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Organic Geochemistry Wk. 1• Acetogenic lipids- most common form of sedimentary
lipid– Fatty acids and derivative lipids– Fatty alcohols and wax esters (bacteria, algae,
– Polymethylenic biopolymers (algeanans marine and non-marine microalgae; cutans)
Introduction To Organic Geochemistry 2nd Edition KillopsS and Killops V
An Introduction to Organic Geochemistry explores the fate of organic matter of all types, biogenic and man-made, in the Earth System.
The global carbon cycle and related elemental cycles. The influence of the evolution of life on the carbon cycle. Production and chemical composition of biogenic matter. Degradation vs. preservation of sedimentary organic matter in various environments. Biological and thermal alteration in sediment, soil and water column. Molecular and isotopic stratigraphy. Greenhouse gases and palaeoclimatic variation. Man's influence on biogeochemical cycles and global climate change. Factors affecting the behaviour of pollutants in the environment.
This image has been removed due to copyright restrictions.Please see the book cover of Gaines, S. M., G. Eglinton, J., Rullkötter. "Echoes of Life." In Echoes of life: What Fossil M
Oxford University Press, New York.2009. New York.
This image has been removed due to copyright restrictions.Please see the book cover of "An Introduction to Organic Geochemistry."
n-Alkyl lipids are essentially polymers of acetate – acetogenic lipids
Acetate Methyl-C and Carboxyl-C are isotopically distinct and determined by its metabolic source and the profound isotope effect of pyruvate dehydrogenase
Thermophilic bacteria and some SRBsn-1-akylglycerol monoetherssn-1,2-dialkylglycerol dietherssn-1,2-alkylacyl glycerols
Archaeasn-2,3-diakylglycerol diethers
Archaea
Bacteria & EukaryaCH2
CH2
H2C
H2C
C
C
C
O
O
O
O
O
O
C
C
C
H
H
O
O
O-O-P
=
O-
OO
O-P
=
=
=
Branched isoprene chains
Unbranched fatty acids Ester linkage
Ether linkage
L-glycerol
D-glycerol
Figure by MIT OpenCourseWare.
Lip-1.13. Stereospecific Numbering. In order to designate the configuration of glycerol derivatives, the carbon atoms of glycerol are numbered stereospecifically. The carbon atom that appears on top in that Fischer projection that shows a vertical carbon chain with the hydroxyl group at carbon-2 to the left is designated as C-1. To differentiate such numbering from conventional numbering conveying no steric information, the prefix 'sn' (for stereospecificallynumbered) is used. This term is printed in lower-case italics, even at the beginning of a sentence, immediately preceding the glycerol term, from which it is separated by hyphen. The prefix 'rac-' (for racemo) precedes the full name if the product is an equal mixture of both antipodes; the prefix 'X-' may be used when the configuration of the compound is either unknown or unspecified (cf. Lip-1.10).Examples:
(a) sn-glycerol 3-phosphate for the stereoisomer (VII = VIII), previously known as either L-α-glycerophosphate or as D-glycerol 1-phosphate;(b) rac-1-hexadecylglycerol;(c) 1,2-dipalmitoyl-3-stearoyl-X-glycerol.
Trans fatty acids do occur in nature but, our diet, largely result from processing
These images have been removed due to copyright restrictions.Please see the three images on http://library.med.utah.edu/NetBiochem/FattyAcids/3_3.html.
Trans fats in foodThough some trans fats are found naturally (in the milk and body fat of ruminants such as cows and sheep), the majority are formed during the manufacture of processed foods (see below for details). In unprocessed foods, most unsaturated bonds in fatty acids are in the cis configuration.Trans fat from partially hydrogenated vegetable oils has displaced natural solid fats and liquid oils in many areas.Partial hydrogenation increases the shelf life and flavor stability of foods containing these fats. Partial hydrogenation also raises the melting point, producing a semi-solid material, which is much more desirable for use in baking than liquid oils. Partially hydrogenated vegetable oils are much less expensive than the fats originally favored by bakers, such as butter or lard. Because they are not derived from animals, there are fewer objections to their use.In the US, snack foods, fried foods, baked goods, salad dressings, and other processed foods are likely to contain transfats, as are vegetable shortenings and margarines. Laboratory analysis alone can determine the amount. Outside the US, trans fats have been largely phased out of retail margarines and shortenings. US food manufacturers are now also phasing out trans fats, but at present, most US margarines still have more trans fat than butter. In the 1950s advocates said that the trans fats of margarine were healthier than the saturated fats of butter, but this has been questioned. See the saturated fatspage for details.A trans configuration of hydrogen atomsChemistry of trans fats
Trans fatty acids are made when manufacturers add hydrogen to vegetable oil, in the presence of small amounts of
catalyst metals such as nickel, palladium, platinum or cobalt -- in a process described as partial hydrogenation. If the hydrogenation process were allowed to go to completion, there would be no trans fatty acids left, but the resulting material would be too solid for practical use. A claimed exception to this is Kraft Foods' new trans fat free Crisco which contains the wax-like fully hydrogenated cottonseed oil blended with liquid vegetable oils to yield a shortening much like the previous Crisco which was made from partially hydrogenated vegetable oil. However any hydrogenated or partially hydrogenated oil will contain trace amounts of the metals used in the process of hydrogenation. In a natural fatty acid, the hydrogen atoms usually form a double bond on the same side of the carbon chain. However, partial hydrogenation reconfigures most of the double bonds that do not become chemically saturated, so that the hydrogen atoms end up on different sides of the chain. This type of configuration is called trans (which means "across" in Latin). The structure of a trans unsaturated chemical bond is shown in the diagram.
