Tim Soderberg

Associate Professor of Chemistry
University of Minnesota, Morris

Office: Science 1320
Phone: (320) 589-6331
Email: soderbt

I am on sabbatical for the 2013-2014 academic year, but can be reached at the email address above


 

I teach Organic and Bioorganic Chemistry at UMM, as well as General Chemistry labs. I received a B.A. in English from Amherst College in 1987, and a California teaching credential from San Francisco State University in 1989. After teaching English as a Second Language in Tokyo, Japan for about five years, I returned to the United States and enrolled at Sonoma State University where I completed all of the undergraduate Chemistry, Calculus, and Physics courses necessary to enter a graduate Chemistry program. I came to UMM in the Fall of 2000 after receiving my Ph.D. in Biological Chemistry from the University of Utah under the direction of Professor C. Dale Poulter. My graduate research focused on the enzymology of two prenyltransferase enzymes: one that modifies tRNA, and one that is involved in the early biosynthesis of ether-linked membrane lipids in archaea. My current research involves the discovery and characterization of novel enzymes (see below).

I am also currently involved in ongoing development of a new organic chemistry textbook in which the central focus is on molecules and reactions of biological interest. The text is now part of the Chemwiki dynamic chemistry texbook project at the University of California, Davis.


 

Courses:

Chem 2301 (Organic Chemistry I)
Chem 2311 (Organic Chemistry Lab I)
Chem 2304 (Organic Chemistry II With a Biological Emphasis)
Chem 2321/2322 (Intro to Research)
Chem 4351 (Bioorganic Chemistry)

(on sabbatical for the 2013-2014 academic year)


If you are interested in curriculum innovation in organic chemistry education, please visit
Organic Chemistry With a Biological Emphasis

Click here to visit the UMM student premed web page


Research


My research interests lie in the area of bioorganic chemistry, the organic chemistry that occurs via enzymatic catalysis in biological systems. More specifically, I am interested in trying to better understand biochemical pathways in a group of organisms called Archaea. These microscopic prokaryotes, which make up a separate kingdom of life distinct from Bacteria and Eukarya, are fundamentally different- in terms of their genetic evolutionary history and in many cases their biochemistry- from organisms in the two other kingdoms. Archaea thrive in conditions that until recently were thought to be incompatible with living things: in the boiling, sulfurous waters of hot springs, for example, in 4M salt water, and near geothermal vents thousands of feet under the ocean, far from any sources of light or molecular oxygen.

As part of the advent of massive DNA sequencing projects, several complete genetic blueprints for archaeal species have been published, revealing that the archaea are missing many genes that were previously thought to be essential for all living things.   Many archaeal species, for example, are missing genes encoding enzymes of the pentose phosphate pathway (PPP), a series of biochemical reactions that converts abundant 6-carbon sugars   like glucose and fructose into important five and four-carbon sugars. Ribose-5-phosphate, a five-carbon sugar, is required for the synthesis of DNA and RNA, while erythrose-4-phosphate, a four-carbon sugar, is required for making amino acids such as phenylalanine and tyrosine.   The enzymes of the PPP are the only known route to ribose and erythrose, so the source of these critical precursor sugars in archaea is still unknown.   It is possible that the genes may exist but are not recognizable by current sequence analysis techniques. Alternate pathways may also play key roles.   The goal of my project is to learn more about the PPP in archaea, and to explain how the sugar precursors for DNA and amino acids are synthesized in these species.

Three archaeal genomes do contain putative genes for nonoxidative phase of the PPP, but until recently these genes had never been cloned or characterized from any archaeal sources.   A starting point for my research, then, was to study these archaeal genes that appear to encode the PPP enzymes transaldolase, transketolase, and ribulose-5-phosphate epimerase. Since the project's inception in spring 2001 we have cloned the genes for these three enzymes, and have been able to demonstrate the ability to insert the cloned genes into E. coli bacteria and produce recombinant protein.   We have purified and characterized recombinant, heat-stable transaldolase from M. jannaschii, and a paper describing the results has been published (Soderberg, T. and Alver, R. C. 'Transaldolase of Methanocaldococcus jannaschii ' Archaea 2004, 1, 255).

A related functional genomics project has resulted in a possible explanation for the enigmatic patterns of inheritance observed for the PPP genes in archaeal genomes, and suggests that, in some archaeal species which are missing the PPP genes, ribose phosphate synthesis may be accomplished instead by enzymes of the ribulose monophosphate pathway. A paper describing this study has been published (Soderberg, T. 'Biosynthesis of ribose-5-phosphate and erythrose-4-phosphate in archaea: a phylogenetic analysis of archaeal genomes' Archaea 2005, 1, 347-352).

Both of these papers have been cited in a recently published book, Archaea: new models of prokaryotic biology (Paul Blum, ed.) and also in numerous research reports and reviews.

This research was supported by start-up funding from the University of Minnesota, Morris, and by a Cottrell College Science Award from the Research Corporation.

 

Genome/structure analysis links

NCBI (Genebank)
CMR (Comprehensive Microbial Resource)
PDB (Protein DataBank
ClustalW (sequence alignments)
JMol
Rasmol

 


The views and opinions expressed in this page are strictly those of the page author. The contents of this page have not been reviewed or approved by the University of Minnesota.


The views and opinions expressed in this page are strictly those of the page author. The contents of this page have not been reviewed or approved by the University of Minnesota.