Molecular Fossils : Biomarkers
Term ‘Biomarker’ also used in
relation to health of ecosystems and
humans Prognostic and Predictive
Indicators
Readings
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Hinrichs et al., Nature 1999
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Thiel et al., GCA 1999
– Both papers on linking biomarkers to AOM
– Potential examination material
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Fogel and Cifuentes 1994, Isotopic (esp.13C)
fractionation during primary production
– Potential examination material

Hayes 2002, 13C and 2H-fractionation during
biosynthesis
– For the really committed!!!!!!; mostly not examinable
Dimensions of Organic Geochemistry
Based on a chemical perspective Size scales range from atomic to
global, timescales to 100’s of millions yrs Generally concerns nonliving
organic matter Can involve any natural environment, modern and
ancient Overlaps with societal issues:
petroleum exploration, fuels research, pollution, water quality,
waste disposal, soil fertility, forestry, forensic chemistry, archaeology,
natural products studies, drugs
Why is nonliving natural organic matter important?
food, fuel, structural materials, drugs plays an important role in global
cycles of C, O, N, P, S, metals etc affects soil fertility and structure,
redox chemistry, photochemistry, light transmission record of
environmental conditions, history and reactions (molecular fossils)
Data richness
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large number of information units = isotopes, atoms, molecules,
stereochemistry
a. 1 drink of water = 250 ml, at 4 mg/L of organic matter ª 1 mg organic
matter, at an average of 1000Da / molecule ª 10-6 moles of molecules, at 6 x
1023 molecules/mole ª 6x1017 organic molecules in the cup.
b. every 1000 Da molecule contains about 50% carbon ª 500 Da of
carbon,at 12 Da per C atom ª 40 carbon atoms ª lots of potential for
structural diversity (e.g. at least 10 structural variants for an acyclic 7carbon hydrocarbon).
c. since ≒1/100 all carbons is 13C, about 40% of all molecules will have one
13C,that one 13C could be in up to 40 different sites the individual molecules.
d. about 1/1012 carbons in the contemporary biosphere is a 14C, although
the odds of any one molecule having a 14C is less than 1/1011, there will be
about 40 x 1017/1012 ≒ 4x105 radioactive molecules in the cup of water,
decaying at a predictable rate.
e. organic matter has also: 1H, 2H, 3H, 14N, 15N, 16O, 17O, 18O, P, and 32S, 33S
34S and 36S, each of which adds to structural diversity and information
richness.
every asymmetric carbon has two possible stereoisometric forms, making
the maximal number of stereoisometric forms equal to 2n, where n=number
of asymmetric carbons. If only 10% of the carbons in this hypothetical
molecule are chiral, that molecule will have up to 16 different forms.
Organic matter traces biological and geographic sources
“biomarkers”:
1. vanillin  lignin  vascular plants  terrigenous origin
2. syringealdehyde  lignin  vascular plant  angiosperms
3. C37:3 alkenone  coccolith  marine
4. stable carbon isotopes trace carbon atoms through diets
and up food webs
Record time/maturation histories:
1.14C ticks away after removal from its atmospheric source
2.heating causes amino acids to racemize over time (Lalanine Æ D-alanine)
Record past events and processes
histories (often cumulatively)
white-rot fungal degradation of lignin
increases the yield of vanillic acid
versus vanillin from CuO oxidation of
the wood remains 
heating scrambles natural to unnatural
structures 
herbivory clips phytol tail off of chlorophyll
molecule
passage up through food webs fractionates
nitrogen and carbon
Record paleoenvironmental
conditions
1.temperature  number of
C37:3 alkenone double bonds
increases with decreasing water
temperature
2.paleooxicity  reflected by
some pigments and lipids
3.paleosalinity  reflected by
some lipids
Organic information comes in useful
“shells”
1. optical, microscopic, isotopic and bulk
chemical (NMR, IR, CHN)
characterizations are typically the most
representative, but have limited
information potential
2. molecular (biomarker)
characterizations carry a wealth of
information (including isotopic), but can
often be unrepresentative of bulk
organic mixtures which contain many
organic components with different:
a. sources
b. physical forms
c. ages
d. reaction histories
The Major Biochemicals
General Rules for major biochemicals (beware
of exceptions)
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Macromolecules that are highly reactive within living cells also tend
to be reactive outside the cell.
