DNA structure and replication

Question 1

What are the role of nucleotides?

Answer 1

Nucleotides are monomers of nucleic acids, like DNA, RNA and ATP.
Phosphorylated nucleotides, like ADP and ATP, are used in energy-requiring metabolic processes.
They can be components of many coenzymes.

Question 2

What are the three components of nucleotides (DNA or RNA)?

Answer 2

Pentose sugar, nitrogenous base and phosphate group.

Question 3

Describe what bonds are found in a nucleotide and where they are found.
How do these bonds form?

Answer 3

On carbon 1 of the pentose sugar, there is a glycosidic bond between the pentose sugar and nitrogenous base. On either carbon 3 or carbon 5 of the pentose sugar, there is a phosphodiester bond between the pentose sugar and phosphate group.
These bonds form through condensation reactions.

Question 4

How does a nucleotide of DNA and RNA differ from each other?

Answer 4

DNA contains pentose sugar, deoxyribose, whereas, RNA contains pentose sugar ribose. DNA has nitrogenous bases A, T, C, G. In RNA, instead of thymine, we have uracil.

Question 5

In nucleotides of DNA, there are 4 types. How do these 4 nucleotides differ from each other?

Answer 5

Each nucleotide has a different nitrogenous base. The 4 types of nitrogenous bases are thymine, guanine, cytosine and adenine.

Question 6

What does it mean if the bases are purine?
What does it mean if the bases are pyrimidine?

Answer 6

Purine bases refer to adenine and guanine as they have 2 carbon rings in their structure.
Pyrimidine refers to cytosine and thymine as they have 1 carbon ring in their structure.

Question 7

DNA is made from 2 polynucleotide strands. How are they joined together?
Why are the strands described as ‘antiparallel’?

Answer 7

The polynucleotide strands are joined together is joined together between hydrogen bonding between nitrogenous bases. Between adenine and thymine, 2 hydrogen bonds form. Between cytosine and guanine, 3 hydrogen bonds form.
The strands are described as ‘antiparallel’ as the strands run in opposite directions.

Question 8

Why is DNA described as having a sugar-phosphate backbone?

Answer 8

It is described as this as the deoxyribose sugar and phosphate is found on the exterior of the DNA molecule- the backbone. Whereas the nitrogenous bases are found in the middle.

Question 9

How is DNA found in eukaryotic cells?
How is DNA found in prokaryotic cells?

Answer 9

In eukaryotic cells, DNA exists in a nucleus. Each large molecule of DNA is wound around histone proteins, to form chromosomes- hence, each chromosome is one molecule of DNA. DNA also found in mitochondria and chloroplasts.
In prokaryotic cells, DNA is freely lying in the cytoplasm. It is not wound around any histone proteins, and hence described as being ‘naked’.

Question 10

How are RNA molecules different to DNA molecules?

Answer 10

RNA has a ribose sugar; DNA has a deoxyribose sugar.
RNA has nitrogenous base uracil (instead of thymine); DNA has thymine.
RNA is single stranded; DNA is double stranded.
RNA molecule is shorter; DNA is longer.

Question 11

Why is genetic code described as ‘near universal’?

Answer 11

In nearly all living organisms, the same triplet of bases (codon) codes for the same amino acid.
Also genetic code is not overlapping.

Question 12

Why is genetic code described as degenerate? Why is this beneficial?

Answer 12

For almost all amino acids (except methionine and tryptophan), different combination of bases can still code for the same amino acid. In the case of a mutation of base, there is a chance that a change in base can still code for the same amino acid, and hence, has no effect.
Also genetic code is not overlapping.

Question 13

Why is DNA replication described as semi-conservative?

Answer 13

In each of the two daughter DNA molecules synthesised, one strand comes from the parent molecule and one is a newly synthesised strand, hence semi-conservative.

Question 14

What does it mean if DNA is ant-parallel?

Answer 14

One strand of DNA runs in the 5’ to 3’ direction and one strand runs in the 3’ to 5’ direction (basically they run in opposite direction). The number refer to the number of carbon on the deoxyribose sugar.

Question 15

During replication, nucleotides are being added to the synthesised DNA strand. What are the initial structure of these nucleotides?

Answer 15

The nucleotides initially has a deoxyribonucleic triphosphate structure. This means it contains a deoxyribose sugar, a nitrogenous base and 3 phosphate groups.