These images have been removed due to copyright restrictions.Please see the images on http://library.med.utah.edu/NetBiochem/FattyAcids/4_1.htmland http://library.med.utah.edu/NetBiochem/FattyAcids/4_1d.html.
• Electron Impact Ionization– High energy, fragmentation = information
• Chemical Ionization– Low energy collisions with a gas such as CH4,
C4H10, NH3
• Fast Atom Bombardment• Electrospray LC-MS• Atmospheric Pressure CI LC-MS
Formation of the mass spectrum
•Compound ionises in source•Molecular ions fragments as a result of excess energy imparted by the ionising electrons (standard energy 70eV)•Ions pushed from source with repeller•Accelerated by high voltage•Ions separated by mass analyser•Ions counted and recorded
Calibration and leak checking
•Perfluorokerosene (PFK) - a mixture of fluoroalkanes with ions to > 900 dalton69, 100, 119, 219, 231 ……..
•Heptacosafluorotributylamine - a single compound MW 614 with 69, 119, 219 ...
•Background spectrum should look like air:17,18,28-32 and 40 Da
•Average spectrum has 250 bits of information•Molecular ion and its isotopic abundances•Ionisation energy and structure determine degree of fragmentation; 70 eV is standard•Fragment abundances reflect to relative stabilities of the fragment ions - most abundant are the most stable•Multiply charged and metastable ions lost in data reduction
Viable Phormidium zone with high polar lipid, C18 PUFA & abundant
DMA
FPP Submerged Mat F4-2cyanobacterial hydrocarbons
internal standard (overloaded)
20:00 28:00 36:00 Time
n-C17n-C19
V. high pCO2 low MA~290 ng/mg lipidδ13C -32.5 ‰ n-C19:1
7-Me-C18
δ13Cphytol -26.2 ‰
hopanol -26.9 ‰2-Me-hop -24.4 ‰
20:00 28:00 36:00 Time
FPP Exposed & Silicified Mat F5FPP Exposed & Silicified Mat F5cyanobacterial hydrocarbons
internal standard
n-C17
n-C18
n-C19
7-Me-C18
Di-Me-C19
n-C19:1
low pCO2 high MA~1907 ng/mg lipid-26.5 ‰
δ13Cphytol -26.2 ‰
hopanol -24.5.0 ‰2-Me-hop -24.6 ‰
Alkanes Bacteriohopanepolyols (BHP)
Normal Methyl Dimethyl 2MeC31 C31 2MeC32 C32
Phormidium luridum ++
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Chlorogloeopsis fritschii
Synechococcus lividus
Cyanothece RCB4*
Phormidium RCG3*
Phormidium FPGF4*
Phormidium FPOS4*
Phormidium OSS4*
Oscillatoria amphigranulata
Fischerella sp.
Phormidium RCO4*
Cyanobacterium
Lipid Biomarker Diversity Associated With Cyanobacteria.
*YNP cyanobacteria isolated for this study. Suffix codes refers to isolation source mat (RC, Rabbit Creek Spouter; FP, Fountain Paint Pots; OS, Octopus Spring).
Figure by MIT OpenCourseWare.
Mono-, di- and trimethyl-branched alkanes in cultures of the filamentous cyanobacterium Calothrix scopulorum
JuÈ rgen KoÈ ster a,*, John K. Volkman b, c, JuÈ rgen RullkoÈ tter a,Barbara M. Scholz-BoÈ ttcher a, JoÈ rg Rethmeier d, Ulrich Fischer daInstitut fuÈr Chemie und Biologie des Meeres (ICBM), Carl von Ossietzky UniversitaÈt Oldenburg, Postfach 2503,D-26111 Oldenburg, GermanybHanse-Wissenschaftskolleg, Postfach 1344, D-27749 Delmenhorst, GermanycCSIRO Marine Research, GPO Box 1538, Hobart, Tasmania, AustraliadAbteilung fuÈr Marine Mikrobiologie, UFT und Fachbereich 2, UniversitaÈt Bremen, Postfach 330440, D-28334 Bremen, GermanyReceived 10 December 1998; accepted 13 July 1999(returned to author for revision 25 March 1999)
Organic Geochemistry 30 (1999) 1367-1379
Courtesy Elsevier, Inc., http://www.sciencedirect.com. Used with permission.