EXAMPLE: structural cellular components (proteins, lipids, etc.) turn
over in the cell more slowly than muscle, energy storage lipids and
carbohydrates or enzymes, and are more likely to be detected in
natural samples
EXCEPTION: unusual structural characteristics or environmental
circumstances can reduce the reactivity of molecules (DNA
fossilized in bone).
The reactivity of organic matter depends greatly on the environment.
Redox conditions, presence/absence of a mineral phase (biogenic
or sedimentary) or light, and temperature can all dramatically
change microbial reactivities.
EXAMPLE: preservation of DNA requires isolation of material from a
microbial community and also from oxygen (DNA in amber)
DNA/RNA
(avg comp: C10H12N4O4)
Deoxyribonucleic acid and ribonucleic acid
The greatest potential as a biomarker, but usually poorly
preserved in the environment
 Structural unit is composed of a 5-C sugar (ribose), a
nitrogen-rich cyclic base, and a molecule of phosphoric
acid. The name of the compound is derived from its base
(either a pyridine or purine ring).
 DNA: genetic blueprint of the organism; machinery of
evolution
 RNA: messenger and transfer. RNA turns over rapidly
between monomeric and polymeric form. It is recycled
through the cell and is constantly being replaced.
adenosine
guanosine
uridine
cytosine
Strengths of DNA/RNA as geochemical tools:
Ultimate biomarker
Nitrogen-rich, but not in amide form, thus different from
proteins
Brings the biochemist into the geochemistry realm
Weaknesses:
poorly preserved except under extreme conditions
Brings the biochemist into the geochemistry realm
CARBOHYDRATES
Cx(H2O)y
Most abundant biochemical class on earth due to cellulose and chitin
A. Monomer (sugar)
 most sugars have 5 (pentose) or 6 (hexose) carbon atoms
 generally, carbohydrates are highly soluble in water and insoluble in
non-polar solvents, and tend to decompose (caramelize) rather than
melt
 have a carbonyl group (HC=O) present as either an aldehyde
(terminal) or a ketone (within the chain)
 usually drawn as open chains but actually found as O-linked rings
 ‘simple sugars’ usually include di- and tri-saccharides because they
are sweet (table sugar = glucose-fructose)
B. Diversity: there are many carbohydrates
 chitin (n-acetyl glucosamine polymer) is unique to arthropods and
fungi
 bacteria make hundreds of unique deoxy, acidic, basic and O-methyl
sugars
C. Common Carbohydrates
#
Category
Examples
Carb
Name
ons
3
Triose
glyceraldehyde,
dihydroxyaceto
ne
4
Tetrose
erythrose
5
Pentose
ribose, ribulose,
xylulose
6
Hexose
glucose, galactose,
mannose,
fructose
7
Heptose
sedoheptulose
. Polymer formation: dehydration to form
etherlinkages. Sucrose is composed of
glucose andfructose through an a-(1,2)b glycosidic bond. 
Lactose is found exclusively in the
milk of mammals and consists of
galactose and glucose in a b-(1,4)
glycosidic bond. 
Polysaccharides: the most abundant polysaccharides are
cellulose, chitin, amylose, hemicellulose and pectin. With the
exception of hemicellulose and pectin, all are homopolysaccharides
(one sugar, usually glucose) linked together with chain lengths of
~1000-2000 units.
Utility of carbohydrates as geochemical tools:
 very abundant in living organisms
 great deal of variability in the types of sugars made by
microorganisms
 optically active
 Weaknesses of carbohydrates as geochemical tools:
 Difficult to analyze; many different types ofcarbohydrates require
multiple techniques
 Instability of carbohydrates under many hydrolysis conditions
adds to analytical difficulty
 Wide variety of degradation rates makes bulkcarbohydrate
measurements difficult to interpret
AMINO ACIDS
C3.75H6N1O1.5
Forms:
– Twenty common amino acids used to synthesize proteins.
– More than 150 other amino acids are either used in cells for
special purposes (taurine is used as an osmolyte in bivalves), as
precursors to protein amino acids, created during certain typs of
degradation sequences, or created abiotically.
– Amino acid functional groups show great diversity: R=H for glycine
but can contain rings (phenylalanine), sulfur (methionine), etc.
– All amino acids (except glycine) contain 1 or more chiral carbons
– Amino acids are zwitterions, having both basic and acidic groups.
This leads to high solubility in water, low volatility and a tendency
to decompose before melting
 Polymer Formation: dehydrogenation reaction forms peptide bond
(amide linkage) analogous to the glycosidic linkages in
polysaccharides
 Protein functions are varied and include enzymes, storage proteins,
transport proteins, antibodies, toxins, hormones and structural
proteins.
