Introduction to Organic and Biochemistry

Internet resources

This page was originally developed to provide supplementary materials for a one semester introductory (survey) course in organic and biochemistry. Links to the home page for the course, to the home page for this site, and contact information are in the navigation bar at the top of this page; they are also at bottom of page.

Most of the sections below are listed in the order they first become relevant in my Intro Organic/Biochem course. Chapter references are shown for the textbook by Ouellette, 2/e. Some items are intended as general; these are at the end of the list.
Introduction; alkanes (Ch 3)
Alkenes (Ch 4) (Afrikaans, French, Italian, Portuguese, Russian, Spanish)
Aromatic compounds (Ch 5)
Stereochemistry (Chirality) (Ch 6)
Alcohols, ethers, sulfur compounds (Ch 8-9)
Aldehydes and ketones (Ch 10)
Carbohydrates (Ch 11)
Carboxylic acids, etc (Ch 12)
Lipids (Ch 13) (Spanish) + New 3/10/14, 4/4/14, 8/5/14, 9/22/14, 11/21/14.
Amines, amides (Ch 14)
Amino acids, proteins, genes (Ch 15, 16) (German)
Metabolism (supplemental handouts)

Spectroscopy (Ch 18)
Energy resources + New 12/11/13, 1/6/14, 1/21/14, 4/7/14, 4/8/14, 5/2/14, 8/18/14, 9/12/14, 9/30/14, 10/26/14.

General (Spanish)
Bottom of page; return links and contact information
Links to external sites will open in a new window.
You may find links of interest on my other pages of Internet Resources, either for other specific courses or the chem-miscellaneous, miscellaneous, or introductory pages. All of these are available from the List of pages of Internet resources.


Introduction; alkanes (Ouellette 2/e Ch 3)

Posts in my Musings newsletter on alkanes include:
* Svalbard is leaking (March 7, 2014).
* Quiz: NASA's boat (June 29, 2011).
* Ice on fire (August 28, 2009). More posts about methane hydrates are linked there.

* Other Musings posts about methane and natural gas are listed below in the section Energy resources.

For information about using the UC Libraries, including the electronic resources, see the Library Matters page at the web site. That page also includes information about doing searches of the scientific literature, to find articles on a topic that interests you. Major topic areas there include: UC Berkeley library; electronic journals; journal articles; PubMed (Medline) searches; citation searches.

The "General" section of this page has links to sites for a range of organic chem and biochem courses, both at the introductory and regular university levels. Some of the intro sites may be particularly useful for those who would like more materials at the basic level.

Cycloalkanes (cis, trans; axial, equatorial). Dr Phil Bays (St. Mary's College, Indiana) has a good set of practice problems on stereochemistry. The structures are clear, and the questions appropriate. Instant feedback. Although some parts of this are for Ch 6, some parts are useful here with cycloalkanes. http://sites.saintmarys.edu/~pbays/Stereochemistry.html. For now, choose the sections that have cycloalkanes in the title. This site is also listed below for stereochemistry, Ch 6.

Do plants make methane?. In 2006 a group reported that plants make methane. A lot of methane -- enough to suggest that plants were major contributors to our global methane budget. This was a surprising finding, since it was inconsistent with our understanding of how methane is made. The paper explored how this might occur, with no clear conclusions; in the absence of any reasonable mechanism, many were skeptical. Since the initial report, others have examined this; results varied, but the emerging consensus was that the initial report was either wrong or exaggerated. This report by Nisbet et al offers a new view. They show that the plants lack any known pathway for making methane. Importantly, they report that plants serve as efficient conduits of methane from the soil, via transpiration. Thus they really do emit methane, but it is not their own production. This proposal makes sense, and accommodates the variable results obtained by others. Is this the last word? Let's see. A news story: Challenge to plant methane link, January 14, 2009. http://news.bbc.co.uk/2/hi/science/nature/7827106.stm. The paper is R E R Nisbet et al, Emission of methane from plants. Proc Royal Soc B 276:1347-1354, 4/09. This paper is listed in the chapter handout for alkanes: Organic/Biochem Chapter handout: Alkanes (pdf file). (All the chapter handouts are available at: Organic/Biochem Chapter handouts).

Anaerobes Appear Key in Converting Poorly Accessible Oil to Gas. Microbe 3:114, 3/08. Microbe is the news magazine of the American Society for Microbiology. This news story discusses a recent paper by Jones et al (2008), which is listed in the chapter handout. Free online: http://forms.asm.org/microbe/index.asp?bid=56841. The next item below may well be related.

New Petroleum-Degrading Bacteria Found at Rancho La Brea Tar Pits in Los Angeles. http://newsroom.ucr.edu/news_item.html?action=page&id=1583. Methane-producing bacteria are responsible for the bubbles seen at the tar pits. News release, May 10, 2007, on the work of J-S Kim & D E Crowley, Univ Calif Riverside.

On a lighter note... the Periodic Table According to Organic Chemists: http://www.uccs.edu/Documents/danderso/orgpt.pdf. From D R Anderson, University of Colorado at Colorado Springs.

My page on Writing, drawing and viewing chemical formulas points to some free programs that may be useful to you both during the course and for your personal use outside the course. These include:
* RasMol, a program for viewing molecular structures. I encourage you to give it a try early in the course, with some small molecules, so you have some experience with it by the time we get to proteins (Ch 15).
* ChemSketch and ISIS/Draw, programs for drawing organic chemical structures. These are useful for drawing structures for word processing documents. Further, the structures you draw can be converted to files that can be viewed as 3D models. Many students find it fun to try this -- drawing your own structures and converting them to 3D models. Both programs will name structures that you draw.

My page Rings: Showing cis/trans and axial/equatorial relationships discusses these particular aspects of cyclohexane rings.

Other pages at my web site that have been mentioned for Ch 3: Library Matters; Terms: Primary, Secondary, Tertiary, Quaternary; Glossary; Omitting numbers; Books: Suggestions for general reading. The web site also contains a nice periodic table, current through element #118, on the Download page; that page also contains ChemFormula, a macro to help you format chemical expressions in Microsoft Word.

Also see the section on Energy resources. Some of the items it contains used to be listed in this section or under Alcohols, ethers, sulfur compounds.

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Alkenes (Ouellette 2/e Ch 4)

The following two items are related to papers listed in the Further Reading section of the Chapter handout. Both involve work from UC Berkeley.

A UC Berkeley group led by Jay Keasling is working on production of artemisinin, a new type of anti-malarial drug, in microbes (bacteria and yeast). There is an article about this listed in the chapter handout.
* Here is a campus news story on the funding of this project by the Gates Foundation: "QB3 + Gates' millions = a cure? Helped by Microsoft's founder, Jay Keasling and his industry partners hope to create an inexpensive treatment for malaria". January 12, 2005. http://www.berkeley.edu/news/berkeleyan/2005/01/12_keasling.shtml.
* A status report -- a news story, June 4, 2008. "Synthetic yeast to brew up vital malaria drug." http://www.newscientist.com/article/dn14059-synthetic-yeast-to-brew-up-vital-malaria-drug.html.
This group of items is also listed for the Biotechnology in the News (BITN) topic Malaria.