This image has been removed due to copyright restrictions.Please see: Figure 2, Jürgen Köster, et al. "Mono-, Di- and Trimethyl-Branched Alkanes in Cultures of the Filamentous Cyanobacterium Calothrix Scopulorum."Organic Geochemistry 30, no. 11 (November 1999): 1367-1379.
Botryococcus braunii
O
O
OR
O
OHx= 15, 17, 19m= odd, 15-21n=even, 14-20R= oleyl and palmytyl
CH3(CH2)7CHCH(CH2)n
CHOCH
CH2CHCH3 (CH2)7
(CH2)m
(CH2)XCH
CH
CH
CH(CH2)7CH3
14
14
MACROMOLECULAR NETWORK
C
Hypothesized structures of Botryococcus algeanans for A&B races (polymethylenic) and L race(polyisoprenoid)
Largeau, Derenne, Metzger et al., 1985-1995; Tegelaar 1989-1995
Scenedesmus quadricauda
Image courtesy of Sylvie Derenne. Used with permission.
Scenedesmus quadricauda
Image courtesy of Sylvie Derenne. Used with permission.
Scenedesmus quadricauda isolated algeanan
Image courtesy of Sylvie Derenne. Used with permission.
Elucidation of Algeanan Structures
• Lyophilized cells• Lipid isolation by solvent extraction• Residue subjected to strong acid hydrolysis
(2N H2SO4; 6N HCl or TFA) followed by strong alkali hydrolysis (refluxing 5% KOH in MeOH or EtOH)
Elucidation of Algeanan Structures
• Spectroscopy– FTIR, solid state 13C nmr
• Pyrolysis– Flash pyrolysis (products swept as generated alkanes & enes)– Sealed-tube pyrolysis, hydrous pyrolysis (alkanes)– Hydropyrolysis (Love et al.,199; catalytic, high pressure hydrogen
& products swept as generated alkanes & enes)• Chemical degradation
– Saponification, HI ether cleavage, RuO4 oxidation• Thermochemolysis (Pyrolysis with tetramethylammonium
hydroxide, Allard et al., 2002)
Text has been removed due to copyright restrictions.Please see: Abstract, Peter Blokker, et al. "Chemical Structureof Algaenans from the Fresh Water Algae Tetraedron Minimum,Scenedesmus Communis and Pediastrum Boryanum."Organic Geochemistry 29, no. 5-7 (November 1998): 1453-1468.
Courtesy Elsevier, Inc., http://www.sciencedirect.com. Used with permission.
This image has been removed due to copyright restrictions.Please see: Figure 4, Peter Blokker, et al. "Chemical Structure ofAlgaenans from the Fresh Water Algae Tetraedron Minimum,Scenedesmus Communis and Pediastrum Boryanum." OrganicGeochemistry 29, no. 5-7 (November 1998): 1453-1468.
This image has been removed due to copyright restrictions.Please see: Figure 5, Peter Blokker, et al. "Chemical Structure ofAlgaenans from the Fresh Water Algae Tetraedron Minimum,Scenedesmus Communis and Pediastrum Boryanum." OrganicGeochemistry 29, no. 5-7 (November 1998): 1453-1468.
This image has been removed due to copyright restrictions.Please see: Figure 10, Peter Blokker, et al. "Chemical Structure ofAlgaenans from the Fresh Water Algae Tetraedron Minimum,Scenedesmus Communis and Pediastrum Boryanum." Organic Geochemistry29, no. 5-7 (November 1998): 1453-1468.
Elucidation of Algeanan Structures• Spectroscopy
– FTIR, solid state 13C nmr highly aliphatic with carbonyl, ether, hydroxyl functions and some indiaction of unsaturation
alkane/alkene chains with some distinctiveness; elevated C25, C31 or C33– Sealed-tube pyrolysis, hydrous pyrolysis (alkanes)– Hydropyrolysis (Love et al.,199; catalytic, high pressure hydrogen &
products swept as generated alkanes & enes) strong even/odd predominance and distinctive carbon number patterns
• Chemical degradation– Saponification, HI ether cleavage, RuO4 oxidation fatty diols + acids,
ω-OH acids, diacids, sat’d and unsat’d with strong carbon number predominances
• Thermochemolysis (Pyrolysis with tetramethylammonium hydroxide, Allard et al., 2002) very long chains up to C120 by DCI-MS on thermochemolysis products
Elucidation of Algeanan Structures
• Polyether linked long-chain n-alkyl chains (up to C36) (Gelin et al., 1997); precursors are long-chain diols; used TFA in isolation; restricted to chlorophytes eustigmatophytes, rare in dinos absent in diatoms, haptohytes (Gelin et al., 1999).
• Linear polyester chains cross-linked by ether bonds chains of 27, 29, 31 and 28, 30, 31; unsaturation source of rare ether cross-linking via epoxidation( Blokker et al., 1998)
• Outer walls of linear polyester chains chains up to C80 and algeanans with dicarboxylic acids up to C120 ( Allard et al., 2002)
• “Bacterans’ are artifactual macromolecules with a melanoidin-like structure (Allard et al., 1997)