Websites of note

Barry Ganong is a teacher in the Department of Chemistry and Physics at Mansfield University, Northern Pennsylvania. He has created a suite of laboratory practicals beginning in 1992, developing his own resources after adapting third party sources. Three courses in biochemistry are offered at Mansfield University. 1) Organic and Biochemistry: taken by environmental sciences and dietetics majors and by others for general education science credit. 2) Introduction to Biochemistry: taken by dietetics majors, fairly in-depth, emphasizing in particular the biochemistry relevant to human nutrition. 3) Biochemistry: one-semester upper-division for science majors. Ganong has developed biochemistry laboratory exercises for each of these courses, which are instructive and easy to source materials at low-cost. Most of them strike me as being good fun as well. For example, the following is a precis of the laboratory session Tests for Carbohydrates. In the first part, students perform four qualitative tests on eight sugars. The tests are Benedict's (reducing sugars), Barfoed's (monosaccharides), Seliwanoff's (ketoses), and Bial's (pentoses). The sugars given are glucose, fructose, lactose, maltose, ribose, sucrose, sorbose, and xylose (1% solutions). Structures for the first six are in most texts. The latter two are usually not mentioned and serve effectively as “unknowns.” In the second part, students use these qualitative tests to determine the characteristics of sugars in four natural mixtures: corn syrup, honey, and acid hydrolysates of sawdust and dandelion root starch. Corn syrup used to be glucose. Using a 2% solution of corn syrup in water, students got a variable ketose test. It turns out to be a mixture of real corn syrup and high-fructose corn syrup. Students thus miss the point that traditional corn starch is all glucose, but gain the message that industrial processing converts glucose to fructose in corn syrup to increase its relative sweetness. Honey is made up as a 2% solution in water, and gives the expected test for ketose. Ganong states I made the wood and dandelion root extracts by adding 40 mL of 0.5 M HCl to 10 g sawdust (local sawmill) or 10 mL 1 M HCl to 4 g chopped dandelion roots (my yard) and incubating in sealed bottles in a 65 degree oven for three days. To each, I added 20 mL water, mixed well, and decanted into separate flasks. I then added 20 mL water to the sawdust and the roots and heated in a microwave oven for one minute, then vacuum filtered and pooled the filtrates. Adding 50% NaOH dropwise, I neutralized both extracts, then added 1 g Norit, mixed, and filtered through GF/C glass fiber filters. The filtrates were clear and pale yellow. The wood extract yielded pentose (xylose from hemicellulose), monosaccharide, and reducing sugar. Dandelion roots store sugar as inulin, a fructose polymer, and students' results were consistent with this, showing reducing sugar, monosaccharides, and ketose. There is a large range of chemical and biochemical laboratory sessions described at this site. Vitamin D has long been just another vitamin in textbooks, with the ability to prevent rickets and osteomalacia. However, recent findings suggest that it has an additional role in maintaining an active immune system and it has become a vitamin essential for a range of processes [1]. The current resurgence in interest also relates to lifestyle modifications of sunlight exposure, with some groups getting little exposure such as the elderly in some situations. Of course the dangers of high exposure to UV light act as a foil to excess sun exposure. This fact sheet from the National Institutes of Health is an authoritative and extensive treatment of what vitamin D is, the sources of vitamin D, the recommended intake for vitamin D, when vitamin D deficiency can occur, who may need extra vitamin D, current issues and controversies about vitamin D, the health risks of too much vitamin D, and selecting a healthy diet. Just to remind you of the nature of vitamin D the fact sheet begins by relating that it exists in several forms, each with a different level of activity. Calciferol is the most active form of vitamin D. Other forms are relatively inactive in the body. The liver and kidney help convert vitamin D to its active hormone form. Once vitamin D is produced in the skin or consumed in food, it requires chemical conversion in the liver and kidney to form 1,25 dihydroxy-vitamin D, the physiologically active form. Active vitamin D acts on the absorption of calcium and phosphorus. New knowledge is extending the roles of vitamin D from this classic picture. After viewing this fact sheet, change the URL to ods.od.nih.gov/factsheets and you will have a comprehensive alphabetical list of dietary supplements. For the letter A alone you will find aloe vera, anabolic steroid abuse, antioxidants against cancer (Vitamin C, Vitamin E, Coenzyme Q10), antioxidants against cardiovascular disease (Vitamin C, Vitamin E, Coenzyme Q10), and Astragalus. Although completed in 2003, the Human Genome information site continues to be updated and maintained by the U.S. Department of Energy and the National Institutes of Health. As would be expected the history of the multination collaboration is related here. The introduction asserts that the project goals were to 1) identify all the ∼20,000–25,000 genes in human DNA; 2) determine the sequences of the 3 billion chemical base pairs that make up human DNA; 3) store this information in databases; 4) improve tools for data analysis; 5) transfer related technologies to the private sector; and 6) address the ethical, legal, and social issues that arise from the project. It is interesting to see how history has been rewritten in these goals because prior to 2000 the chief investigators were convinced that they would find 100–120,000 genes. The ongoing analyses of the data are reported on a progress page that is mostly a collection of links to primary sources, notably papers published in the journal Nature. Selecting the Education banner, from the alternative main choices of Medicine and Ethics, produces an extensive list of resources that are online or can be acquired from the U.S. Department of Energy. The resources are human genome publications, downloadable teaching aids, lesson plans, teacher guides, student activities, online educational modules, genetics, videos, webcasts, graphics, animation, posters, presentations, teaching aids for purchase, software, activity kits, books, workshops, training, and links to genetics sites. This website at Washington State University, USA (not Vancouver Canada), has a guide written by Steve Sylvester, which I could have written myself. Sadly there are no other gems at this site, only course information and textbook references. Steve Sylvester states Biochemistry is frequently considered to be one of the most difficult courses in the undergraduate curriculum. Biochemistry is