Further reading: Old articles

Introduction

Articles for:
   Chemistry (Intro, General)
   Chemistry (Organic, biochemistry)
   Molecular biology

Other sources of Further reading at this web site

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Introduction

This is an archive of older articles that used to be listed in one or another chapter handout. I try to limit the handouts to fairly recent items, but some articles seem worth keeping -- so here are some of them. This page is loosely organized by course and topic, but browsing is encouraged; one reason for including some of these is that they are of wider interest.
 
Links to some articles are shown, when I am fairly sure that they are freely available online. For now, this applies mainly to articles in Science (registration -- free -- may be required for full access). Many of the other articles are available, certainly from UC computers.

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Chemistry (Intro, General)

N M Senozan & M P Christiano, Iron as nutrient and poison. J Chem Educ 74:1060, 9/97.

T P Silverstein, The real reason why oil and water don't mix. J Chem Educ 75:116, 1/98. A discussion -- in chemical terms, with thermodynamic data -- of the "hydrophobic" interaction. The key point is that the effect is driven by entropy, with both solute and solvent being restricted when a hydrocarbon dissolves in water. (Enthalpy changes for dissolving hydrocarbons in water are actually favorable, in many cases.) Silverstein also discusses why methane is quite soluble in water at low temperature with high pressure -- leading to the storage of considerable amounts of hydrocarbons in cold oceans at great depths.

G Giuliani et al, Oxygen isotopes and emerald trade routes since antiquity. Science 287:631, 1/28/00. (+ News, Stokstad, p 562.) They use measurements of oxygen isotopes to distinguish the source of gemstones. The Giuliani article is free online at: http://science.sciencemag.org/content/287/5453/631.

J E Posey & F C Gherardini, Lack of a role for iron in the Lyme disease pathogen. Science 288:1651, 6/2/00. The insolubility of Fe(III) presents a serious problem for most aerobic organisms. Fe(III), the common form of Fe under oxidizing conditions, is generally essential, but is quite insoluble. Thus most organisms, from bacteria to humans, have complex systems for obtaining the Fe they need. Bacteria that invade humans have systems for obtaining Fe from the host. Here, Posey & Gherardini show that a bacterium with a very small genome (Borrelia burgdorferi, the causal agent of Lyme disease) has "learned" to live without Fe. One reason it can grow without Fe is apparently that it uses Mn for some functions where Fe is more commonly used. Free online at: http://science.sciencemag.org/content/288/5471/1651.

1) K E Kolb & D K Kolb, Glass - Sand + Imagination. J Chem Educ 77:812, 7/00. 2) S J Hawkes, Glass doesn't flow and doesn't crystallize and it isn't a liquid. J Chem Educ 77:846, 7/00. A couple of informative and delightful articles about a common and complex solid. (The issue also contains an article on an artificial glass, which is listed here under Chisholm 7/00.)

G Frenking, Chemistry: Another noble gas conquered. Nature 406:836, 8/24/00. News. Discussion of synthesis of a "stable" compound of argon, HArF. It is stable under some rather special conditions, below 27 K in a matrix of solid Ar. Nevertheless, one more element can no longer be called "inert." Interestingly, they speculate that the method used to make this compound might work for Ne and He -- the only two elements left for which no stable compounds have been made. Also see Khriachtchev, 6/03 for some krypton chemistry.

L Rosenfeld, Discovery and early uses of iodine. J Chem Educ 77(8):984, 8/00. Iodine is a rather rare element, but one essential for human health, because of one specific role. This article tells how the element was discovered, and how its role in human health was worked out.

J-M Tarascon & M Armand, Issues and challenges facing rechargeable lithium batteries. Nature 414:359, 11/15/01. Part of a feature section on "Materials for clean energy". Other articles include: photoelectric cells, fuel cells, hydrogen storage, superconductors.

A S Ellis et al, Chromium isotopes and the fate of hexavalent chromium in the environment. Science 295:2060, 3/15/02. (+ News, Blowes, p 2024.) Cr is both biologically and geologically important. Cr(VI) is toxic -- a carcinogen; Cr(III) is probably a useful trace nutrient. The former is quite soluble, the latter rather insoluble, especially under geological conditions. Groundwater contamination, as from industrial sources, is typically the toxic Cr(VI). The current work reports methodology to track Cr in groundwater, using isotope analysis. This may also be useful in evaluating water treatments. The News story is a good readable introduction to the Cr issues. The Ellis article is free online at: http://science.sciencemag.org/content/295/5562/2060.

