DNA Sequencing and the Uses of DNA Sequencing

Question 1

What does DNA sequencing allow?

Answer 1

It allows the nucleotide base sequence of an organism’s genetic material to be identified.

Question 2

What is Sanger Sequencing?

Answer 2

A chain termination method of sequencing that was developed by Frederick Sanger and his colleagues that uses modified nucleotides; dideoxynucleotides.

Question 3

What has also been developed due to advances in technology? Allow?

Answer 3

High-throughput sequencing methods that allow scientists to rapidly sequence the genome of organisms.

Question 4

How does dideoxynucleotides in modified nucleotides differ from deoxynucleotides in DNA?

Answer 4

They both have slightly different structures to one another.

Question 5

How does sanger sequencing work in summary?

Answer 5

The dideoxynucleotides pair with complementaty base nucleotides on the template strand in DNA replication. When DNA polymerase comes across these on the developing strand, it stops replicating, hence the name, producing a shortened DNA strand.

Question 6

What is the method for Sanger Sequencing?

Answer 6

1. 4 test tubes are prepared that contain the DNA to be sequenced, DNA polymerase, primers, free nucleotides and dideoxynucleotides.
2. Test tubes are incubated at a temperature that allows DNA polymerase to function. Primer anneals to the start of the single stranded template, producing a short section of double stranded DNA at the start of a sequence.
3. DNA polymerase attaches to this double stranded section and begins doubling the DNA using free nucleotides in the test tube, forming H2 bonds between the bases on the nucleotides.
4. At any time, DNA polymerase can insert dideoxynucletides to terminate the doubling of DNA. For example if a test tube has ‘A’ dideoxynucleotide, the final nucelotide of every chain is A, so vary in lengths.
5. Once incubation stops, the complementary DNA chains are separated from the template DNA.
6. The resulting single stranded DNA chains are separated according to length using gel electrophoresis. If the furthest band on the gel comes from ‘C’ then the first base is C, the next furthest band in the ‘T’ well then the 2nd base is T.

Question 7

What is bioinformatics?

Answer 7

The development of the software and computing tools needed to organise/analyse raw biological data.

Question 8

What do bioinformatics generate data on?

Answer 8

DNA sequences, RNA sequences, and protein sequences, as well as on the relationship between genotype and phenotype.

Question 9

What is the process of using bioinformatics to analyse raw biological data?

Answer 9

1. High-power computers are required to create databases.
2. The databases contain information about an organism’s gene sequences and amino acid/protein sequences.
3. Once a genome is sequenced, bioinformatics allow scientists to make comparisons with the genomes of other organisms using the many databases available.
4. This can help to find the degree of similarity between organisms which then gives and indication of how closely related the organisms are.

Question 10

What has bioinformatics contributed to the studies of?

Answer 10

• Genetic variation.
• Evolutionary relationships.
• Genotype-phenotype relationships.
• Epidemiology.

Question 11

How has gene sequencing allowed for the sequences of amino acids in polypeptides to be predicted?

Answer 11

1. The genetic code can be used to predict the amino acid sequence within a protein.
2. Once scientists know the amino acid sequence they can predict how the new protein will fold into its tertiary structure.
3. This information can be used for a range of applications, such as in synthetic biology.

Question 12

How can genetic variation be investigated using DNA sequencing?

Answer 12

1. Many individuals of the same species have their genomes sequenced and compared.
2. A species that has a high level of genetic variation will exhibit a large number of differences in base sequences between individuals.

Question 13

How can evolutionary relationships be investigated using DNA sequencing? Example?

Answer 13

1. It can be investigated by comparing the genomes of different species.
2. Species with a small number of differences between their genomes are likely to share a more recent common ancestor than species with a large number of differences.
   - E.g. The protein cytochrome c is involved in respiration, and so is found in a large number of species. For this reason it is especially useful for making comparisons between different species.

Question 14

How can genotype-phenotype relationships be investigated using DNA sequencing?

Answer 14

1. Genotype-phenotype relationships are explored by stopping the expression of different genes and observing the effect it has on the phenotype of an organism.
2. When an organism’s genome sequence is known, scientists can target specific base sequences to knock out/stop the expression of.

Question 15

How can epidemiology be investigated using DNA sequencing?

Answer 15

1. Epidemiologists study the spread of infectious disease within populations.
2. The genomes of pathogens can be sequenced and analysed to aid research and disease control.
   - Highly infectious strains can be identified.
   - The ability of a pathogen to infect multiple species can be investigated.
   - The most appropriate control measures can be implemented based on the data provided.
   - Potential antigens for use in vaccine production can be identified.

Question 16

How do scientists analyse the human genome?

Answer 16

1. A genome project works by collecting DNA samples from many individuals of a species.
2. These DNA samples are then sequenced and compared to create a reference genome.
3. More than one individual is used to create the reference genome as one organism may have anomalies/mutations in its DNA sequence that are atypical of the species.

Question 17

What is the Human Genome Project?

Answer 17

The Human Genome Project is an international, collaborative research programme where DNA samples were taken from multiple people around the world, sequenced, and used to create a reference genome.
Laboratories around the globe were responsible for sequencing different sections of specific chromosomes. It was decided that the data created from the project would be made publicly available. As a result, the data can be shared rapidly between researchers. The information discovered could also be used by any researcher and so maximised for human benefit.

Question 18

What is synthetic biology?

Answer 18

Synthetic biology is a recent area of research that aims to create new biological parts, devices, and systems, or to redesign systems that already exist in nature.

Question 19

What are 4 different techniques that synthetic biology uses?

Answer 19

1. Genetic engineering: a single change in a biological pathway or genetic modification of an entire organism.
2. Use of biological systems or parts of biological systems in industrial contexts, e.g. the production of drugs from microorganisms.
3. The synthesis of new genes to replace faulty genes, e.g. cystic fibrosis faulty genes are looking at being replaced by functional genes synthesised in a laboratory.
4. The synthesis of an entire new organism

Question 20

What is a proteome?

Answer 20

A set of proteins produced in an organism, system, or biological context.

Question 21

What is proteonomics?

Answer 21

The study and amino acid sequencing of an organism’s entire protein complement.

Question 22

In what 2 ways is the proteome larger than the genome?

Answer 22

1. Alternative splicing.
2. Protein modification.

Question 23

How is alternative splicing done in genomics and proteomics?

Answer 23

1. ‘Pre-mRNA’ is modified whereby the introns are removed and some extrons may be removed as well.
2. The exons to be translated are joined together by enzyme complexes known as splicesomes to give the mature functional mRNA.
3. The splicesomes may join the same exons in a variety of ways, so a single gene may produce several versions of functional mRNA, which in turn would code for different arrangements of amino acids, giving different proteins and resulting in different phenotypes.

Question 24

How is protein modification done in genomics and proteomics?

Answer 24

1. Some proteins are modified by other proteins after they are synthesised.
2. A protein that is coded for by a gene may remain intact or it may be shortened or lengthened to give a variety of other proteins.