A post in my Musings newsletter with another example of metabolic engineering of microbes: A better way to divide 6 by 2: A more efficient way to use sugar (November 10, 2013). This post is also noted below in the section Energy resources.

UCB researchers have shown a role for carotenoids in carrying off excess energy that is absorbed during photosynthesis. Here is a news story on this project in the UCB student newspaper, Daily Cal: The fight against light - Plant molecule functioning in self defense discovered, http://archive.dailycal.org/article.php?id=17463. The work was published: N E Holt et al, Carotenoid cation formation and the regulation of photosynthetic light harvesting. Science 307:433, 1/21/05. The paper is free online at: http://www.sciencemag.org/content/307/5708/433.abstract.


Other

Dr Tom Newton at the University of Southern Maine developed an animation showing how a double bond is formed in terms of orbitals. Here is a copy of the figure: Newton's Figure 3, on double bond [link opens in new window]. In particular, note how two p orbitals, one from each bonding C, overlap sideways. This sideways overlap of elongated orbitals is called π (pi) bonding. It provides an easy way to explain why free rotation is not possible around a double bond. ["Regular" bonding is called σ (sigma) bonding.] In effect, this is an animated version of the right hand side of Fig 1.6.

Newton's organic chemistry site is now maintained at the University of Hamburg. To get to this item... http://www.biologie.uni-hamburg.de/b-online/library/newton/Chy251_253/Topics.html. Choose "Shapes: hybridization"; scroll down to Fig 3, DoubleBond.gif. The Newton site is also listed below as a General resource for organic chemistry.

Ozonolysis of Alkenes. http://www.chem.ucalgary.ca/courses/351/Carey5th/Ch06/ch6-10.html. We make the general point that the characteristic reaction type of alkenes is addition. However, the oxidation reactions that Ouellette presents in Sect 4.7 certainly do not appear to be additions, given their overall description. These are complex reactions, but the first step really is an addition to the double bond. This page shows the details of the ozonolysis reaction, and shows the primary addition step; look at the malozonide. The page is part of a more comprehensive organic chem site at the Univ of Calgary.

http://www.pslc.ws/macrog.htm. The Macrogalleria site on polymers, at the University of Southern Mississippi: "A cyberwonderland of polymer fun". It is a major educational resource on polymers, and is very readable over a wide range of topics. "AND... for the young and the young at heart, we have the Kid's Macrogalleria that contains much info and much fun, with activities, demos, and even games that are related to polymers." Also available in Afrikaans, French, Italian, Portuguese, Russian, Spanish. (It is also listed on the Internet resources: Chemistry - Miscellaneous page, under Organic.)

World's first 'green' linear polyethylene launched. Press release, Macrh 31, 2008, from the Royal Society of Chemistry about a Brazilian company making ethylene (ethene) -- and then polyethylene -- from bio-ethanol. We note in class that both directions of the simple interconversion between ethanol and ethylene are industrially useful, with the balance typically depending on the price of oil. Brazil has particularly favorable economics of making ethanol, from sugarcane. Now they have extended this: sugarcane --> ethanol by fermentation --> ethylene by chemical dehydration --> polyethylene, as usual. http://www.rsc.org/chemistryworld/News/2008/March/31030801.asp.

The 2000 Nobel Prize in Chemistry was awarded to three scientists (including Alan Heeger at UC Santa Barbara) for the discovery of electrically conductive polymers. The polymers are polyacetylenes. You can think of polyacetylene the same way as polyethylene: the polymer is made by addition; the polymer itself has alternating single and double bonds. See the Nobel site: http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2000/. The article includes an animation of the charge transfer along a polymer molecule, and between a polymer molecule and the dopant.

The 2005 Nobel Prize in Chemistry was awarded to three scientists for the development of alkene metathesis. The idea is to combine smaller alkenes into larger ones, by a process that formally looks something like double replacement (i.e., a rearrangement). See the Nobel site: http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2005/index.html.

For more about farnesol (p 128, bottom), to the tune of Jingle Bells: http://www.lyricsbay.com/farnesol_lyrics-unknown.html.

Self-healing polymers. Biological materials incur damage or decay over time; biological processes restore them. But ordinary chemical materials? Now there is work to design a polymeric material with self-repair capability. http://autonomic.beckman.illinois.edu/. (The work described at this site was pioneering work on self-healing polymers. More has followed. One interesting new approach is described in a 2008 paper now listed in the Ch 14 handout.)

Recycling information: http://www.co.contra-costa.ca.us/depart/cd/recycle/. Among other things, check the "Reuse and Recycling Guide." From Contra Costa County; includes links to recycling agencies in some other local areas. [An article about the merits of burning vs burying plastics, Piasecki et al (1998), is on the Further reading: Old articles web page.] (You can obtain a copy of the Recycling Guide at the county Recycling Hotline, 1-800-750-4096.)

Alameda County recycling: http://www.stopwaste.org

A kit that lets you make your own C60 "buckyballs" is available, on the Download page. The kit may be suitable for ages 8+.

The The E-Z system for naming alkenes; examples of using the CIP rules. Ouellette covers this fine in Ch 4. The page now includes more examples, including how to apply the CIP priority rules.

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Aromatic compounds (Ouellette 2/e Ch 5)

Posts in my Musings newsletter on graphene include:
* Loudspeakers: From gold-coated pig intestine to graphene (April 27, 2013).
* Graphene bubbles: tiny adjustable lenses? (January 15, 2012).
* Image of a carbon atom that isn't there (August 17, 2008).

Dr Tom Newton at the University of Southern Maine developed an animation showing the bonding in benzene in terms of orbitals. Here is a copy of the figure: Newton's Figure 2, on the aromatic ring [link opens in new window]. In particular, note the loop formed by six p orbitals, one from each bonding C, overlapping sideways. This continuous loop of sideways-overlapping p orbitals, with six electrons, is responsible for the aromatic character. This item builds on the item posted above for Alkenes on π bonding in alkenes, also from Dr Newton. (This page also gives you more explanation of the basis of Hückel's rule, though the level is fairly difficult.) For a broader view of what aromaticity entails, see my page on this topic, listed in this section below.

Newton's organic chemistry site is now maintained at the University of Hamburg. To get to this item... http://www.biologie.uni-hamburg.de/b-online/library/newton/Chy251_253/Topics.html. Choose "MO theory and Huckel's rule"; scroll down to Fig 2, Deconstruction.gif. The Newton site is also listed below as a General resource for organic chemistry.

The 2010 Physics Nobel Prize was awarded to Andre Geim and Konstantin Novoselov, University of Manchester, "for groundbreaking experiments regarding the two-dimensional material graphene". See the Nobel page The Nobel Prize in Physics 2010.

The following pages at my site are relevant to this chapter:

The Phenyl group page will help you with this and related terms. The page shows structures.

The Aromatic page addresses the broader question, What does "aromatic" really mean? I encourage you to browse it, and enjoy the pictures!

