand of dsDNA having five codons (15 nucleotides).

DNA, short for deoxyribonucleic acid, is the molecule that contains the genetic code of organisms.DNA is made up of molecules called nucleotides. Each nucleotide contains a phosphate group, a sugar group and a nitrogen base. The four types of nitrogen bases are adenine (A), thymine (T), guanine (G) and cytosine (C). The order of these bases is what determines DNA's instructions, or genetic code.

A codon is a sequence of three DNA or RNA nucleotides that corresponds with a specific amino acid or stop signal during protein synthesis. Each codon consists of three nucleotides,

For making our own strand of dsDNA, we have to use 4 nitrogen bases in random. As 1 codon is made up of 3 nucleotide so, for making ds DNA with 5 codon we have to use 15 nucleotides.

We have to follow complementary base pairing rule in order to make dsDNA. Complementary base pairing is the phenomenon where in DNA guanine always hydrogen bonds to cytosine and adenine always binds to thymine. The bond between guanine and cytosine shares three hydrogen bonds compared to the A-T bond which always shares two hydrogen bonds.

so our final dsDNA is- 5’ AGCCGTGATGCACGA 3’

3’ TCGGCACTACGTGCT 5’

Where , 5' and 3' mean "five prime" and "three prime", which indicate the carbon numbers in the DNA's sugar backbone. The 5' carbon has a phosphate group attached to it and the 3' carbon a hydroxyl (-OH) group. This asymmetry gives a DNA strand a "direction"

2- Replicate your DNA

1) The first step in DNA replication is to ‘unzip’ the double helix structure of the DNA molecule.This is carried out by an enzyme called helicase which breaks the hydrogen bonds holding the complementary bases of DNA together (A with T, C with G). So, by this our 2 strands will seprate out-

5’ AGCCGTGATGCACGA 3’

  3’ TCGGCACTACGTGCT 5’

The separation of the two single strands of DNA creates a ‘Y’ shape called a replication ‘fork’. The two separated strands will act as templates for making the new strands of DNA.

2) One of the strands is oriented in the 3’ to 5’ direction (towards the replication fork), this is the leading strand. The other strand is oriented in the 5’ to 3’ direction (away from the replication fork), this is the lagging strand. As a result of their different orientations, the two strands are replicated differently.

5’ AGCCGTGATGCACGA 3’- leading strand

  3’ TCGGCACTACGTGCT 5’- lagging strand

3) A short piece of RNA called a primer (produced by an enzyme called primase) comes along and binds to the end of the leading strand. The primer acts as the starting point for DNA synthesis.

primer for leading strand will be- 5' TCAT 3' and for lagging strand 5' AGCC 3'

4)On leading strand- DNA polymerase binds to the leading strand and then ‘walks’ along it, adding new complementary nucleotide bases (A, C, G and T) to the strand of DNA in the 5’ to 3’ direction.

This sort of replication is called continuous.

5’ AGCCGTGATGCACGA 3’- leading strand

-TCAT5'- primer

5) On lagging strand- Numerous RNA primers are made by the primase enzyme and bind at various points along the lagging strand.Chunks of DNA, called Okazaki fragments, are then added to the lagging strand also in the 5’ to 3’ direction.this type of replication is called discontinuous as the Okazaki fragments will need to be joined up later.

   Primer -5' AGCC GTGA-----

3’ TCGGCACTACGTGCT 5’- lagging strand

6)Once all of the bases are matched up (A with T, C with G), an enzyme called exonuclease strips away the primer(s). The gaps where the primer(s) were are then filled by yet more complementary nucleotides.

7) Finally, an enzyme called DNA ligase seals up the sequence of DNA into two continuous double strands.

5’ AGCCGTGATGCACGA 3’- leading strand

3’ TCGGCACTACGTGCT 5’

5’ AGCCGTGATGCACGA 3’​​​​​​​

3’ TCGGCACTACGTGCT 5’- lagging strand

3- Indicate the new and old strands-

The result of DNA replication is two DNA molecules consisting of one new and one old chain of nucleotides. This is why DNA replication is described as semi-conservative, half of the chain is part of the original DNA molecule, half is brand new.

5’ AGCCGTGATGCACGA 3’​​​​​​​- old strand

3’ TCGGCACTACGTGCT 5’- new strand

5’ AGCCGTGATGCACGA 3’​​​​​​​ new strand

3’ TCGGCACTACGTGCT 5’- old strand

4- Show the 5’ and 3’ ends of all strands-

5’ AGCCGTGATGCACGA 3’​​​​​​​- old strand

3’ TCGGCACTACGTGCT 5’- new strand

5’ AGCCGTGATGCACGA 3’​​​​​​​ new strand

3’ TCGGCACTACGTGCT 5’- old strand

5- How many hydrogen bonds are between the bases holding the double helices together.

For -

5’ AGCCGTGATGCACGA 3’​​​​​​​- old strand

3’ TCGGCACTACGTGCT 5’- new strand

39 hydrogen bonds are formed.

According to Complementary base pairing , the phenomenon where in DNA guanine always hydrogen bonds to cytosine and adenine always binds to thymine. The bond between guanine and cytosine shares three hydrogen bonds compared to the A-T bond which always shares two hydrogen bonds.

So, in given strand we have 6 pairs of AT and 9 pairs of GC

1 AT pair = two hydrogen bonds. 6 AT pairs = 12 hydrogen bonds.

1 GC pair= three hydrogen bonds, 9 GC pairs = 27 hydrogen bonds

Total is 39