Retrieval activity

DNA/RNA revision
sheet
DNA sequencing

Process of determining the precise order of nucleotides

within a DNA molecule.

DNA contains genes, this ‘coding DNA’

only forms a small part of an organisms
DNA (1.5% in humans)

Non coding DNA (junk DNA), this DNA

will often carry out regulatory functions
Genomics is the study of genomes. It uses DNA
sequencing methods and computational Biology to
analyse the structure and function of genomes.

Comparing genes and regulatory sequences of

different organisms will help us to understand the
role of genetic information in a range of areas
including health, behaviour and evolutionary
relationships between organisms.
Automated DNA sequencing

Based on interrupted PCR and electrophoresis.

PCR is initiated but some of the free nucleotides carry

a fluorescent marker. These ‘throw’ off DNA
polymerase, so replication of the chain stops.

Each nucleotide type has a different coloured

fluorescent marker.

The fragments produced by PCR vary in length with

each end nucleotide being tagged with a specific
colour.

These strands run through a machine (like they do in

electrophoresis) and the colour sequence is read by a
laser.
Stages

1. Genome is mapped
2. Samples of genome are sheared into smaller
sections.

3. These sections are placed into separate

bacterial artificial chromosomes (BACs) and
transferred to E.coli. The cells
grow/reproduce to form clones. Called Clone
libraries.
Sequencing a BAC section using overlapping fragment
analysis

Using an
automated
process
Initially the process was carried out manually so was time
consuming. DNA sequencing was originally carried out on
organisms with short sequences of bases (viruses and
bacteria).
 Computational Biology and Bioinformatics

Builds theoretical models of

biology systems using the Development of the
software and computing software and
tools developed computing tools to
process the data
recorded
Human Genome Project

Started in 1990 an international project between scientists from

a number of countries working together to map the entire
human genome. The data was freely available to scientists all
over the world.

The aim was to complete it in 15 years but due to automated

sequencing and more powerful faster computers, the first
complete sequence was published in 2003.

2 years early and under budget!!!

Next – generation sequencing

Technology developments have led to new automated, high-

throughput sequencing process.

Sequencing reactions now occur on a plastic slide (flow cell)

instead of using gel. Millions of pieces of DNA are attached to
the slide and replicated in situ using PCR. The clusters of DNA
are sequenced and imaged at the same time, sometimes called
‘massively parallel sequencing’.

High-throughput methods can sequence the 3 billion base pairs

of human genomes in days, its also cheaper.
Comparing genomes

A wide variety of organism genomes have been sequenced already.

Applications

1. Identify genes for proteins found in all/many organisms.

2. Identify evolutionary relationships.
3. Modelling the effects of changes to DNA/genes.
4. Comparing genomes from pathogenic and similar but non
pathogenic organisms. Can be used to develop new
drugs/treatments/vaccines.
5. DNA of individuals can be analysed to identify mutant alleles or
alleles that increase risk of certain disease e.g. heart disease,
cancer.
Homework/ groups work in class

Using the specification points below, give examples for each

application of gene sequencing.

Learners should be able to demonstrate and apply their

knowledge and understanding of:

(i) how gene sequencing has allowed for genome-wide

comparisons between individuals and between species
(ii) how gene sequencing has allowed for the sequences of amino
acids in polypeptides to be predicted
(iii) how gene sequencing has allowed for the development of
synthetic biology
View this only after homework completed

(i) how gene sequencing has allowed for genome-wide

comparisons between individuals and between species

1. Analysing the human genome

Genomes analysed and compared to identify patterns in the

DNA we inherit and diseases to which we are vulnerable.

Implications in health management and medicine

2. Analysing the genomes of pathogens.

• Enables doctors to identify antibiotic resistant strains – so

only effective antibiotics can be used.
• Enable doctors to find the source of infection eg bird flu or
MRSA
• Track the progress of an outbreak eg Ebola virus
• Identify markers for vaccines.

3. Identifying species – Aids classification and evolutionary

relationships.
(ii) how gene sequencing has allowed for the sequences of amino
acids in polypeptides to be predicted

Proteomics – the study and amino acid sequencing of an

organisms proteins.

It is not as simple as one gene codes for one protein. Scientific

evidence is emerging that suggests the relationship between
genotype and phenotype is complex.

Some genes code for many different proteins, environment

influences gene expression…
 mRNA transcribed from DNA contains exons and introns, this is
modified before translation occurs at the ribosome

The process is aided by spliceosomes, which are small RNA molecules that
recognize the beginning of introns (usually GU) and the end (usually AG) and
catalyze splicing at these sites. 
Sometimes exons may also be removed – creating a different
protein from the same gene.

Exons may be joined in a variety of ways, creating different

functional mRNAs, which would translate into different proteins.
Therefore one gene may account for several different phenotypes
(iii) how gene sequencing has allowed for the development of
synthetic biology

Definition – An emerging area of research that can broadly be

described as the design and construction of novel artificial
biological pathways, organisms or devices or the redesign of
existing natural biological systems.
Examples of Synthetic biology

• Genetic engineering – changing a biological pathway or

genetic modification of an organism
• Using biological systems in industry eg fixed or immobilised
enzymes, microorganisms producing drugs.
• Gene therapy. New gene to replace faulty gene (used in cystic
fibrosis treatment)
• Synthesis of an entire new organism. In 2010, scientists
announced they produced an artificial genome for a bacterium
and successfully replaced the original genome with this new,
functioning genome.