91

Task 7.12

What are “moonlighting” enzymes? Find an example.

Task 7.13

Higher sensitivity of metabolic regulation due to simultaneous outward and reverse

reaction:

(a) Consider for which biochemical processes it can actually make sense what is con­

stantly going on in the cell (in the “bubbling soup”), namely that outward and

reverse reactions can take place simultaneously.

(b) Carry out a calculation example for this.

Useful Tools and Web Links

PDB

https://www.rcsb.org/pdb/home/home.do

RNAAnalyzer

https://rnaanalyzer.bioapps.biozentrum.uni-­wuerzburg.de/

Functional Glycomics

https://www.functionalglycomics.org/; https://ncfg.hms.harvard.

edu/

ENCODE

https://www.encodeproject.org (see Diehl and Boyle 2016).

• This is an important link to the human genetic code, namely the famous “Encyclopedia of

DNA Elements” of the human genome, which you can both look up and analyze here. There

is also much original literature describing it.

OMIM: https://www.omim.org

• “Online Mendelian Inheritance in Man” makes it very clear how a wrong letter (a genetic

mutation) leads to disease.

Lipid-Pro: https://www.neurogenetics.biozentrum.uni-­wuerzburg.de/services/lipidpro/

• This is the software we developed that helps classify lipids and decode their code.

Bionumbers: https://bionumbers.hms.harvard.edu

• Here, the number codes that play a role in numerous biological processes are explained

nicely and engagingly (Milo et al. 2010).

Literature

Ahmed Z, Mayr M, Zeeshan S et al (2015) Lipid-Pro: a computational lipid identification solution

for untargeted lipidomics on data-independent acquisition tandem mass spectrometry platforms.

Bioinformatics 31(7):1150–1153. https://doi.org/10.1093/bioinformatics/btu796. (* This is soft­

ware we developed that helps classify lipids and decode their code.)

AlQuraishi M (2019) End-to-end differentiable learning of protein structure. Cell Syst. 8(4):292–301.

e3. https://doi.org/10.1016/j.cels.2019.03.006

Diehl AG, Boyle AP (2016) Deciphering ENCODE.  Trends Genet 32(4):238–249. https://doi.

org/10.1016/j.tig.2016.02.002. (Review. PubMed PMID: 26962025 * A very nice overview of

the results of ENCODE.)

7.5  Literature