Exercises: DNA Sequencing and Genome Databases

Define the terms genome and DNA sequencing.

In a DNA sequencing gel, fragments are separated by size.

1. a) State the technique used to separate the fragments.

1. b) State which fragments move furthest through the gel.

1. c) State how the fragments differ from each other.

Name two uses of publicly available genome databases.

In a sequencing reaction, a newly synthesised strand is built from a template. Fragments of the following lengths were found on a gel, each ending in a labelled terminating nucleotide:

• 1 nucleotide: T

• 2 nucleotides: A

• 3 nucleotides: G

• 4 nucleotides: G

• 5 nucleotides: C

• 6 nucleotides: A

1. a) Write the sequence of the newly synthesised strand in the order $5' \to 3'$.

1. b) Write the sequence of the template strand it was made from, in the order $3' \to 5'$.

1. c) Explain why the shortest fragment is read first.

A sequencing method uses template DNA, primer, DNA polymerase, free nucleotides and a small amount of modified nucleotides that stop chain elongation.

1. a) State the role of the primer.

1. b) Explain why the modified nucleotides produce fragments differing in length by one nucleotide.

1. c) Explain why the fragments need to be labelled in order to read the sequence.

A researcher at a university in Dublin compares the sequence of a gene from a patient with the reference sequence in a genome database:

• Reference: 5′-ATGGCCTTAAGC-3′

• Patient: 5′-ATGGCCATAAGC-3′

1. a) Identify the type of mutation and its position.

1. b) Explain how a database helps the researcher in this comparison.

1. c) State one way in which this type of mutation could have no effect on the protein.

Next-generation sequencing machines can sequence an entire human genome in a day, whereas the Human Genome Project took over a decade.

1. a) Explain why a sequenced genome alone does not tell us the function of every gene.

1. b) Discuss two benefits of the availability of sequence data in public databases to medicine.

1. c) Discuss one ethical or privacy concern arising from the sequencing of individuals' genomes.

The following fragments were read from a gel, from shortest to longest, with the terminating base for each: C, A, T, T, G, C, A, G.

1. a) Deduce the sequence of the new strand in the order $5' \to 3'$.

1. b) Deduce the complementary template sequence and state its polarity.

1. c) Explain what the result would show if the gel were run for too short a time, and how this would affect the reliability of the sequence.

Scientists compare the gene for cytochrome c in humans, chimpanzees and yeast stored in a genome database. The amino acid sequences of the encoded protein are identical (0 differences) in human and chimpanzee, although their DNA sequences differ at a few positions; between human and yeast, both the DNA and the amino acid sequences differ at many positions.

1. a) Interpret these results in terms of evolutionary relationships.

1. b) Explain why a protein-coding gene is a good marker for comparing species.

1. c) Explain why the amino acid sequences may be more similar between species than the DNA sequences, using the properties of the genetic code.