Conserved sequences in genes – Database activity
IB learner profile: Thinker ATL: Thinking skills – Experimenting with
new strategies for learning
Time: 30 minutes Formative Inquiry
Task instructions:
Work in pairs and follow the task instructions carefully.
Answer the questions on a separate document that you both submit on MB.
Background information:
Clustal Omega is a free online tool designed to facilitate the comparison of nucleotide and amino
acid sequences. It offers the ability to compare multiple sequences simultaneously, allowing for
the construction of multiple alignments.
Important terms:
• Conserved gene sequences:
Gene sequences that remain identical or similar across a species or group of species,
• Highly conserved sequences
Gene sequences that remain similar over long periods of evolution
• Gene sequence homology
Species with close evolutionary relationships usually share a high degree of gene
sequence.
Two possible hypotheses for Evolution:
1. The gene sequences are functional constraints. Functional constraints refer to the
selective pressures that prevent the accumulation of mutations that disrupt the function
of a gene or its products. Mutations that alter the structure or function of a protein can
have detrimental effects, particularly if the protein is involved in essential cellular
processes. As a result, these mutations are less likely to persist in a population over time.
2. Slower rates of mutation suggest that natural selection pushes mutation rates down to a
lower limit set by the power of random genetic drift rather than by intrinsic physiological
limitations. This results in reduced levels of replication, transcription, and translation.
The CHRNE gene is responsible for encoding the cholinergic receptor epsilon, a crucial protein
involved in transmitting signals within the nervous system. The ability to compare these nucleotide
sequences from different organisms aids in understanding the genetic variations and similarities
across different species.
(Adapted from Kognity, 2023)
You will need the following links:
- File with gene sequences
https://old-ib.bioninja.com.au/standard-level/topic-3-genetics/31-genes/sequences.txt
- Clustal Omega website
https://www.ebi.ac.uk/jdispatcher/msa/clustalo
- How to read the results
https://www.labxchange.org/library/items/lb:LabXchange:5b84cc84:html:1
Steps:
- Open the file with the gene sequence and the Clustal Omega website.
- Make sure that you are open in the “Input form tab”.
- Change the input sequence type to DNA (You can change it later to protein)
- Paste the CHRNE sequences in the space provided. You have to copy more than one
sequence e.g. human and chimpanzee, or all of them. It is easier to start with two so that
you can see how the website works.
- Make sure that the species name is preceded by a forward arrow (e.g. '>Human’). You can
copy it as is from a file with gene sequences.
- Once you have added all sequences, scroll down and click ‘Submit’.
- Analyse the sequence alignment by observing where the nucleotides are the same between
species and where they are different.
Questions:
1. How does Clustal Omega help in identifying similarities and differences between DNA
sequences?
2. What can multiple sequence alignments reveal about the genetic variations among different
species?
3. What are conserved regions in DNA sequences and why are they important?
4. How can the comparison of DNA sequences be using Clustal Omega aid in understanding
evolutionary relationships?
5. Can you identify any functional domains within the CHRNE gene using the sequence
alignment results from Clustal Omega?
6. What are some potential applications of Clustal Omega and DNA sequence comparison in
the field of molecular biology and bioinformatics?