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Stereochemistry (Chirality) (Ouellette 2/e Ch 6)

Dr Phil Bays (St. Mary's College, Indiana) has a good set of practice problems on stereochemistry. The structures are clear, and the questions appropriate. Instant feedback. http://sites.saintmarys.edu/~pbays/Stereochemistry.html. (Part of this site was recommended for use with cycloalkanes, Ch 3.)

The 2001 Nobel prize in Chemistry was awarded to three scientists for their work in developing practical methods for making the correct isomer of drugs, that is for doing chiral synthesis. See the Nobel site, http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2001/. Also see "Further reading" items on this topic, in chapter handout.

Everything has a mirror image? Even Google? Try it, at http://elgoog.im/. (The story is that this was introduced as an attempt to circumvent censorship of search engines in certain countries. It worked.) This site is also featured in the Musings post elgooG (October 12, 2009).

Ch 6 introduces the R,S system for naming chiral isomers. As noted, The E,Z system is a rigorous IUPAC system for naming alkene isomers, using the same general approach -- and same priority rules. See my page The E-Z system for naming alkenes; examples of using the CIP rules. (This was mentioned earlier, under Alkenes.)

You may also want to look at some stereoisomers of chiral compounds in RasMol. See my RasMol page.

H Prior et al, Mirror-induced behavior in the magpie (Pica pica): Evidence of self-recognition. PLoS Biol 6(8):e202, 8/08. The ability to recognize oneself in a mirror is a trait sometimes considered characteristic of only humans and apes. Over recent years, evidence accumulated that elephants and dolphins, too, show this aspect of self-recognition. Here is evidence that some birds recognize themselves in the mirror. Very readable paper, with interesting methodology. The paper is freely available online: http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0060202. The article is listed in the handout for Ch 6.

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Alcohols, ethers, sulfur compounds (Ouellette 2/e Ch 8-9)

For animations of elimination and substitution reactions, see http://www.bluffton.edu/~bergerd/classes/CEM221/sn-e/home.html. These are types of reactions used in Sections 8.5 & 8.6; they were introduced, with mechanisms, in Ch 7, which we skip. These animations will usefully reinforce these basic reaction types even if you do not worry about the mechanisms for now. For those going on in organic chemistry, this is essential material -- and these are nice animations. (Both Flash and gif animations are available. If possible, try the Flash animations first.) From Daniel Berger, Bluffton College.

Removing stains at home, from the Department of Fiber Science & Apparel Design at Cornell. A practical guide to removing stains. Chemistry underlies much of this... what is soluble in what, largely determined by polarity. Go to the Department's outreach page: http://www.human.cornell.edu/fsad/outreach/index.cfm. Near the end of the first paragraph is a link to "Removing stains at home" (pdf file).

MTBE = methyl t-butyl ether; it is a controversial gasoline additive. A report from the National Academy of Sciences summarizes the key issues in the debate on oxygenated fuels (using mainly MTBE or ethanol). Go to the National Academy Press, at http://www.nas.edu. Search on MTBE. Doing this will give you any current information that may be available there, but the main point for now is the 1996 book "Toxicological and performance aspects of oxygenated motor fuels." I suggest you start with the Executive Summary.

Thimerosal. This is the mercury-containing compound that is used as a preservative in some vaccines. It is controversial because of concerns about possible toxicity. It is relevant here because the Hg is attached to a sulfur atom; one can think of it as a Hg-substituted thiol. I have posted two items on this. My thimerosal page shows the structure of thimerosal and some related compounds, including aspirin. I have also posted a short note about thimerosal on BITN - Miscellaneous; section on vaccines. This includes a link to an FDA site, which should be a good starting point for a broader consideration of the compound. The FDA page should not necessarily be considered a final answer, but it is well organized, and should serve to at least outline the issues. Let me know of questions. This topic is also listed under Introductory Chemistry Internet Resources: Thimerosal.

A particular question that came up was about the behavior of methyl mercury vs ethyl mercury. My bottom line is that this is not very clear. Although there is some evidence that the ethyl mercury may be less toxic, the evidence seems very limited. There are two factors to consider in making this comparison. One is chemical/physical behavior. Both are non-polar, and thus relatively soluble in fat. Offhand, I would not want to predict any difference between them on this point. The second issue is their precise biological action. I don't know of any detailed work on this; as already noted, the evidence that the ethyl mercury may be less toxic is weak, and I have not seen any detailed analysis or explanation of it.

Also see the section on Energy resources. Some of the items it contains used to be listed in this section or under Introduction; alkanes.

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Aldehydes and ketones (Ouellette 2/e Ch 10)

This listing added November 2014. The following post in my Musings newsletter is on the biology of aldehydes:
* Alcohol consumption, an "ethnic" mutation, and a possible new drug (October 28, 2014).

"I Have Seen the Light! Vision and Light-Induced Molecular Changes." How vision works, including the chemistry of the photoreceptor. That chemistry involves an aldehyde reaction, and also cis-trans isomerization. http://www.chemistry.wustl.edu/~edudev/LabTutorials/Vision/Vision.html. Includes good graphics, at molecular and biological levels. From R Casiday and R Frey of Washington Univ. (Another of their set, on oxidative phosphorylation, is listed below, for Metabolism.)

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Carbohydrates (Ouellette 2/e Ch 11)

Salivary amylase is the first enzyme that helps us digest starch -- in the mouth. Humans in societies with high starch consumption have more salivary amylase -- and more copies of the gene for it -- than humans in societies with low starch consumption. This suggests that natural selection has been occurring in humans for this trait, and also supports the emerging idea that copy number variation is important. The paper also notes limited data supporting the same correlation with other primates. This work was published as G H Perry et al, Diet and the evolution of human amylase gene copy number variation. Nature Genetics 39:1256, 10/07. It is listed in the chapter handout under Novembre et al, the accompanying news story in the same issue. A news story that is freely available: Starch 'fuel of human evolution' -- Man's ability to digest starchy foods like the potato may explain our success on the planet, genetic work suggests. http://news.bbc.co.uk/2/hi/health/6983330.stm.

An interesting story of the development of an artificial sweetener, using an uncommon and unmetabolized sugar. The article also discusses the sweetness of L-sugars; these might be suitable as artificial sweeteners, but are not economically practical. "A natural way to stay sweet": http://spinoff.nasa.gov/Spinoff2004/ch_4.html.

Electricigenic bacteria -- bacteria that can couple their electron transport directly to an external electrode, and thus can serve as the basis of a microbial fuel cell. One possible application is the use of waste organics, including sugars, to make electricity. One of the examples most studied is the genus Geobacter (a genus that does not itself use sugar). http://www.geobacter.org. From Derek Lovley, Univ Massachusetts. Also see: D Lovley, Microbial energizers: Fuel cells that keep on going. Microbe 1:323, 7/06. This article is in the publications file at the Microbial fuel cells site (listed below): http://www.microbialfuelcell.org/www/index.php/component/option,com_jombib/id,157/task,showbib/.

The Figure is Fig 4 of the paper in Microbe; it is also shown at the Geobacter site.
A calculator, operating on a set of bacterial fuel cells. Fig 4 of the Lovley paper.

