Jeffrey L. Bada

Amino Acid Racemization and the Preservation of Ancient DNA

The extent of racemization of aspartic acid, alanine, and leucine provides criteria for assessing whether ancient tissue samples contain endogenous DNA. In samples in which the D/L ratio of aspartic acid exceeds 0.08, ancient DNA sequences could not be retrieved. Paleontological finds from which DNA sequences purportedly millions of years old have been reported show extensive racemization, and the amino acids present are mainly contaminates. An exception is the amino acids in some insects preserved in amber.

Aspartic acid racemisation in dentine as a measure of ageing

THE L-amino acids initially present in bone protein undergo slow racemisation over geological time at a rate which is proportional to temperature1,2. We have shown3 that at the human body temperature of ∼37°C aspartyl residues in tooth enamel protein also undergo racemisation at a rate which corresponds to an enrichment in the D-aspartic acid content of ∼0.1% per year. No D-aspartic acid increase was detected in haemoglobin, a protein with a more rapid turnover. We concluded that D-aspartyl residues accumulate in the metabolically stable protein in tooth enamel during the human lifetime as a result of in situ racemisation. We proposed that the irreversible first-order rate equation calculated from the enamel results could be used to deduce the age of any stable protein from a long lived mammal and thus the age of the organism itself. The error among samples from old individuals was large, however, probably because attrition and caries reduce the amount of uncontaminated enamel, and thus tend to limit the usefulness of tooth enamel for age determinations. In this report, we show that tooth dentine is a more suitable material, and the extent of aspartic acid racemisation in this fraction can be used as a reliable indicator of mammalian age.

Aspartic acid racemisation in the human lens during ageing and in cataract formation

D-ASPARTIC acid has been shown to accumulate with age in human tooth enamel1 and dentine2 at a rate of about 0.1% yr−1. We have predicted that racemisation should take place in any metabolically stable protein in long-lived mammals and that, as a consequence of racemisation, these proteins will have altered conformations which would probably produce changes in their biological activities or chemical properties3. We have extended these studies to soft tissue proteins, in particular those in the human lens. The proteins in the central portion of the lens are among the most stable in the human body4. Numerous changes in the properties of the lens proteins occur with age and cataract formation—denaturation5, increasing pigmentation6, cross linking5,6 insolubility6–9, and fluorescence10. Pirie11 has suggested that physicochemical processes may be responsible for these changes. We report here the results of D/L enantiomeric analyses of normal human lenses and cataracts: aspartic acid racemisation was seen during ageing and cataract formation.

Extraterrestrial Organic Compounds in Meteorites

Many organic compounds or their precursorsfound in meteorites originated in the interstellar or circumstellarmedium and were later incorporated intoplanetesimals during the formation of thesolar system. There they either survivedintact or underwent further processing tosynthesize secondary products on themeteorite parent body.The most distinct feature of CI and CM carbonaceouschondrites, two typesof stony meteorites, is their high carbon content(up to 3% of weight), either in theform of carbonates or of organic compounds. The bulkof the organic carbon consistsof an insoluble macromolecular material with a complexstructure. Also present is asoluble organic fraction, which has been analyzedby several separation and analyticalprocedures. Low detection limits can be achievedby derivatization of the organicmolecules with reagents that allow for analysisby gas chromatography/massspectroscopy and high performance liquidchromatography. The CM meteoriteMurchison has been found to contain more than70 extraterrestrial amino acids andseveral other classes of compounds includingcarboxylic acids, hydroxy carboxylicacids, sulphonic and phosphonic acids, aliphatic,aromatic and polar hydrocarbons,fullerenes, heterocycles as well as carbonylcompounds, alcohols, amines and amides.The organic matter was found to be enriched indeuterium, and distinct organiccompounds show isotopic enrichments of carbon andnitrogen relative to terrestrialmatter.

The fluorescence of dissolved organic matter in seawater

A total of 28 vertical profiles of seawater fluorescence was measured in the Sargasso Sea, the Straits of Florida, the Southern California Borderlands, and the central Pacific Ocean. In all cases, surface seawater fluorescence was low as a result of photochemical bleaching which occurs on the timescale of hours. Fluorescence of deep water was 2–2.5 times higher than that of surface waters, and was constant, implying a long residence time for fluorescent organic matter, possibly of the order of thousands of years. Fluorescence correlates well with nutrients (NO3−, PO43−) in mid-depth waters (100–1000 m) in the Sargasso Sea and the central North Pacific, consistent with results in the central Pacific and the coastal seas of Japan. This suggests that regeneration or formation of fluorescent materials accompanies the oxidation and remineralization of settling organic particles. The various sources and sinks of fluorescent organic matter in the global oceans are assessed. The major sources are particles and in situ formation; rivers, rain, diffusion from sediments, and release from organisms are minor sources. The major sink is photochemical bleaching.