The hydrolysis of the deoxyribonucleotide triphosphate into a deoxyribonucleotide phosphate and a diphosphate, provides energy for DNA polymerase to form a phosphodiester bond between the deoxyribose sugar of one nucleotide and a phosphate group of another nucleotide.

Question 16

In what direction does DNA polymerase work, and how does it work?

Answer 16

DNA polymerase works in a 5’ to 3’ direction.
It works by forming a phosphodiester bond between the hydroxyl group (on carbon 3) of the last nucleotide in the chain and the phosphate group of the next nucleotide to be added (which is attached to carbon 5).

Question 17

What is the Origin of Replication?

Answer 17

The origin of replication is the area along the DNA strand where replication is initiated.

Question 18

What is the difference between eukaryotic and prokaryotic cells, in terms of the Origin of Replication?

Answer 18

In prokaryotic cells, there is only one Origin of replication in the DNA strand.

In eukaryotic cells, there are thousands of Origins of replication in the DNA strand.

Question 19

When looking at DNA strands in a micrograph, how do you know where the Origin of replication is?

Answer 19

In a micrograph, there will be bubbles along the DNA strand. These bubbles are the Origin of Replication.

Question 20

When looking at the Origin of replication, we can say replication can be bi-directional. What does this mean?

Answer 20

It means that from the Origin of replication, DNA replication can occur in either direction.

Question 21

What are the rules for DNA Polymerase to function?

Answer 21

1. DNA needs to be in a single-stranded state.
2. The enzyme will add nucleotides to an existing chain (RNA primers?).
3. The enzyme only functions in a 5’ to 3’ direction.

Question 22

What are RNA primers?

Answer 22

RNA primers are small strands of RNA nucleotides, that are bound and complementary to a short length along the DNA strand.

The presence of RNA primers along the DNA strand gives the DNA polymerase a starting point for replication, as they cannot start synthesising from scratch.

RNA primers are useful in this way and especially useful when synthesising the lagging strand, where it jump ahead and start synthesising an entirely new fragment. The many RNA primers along this strand provides DNA polymerase with a hydroxyl group to for phosphodiester bonds.

Question 23

What enzyme synthesises RNA primers?

Answer 23

Primase synthesises RNA primers.

Question 24

Why do RNA primers need to be taken out of the replicated DNA?

Answer 24

After replication, RNA primers needs to be taken out because RNA primers are not in the form of DNA.
One, RNA has a ribose sugar rather than a deoxyribose sugar. Two, RNA has a uracil base instead of thymine.
These changes in the DNA structure can affect the DNA’s structure as some enzymes won’t be able to read the DNA during future processes of DNA replication and transcription.
Instead, the RNA primers are taken out and replaced with DNA nucleotides.

Question 25

After RNA primers are taken out, what enzyme forms phosphodiester bonds between the new DNA nucleotides (that replaced RNA primers) and other fragments of replicated DNA?

Answer 25

The ligase enzyme.

Question 26

The function of DNA polymerase is so that it works in a 5’ to 3’ direction. How is it limited to its function in the fact that the DNA strands are anti-parallel?

Answer 26

Firstly, it is the 5’ to 3’ direction that DNA polymerase works in; the 5’ to 3’ direction is not referring to the direction that the template DNA is running in.
As DNA is anti-parallel, then if the direction of one of the template strands is 3’ to 5’, then the strand being synthesised should be 5’ to 3’ (which supports the fact that DNA is anti-parallel). In the synthesis of this strand, DNA polymerase will work smoothly and create a non-fragmented strand; this is called the leading strand.
If the template strand above is 3’ to 5’, then the other template strand of the DNA molecule must be 5’ to 3’. Hence the DNA strand being synthesised for this template strand must be 3’ to 5’. This is where DNA polymerase is LIMITED because it cannot work in this direction.
To compensate for this, DNA polymerase undergoes a backstitching mechanism. This is where DNA polymerase works away from the unwinding of the DNA so it works in the 5’ to 3’ direction, and then jumping ahead in the strand to replicate the next part of the DNA; this is called the lagging strand.

Question 27

What is the difference between the lagging and leading strand?