T Walczyk & F von Blanckenburg, Natural iron isotope variations in human blood. Science 295:2065, 3/15/02. Iron is a critical nutrient for humans (and for all aerobic organisms). However, it can be a problem nutrient, because the common form of iron, iron(III), is quite insoluble. In humans, absorption is a complex issue. Here they show that the ratio of iron isotopes varies among individuals, and among tissues in an individual. Some of the reasons are understood; they suggest that studying iron isotope ratios in human blood could be useful in understanding iron metabolism, including individual differences. Free online at: http://science.sciencemag.org/content/295/5562/2065.

K Powell, Heavy elements: A very brief encounter. Nature 418:815, 8/22/02. News. The work discussed here explores the chemistry of hassium (Hs; Z=108), using only seven atoms of a recently discovered isotope that has a half life of about ten seconds. It behaves about as expected for its group. A paper on the chemistry of ununbium (Z=112), from May 2007, is listed in the Ch 10 handout.

T Mitsui et al, Water diffusion and clustering on Pd(111). Science 297:1850, 9/13/02. They watch individual water molecules and clusters move across a metal surface, using a form of atomic force microscopy. They show that small clusters move more quickly than single molecules, but larger clusters move more slowly. Why? They suggest that the precise geometry of single water molecules makes it hard for them to jump from one binding spot on the surface to another, whereas small clusters, which make more contacts, can bridge between binding spots better. On the other hand, larger clusters bind too tightly to move much. Free online at: http://science.sciencemag.org/content/297/5588/1850.

P Moller & A J Sierk, Nuclear physics: Into the fission valley. Nature 422:485, 4/3/03. News. Discussion of some of the issues in making new elements. New elements are made by fusing two lighter nuclei, and there seem to be competing reactions -- including fission of the new nuclei, particularly during the intermediate stages of forming a new nucleus. Some of this is rather technical, but browsing this news story may be fun and somewhat useful. Remember that the "reason" for making new elements is to test theories of nuclear stability. More about new elements is on the page of Intro Chem Internet Resources.

L Khriachtchev et al, A gate to organokrypton chemistry: HKrCCH. JACS 125:6876, 6/11/03. The first compound of a noble gas was made in the early 1960s. The first reasonably legitimate argon compound, HArF, was reported in 2000 (Frenking, 8/00). Here is a report of a krypton compound, which they think may be useful as an intermediate in carrying out reactions with certain organic compounds.

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Chemistry (Organic, biochemistry)

C M Friend, Catalysis on surfaces. Sci Amer 4/93, p 74. Specific reactions discussed include: breakdown of NO and CO in catalytic converter; desulfurization of fuels.

J P Changeux, Allosteric proteins: from regulatory enzymes to receptors. BioEssays 15:625, 9/93. A key player in the development of the idea of allostery tells his story. Part of the work was done in the Molecular Biology Dept at UC Berkeley.

N Kurti & H This-Benckhard, Chemistry and physics in the kitchen. Sci Amer 4/94, p 66. Well, it is at least partially about fats.

N Barkal & S Leibler, Robustness in simple biochemical pathways. Nature 387:913, 6/26/97. (+ accompanying news item by Hartwell, p 855.) The set of biochemical pathways can be thought of as a computational device, for ensuring the correct amount of each required chemical. Here, they analyze one group of pathways, using computer simulation, and show that the network is "robust" -- that the result is not very sensitive to changes in the inputs, because of all the interconnections. They argue that this should be so.

E Doyle, Trans fatty acids. J Chem Educ 74:1030, 9/97. Chemical processing of fats, such as in partial hydrogenation, can lead to trans double bonds, thus making what is referred to as "trans fatty acids" (TFA). TFA are now believed to be a harmful form of fat, perhaps worse than saturated fat. The FDA has announced a rule that will require TFA content to be shown on nutrition labels. This article, though somewhat dated, is a good introduction to TFA basics.