Microbial fuel cells. A new site broadly on that same topic: http://microbialfuelcell.org/. Explanatory material, and links.

Glycomics. Article: A A Weiss & S S Iyer, Glycomics aims to interpret the third molecular language of cells. Microbe 2:489, 10/07. Microbe, the news magazine of the American Society for Microbiology, is free online; this item is at http://forms.asm.org/microbe/index.asp?bid=53398 (HTML) or http://forms.asm.org/ASM/files/ccLibraryFiles/Filename/000000003341/znw01007000489.pdf (PDF). A nice overview, written for a general audience, of the role of carbohydrates on cell surfaces. The sugars are found as part of glycolipids and glycoproteins (more about these in later chapters, on lipids and proteins). Many receptors for viruses and toxins involve sugar residues -- hence the connection to microbiology. The article discusses influenza virus and botulinum toxin among the examples where the sugar residues are key in determining the specificity of the agent.

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Carboxylic acids, etc (Ouellette 2/e Ch 12)

Organic Acids In Wine. Why they are there, what they do, and what to do about them. https://people.ok.ubc.ca/neggers/Chem422A/Organic%20acids%20in%20wine.pdf. From Nigel Eggers, Univ British Columbia - Okanagan. For more, see the main page for his "Biochemistry of Wine" course: https://people.ok.ubc.ca/neggers/Chem422A.htm. This site was recommended by an X402 student.

For more about polymers, see the Macrogalleria site, listed above for Alkenes.

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Lipids (Ouellette 2/e Ch 13)

Posts in my Musings newsletter that are relevant to this topic include:
* Added November 21, 2014. Mutations that lead to reduced risk for heart disease (November 21, 2014).
* Added September 22, 2014. Cachexia: is it BAT run amok? (September 22, 2014).
* Added August 5, 2014. Could we treat obesity with probiotic bacteria? (August 5, 2014).
* Added April 4, 2014. YY in the mouth? (April 4, 2014).
* Added March 10, 2014. Why exercise is good for you, BAIBA (March 10, 2014).
* Brown fat: different kinds respond differently to cold (September 20, 2013).
* How good is "good cholesterol" (HDL)? (September 21, 2012).
* Bacteria induce simple "pre-animal" to become colonial (September 8, 2012).
* Heart health and python blood (December 28, 2011).
* Turning sewage into profit -- via rocket fuel (September 15, 2010).
* Omega-3 fatty acids; fish oil (March 29, 2010).
* How do you make phospholipid membranes if you are short of phosphorus? (November 1, 2009).
* Brown fat (May 21, 2009).

A new type of hormone. An idea that has been developing in recent years is that adipose (fat) tissue is "active" -- that it sends out hormonal signals that affect metabolism. The first and most famous of the adipokines -- hormones made by adipose tissue -- is leptin. Now we have evidence, from mice, for an adipokine that is itself a fatty acid. The fatty acid is cis-9-hexadecenoic acid, popularly called palmitoleic acid. A news story: A New Class of Hormone from Healthy Fat Cells Benefits Body Metabolism, HSPH Researchers Find in Mice -- Discovery of 'lipokine' signaling could eventually lead to new treatments for obesity-related conditions. September 18, 2008. http://www.hsph.harvard.edu/news/press-releases/new-class-of-hormone-from-healthy-fat-cells-benefits-body-metabolism-mice/. The article, which is listed in the chapter handout, is: H Cao et al, Identification of a lipokine, a lipid hormone linking adipose tissue to systemic metabolism. Cell 134:933-944, 9/19/08.

Stress and neuropeptide Y. Stress may lead to fat accumulation. In mice, it has now been shown that part of this story is the key role of neuropeptide Y (NPY). News story: Scientists Discover How Stress Causes Obesity And How Fat Can Be Removed Using A Simple Injection. http://www.medicalnewstoday.com/articles/75768.php. The paper is L E Kuo et al, Neuropeptide Y acts directly in the periphery on fat tissue and mediates stress-induced obesity and metabolic syndrome. Nature Medicine 13(7):803, 7/07. Accompanying news story: J P Warne & M F Dallman, Stress, diet and abdominal obesity: Y? Nature Medicine 13(7):781, 7/07.

Adipose Tissue. One of the important general findings of recent years is the active role of fat tissue. Leptin is but one example of a hormone made by such tissue. For a brief overview: http://www.nugo.org/nip/26003. This page is part of the NuGO site, which is listed as a general web site for Further reading: Medical topics under Web Sites and for Biotechnology in the News (BITN), under DNA and the genome - Examples of how genome information is useful.

Leptin in baby formula? In mice, giving large doses of the hormone leptin during infancy ensures that they never become obese -- and never get diabetes. Would this work in humans? It is being discussed. A news story: Scientists working on formula milk that prevents child obesity. http://www.theguardian.com/science/2007/apr/23/medicalresearch.ethicsofscience. (The Guardian, April 22, 2007.)

Aspirin works by inhibiting cyclooxygenase (COX), a key enzyme in the synthesis of prostaglandins from arachidonic acid (p 372). More recently, we have understood that there are (at least) two COX enzymes, with distinct biological roles. This knowledge led to the development of a new class of anti-inflammatory drugs that specifically inhibit COX-2 (e.g., Celebrex and Vioxx), thus avoiding some of the classic side effects of aspirin. The recent news has been about problems with these drugs -- and perhaps with a wider range of anti-inflammatory drugs. The following site, from the FDA, provides information on these drug issues: COX-2 Selective (includes Bextra, Celebrex, and Vioxx) and Non-Selective Non-Steroidal Anti-Inflammatory Drugs (NSAIDs), http://www.fda.gov/Drugs/DrugSafety/PostmarketDrugSafetyInformationforPatientsandProviders/UCM103420. Among other things, see the "Questions and Answers".

The news referred to above certainly has a negative tone, as the emphasis has been on negative effects of the drugs, and perhaps the failure of our drug regulation system to recognize these effects soon enough. But also bear in mind that there is a fascinating biology story developing here. We start with a common useful drug (aspirin), long used with no understanding of how it works. We now have an idea how it works, and that story gets more and more complicated as we learn more. The current drug story has at least two underlying causes: the drugs are not as specific as we sometimes say in casual discussion, and the roles of the COX enzymes are more complex than we suspected. More will be learned, for better and worse. There are at least hints that COX inhibitors may be useful for treating some cancer and other diseases.

FDA page on Trans Fat Now Listed With Saturated Fat and Cholesterol. A page of consumer-oriented information about trans fatty acids (TFA), and about food labeling. http://www.fda.gov/Food/IngredientsPackagingLabeling/LabelingNutrition/ucm274590.htm. Also in Spanish.

The zero trans fat cooking oil contest and related materials. The goal is to help restaurants eliminate the use of trans-fats in cooking. Useful information, and fun. http://frytest.com/index.php.

The following sites have good sections on biological membranes, including the role of cholesterol.
* http://cytochemistry.net/cell-biology/membrane_intro.htm. From Gwen Childs, University of Arkansas for Medical Sciences.
* http://en.wikibooks.org/wiki/Cell_Biology. Scroll down to: Parts of the cell, Membranes. From Wikibooks, the open-content textbooks collection; this book is based on the cell biology textbook started by Mark Dalton, University of Minnesota.