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Strengths of amino acids as geochemical tools:
– Structural diversity reveals a wide variety of processes
and reactions
– Reactions of epimerization and racemization provide an organic
‘clock’ reflecting temperature and time history
– Sampling methodologies reasonably well worked out
– Degradation of amino acids typically leads to a characteristic
buildup of non-protein amino acids, yielding a relative index of
degradation “freshness”
– Some amino acids and proteins could provide source information
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Weaknesses of amino acids as geochemical tools:
– Little source information: nearly all organisms look similar in bulk
amino acid composition
– AA’s are typically quite reactive and can be rapidly lost from
environmental samples
LIPIDS although certain characteristics are common across
the compound class, lipids are very heterogeneous.
 Lipids are operationally defined as being extractable by a
nonpolar solvent
 Common lipids: glycerides, waxes (including cutin and
suberin), hydrocarbons, terpenoids (sterols, phytols,
carotenoids), plus common heteromolecules
(lipopolysaccharides, phospholipids, lipoproteins).
 Cores are ‘polymethylenic’ (chains constructed from
acetate units) or ‘polyisoprenoid’ ( chains or rings
constructed of isoprene units)
2 general categories of lipids are saponifiable and
nonsaponifiable (saponic = ‘soap producing”) based on
presence of ester linkages
saponic lipids are composed of fatty acids and alcohols, which
are released as monomers in boiling base. An example is
palmitic acid (e.g. Palmolive), the most common fatty acid.
All fatty acids contain a terminal carboxyl group. All fatty
alcohols contain a terminal alcohol group.
General characteristics: low solubility, melt rather than
decompose,highly surface active, Saturated = full of hydrogen,
no double bonds
Forming the lipid bond:
In general, fatty acids are linked to a
polyalcohol glycerol by ester linkages.
ii. Glycerides: 1,2 or all 3 of the alcohols on
the glycerol can link with a fatty acid to form
a glyceride. Chain length: ~C12-C36
Forming the lipid bond 2:
All archaea and some specific kinds of thermophilic bacteria
synthesis glycerol ethers as opposed to glycerol esters.
In archaea the chains are isoprenoidal while they are
polymethyleneic in bacteria
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In general, animal fats are saturated, plant fats
are unsaturated. For a given chain length,
unsaturation leads to a lower melting point (lard
is solid and canola oil is liquid at room
temperature). In plants, the major fats are C18
(mono-, di- or tri-unsaturated).
Fatty acids are of even carbon number because
they form from acetyl units H3C-CO-.
Function in cell: energy storage. For a given
weight of compound, lipids yield ~2X more
energy than carbohydrate.
Why?
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Waxes: an ester bond between a fatty acid and a fatty
alcohol produces a wax ie wax ester. ‘Wax’ also refers to
high MW hydrocarbons
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Primary use in plants and insects as a protective coating and
also as energy storage
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Average chain length C24-C28 each end for a total of C48-C52
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some waxes contain ketones, branched alkanes, or aldehydes.
When they contain alkanes, the number of carbon atoms
becomes odd because the alkanes are formed by
decarboxylation of fatty acids
More on lipids…………
Terpenoids: highly diverse in structure
and purpose, but all
are divisible into isoprenoid
units (± a couple of carbons).
Monoterpenes (C10 = 2 isoprene units)
are usually volatile, used as
pheromones and stimulants (menthol,
chrysanthemic acid)
Sesquiterpines (3 units): oils and
antibiotics
Diterpenoids (4 units): Phytol side
chain in chlorophyll. Most diterpenes
are di- or tri-cyclic. Examples include
gibberellins, abietic acid, vitamin A.
testosterone
Triterpenoids (6 units) are all derived from
squalene. Can be acyclic, tetra- or pentacyclic. The most common tetracyclic ones
are known as steroids. Major precursors to
biomarker hydrocarbons in petroleum.
steroids: tetracyclic triterpenoids used to provide rigidity in
group, 1 double bond in the primary ring and a
Pentacyclic triterpenoids are divisible into 4 classes:
chain off the D-ring. oleananes, ursanes, lupines and
hopanes. The first three are resins in vascular plants and
they all have E-rings with 6 carbons. Hopanes are
predominant in bacteria and have E-rings with 5 carbons.