R Hoffmann, Dobereiner's lighter. American Scientist 86:326, 7/98. http://www.jstor.org/stable/27857054. A copy is freely available from the author: http://www.roaldhoffmann.com/sites/all/files/dobereiners_lighter.pdf. One of the first reactions one learns in organic chem is hydrogenation of alkenes. A noble metal catalyst, such as platinum, is used. The Pt works because the H2 adsorbs to the surface of the metal. Under appropriate conditions, Pt can catalyze fire production -- from H2 + O2. Whence the H2? From the common reaction of Zn + H2SO4. Delightful article.

B Piasecki et al, Is combustion of plastics desirable? Amer Sci 86:364, 7/98. An analysis of whether it would make more sense to burn plastic than to bury it.

P E Marszalek et al, Polysaccharide elasticity governed by chair-boat transitions of the glucopyranose ring. Nature 396:661, 12/17/98. Polysaccharides are common biological materials, and they stretch. What is the molecular basis of that stretching? Here, they show that stretching is due to a change in the ring conformation, from chair to boat. Part of the work involves observing the stretching behavior of single molecules, using atomic force microscopy (AFM). For more about AFM, see my web page for Internet - Intro Chem.

P A Kiberstis, Mitochondria make a comeback. Science 283:1475, 3/5/99. This is the introduction to a feature section on mitochondria, with articles on mitochondrial genetics, diseases, and biochemistry.

C J Pereira, Perspectives: Chemical engineering -- New avenues in ethylene synthesis. Science 285:670, 7/30/99. News. Discusses new technical developments in the production of ethene (ethylene) from petroleum, by catalytic dehydrogenation of ethane. The article contains a pie chart showing what ethylene is used for -- about 24 billion kg in the US in 1998, mostly for plastics.

S H Leung, Amino acids, aromatic compounds, and carboxylic acids: How did they get their common names? J Chem Educ 77:48, 1/00. For fun. (Erratum. Leung incorrectly says that L-cysteine is S; in fact, it is R. You should be able to verify this. This point was noted by G Lentini, JCE 79:558, 5/02. The point is also raised in a question on my Practice quiz: Amino acids and proteins.)

D S Goodsell, Biomolecules and nanotechnology. Amer Sci 88:230, 5/00. http://www.americanscientist.org/issues/feature/2000/3/biomolecules-and-nanotechnology. Goodsell discusses the organization of biomolecules, mainly proteins, and considers the implications for designing useful molecule-sized devices. Lots of pictures!

M S Chisholm, Artificial glass - The versatility of poly(methyl methacrylate) from its early exploitation to the new millennium. J Chem Educ 77:841, 7/00. Nice discussion of the history and properties of an addition polymer -- commonly known as Plexiglas or Lucite (Ouellette Table 4.2). (The issue also contains some articles on glass, which are listed here under Kolb 7/00.)

R D Hancock & B J Tarbet, The other double helix - The fascinating chemistry of starch. J Chem Educ 77:988, 8/00. Issues include how plants lay down starch granules, how iodine stains starch, and how starch behaves during cooking. Much more starch is used for industrial purposes than for food.

K E Berge et al, Accumulation of dietary cholesterol in sitosterolemia caused by mutations in adjacent ABC transporters. Science 290:1771, 12/1/00. (Plus accompanying news story: H Allayee et al, Biochemistry: An absorbing study of cholesterol. Science 290:1709, 12/1/00.) Cholesterol is characteristic of animal cell membranes. Plants contain, instead, a closely related sterol, called sitosterol. In general, animals do not absorb the plant sterol. However, there are people who have a genetic disease that allows them to absorb sitosterol; they have high levels of cholesterol, with the resulting problems. This article discusses sterol absorption, and the discrimination of plant and animal sterols. The Berge article is free online at: http://science.sciencemag.org/content/290/5497/1771.

1) R Kleinberg & P Brewer, Probing gas hydrate deposits. Amer Sci 89:244, 5/01.
2) C Zimmer, Biogeochemistry: 'Inconceivable' bugs eat methane on the ocean floor. Science 293:418, 7/20/01. News.
3) R E Pellenbarg & M D Max, Gas hydrates: From laboratory curiosity to potential global powerhouse. J Chem Educ 78:896, 7/01.
4) D Adam, Methane hydrates: Fire from ice. Nature 418:913, 8/29/02. News feature.
Recent articles on an intriguing subject, methane gas deposits on the ocean floor. Although methane is usually considered to be insoluble in water, in fact methane and water form an unusual cluster structure under high pressure. The practical reason for being interested? This could be quite an energy reserve, if only we could figure out a practical way to harvest it. The Zimmer news story discusses recent work on anaerobic biodegradation of methane, a major process near these methane deposits in the ocean. More in the Organic/Biochem Ch 3 handout [pdf file]; see "Further Reading" section.

