Principles of metabolism

This is the home page for the Principles of Metabolism PhD course at KI, march 2017.

Schedule and location

The course will run half-time over two weeks, March 20—31.  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).

Detailed schedule for the 2017 course.

All seminars are at Retzius väg 13, Karolinska Campus Solna. See this map.

Course materials

Video lectures

Video lectures (YouTube) and handouts (PDF) are available below.

Lecture 1, Introduction.  Video  PDF

Lecture 2, A cell’s material & energy budget.  Video  PDF
Further reading: Zu & Guppy 2004, Rolfe & Brown 1997

Lecture 3, Oxidation and reduction.  Video  PDF
Further reading: Hanson 1990

Lecture 4, Carbohydrates.  Video  PDF
Further reading: Bar-Even 2012 (challenging!), Westheimer 1987  (phosphates)

Lecture 5, Metabolic Networks and Fluxes.  Video  PDF

Lecture 6, Isotope tracing.  Video  PDF
Further reading: Buescher et al, 2015, Fan et al 2014.

Lecture 7, The TCA cycle.  Video  PDF
Further reading: Owen et al 2002.

Lecture 8. Cofactors and vitamins.  Video  PDF

Lecture 9. Energetics and enzyme catalysis.  Video  PDF

Lecture 10. Respiration and oxygen.  Video  PDF

Lecture 11. Enzyme classes.  Video  PDF

Lecture 12. Amino acids and nutrient starvation.  Video  PDF

Lecture 13. Measuring metabolism.  Video  PDF

Lecture 14. Fatty acids and sterols.  Video  PDF

Lecture 15. Nucleotides  Video  PDF

Lecture 16. One-carbon units and methylation.  Video  PDF

Lecture 17. Experimental considerations.  Video  PDF

Lecture 18. Compartmentalization and Transport.  Video  PDF

Lecture 19. Genomics.   Video   PDF

Databases and websites

HumanCyc database

Kyoto Encyclopedia of Genes and Genomes (KEGG)

BiGG model repository @ UCSD

Human Metabolome Database (HMDB)

BRENDA, the comprehensive enzyme information system

BioGPS gene expression portal

Problem collections for seminars

Seminar 1: Energy and material; oxidation and reduction; carbohydrates.  PDF

Seminar 2: Isotope tracing; The TCA cycle.  PDF

Seminar 3: Energetics, Respiration; Enzyme classes; Amino acids.  PDF

Seminar 4: Measuring metabolism; lipids; nucleotides.  PDF

Seminar 5: Compartmentalization and transport.  PDF

Flux balance analysis lab. PDF  Excel file.

Literature

We will use Stryer’s Biochemistry as a reference text, complementing online materials. The below sections are most relevant to the course; you may want to skim through these sections early on.  We will also cover this material in lectures and classroom sessions, but from a somewhat different angle.

  • Chapter 8, Enzymes: Basic concepts and kinetics. pp. 205 – 212.
  • Chapter 15, Metabolism: Basic concepts and design. pp. 409 – 430.
  • Chapter 16, Glycolysis and gluconeogenesis. pp.
  • Chapter 17, The citric acid cycle. (can skip section on the glyoxylate cycle)
  • Chapter 18, Oxidative phosphorylation. pp. 501 – 503, 506 – 522, 527 – 532.
  • Chapter 20, The Calvin cycle and the pentose phosphate pathway. pp. 577 – 585.
  • Chapter 22, Fatty acid metabolism. pp. 617 – 626, 631 – 641.
  • Chapter 23, Protein turnover and amino acid degradation, pp. 656 – 663, 666 – 672.
  • Chapter 24, The biosynthesis of amino acids. pp. 683 – 693, 700 – 705.
  • Chapter 25. Nucleotide biosynthesis. pp. 709 – 723.
  • Chapter 26. The biosynthesis of membrane lipids and steroids. pp. 732 – 742.
  • Chapter 27. The integration of metabolism. pp. 760 – 770.

Section and page numbers refer to the 6th edition.