Life on Mars

Student Notes

Life on Mars?!

Welcome to the MARSLANDER laboratory. Today you will to be analysing samples collected on Mars, looking for signs of life. We have been given samples from a number of Martian locations:

  1. A desert area in the northern hemisphere
  2. The foot of an extinct volcano in the southern hemisphere
  3. The floor of a large canyon system
  4. A rocky equatorial region
  5. The northern polar region.
  6. The southern polar region.

We will be looking for DNA (deoxyribonucleic acid), the chemical that carries the instructions for all life on Earth. Using a very powerful technique called PCR (polymerase chain reaction) it is possible to amplify short sections of DNA to detectable levels, using very small biological samples. Click here to see a short clip explaining how this done.

In addition to analysing the samples from Mars it is important to carry out control experiments. A ‘positive control’ PCR, using a sample we know contains DNA is used to check that the PCR is working. A ‘negative control’, without DNA, is carried out to check that samples have not been contaminated during PCR preparation. Positive controls can also be used to exclude so-called “false-positive” results.

Practical session – Laboratory

First you will practise using micro-pipettes and then you will run out the products of the PCR reactions on a gel over the course of this session, as described below.

Agarose Gel Electrophoresis for Size-Separation of DNA

In order to identify the different sizes of DNA you will need use a process called agarose gel electrophoresis. This process uses an electric current passed through a gel to separate DNA fragments by size. An agarose gel is made by heating powdered agarose (a seaweed extract) and a buffer solution. This produces a thick liquid which is poured into a sealed tray and allowed to set. The gel is then put into a buffer solution, and DNA samples are put into special holes called “wells” that have been created in the gel. An electric current is passed through the gel, and because the DNA fragments are negatively charged, they are drawn towards the positive electrode. The smaller the DNA fragment, the faster it travels along the gel. This results in DNA separation by size, with the smaller fragments migrating further than the larger fragments on the gel. DNA fragments can be visualised under UV lights.

You will be given your PCR products. There are 8 tubes (labelled 1- 8) and a

tube labelled “M”. Tube M is the DNA size marker which allows you to estimate the size of your bands.

Your demonstrator will give you some loading dye. We have to add this to the DNA samples in order to see where we are loading them on the gel, and the dye also makes the samples heavy so they will sink to the bottom of the wells of the gel.

Add 2µl of loading dye to each sample. Carefully mix the dye in the sample by pipetting up and down.

Load 10µl of each sample in order i.e. DNA Marker first, followed by tubes 1-8. Your demonstrator will show you how to load a sample on a gel. Once all the samples have been loaded your demonstrator will then plug the gel in and allow it to run.

Practical Session – Computer Section

Below is an example of samples that we have previously examined from Mars. What is your initial deduction from the results below?

  • DNA marker ladder (to estimate the size of the unknown samples)
  • negative control – to show that the PCR has worked without cross-contamination from other samples
  • positive control – human GAPDH gene. We use it to test that the PCR has worked properly and helps to show us that we have excluded human contamination in our samples
  • sample 1 - a desert area in the northern hemisphere
  • sample 2 - the foot of an extinct volcano in the southern hemisphere
  • sample 3 - the floor of a large canyon system
  • sample 4 - a rocky equatorial region
  • sample 5 - the northern polar region
  • sample 6 - the southern polar region

Analysing the PCR products

What can we do next with the samples? The next step is to try and identify in more detail what the samples may be. We have already analysed your PCR products by a process called “DNA sequencing” in order to deduce the order of the individual bases in the PCR product.

We sequenced the DNA band from samples 2 (foot of extinct volcano) and 4 (rocky equatorial region), and we have got the sequences on the computers for you to analyse.

You will need to look at the Word files containing the DNA sequences of your PCR products. For example, the sequence from Sample 4 is about 476 base pairs long and the translated protein sequence deduced from this DNA sequence, is shown on page 9.

We are going to compare the sequence we have identified by copying and pasting the sequence into a DNA sequence computer search engine called BLAST. The BLAST programme allows you to input a DNA sequence of interest and BLAST will identify regions of similarity between sequences that are stored on its DNA database. The program compares nucleotide (or protein) sequences to sequence databases and calculates the statistical significance of matches. The results of the search identifies genes that are found in organisms (e.g. human, mouse or bacterial), that are most closely matched to your sequence. It will give us a percentage identity, i.e. how many of the input sequence bases match bases from the gene in the matched organism.

Today we are going to BLAST our sequences from our PCR products and see if they resemble any life forms that we know about on earth. If we do get a match this could indicate that there is, or has been, life on Mars.

What do you need to do?

  1. Open the Word file named “DNA Sequence Samples”.
  2. Copy the DNA sequence “Sample 4”.
  3. Maximise the internet browser and go the following website:-

Choose the program called Nucleotide Blast, about half way down the page.

  1. Paste the sequence into the box which says “Enter query sequence”
  2. Scroll down the web page to where it says “Choose search set”. Here you can choose what database to search in. You can choose from the Human Genome, Mouse Genome or Others. Try the search with all three databases and see if any of them give you a match.
  3. Once you have chosen a search set, scroll down and click on the button that says BLAST. Now the database is performing the search of your sequence against all of the other sequences contained in the database.
  4. Scroll down the page once you have your results.

What areas of Mars did you amplify DNA from?

Did you get a BLAST match?

What organism did your sequence match against?

What was the DNA sequence identified similar to?

Can you tell how similar the sequence you pasted in is to the sequence it matches?

Repeat this with the DNA sequence “Sample 2”.

What can you conclude about your 2 sequences?

If your DNA sequence is part of a gene that codes for a protein then we can identify from the DNA sequence what the amino acid sequence is. Amino acids are the building blocks of proteins.

Your first DNA sequence that you looked at has been translated into an amino acid sequence and is written below. By looking at the amino acid sequence can you work out which amino acids are present from the 1-Letter codes? There are quite a lot of them!

ETSPSSIFTSASSAWASYSITSRMVMAILLVGSVLILVPPSARARRNMSLMTLSILCRSSRLETSISSSERS.RLELNASSVSPISVANGVLNSCARLALNWPSSGISTSFDRVTRTGQSRGEFLLQSPSLQAARQAAPETALRPGYSMHRSGPGP

Amino acid name 3-Letter code1-Letter code

Valine ValV

TYrosine TyrY

Tryptophan TrpW

Threonine ThrT

Serine SerS

Proline ProP

Phenylalanine PheF

Methionine MetM

Lysine LysK

Leucine LeuL

Isoleucine IleI

Histidine HisH

Glycine GlyG

Alanine AlaA

Glutamic Acid GluE

Glutamine GlnQ

Cysteine CysC

Aspartic Acid AspD

Asparagine AsnN

Arginine ArgR

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