Extraterrestrial amino acids in Orgueil and Ivuna: Tracing the parent body of CI type carbonaceous chondrites

Amino acid analyses using HPLC of pristine interior pieces of the CI carbonaceous chondrites Orgueil and Ivuna have found that β-alanine, glycine, and γ-amino-n-butyric acid (ABA) are the most abundant amino acids in these two meteorites, with concentrations ranging from ≈600 to 2,000 parts per billion (ppb). Other α-amino acids such as alanine, α-ABA, α-aminoisobutyric acid (AIB), and isovaline are present only in trace amounts (<200 ppb). Carbon isotopic measurements of β-alanine and glycine and the presence of racemic (D/L ≈ 1) alanine and β-ABA in Orgueil suggest that these amino acids are extraterrestrial in origin. In comparison to the CM carbonaceous chondrites Murchison and Murray, the amino acid composition of the CIs is strikingly distinct, suggesting that these meteorites came from a different type of parent body, possibly an extinct comet, than did the CM carbonaceous chondrites.

The Miller volcanic spark discharge experiment

Millers 1950s experiments used, besides the apparatus known in textbooks, one that generated a hot water mist in the spark flask, simulating a water vapor‐rich volcanic eruption. We found the original extracts of this experiment in Millers material and reanalyzed them. The volcanic apparatus produced a wider variety of amino acids than the classic one. Release of reduced gases in volcanic eruptions accompanied by lightning could have been common on the early Earth. Prebotic compounds synthesized in these environments could have locally accumulated, where they could have undergone further processing.

The chemical conditions on the parent body of the murchison meteorite: Some conclusions based on amino, hydroxy and dicarboxylic acids

Amino and hydroxy acids have been identified in the Murchison meteorite. Their presence is consistent with a synthetic pathway involving aldehydes, hydrogen cyanide and ammonia in an aqueous environment (Strecker-cyanohydrin synthesis). From the various equilibrium and rate constants involved in this synthesis, four independent estimates of the ammonium ion concentrations on the parent body at the time of compound synthesis are obtained; all values are about 2 x 10(-3) M. Succinic acid and beta-alanine have also been detected in the Murchison meteorite. Their presence is consistent with a synthesis from acrylonitrile, hydrogen cyanide and ammonia. Using the equilibrium and rate constants for this synthetic pathway, and the succinic acid/beta-alanine ratio measured in the Murchison meteorite, an estimate of the hydrogen cyanide concentration of 10(-3) to 10(-2) M is obtained. Since hydrogen cyanide hydrolyzes relatively rapidly in an aqueous environment (t1/2 < 10(4) yrs) this high concentration implies a period of synthesis of organic compounds as short as 10(4) years on the Murchison meteorite parent body.

A review of the geochemical applications of the amino acid racemization reaction

Abstract A method of geochronology based on the chemical racemization of amino acids has been developed within the last few years. The various amino acids that make up the proteins of all living organisms consist virtually entirely of the l -enantiomer. After death, the l -enantiomer for each amino acid is slowly racemized over geological time and eventually forms an equilibrium mixture consisting of equal amounts of the d - and l -enantiometer. The increase in D/L ratio can be used to obtain a measure of the time that has elapsed since the organism died. The range of applicability of this method is the Pleistocene and may eventually be useful throughout the Pliocene in some cases. This paper presents a review of the literature on these applications as well as several suggested areas for future research. Unlike radionuclide decay rates, chemical reaction rates are sensitive to changes in such common environmental parameters as temperature, pH, solvent-medium, etc. For this reason, kinetic studies have been conducted at elevated temperatures in various “fossil-types” in order to simulate the changes that occur over long periods of time at the low temperatures found on the surface of the earth. Such studies, while of somewhat limited value for precise extrapolation, do nevertheless provide valuable information on which to base the theoretical concepts necessary for a complete understanding of the geochemical implications of the racemization reaction. Skeletal remains form the most suitable fossils for chronological study. Proteinaceous material is found embedded within the carbonate exoskeletons of invertebrates and the phosphatic endoskeletons of vertebrates. Most of the geochemical racemization studies have been conducted on foraminiferal shells and on bones. However, some work has also been reported on shells of other invertebrates, marine and lacustrine clays, and a few abiogenic concretions. Since the racemization reaction is temperature dependent, it has been used as a paleothermometer to estimate the average temperature to which bones and shells of independently known age have been exposed since their deposition. These average temperatures as a function of time have then been converted into estimates of the magnitude of the Holocene postglacial/Wisconsin glacial temperature change on land. They have also been used to obtain estimates of the “time-averaged” thermal gradient in deep-sea sediments using foraminifera isolated from the sediments.

Amino acid racemization reactions and their geochemical implications

The amino acids present in living organisms consist mainly of the L-enantiomers. Over long periods of geological time, amino acids undergo a slow racemization, producing the z~-enantiomers. The amino acids contained in fossil materials show an increasing extent of racemization with age. The kinetics and mechanism of amino acid racemization and the applications of this reaction in geochronology and paleothermometry are discussed.