The 2003 Nobel prize in chemistry was awarded to two scientists for their work on transport channels, for water and ions, in biological membranes. For more: http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2003/index.html

The 1982 Nobel prize in medicine was awarded to three scientists "for their discoveries concerning prostaglandins and related biologically active substances." For more: http://www.nobelprize.org/nobel_prizes/medicine/laureates/1982/index.html.

e.hormone: Environmental estrogens and other hormones. The general theme is hormone mimics: chemicals that are not a normal part of the human body but which may behave like hormones in the body. These include chemicals found in nature either naturally (e.g., the so-called phytoestrogens in plants) or derived from pesticides etc. The site is from the Center for Bioenvironmental Research, at Tulane and Xavier Universities, in New Orleans. http://e.hormone.tulane.edu/

For more references related to the broad topic of Lipids, especially those with medical implications, see my page Further reading: medical topics.

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Amines, amides (Ouellette 2/e Ch 14)

Structures of melamine and cyanuric acid. Spring 2007 brought stories of pets dying from contaminated pet food. Why? Various theories were brought forward, some with little credibility. In fact, the one that now seems to be correct had little credibility at first. The melamine story. Melamine is an organic amine used to make plastics known as, well, melamines. For example, a plastic made with melamine and formaldehyde is Formica. Apparently it may have been added to commercial wheat gluten in order to enhance the apparent protein content. After all, melamine has lots of N, and the common protein assay simply measures N. However gruesome this might seem, the story had a flaw, a fairly serious flaw. Melamine is a well known chemical, and it just isn't very toxic. Well, it seems that melamine was indeed the culprit, but not alone. The problem was a combination of two compounds, melamine and cyanuric acid. From looking at their structures, one can easily see how they could interact with each other. Together, they are much less soluble than either alone. And indeed the crystals found in the urinary tracts of the poisoned animals contained melamine + cyanuric acid. (Where the cyanuric acid came from was originally unclear, but it now seems that it was in the gluten, too.)

The following two links give glimpses of this story as it emerged.
* How two innocuous compounds combined to kill pets. A news story, May 7, 2007. http://www.washingtonpost.com/wp-dyn/content/article/2007/05/06/AR2007050601034.html.
* Melamine Pet Food Recall - Frequently Asked Questions. A site from the US FDA Center for Veterinary Medicine that was actively maintained during the pet food incident. http://www.fda.gov/AnimalVeterinary/SafetyHealth/RecallsWithdrawals/ucm129932.htm.

Fall 2008, and more melamine. In food for humans. Details not clear at this writing, but it is the same melamine discussed above. Apparently, it was added to milk, to boost the apparent protein content of the milk. The milk, in turn, gets used for a range of products, including infant formula.

Two sites on the melamine contamination of milk products:
* Melamine Contamination in China. (1/9/09.) An FDA page, now archived at: http://foodconsumer.org/7777/8888/L_aws_amp_P_olitics_42/010908392009_Melamine_Contamination_in_China.shtml.
* Wikipedia: 2008 Chinese milk scandal. http://en.wikipedia.org/wiki/2008_Chinese_milk_scandal.

An article analyzing the pet food incident has been published. The paper describes the incident, the identification of melamine and cyanuric acid -- both in the gluten, and the toxicology of individual components as well as mixtures. Most of the work is from Procter & Gamble. The paper is: R L M Dobson et al, Identification and Characterization of Toxicity of Contaminants in Pet Food Leading to an Outbreak of Renal Toxicity in Cats and Dogs. Toxicological Sciences, 106(1):251-262, 11/08. The abstract -- very informative -- is available at PubMed: http://www.ncbi.nlm.nih.gov/pubmed/18689873.

Posts in my Musings newsletter that are relevant to this topic include:
* The possible role of bacteria in determining the toxicity of melamine... Melamine toxicity: possible role of gut microbiota (April 21, 2013).
* A study of the possible origin of RNA, turns out to deal with chemical subunits very similar to those discussed here... A novel type of polymer -- and its possible relevance to the origin of life (March 15, 2013).

For more about the properties of amides, see my page on Amides. The page discusses the non-basicity and the planarity of the amide linkage, and presents the resonance structures that account for these properties. Also relevant to Ouellette Ch 15, on proteins.

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Amino acids, proteins, genes (Ouellette 2/e Ch 15, 16)

The 2002 Nobel Prize in Chemistry was awarded to three scientists for the development of methods for use of mass spectrometry (MS) and nuclear magnetic resonance (NMR) with proteins. See the Nobel site: http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2002/. Also see related articles in JCE: 1) M S Vestling, Using mass spectrometry for proteins. 2) S Cavagnero, Using NMR to determine protein structure in solution. J Chem Educ 80:122 & 125, 2/03.

The 2004 Nobel Prize in Chemistry was awarded to three scientists for their key roles in understanding how proteins are degraded. Specifically, they discovered the role of ubiquitin, a special protein that is attached to proteins to tag them for degradation. The bigger story is the increasing recognition of the importance of protein degradation. Many proteins are made defective, and must be degraded rapidly. Some proteins are supposed to act for only a brief time, and must be promptly degraded. And some mutations lead to proteins that are unstable, and get marked for rapid degradation. See the Nobel site: http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2004/. This site is also listed for Internet resources for Molecular Biology: Transcription - eukaryotes.

A good Internet site to view the amino acids: http://www.chemie.fu-berlin.de/chemistry/bio/amino-acids_en.html. Also available in German.

This is part of a larger site from The Institute of Chemistry, Free University of Berlin, with diverse resources in general, organic, and biochemistry. This site is listed on my page of Internet resources: Chemistry - Miscellaneous.

To view some of the structure files, you need the RasMol viewer. See my RasMol page for a tutorial on using this program. Also see the Writing, drawing and viewing chemical formulas page.


For more about the properties of peptide bonds, which are amide linkages, see my page on Amides. The page discusses the non-basicity and the planarity of the amide linkage, and presents the resonance structures that account for these properties. This page was originally mentioned along with Ch 14, on amides.

The Univ Akron site, listed below as a General resource, includes animations of the processes of DNA replication, RNA synthesis and protein synthesis. They all simplify the processes, but are still helpful. The one on protein synthesis is probably the best. Go to http://ull.chemistry.uakron.edu/genobc/, choose Animations, and go to "Ch 21".

J Winkler, Misfolded proteins and Parkinson's disease. Engineering & Science Vol LXVIII #3, 2005, p 14. Available online: http://calteches.library.caltech.edu/4140/. This article is based on a public lecture, and much of it should be at a level appropriate for X402 students. It generally discusses proteins and how they fold, and focuses on the specific case of a protein whose misfolding is implicated in Parkinson's disease.