Tetraterpenoids (8 units)
usually form chains,
important components of thic
group include carotenoid
pigments. Highly
unsaturated, cyclicized at
each end. Found in almost
all organisms. Specific
distributions of the
carotenoids are
characteristic of different
organisms, especially
photosynthetic organisms.
Characteristics of Biological
MarkerCompounds – Optical Isomerism
CCH3HCOOHCH3CHHOOCH2NNH2L alanineD alanine
The D- and L-enantiomers of alanine are mirror image structures that cannot be
superimposed. They can be distinguished by the direction in which they rotate a beam of
mixtures and do not rotate the polarised light because the effect of the D-enantiomer is
exactly cancelled by its L-counterpart. Unequal mixtures are said to be optically active
and a compound comprising 100% of the D-enantiomer gives the maximum rotation
clockwise or to the right while 100% of the L-enantiomer results in full anticlockwise (to
the left) rotation. Most terrestrial organisms exclusively synthesise and use a-amino acids
in the L-form.
Characteristics of Biological Marker
Compounds – Limited # of Stereoisomers
Stereoisomerism in tartaric acid. B and C are enantiomers.
A, B and A, C are pairs of diastereomers.
Characteristics of Biological
MarkerCompounds – Limited Stereoisomers
Structure of cholesterol with its eight asymmetric carbon atoms
identified with their position n umber. Theoretically, this compound
could exist in as many as 256 (28) possible stereoisomers and yet
biosynthesis produces only the one illustrated (Peters and Moldowan,
1993).
Characteristics of
Biological Marker
Compounds –
Limited Structural
Isomers
Structures of a group of plant-derived C10 natural products
(monoterpenes). The diphosphate ester of geraniol, itself formed by
dimerization of D3isopentenyldiphosphate, is the biochemical precursor
of the other structures. Limonene, myrcene and a-pinene are just three
of the biologically-generated constitutional isomers with a molecular
formula C10H16. There would be many hundreds of possibilities for
non-natural isomers with the same formula.
Characteristics of Biological Marker Compounds –
Repeating Sub-units (eg C2 or C5)
Structure of the diterpenoid phytol composed of four head-tail linked C5
('isoprene') units. Also note that phytol has two sites of asymmetry
and a double bond each of which could deliver additional isomers if
they were produced in other than natural circumstances. Phytol occurs
uniquely as the E-3, 7R, 11R, 15-tetramethylhexadecene-2-enol
structure
Characteristics of
Biological Marker
Compounds –
Biologically
defined Structures
Structures of some regular, irregular and cyclic C20 isoprenoid
(diterpenoid) hydrocarbons that have been identified in bitumen and
which illustrate a variety of biosynthetic patterns based on repeating C5
dodecane are irregularly branched compounds while phytane, labdane
and kaurane are constructed from four head-tail linked isoprene units.
These compounds also illustrate how different structures can be
diagnostic for specific physiologies (phytane for photosynthesis;
crocetane for methanotrophy) or specific organisms (2,6,10-trimethyl-7(3- methylbutyl)-dodecane for diatoms; labdane and kaurane for
conifers).
Characteristics of Biological Marker Compounds –
Systematic Isotopic Ordering at Molecular and
Intramolecular Levels
Cleavage of this
bond in pyruvate
induces fractionation
An important consequence of
the pyruvate to acetate
isotopic fractionation is
‘lightness’ of lipids
Alternate carbons derived from acetate carboxyl
down acetogenic lipidbackbones are light. In
general lipids are also light, but not as light.
DIAGNOSTIC MOLECULES
MODERN & FOSSIL FORMS
dinosterol
modern dinoflagellates
dinosterane
Triassic-Recent
DIAGNOSTIC MOLECULES
MODERN & FOSSIL FORMS
C34 botryococcene
B-race of B. braunii
C34 botryococcane
lacustrine sediments
Cenozoic-Recent
DIAGNOSTIC MOLECULES
BACTERIAL LIPIDS
REFLECT PROCESSES
DIAGNOSTIC FOR
PALAEOENVIRONMENT
EUKARYOTE LIPIDS
STRUCTURAL VARIETY
DIAGNOSTIC FOR
ORGANISMS & AGE
DIAGNOSTIC MOLECULES
MODERN & FOSSIL FORMS
oleanane
β-amyrin
modern angiosperms
ubiquitous in sediments
L. Cretaceous-Recent
DIAGNOSTIC PIGMENTS
isorenierateneChloro
bium carotenoid
aryl isoprenoidsanoxia
in photic zone