Answer 27

The leading strand is the strand that was synthesised in the 5’ to 3’ direction, and is one continues strand with no fragments.
The lagging strand is the 3’ to 5’ strand (also synthesised in the 5’ to 3’ direction because DNA polymerase only works in this direction) that was synthesised into fragments, then glued together with the ligase to make a complete strand.

Question 28

What is the Okazaki fragments?

Answer 28

The Okazaki fragments are the fragments synthesised in the lagging strand of the replicated DNA.

Question 29

What enzyme joins gaps in the DNA backbone?

Answer 29

DNA ligase.

Question 30

What are some enzyme responsible in the DNA replication process in prokaryotes?

Answer 30

In prokaryotes, DNA polymerase III is responsible for replication.
Additionally, DNA polymerase I is responsible for repair and removing primers.

Question 31

Name some DNA polymerases responsible for chromosome replication, that are found in eukaryotes.

Answer 31

DNA polymerase alpha and delta.

Question 32

By what process does prokaryotic cells divide?

Answer 32

Binary fission.

Question 33

What is the ‘end replication problem’?

Answer 33

The end replication problem refers to only the lagging strand. This problem talks about the last fragment of the lagging strand that needs to be synthesised.

To synthesise DNA strands, DNA polymerase uses hydroxyl group on carbon 3 (of the last nucleotide) in an RNA primer as a starting point to start synthesising DNA fragments. After this is done, the RNA primers are taken out, then the hydroxyl group on carbon 3 (of the last nucleotide) of the DNA fragments is used as a starting point to start adding DNA nucleotides.

The problem with the last synthesising the last fragment on the lagging strand, is that there is no RNA primer after that to act as a starting point. Even if there was an RNA primer, it would need to be later removed, however there would be no DNA fragment after that to act as a starting point for adding DNA fragments.

Question 34

What is a telomere?

Answer 34

A telomere is referring to the ends of chromosomes, which has a repeating sequence of nucleotides (just G and T bases?).

Question 35

What enzyme is responsible for resolving the ‘end-replication’ problem?

Answer 35

Telomerase.

Question 36

How does telomerase overcome this end-replication problem?

Answer 36

Telomerase is an enzyme that is able to recognise the tip of a telomere.
Telomerase uses a short template of an RNA strand it holds to elongate the DNA strand further, by using complementary bases to this RNA strand template.
DNA polymerase alpha then comes along to this strand. DNA polymerase alpha has DNA primase as one of its sub-units and is able to synthesise the RNA primer, by using the complementary strand (which is attached at the end of the DNA strand) that telomerase synthesised.
The RNA primer synthesised provides a hydroxyl group as a starting point for DNA polymerase alpha to synthesise the last fragment on a lagging strand.

Question 37

Briefly state the steps in DNA replication

Answer 37

1. DNA helicase unwinds and separates DNA strands, to give DNA in a single stranded form.
2. DNA polymerase starts synthesising the new strand, using RNA primers as a starting point.
3. The DNA is replicated, but then RNA primers are taken out and replaced with DNA nucleotides.
4. For the lagging strand, all fragments are glued together using the ligase enzyme, to form a whole strand.

Question 38

What is the function of DNA helicase?

Answer 38

DNA helicase unwinds the DNA strand, and separates it into two different strands, by breaking the hydrogen bonds.
ATP is needed helicase to move along the DNA molecule to break the hydrogen bonds.

Question 39

How does DNA structure remain stable while replication is happening (why is it not flowing around and sticking togther)?

Answer 39

Single stranded Binding proteins (formed by helicases?) binds to the DNA to straighten it out for replication to occur.

Question 40

How does DNA polymerase add new nucleotides to the synthesising strand?

Answer 40

By forming phosphodiester bonds, which occurs via a condensation reaction.

Question 41

How does DNA polymerase reduce the risk of mutations during DNA replication?

Answer 41

DNA polymerase is able to proof-read the DNA for any faulty nitrogenous bases.
If there were to be an error, DNA polymerase is inhibited from moving to the next nitrogenous base along the template DNA strand, so it gives an opportunity for correction of the base.

Question 42

How is DNA prevented from tangling and coiling during replication?

Answer 42

The enzyme topoisomerases prevents the DNA tangling and coiling during replication.
Type 1 topoisomerases prevents coiling in one DNA strand.
Type 2 topoisomerases prevents coiling in both DNA strands, and untangle DNA helices.