C Wong Po Foo et al, Novel nanocomposites from spider silk-silica fusion (chimeric) proteins. PNAS 103:9428-9433, 6/20/06. Silk protein is a classic example of a fibrous protein rich in (-sheets (p 439). It is a particularly interesting protein because of its strength. Silk strength depends both on the source and on the spinning technique. Silkworm silk and spider silk both get much attention, and one company is producing spider silk in goat milk. In this paper, they explore making composite materials, containing silk and silica -- somewhat like what is found in diatom skeletons. They start by making a chimeric protein that contains silk plus key regions of diatom proteins required to promote bio-silica formation. Available online: http://www.pnas.org/content/103/25/9428.abstract.

There are Musings posts about developments with silk, both from spider and silkworm. These include:
* Silk-clothed electronic devices that disappear when you are done with them (October 19, 2012).
* Spiders and violins (May 4, 2012).
* Spider silk: Can you teach an old silkworm new tricks? -- Update (February 11, 2012).

A Protein Primer: A Musical Introduction to Protein Structure. Assign pitches to the amino acids -- etc etc etc. Certainly fun, and possibly even a useful introduction to protein structure. Covers the genetic code and various levels of protein structure. The site has several MP3 files to illustrate the system. http://www.whozoo.org/mac/Music/Primer/Primer_index.htm. From M A Clark, Texas Wesleyan University.

For more related to this chapter, see my page of Molecular Biology Internet resources, especially the section on Protein synthesis. The level of that page is generally more advanced than this page, but there is considerable overlap.

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Metabolism (Ouellette 2/e supplemental handouts)

* Required

The web site for Worthington Biochemical Corp contains a nice Introduction to Enzymes, which they maintain for the benefit of beginning biology or biochem students. http://www.worthington-biochem.com/introBiochem/beginBiochem.html. This is a required reading assignment for my X402 class.

* Metabolic charts

The small metabolic chart I show is available online from Sigma, as a pdf file. Go to Sigma's Metabolic Pathways page, part of their Enzyme Explorer, http://www.sigmaaldrich.com/life-science/metabolomics/learning-center/metabolic-pathways.html. This page gives you the link to the pdf file; if you would like a paper copy, see the purchase information on the page.

That Metabolic Pathways page at Sigma, above, also includes additional resources on metabolism. There are several animations of metabolic processes, and a link to a list of enzymes by EC (Enzyme Commission) number.

The big chart I (sometimes) show is from Boehringer Mannheim, which is now part of Roche. The chart is called "Biochemical Pathways". It seems to be no longer available.

A smaller metabolic chart, approximately equivalent to the Sigma chart, is at http://www.bmb.leeds.ac.uk/illingworth/metabol/index.htm. It shows the metabolism of mammalian liver, but remember that much of this is universal. You can save the gif file that is shown or download a pdf file with a link just below; each is about 60 kB. From J A Illingworth at the Univ of Leeds.

* Journal articles listed in Further Reading

Many journal articles are available online, though free access may be restricted. I list here only occasional ones, that I know are open to free access. Others may have free access, and many more will be available to those who use the university access.

F Berg et al, The Uncoupling Protein 1 gene (UCP1) is disrupted in the pig lineage: A genetic explanation for poor thermoregulation in piglets. PLoS Genetics 2(8):e129, 8/06. If we could just burn our food without capturing the energy, we could eat more with less weight gain. A way to avoid energy capture would be to somehow dissipate the energy from NADH oxidation, avoiding coupling it to ATP formation. In fact, "uncoupling proteins" (UCP) allow just that. Mice have them, in brown fat. Humans have them, but only in infancy. Pigs do not have them, and this paper explores the genetic basis of that defect. Free online at: http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020129.

* Other

Physiology of Respiration. http://historyofscience.free.fr/Lavoisier-Friends/a_chap4_lavoisier.html. This page describes how Lavoisier made the connection between ordinary combustion and burning our food. From Jean Pierre Poirier author of "Lavoisier, Chemist, Biologist, Economist" (University of Pennsylvania Press, 1996). I have also listed this page under Internet Resources for Intro Chemistry: Reactions, and I have listed the larger Lavoisier site under Miscellaneous Chemistry Internet Resources: History.

A good source of the complete glycolysis pathway is http://www.bio.davidson.edu/Courses/Molbio/MolStudents/spring2005/Gemberling/protein.html. From a student at Davidson College. The page is on a specific enzyme, but includes the complete glycolysis pathway. You can use this to check yourself if you do Part 1 of the Glycolysis worksheet (my supplementary handout; see Metabolism), or you can just use it as a source of the pathway.

An extensive tutorial on oxidative phosphorylation is included in a fine collection of tutorials at Washington Univ (St Louis) that generally aim to show practical aspects of freshman chemistry. Go to their main site, http://www.chemistry.wustl.edu/~edudev/LabTutorials/, and choose "Energy for the Body: Oxidative phosphorylation". This tutorial includes a quite complex animation of the electron transfer process. Of course, while at the Tutorials site, look around for others that may interest you. (Another of this set, on the biochemistry of vision, is listed above, for Aldehydes and ketones.)

Electron transport and ATP formation. Dr Thomas Terry, Univ of Connecticut, has made available a couple of pages on these processes, including some nice animations. These are now archived: http://web.archive.org/web/20110720074531/http://www.sp.uconn.edu/~terry/images/anim/ETS.html. That page is "Animation of Electron Transport in Mitochondria", and it links to a second page, "Animation of ATP synthesis in Mitochondria".

The final enzyme in the oxidative phosphorylation sequence is the ATPase. This enzyme actually rotates in the membrane as it works to make ATP. The following two sites shows diagrams of this complex enzyme. The first shows a movie of the enzyme rotation, directly observed by attaching a visible propeller to the enzyme. The second has various animations. Both are parts of more extensive sites on metabolism.
* http://www.bmb.leeds.ac.uk/illingworth/oxphos/atpase.htm. From J A Illingworth, Univ of Leeds, UK.
* http://www.k2.phys.waseda.ac.jp/Movies.html. There are several movies listed for "Rotation of F1-ATPase" -- and other topics. From the Kinosita lab, on Single Molecule Physiology, Waseda University.

Recall the Metabolic Pathways page at Sigma, listed above under Metabolic Charts. It also includes additional resources on metabolism, with animations of metabolic processes, including the ATPase.

Rose M Chute (Lone Star College, in the Houston area) maintains an excellent set of Science Animations, Movies & Interactive Tutorial Links over a wide range of biology and the supporting chemistry. http://www.apchute.com/animatio.htm. Of most direct relevance at the moment: look at the section for AP2 (at the left); choose Cellular Respiration. But I encourage you to browse this whole site; I found the quality to be quite high.

For fun... some songs about metabolism:
* from Paul Price, of UC San Diego, for his Metabolic Biochemistry class: http://classes.biology.ucsd.edu/bibc102.SP07/Metabolic%20songs.html. (The songs are apparently from Harold Baum, The Biochemist's Songbook, Pergamon Press, 1982, ISBN 0-08-027370-X.)
* Kevin Ahern's Wildly Popular Metabolic Melodies, original songs from Kevin Ahern, Oregon State Univ: http://www.davincipress.com/metabmelodies.html.

