Biochemical Pathways – The Highways To Life

By A.K. Matai

Biochemical pathways are straightforward. A gene is transcribed and translated into a protein that plays a catalytic role in a biochemical pathway. There are a few variations on the traditional biochemical pathway which are outlined below.

Biochemical Pathways - Highway To Life 3.png

There are usually two types of questions you can encounter when working with the concept of biochemical pathways in a genetics context. In this post, I will work through a sample question for each type question and hopefully clarify the concept of Biochemical pathways.

Biochemical Pathway to Experiment Sample Problem

You have isolated five E.coli mutant strains that are unable to synthesize an essential compound, Adamantine. To determine the biochemical pathway that synthesizes Adamantine, you tested each of the five mutant lines for their ability to grow on minimal media (MM) and minimal media supplemented with compounds Travertine, Peperino, and Adamantine of which compounds Travertine and Peperino are suspected to be in the pathway. The results of growth (+) or no growth (-) are summarized below.

Strain MM MM+ Travertine MM+ Peperino MM+ Adamantine
Mutant 1 + +
Mutant 2 +
Mutant 3 + + +
Mutant 4 +
Mutant 5 + +

Draw a biochemical pathway consistent with these results and indicate the location at which each mutation blocks the pathway.

STEP 1

First, I would rearrange the table so that you get a nice diagonal pattern of + signs as shown below by the red line.

Strain MM MM+ Travertine MM+ Peperino MM+ Adamantine
Mutant 3 + + +
Mutant 5 + +
Mutant 1 + +
Mutant 2 +
Mutant 4 +

STEP 2 

After rearranging the table, a pattern emerges. Any mutant that can survive on MM+ Travertine can also survive on MM+Peperino and MM+Adamantine. This suggests that Travertine is upstream of Peperino and Adamantine. It is further reinforced when a mutant that can survive on MM+Peperino can also survive on MM+Adamantine suggesting that Peperino is downstream of Travertine and upstream of Adamantine.

As for determining where each mutant is blocked in this pathway, one must systemically go through each mutant in the rearranged table.

  • Mutant 3 can survive on MM supplemented with Travertine, Peperino and Adamantine meaning that the mutation is upstream of Travertine in the biochemical pathway.
  • Mutant 5 can survive on MM supplemented with Peperino and Adamantine meaning that the mutation is upstream of Peperino in the biochemical pathway.
  • Mutant 1 can survive on MM supplemented with Peperino and Adamantine meaning that the mutation is upstream of Peperino in the biochemical pathway.
  • Mutant 2 can survive on MM supplemented with Adamantine meaning that the mutation is upstream of Adamantine in the biochemical pathway.
  • Mutant 4 can survive on MM supplemented with Adamantine meaning that the mutation is upstream of Adamantine in the biochemical pathway.

STEP 3

Lastly, use all of these observations to construct a valid biochemical pathway.

Biochemical Pathways - Highway To Life 1.png

Experiment to Biochemical Pathway Sample Problem

You are studying amino acid synthesis in S. cerevisiae. Here is a simplified pathway showing the three enzymatic steps that you are interested in. 

Biochemical Pathways - Highway To Life 3.jpg

You have just isolated a new mutant strain and want to know if it has a mutation in gene1 or gene2 or gene3 (these are the only possibilities). Design a biochemical pathway experiment to find out. All you have to work with is your strain, a wild type strain, and any media plate you want. Show the results you would get if the new mutation turned out to be in gene2.

STEP 1 

  • Make a note of all of the key points required to solve this problem. First, yeast requires Serine (Ser), Glycine (Gly) and Cysteine (Cys) to survive. If any of these essential amino acids are missing, yeast will not grow. And secondly, each experiment requires a positive and negative control.

STEP 2 

Construct a table of expected results.

MM MM+Ser MM+ Gly MM+Cys CM
WT Strain + + + + +
Mutant Strain + +

Note: CM refers to complete media which contains all the things required for the survival of a yeast strain. The mutant strain has a mutation in gene 2 and can’t make Glycine. Therefore, it won’t be able to survive on any media that doesn’t contain Glycine.

Questions, Comments or Concerns?

Feel free to post a your questions, comments or concerns down below!

References

Locke, John; Deyholos, Michael; Harrington, Michael; Canham, Lindsay; Kang, Min, “Open Genetics Lectures (OGL) Fall 2016”

Unknown. Highway Speed Car Motion Lights. 2011. https://pixabay.com/en/highway-speed-car-motion-lights-821487/. Web. 19 Mar. 2017.

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s