This is the home page for the Principles of cellular metabolism PhD course at KI September 2021.
Schedule and location
The course will run half-time over two weeks. The intention is to have a slower pace so as to give a bit more time to absorb new concepts and also allow time to maintain ongoing experiments, etc during the course. There will be 6 sessions in total (1 introduction).
All seminars this year are at Wiederströmska huset, Tomtebodavägen 18a, Karolinska Campus Solna. See this map.
The course is organized around a series of video lectures that highlight important principles and key metabolic pathways. Besides the video lectures, there is required reading. Below, I indicate sections of Stryer’s Biochemistry which is available online, but any major biochemistry textbook (Lehninger / Voet / Devlin) can be used. Details on the enzymatic mechanisms involved can be skipped. Cell Biology by the Numbers by Ron Milo is fantastic for a quantitative understanding of cell biology, and also has some content online.
Material marked further reading is not mandatory, but recommended for those that want to go deeper into specific topics. In the seminars we will also look at some recent examples from the literature.
All video lectures are freely accessible on YouTube.
Further reading: Almaas et al on the “high flux backbone” of metabolism, another high-level model related to the “bow tie” organization.
Rolfe & Brown 1997 for an in-depth discussion of energy-producing and consuming processes in cells (very long article, skip the details.) Cell biology by the numbers online sections: cell size, elemental composition and metabolite turnover.
Stryer (6th ed) ch 15.3, or Stryer online section 14.2.
Further reading: Hanson 1990 on oxidation numbers.
Orth et al 2010 for an introduction to flux balance analysis.
Buescher et al, 2015 for an overview of isotope tracing and flux analysis methods.
Further reading: Fan et al 2014 shows an example where isotopic labeling of a product does not imply a net flux.
Further reading: Goodman et al 2018 provides an up-to-date account of NAD(P) compartmentalization in the liver
Further reading: Park et al 2016 combine absolute concentration and isotope tracing data with thermodynamic laws to estimate metabolic fluxes.
Further reading: Sullivan et al 2015 reports an unexpected role for aspartate in hypoxic cells.
Note: in august 2018, the enzyme commission introduced a seventh class (EC 7) for translocases. For now we use the old EC—EC6 system in the seminar, but we will discuss this change.
Further reading: Wolfson & Sabatini 2017 reviews the sensing mechanisms that help cells respond to amino acid deprivation.
Liu & Locasale 2017 for a recent overview of metabolomics methods.
Ducker & Rabinowitz 2017 provides an in-depth review of one-carbon metabolism in humans.
Further reading: Cantor et al 2017 describe effects of studying metabolism in a growth medium more similar to human plasma.
Stryer (6th ed) Ch 27.2 or Stryer online section 30.2
Databases and websites
MetaCyc database (free with registration)
The eQuilibrator tool for Gibb’s energy calculations
Problem collections for seminars
Problem collections are being updated, and will be handed out at each seminar. I will post each collection here after the seminar.
Excel data file for T-cell gene expression