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Spectroscopy (Ouellette 2/e Ch 18)

Although we do not discuss spectroscopy in X402, it is an important topic in university level organic chemistry. Ouellette's Chapter 18 is a good introduction, and problems are scattered throughout the book (typically at the end of the set of problems for each functional group). Here are some web sites with good presentations of aspects of spectroscopy. Some of these have good animations, and good practice problems.

Thanks to M. Farooq Wahab (Chemistry, University of Karachi) for help getting this section started, and for contributing many of the listings based on his teaching experiences.

http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/Spectrpy/spectro.htm. Introduction to Spectroscopy. Includes mass spectrometry (MS), ultraviolet-visible spectroscopy (UV-Vis), infrared spectroscopy (IR), nuclear magnetic resonance spectroscopy (NMR), plus links to other sources of information and practice problems. From W Reusch (Michigan State Univ), as part of his online textbook of organic chemistry, which is listed below under General.

http://www.chem.queensu.ca/FACILITIES/NMR/nmr/webcourse/. Online NMR course. From F Sauriol (Queen's Univ, Kingston, Ontario, Canada).

http://www.nmrdb.org/predictor. NMR simulation. Draw a molecule, and the web page will draw the expected NMR spectrum. To use it: Find the section labeled "How to proceed ?", at the right. Choose "1. Draw a molecule". Play a little and you will figure out the drawing program. When you have drawn the molecule, press the "Submit molecule" button at the bottom of the Draw window. Note that other options are available for providing the molecule information. (From Luc Patiny, Ecole Polytechnique Federale de Lausanne.)

http://www.ionsource.com. A commercial site, with a major section of educational information, Mass Spectrometry and Biotechnology Resource, by Andrew Guzzetta. Covers mass spectrometry, HPLC, and more.

Why is water blue? http://www.dartmouth.edu/~etrnsfer/water.htm. Discusses in both general and technical terms how the weak blue color of water is related to its structure, including the hydrogen bonding in liquid water. The evidence is based largely on analysis of the wavelengths of vibrational transitions, seen in visible and infra-red spectra. Interestingly, they predict and show that water with the heavy isotope of H, 2H (deuterium), is much less blue. From Charles Braun and Sergei Smirnov at Dartmouth. A delightful page, based on an article originally published in J Chem Educ (70:612, August 1993), but now enhanced with color figures. This page is also listed on my page of Internet resources for Introductory chemistry under Water.

Also see above section on Amino acids, proteins, genes, for an item on the 2002 Nobel Prize in Chemistry for the use of NMR and MS with proteins.

Also see Medicine: Color vision and color blindness section of my Internet resources: Biology - Miscellaneous page for information on the nature of light and color vision.

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Energy resources

Posts in my Musings newsletter on energy include...
* Added October 26, 2014. Fracking: Implications for energy usage and for greenhouse gases (October 26, 2014).
* Added September 30, 2014. Impact of watching movies on global warming (September 30, 2014).
* Added September 12, 2014. Solar energy: A more efficient way to boil water? (September 12, 2014).
* Added August 18, 2014. Quality of oil and gas wells -- fracking and conventional (August 18, 2014).
* Added May 2, 2014. Supercapacitors in the form of stretchable fibers -- suitable for clothing (May 2, 2014).
* Added April 8, 2014. When lightning strikes a tree... (April 8, 2014).
* Added April 7, 2014. Methane leaks -- relevance to use of natural gas as a fuel (April 7, 2014).
* Added January 21, 2014. Windmills for your cell phone? (January 21, 2014).
* Added January 6, 2014. A simple way to make a supercapacitor with high energy storage? (January 6, 2014).
* Added December 11, 2013. Could vibration (or loud music) improve the performance of a solar cell? (December 11, 2013).
* A better way to divide 6 by 2: A more efficient way to use sugar (November 10, 2013). This post is also noted above in the section Alkenes.
* Shale gas recovery using hydraulic fracturing (fracking) (October 7, 2013).
* An artificial forest with artificial trees (June 7, 2013).
* What if your house could sweat when it got hot? (November 30, 2012).
* Engineering E coli bacteria to convert cellulose to biofuel (December 13, 2011).
* Energy wastage: The set-top box (August 1, 2011).
* Making electricity in your windows: sharing the solar spectrum (July 5, 2011).
* A Christmas present: Using concentrated sunlight to split water and CO2 (February 18, 2011).
* Planning (November 23, 2010).
* Cellulosics for energy: an update (October 30, 2010).
* Joint Center for Artificial Photosynthesis (JCAP) (August 16, 2010).
* Hydrogen fuel cell cars (June 8, 2010).
* Making biofuels from cellulose (May 17, 2010).
* Your waste body heat (May 4, 2010).
* MIT invents a better bicycle wheel (April 24, 2010).
* Sustainable Energy - without the hot air (September 16, 2009).
* Materials for solar cells (March 10, 2009).
* Converting Oklahoma to natural gas (October 1, 2008).

Bioenergy Connection from the Energy Biosciences Institute (EBI): http://www.energybiosciencesinstitute.org/content/communication-materials#2. A magazine for the general public on the work of the EBI. This site is also listed under Internet resources: Miscellaneous -- Colleges and universities as an example of online publications from UC Berkeley highlighting research and other university activities.

Alternative energy for a sustainable future. A 2008 issue of Engineering and Science, the Caltech alumni magazine, was devoted to this topic. Good articles, written for the well-educated layman. Go to http://calteches.library.caltech.edu/710/, which is the table of contents for this issue, Volume LXXI, Number 2, 2008. Articles include "The Race for New Biofuels", by Frances H. Arnold; "Solar Fuels I: Rods and Stones", by Douglas L. Smith; "Solar Fuels II: The Quest for the Catalyst", by Harry B. Gray; "From Solar Fuel Back to Electricity", by Marcus Woo. Another good article from this magazine is listed below, under the title "Powering the planet".

Increase Your H2IQ -- an education page for the general public, from the Office of Energy Efficiency and Renewable Energy (EERE), US Department of Energy (DOE). Lots of information and resources. http://energy.gov/eere/fuelcells/increase-your-h2iq. (There is a link to the EERE home page at the top; among the other programs included at the EERE site: Biomass; Geothermal technologies; Solar energy technologies; Vehicle technologies; Wind and hydropower technologies.)

Biotechnology for Biofuels -- a new journal (2008). It is "an open access, peer-reviewed online journal featuring high-quality studies describing technological and operational advances in the production of biofuels from biomass". http://www.biotechnologyforbiofuels.com/.

There is great interest in making biofuels from cellulose rather than from starch. The disadvantage is the difficulty of breaking down cellulose. This difficulty is both inherent in the nature of cellulose and made worse by the presence of lignin. One approach to dealing with the latter is to develop trees with reduced lignin. Vincent Chiang, North Carolina State University, has developed trees with about half the lignin of natural trees. A news story on this work: Through Genetics, Tapping a Tree's Potential as a Source of Energy. November 20, 2007. http://www.nytimes.com/2007/11/20/science/20tree.html.