R G Hollingsworth et al, Pest control: Caffeine as a repellent for slugs and snails. Nature 417:915, 6/27/02. They suggest the use of a 1-2% solution; weaker solutions, on the order of ordinary coffee, may have some effect.

S Imai et al, Plant biochemistry: An onion enzyme that makes the eyes water. Nature 419:685, 10/17/02. The lachrymatory (tear-inducing) factor (LF) of onions is made from an S-containing cellular compound when an enzyme is activated upon cell breakage. Here they show that this is a two-step process, and that step 2 also requires an enzyme. This second, enzyme-catalyzed, step is in competition with a spontaneous reaction that produces a flavor component. They thus speculate that lowering the level of the enzyme that makes the LF could lead both to more flavor and fewer tears.

I J Buerge et al, Caffeine, an anthropogenic marker for wastewater contamination of surface waters. Environ Sci Technol 37:691-700, 2/15/03. Amusing, but also interesting.

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Molecular biology

F Crick, Central dogma of molecular biology. Nature 227:561, 8/8/70. Available online at https://profiles.nlm.nih.gov/ps/access/SCBCCH.pdf. (The source given here is the Profiles in Science site.) This is the article in which Crick addresses attacks on the central dogma that were stimulated by the discovery of reverse transcriptase (RNA --> DNA). He clarifies what he really meant, and how reverse transcription fits right in. I had occasion to re-read this classic recently; I heartily recommend it! The Crick article that Weaver lists for Ch 3 is the original presentation of the Central Dogma. (This site is also included in the section of my Internet - Molecular Biology page for Chapter 3.)

How do you find a copy of an article, such as the one above? One good way is to use Google Scholar. http://scholar.google.com Go to Advanced Search. Put a part of the title in the "with the exact phrase" box, set "where the words occur" to "in the title of the article". Optionally, you can add an author or date; however, title alone is often sufficient. Using Google Scholar for this Crick article yields several sources.

H Varmus, Reverse transcription. Sci Amer, 9/87, p 56. RT is the key first enzyme in making a cDNA library. It is found naturally in the retroviruses, some eukaryotic transposons, and occasionally in bacteria. (Varmus was formerly at UCSF, and was head of NIH.)

K B Mullis, The unusual origin of the polymerase chain reaction. Sci Amer 4/90. p 56. The inventor of the polymerase chain reaction (PCR) tells his story. The work was done at a local biotech company. (Mullis shared the 1993 Nobel prize in chemistry.)

T Lindahl, Facts and artifacts of ancient DNA. Cell 90:1, 7/11/97. Minireview. The focus is the report (in same issue) of isolation and analysis of DNA from a (dead) Neandertal man. The analysis indicates that Neandertal man represented a distinct genetic lineage, not a precursor to modern man. A big issue in any such analysis of "ancient DNA" is establishing the validity of the DNA. Lindahl addresses this. (The following News item is related, and very good: R Ward & C Stringer, A molecular handle on the Neanderthals. Nature 388:225, 7/17/97.)

R V Miller, Bacterial gene swapping in nature. Sci Amer 1/98, p 67. A brief discussion of natural gene transfer between bacteria in nature, by conjugation, transformation or transduction. This is interesting partly for its entirely natural implications in evolution but also in the context of introducing genetically modified organisms into the environment.

A A Lucas et al, Revealing the backbone structure of B-DNA from laser optical simulations of its X-ray diffraction diagram. J Chem Educ 76:378, 3/99. They describe an optical simulation of the X-ray analysis of DNA, to help students visualize how the X-ray data revealed features of the DNA structure.

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Other sources of Further reading at this web site (other than this page)

* Chapter handouts for    Chemistry (Intro, General)    Chemistry (Organic, biochemistry)    Molecular biology
* Materials posted under Biotechnology in the News. BITN
* A page focusing on articles with a medical emphasis; this page relates most directly to the Lipids and Metabolism sections of the Organic/Biochem course, but is becoming more general. Medical topics
* A page describing how to find classic papers. Classic papers


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Last update: August 4, 2017