concept rich and progressively builds upon acquired learning. It is a big mistake to think that you can just review your lecture notes the night before the exam or that you don't have to open the textbook. The best of all practices is to read the text assignment before the lecture and then do practice problems after reviewing the lecture and text. There are study guides available for most biochemistry texts and many include problems and practice exams. If you are more electronic, there are also CDs available. Practice tests on the Internet may be helpful but since these are individualized to the emphasis of a given instructor, there may be questions you are unfamiliar with. The key thing is to study, and to keep up with the lectures. Another important aspect is to practice drawing biochemical structures. Simply seeing the structure in a text or writing it once in your notes is insufficient. You should be able to write structures on the placemat while you are waiting for your food at a restaurant—and if you can't do it there, you probably won't be able to do it in the exam room. But you must practice the correct structures so try them again when you can check them with the text. Getting a study group together weekly is highly beneficial. A group of 3 to 6 is most efficient. Even an e-mail partner can help you keep on track. If you don't understand something, don't let it wait too long, try to find the answer and if you can't, contact the instructor or teaching assistant. These resources cover a broad range of basic biochemistry teaching and feature some good quizzes. Although the site will remain as an archive “for the foreseeable future,” you should visit this site promptly because progressive conversion to the Blackboard Virtual Learning Environment at Leicester means that this site will no longer be updated. The topics are listed for the year in which they are taught. 1) First year: molecular biochemistry, macromolecules in action, biological molecules, metabolism, key skills A and B plus other first-year modules. 2) Second year: structure and function of proteins, informational macromolecules, intermediary metabolism and bioenergetics, targeting biochemical knowledge at medical problems plus other second-year modules. 3) Third year: cancer cell and molecular biology, biochemistry of gene expression, antimicrobial biochemistry, understanding and using enzymes, proteins (structure, dynamics, and engineering), biochemical mechanisms of human disease plus other third-year modules. Some of the material is self-contained, but some is incomplete such as the second year drug design exercise that requires an additional briefing sheet. Nevertheless it is easy enough to envisage what the missing material would say. If you are developing your own curriculum then the structure of these courses and the lecture topics may help you plan your own material. In any event take some of the quizzes. I found myself needing to be more careful in answering the questions after making some elementary mistakes. This resource at the George Washington University, Washington, DC, is a compendium of conventional metabolic pathways drawn in a simple clear style. A potential use for this is to cut and paste individual structures (easily done) into assessment questions so that students need to do just a little extra recognition work relative to using the structures given in their textbook. There are also extra bits of information added, such as the table of energetics for the reactions of glycolysis. The representation of the Krebs–Henseleit urea cycle begins with the summary that one turn of the cycle is Carbomyl Phosphate + Aspartate + 3 ATP + 2 H2O → Urea + Fumarate + 2 ADP + 2 Pi + AMP + PPi. This is plain text and so it is easily copied. Students might find the very simple style more accessible than the embellished pathways shown in many textbooks. The four sections are 1) Carbohydrate Metabolism: glycolysis (and gluconeogenesis), Kreb's cycle, pentose phosphate pathway, glycogen biosynthesis, galactose pathway, and Calvin cycle; 2) Lipid Metabolism: triacylglycerol metabolism, activation of fatty acids, beta-oxidation of fatty acids—even chain and odd chain, beta-oxidation of polyunsaturated fatty acids, alpha-oxidation pathway, de novo biosynthesis of fatty acids, and cholesterol biosynthesis; 3) Amino Acid Metabolism: glutamate reactions, Krebs–Henseleit urea cycle, shikimate pathway, phenylalanine and tyrosine biosynthesis, and tryptophan biosynthesis; 4) Energy Metabolism: oxidative phosphorylation, chemistry of ATP synthesis, photosynthesis, and methane metabolism. I initially arrived at the Micropolitan Museum section of this site to view a world lost to me since undergraduate days; a world of water fleas and plankton. The high-quality renditions of Daphnia and Foraminifera are a great aesthetic tour through a microworld generally neglected by biochemists. The site is enormous and if you choose Home from the locations you will be faced with the enormity of the content. Navigation is a challenge, but start exploring through options that take your interest. The illustrated article Syphilis and the Microscope can be found by choosing Mag and then Micscape; Exploring the Miniature World, Issue 146, December 2007. Kennewick Man is named for the skeletal remains of a 9,200-year-old man found on a bank of the Columbia River near Kennewick, Washington, USA, in 1996. Kennewick Man was discovered by spectators at a hydroplane race on the river. The local newspaper, the Tri-City Herald, now maintains this website dedicated to the facts and developments about who this man was and the ongoing controversy concerning which native groups (if any) can lay claim to the remains. Migration from Asia is widely assumed to be the source of America's original inhabitants, but when this migration (or migrations) occurred is still a matter of conjecture. Kennewick Man is helping science find more information relating to this puzzle, but native Indian groups are opposing the scientific use of the remains. Kennewick man was wounded by an arrow-like stone projectile (may not have been fatal) and died in the age range of 45–55. Anthropologist James Chatters gets the credit for initial collection and analysis of a 150 pieces of bone which made almost a full skeleton. This website provides an archive of the Herald's articles, along with links to other resources including DNA analysis. In some way Kennewick man is an American equivalent to Ötzi, the Iceman, a well-preserved natural mummy of a man who died 5,300 years ago, found in 1991 on the border between Austria and Italy. That body was also contested for ownership. It has been lamented from the time of Charles Darwin that the fossil record of Homo sapiens is one of the poorest in archaeology, but Kennewick man and other specimens are giving us a better knowledge of our genetic prehistory.

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