S Cheng & B E Logan, Sustainable and efficient biohydrogen production via electrohydrogenesis. PNAS 104(47):18871-3, 11/20/07. They use a modified microbial fuel cell. Applying a small voltage allows electrons to be released in the form of hydrogen gas. Free online at: http://www.pnas.org/content/104/47/18871.abstract.

Energy at Berkeley. An article in California, the UC Berkeley magazine for alumni, introducing the range of energy work done here. Lisa Margonelli, Start-up U, with subtitle "With global warming breathing down our necks, energy is hot. And at Berkeley, green ideals are teaming up with that other green - money." September 2007. Free online at: http://alumni.berkeley.edu/california-magazine/september-october-2007-green-tech/start-u.

Water as fuel? Purdue Univ engineers, led by Dr Jerry Woodall, announced an improved process for generating hydrogen. The key chemical reaction is aluminum + water reacting to give hydrogen gas plus aluminum oxide. In the context of a car, the idea is that the car could easily carry aluminum and water, and generate the hydrogen gas as needed. The car would then run on burning the hydrogen. The new work is on the development of a new alloy of aluminum that allows practical generation of hydrogen. This is all quite reasonable. However, it has been misrepresented by some as using water as a fuel -- with the promise of a cheap and plentiful fuel. In fact, the aluminum is consumed in the process, as described above. The process depends on recycling the aluminum oxide product back to aluminum metal, a process done eletrolytically at considerable expense. It is this step that limits the economic merit of the process. Some have skipped over this point entirely, thus misrepresenting the potential of the process. The Purdue group is quite aware of this, and they discuss it in the item listed below. They offer a proposal which they think might adequately address it; I am skeptical of their proposal, but this is not the place for a detailed economic analysis. At least, the Purdue announcement presents not only an interesting technical development, but also the key economic hurdle it must overcome. Press release from Purdue: New process generates hydrogen from aluminum alloy to run engines, fuel cells. May 15, 2007. https://news.uns.purdue.edu/x/2007a/070515WoodallHydrogen.html.

Powering the planet. An article in the Caltech alumni magazine Engineering and Science Vol LXX #2, p 12, 2007. Based on a lecture, May 2007, by Caltech chemistry professor Nate Lewis. http://calteches.library.caltech.edu/4259/ Lewis emphasizes that the more important driving force behind developing new energy sources is the carbon problem, more than any immediate threat of running out of fossil fuels. Also see Lewis's web site at http://nsl.caltech.edu. Try the sections on Research and on Energy. A series of more recent energy articles in this same magazine are listed above, under the title "Alternative energy for a sustainable future".

Fossil fuels. A Nature web focus site on "fossil fuels and society", including the feature set listed under Further Reading (Ch 3) as Hall et al (2003), plus more.
http://www.nature.com/nature/focus/fossilfuels/index.html.

Rating fuels. Whether biofuels are or are not environmentally "better" than the usual fossil fuels depends on the details. Berkeley scientists have proposed a rating system so you can tell. The rating system would apply to specific processes, so that bio-ethanol would have different ratings depending on how it is produced. A UC Berkeley press release, "Green Biofuels Index would aid consumers, market". April 17, 2007. http://www.berkeley.edu/news/media/releases/2007/04/17_greenindex.shtml. The press release links to the full work.

Biofuels page from the US DOE: http://genomicscience.energy.gov/biofuels/.


More from Berkeley...

The Helios project, at Lawrence Berkeley Lab. Broadly, the goal of Helios is to develop new renewable energy sources, using both biological and chemical processes. http://www2.lbl.gov/LBL-Programs/helios-serc/index.html.

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General

Karen Timberlake is the author of a well-regarded textbook for introductory chem, including organic and biochem. She has posted many useful supplementary materials at her site: http://www.karentimberlake.com. The powerpoint presentations, in the "CheModules" section, include practice problems at a fairly basic level. Also see "Quizzes".

http://ull.chemistry.uakron.edu/genobc/. James K Hardy (University of Akron) has made available materials for a similar course. You can view his set of slides, by clicking on the chapter title. You can also view a set of animations.

Ron Rinehart, of nearby Monterey Peninsula College, has a web site for a course at about our level: http://www.mpcfaculty.net/ron_rinehart/30B/default.htm. You may find some of his materials (lecture notes, lab notes) and links useful. Also, check his page for Chem 12, an organic chemistry course.

The following sites are from instructors of general organic chemistry courses, and contain useful pages on various organic topics.
- From Dr W Reusch, Michigan State University: http://www2.chemistry.msu.edu/faculty/reusch/VirtTxtJml/intro1.htm.
- From Dr Thomas Newton, University of Southern Maine:
   * http://www.biologie.uni-hamburg.de/b-online/library/newton/Chy251_253/Topics.html
      and
   * http://www.biologie.uni-hamburg.de/b-online/library/newton/Chy251_253/Topics2.html

Specific topics from the Newton site are referred to above in the sections Alkenes and Aromatic compounds.

The Newton site is now maintained at the University of Hamburg, by Alice Bergfeld & Peter V Sengbusch; the URLs included above reflect that. Interestingly, it is part of a diverse collection of sites under the banner of Botany Online -- The Internet Library - Teaching Botany And Related Topics. The home page for that site is http://www.biologie.uni-hamburg.de/b-online/library/catalog.htm. Look around; it's quite a collection. That site is also listed on my page Internet resources: Biology - Miscellaneous in the section Biology: plants.

http://www.ochem4free.info/node/1. Organic Chemistry for free, an online intro organic book, by Richard & Sally Daley. This book is organized somewhat differently from most organic books. The primary organization is by reaction mechanism, rather than by functional group. Since we do little reaction mechanism in this course, this could be confusing at first. But for those going on with more organic, this book can be a useful complement.

http://www.rpi.edu/dept/bcbp/molbiochem/MBWeb/mb1/MB1index.html. Biochemistry of Metabolism, an extensive set of materials for a biochem course, from Joyce Diwan, Renssellaer.

Medical Biochemistry textbook, from Michael W King, Indiana University School of Medicine - Terre Haute. http://themedicalbiochemistrypage.org/. Also in Spanish.

Kimball's Biology Pages. An excellent biology glossary, plus lots of information. From Dr John Kimball, the biology textbook author retired from Harvard. In fact, the site is almost an online textbook in biology. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/. (This site is also listed for the Molecular Biology course, Ch 1 as a general source of background biology information, and it is listed under Biology: books and glossaries on the Internet resources: Biology - Miscellaneous page.)


For IUPAC naming information for organic chemicals, check the following two sites. The first has the basic IUPAC rules. The second is more comprehensive, but probably more confusing.
1. http://www.acdlabs.com/iupac/nomenclature/
2. http://www.chem.qmul.ac.uk/iupac/

http://www.organicworldwide.net. Organic Chemistry Resources Worldwide, a broad source of organic chemistry information.

Some of the "General" sites listed here -- and many more -- are also listed on my page of Internet resources: Miscellaneous or Internet resources: Chemistry - Miscellaneous. Students are encouraged to browse that page, as well as Internet resources listed for other Chemistry and Molecular Biology classes. All of those are available from the List of pages of Internet resources.

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Last update: November 26, 2014