DNA Replication (DP IB Biology: HL)

Describe the structural features of a DNA molecule.

Describe the process of semi-conservative replication of DNA in eukaryotes. In your answer, include details of any molecules, bonds or enzymes involved.

The diagram below shows one cycle of the polymerase chain reaction (PCR). 

Outline the events that are taking place during stage 1 in the diagram.

Molecule X in the diagram shown in part (a) is a DNA primer.

State the role of a DNA primer in PCR.

Stage 3 in PCR involves an enzyme.

Explain how the enzyme is suitable for its role in PCR.

State two applications of PCR.

The diagram below illustrates a small section of a DNA molecule from the nucleus of a eukaryotic cell.

State the structures labelled X and Y.

A repetitive sequence of DNA occurs at the ends of eukaryotic chromosomes, called a telomere.

Explain the role of a telomere. 

Most of the DNA in an organism is contained within the nucleus. Some of this DNA is unique, whilst some is made up of highly repetitive sequences.

Contrast unique and highly repetitive sequences of DNA

DNA was originally thought of as a protein. In the 1950s, Alfred Hershey and Martha Chase showed that DNA is a factor of heredity responsible for carrying genetic information from one generation to another.

Describe their experiment.

The chain termination process can be used to identify the sequence of base pairs.

Use the image above to identify the order of bases, starting with the smallest, in the block of DNA labelled X, on the right.

Results from a paternity test using gel electrophoresis are shown in the image below. DNA was isolated from a mother, her child and two potential fathers. Primers designed to amplify different satellite DNA regions were used and amplified alleles are shown in the results below.

Use the gel electrophoresis DNA profiles in the image above to determine which male is the child's father.

The DNA fragments separated in the gel electrophoresis in part (c) vary in size from 100 bp (base pairs) up to 5 000 bp. DNA fragments of known size were used to create the plot shown in the graph below.

Use the line of best fit on the graph to determine the base pair length for DNA fragments that travelled 5 cm on the gel electrophoresis plate. Give answers to the nearest whole number.

Outline the steps of DNA replication at a replication fork, describing the role of each of the enzymes involved.

State two features that allow nucleic acids or proteins to be separated by gel electrophoresis.

During gel electrophoresis of a sample of DNA fragments,

(i) Identify which electrode the DNA would move towards. Justify your answer.

(ii) State which component of DNA gives it its charge.

State which class of enzymes can be used to cleave DNA into fragments prior to gel electrophoresis.

Restriction enzymes and gel electrophoresis can be used in genetic screening, to identify genes associated with a disease. The mutation of the Beta-globin gene which gives rise to sickle-cell anaemia removes a recognition site of the restriction enzyme DdeI as shown in the diagram below. The lengths of some fragments are shown in base pairs (bp).

(i) Deduce the size of fragment X. 

(ii) DdeI digested DNA from an individual who was a carrier for the sickle-cell beta-globin gene was analysed with gel electrophoresis as shown below. Draw and label the DNA fragments that would result from a normal individual.

Archaeologists in Pompeii recently discovered the remains of seven human skeletons within a house that was buried under volcanic ash when Mount Vesuvius erupted during ancient Roman times in 79 AD. Researchers were interested to know if the skeletons were from related individuals, they isolated DNA from the skeletons and used it in the Polymerase Chain Reaction (PCR).

PCR utilises multiple cycles of three simple steps, describe these steps and suggest why the researchers used PCR in their investigation.

DNA profiling was carried out on the PCR products to identify if the skeletons came from related individuals. The results are seen in the image below.

It was determined that the three children were siblings and shared the same biological parents. Their mother is Adult B.

(i) Predict which adult is the children’s father. Justify your answer.

(ii) Suggest why the profiles for Child 1 and Child 2 are the same.

Outline the method by which DNA profiling is undertaken and describe why it is a useful technique.

Explain why only bases that are complementary to the bases on the template strand can be added to the new DNA strand during DNA replication. 

Ultraviolet exposure can cause guanine to be oxidised to 8-oxyguanine, which is no longer complementary to cytosine. Instead, during replication, 8-oxyguanine can form bonds with adenine, resulting in a base pair.

Outline the possible consequences of this change.  

In the absence of mutagens, the rate of mutations during DNA replication is very low, approximately 160 bases per cell cycle.

Given that the human genome contains 3.2 billion base pairs, calculate the percentage copying error rate of each cell cycle. 

Discuss the formation of Okazaki fragments during the process of replication on the lagging strand of a DNA molecule.

A group of scientists studied the replication of DNA in Escherichia coli bacteria.

During their investigation, radioactive nucleotides were added to DNA that was actively replicating in a short pulse of about 5 seconds. This allowed the radioactive nucleotides to be incorporated into the new DNA strands. 

This was followed by a "chase" period, during which an abundance of unlabelled nucleotides was added to the DNA for different amounts of time, between 7 and 120 seconds. After the isolation and centrifugation of the DNA molecules, the results were obtained.

The graph below shows the results of their investigation.

Contrast the results obtained at a "chase" period of 7 seconds with those obtained at 120 seconds.

Explain the results obtained at a "chase" period of 60 seconds.

Suggest a possible explanation for the low number of small fragments present at 120 seconds.

Sketch a line on the graph of the predicted results that could be obtained at a "chase" period of 150 seconds.

One round of PCR takes approximately 75 seconds.

Calculate how many copies of DNA would be produced after a single fragment of DNA has been in the thermal cycler for 1.5 hours. Give your answer in standard form.

The diagram below shows the processes involved in the amplification of a sample of viral RNA.

Compare and contrast the process in the image with the process used in the amplification of a fragment of DNA.

The addition of RNAase enzyme occurs between stages 3 and 4 shown in the diagram from part a).

Suggest why this is a necessary part of the process.

Seven skeletons were discovered in a house in Pompeii, three of which were children. It is believed they were inhabitants and workers within the house when Mount Vesuvius erupted in 79 AD.

Researchers were able to isolate very small amounts of DNA from these skeletons. The DNA obtained was used in the polymerase chain reaction (PCR). Genetic fingerprinting was then carried out on this DNA to identify the skeletons.

The image below shows some of the results of the genetic fingerprinting of the three children and four adults.

Explain why the researchers used PCR in their investigation.

It was determined that the three children were siblings and shared the same biological parents. Their mother is Adult B.

Identify, with a reason, which of the other adults was the children’s father.

During PCR DNA is heated to 94 °C and DNA primers, nucleotides and thermostable enzymes are added to the mixture.

Explain the purpose of these steps.