Formation of the Elements
Composition of Earth
Elements in earth
Chemical Equilibrium
   Exists when a system is in a state of
   minimum energy (G)



- Often not completely attained in nature (e.g., photosynthesis leaves products
out of chemical equilibrium)
- A good approximation of real world
-Gives direction in which changes can take place (in the absence of energy
input.)
-Systems, including biological systems, can only move toward equilibrium.
-Gives a rough approximation for calculating rates of processes because, in
general, the farther a system is from equilibrium, the more rapidly it will move
toward equilibrium; however, it is generally not possible to calculate reaction
rates from thermodynamic data.
Reaction Rates/Equilibrium
Acid-Base Equilibria
Bronsted-Lowry definition: acid donates H+; base accepts H+
In aqueous systems, all acids stronger that H2O
generate excess H+ ions (or H3O+); all bases stronger
than H2O generate excess OH-




                        2




                    3

                    3
                3
Acid-Base




Many reactions influence pH
Photosynthesis and respiration are acid base reactions.
aCO2(g) + bNO3- + cHPO42- + dSO42- + f Na+ + gCa2+ + hMg2+ iK+ + mH2O + (b +
2c + 2d -f -2g - 2h - i)H+<-----> {CaNbPcSdNafCagMghKiH2Om}biomass + (a + 2b)O2

Oxidation reactions often produce acidity.
Reduction reactions consume acidity


pH influences many processes
-weathering (Fe and Al more soluble at lower pH)
-cation exchange (leaching of base cations from soil due to acid rain)
-sorption (influences surface charge on minerals and therefore what sticks to them)
Acid-Base

                                        Alkalinity ≈ ANC




Alkalinity = ∑(base cations) - ∑(strong acid anions)
Any process that affects the balance between base
cations and acid anions must affect alkalinity.
Redox
The oxidation state of an atom is defined with the following
convention:
•The oxidation state of an atom in an elemental form is 0.
      In O2, O is in the 0 oxidation state.

•When bonded to something else, oxygen is in oxidation
state -2 and hydrogen is in oxidation state of +1 (except for
peroxide and superoxide).
       In CO32-, O is in -2 state, C is in +4 state.

•The oxidation state of a single-atom ion is the charge on
the ion.
       For Fe2+, Fe is in +2 oxidation state.
Redox
Redox reactions tend to be slow and are often out of
thermodynamic equilibrium - but life exploits redox
disequilibrium.
             Oxidation - lose electrons
             Reduction - gain electrons




       Fe was oxidized, Mn was reduced
Why do we care about redox rxns?

                   O




                Measure of oxidation-reduction
                potential gives us info about
                chemical species present and
                microbes we may find.
Biogeochemistry
Elements in earth
QuickTime™ and a
                      TIFF (Uncompressed) decompressor
                         are needed to see this picture.




Nitrification
ammonia→ nitrite → nitrate
Denitrification
nitrate → nitrite → nitric oxide → nitrous
oxide → N2
N Fixation
N2 →ammonia
What is an isotope?
                          • Isotope- line of equal
                            Z. It has the same #
                            protons (ie. they are
                            the same element)
        14
             N   15
                      N
   12
      C 13C      14
                      C
                            but a diff. # of
10
   B 11B                    neutrons.
How did all this stuff get here?
• 4 types of isotopes, based on how they
  formed:
  – Primordial (formed w/ the universe)
  – Cosmogenic (made in the atmosphere)
  – Anthropogenic (made in bombs, etc)
  – Radiogenic (formed as a decay product)
Stable Isotopes
Light isotopes are fractionated during chemical reactions, phase
changes, and biological reactions, leading to geographical
variations in their isotopic compositions

FRACTIONATION: separation between isotopes on the basis of mass
(usually), fractionation factor depends on temperature

Bonds between heavier isotopes are harder to break
Stable Isotope Examples
• Rayleigh
  fractionation: light
  isotopes evaporate
  more easily, and
  heavy isotopes
  rain out more
  quickly




    δ = {(Rsample – Rstandard) / Rstandard} x 103
Stable Isotope Examples

∀ δ18Ocarbonate in forams
  depends on δ18Oseawater as
  well as T, S
∀ δ18Oseawater depends on how
  much glacial ice there is
   – Glacial ice is isotopically
      light b/c of Rayleigh fract.
   – More ice means higher
    δ18Oseawater
Stable Isotopes
•   C in organic matter, fossil fuels, and hydrocarbon gases is depleted in
    13
      C ==> photosynthesis
     – used as an indicator of their biogenic origin and as a sign for the
       existence of life in Early Archean time (~ 3.8 billion years ago)
•   N isotopic composition of groundwater strongly affected by isotope
    fractionation in soils plus agricultural activities (use of N-fertilizer and
    discharge of animal waste)
•   Particulate matter in ocean enriched in 15N by oxidative degradation
    as particles sink through water column
     – Used for mixing and sedimentation studies
•   S isotopes fractionated during reduction of SO42- to S2- by bacteria
     – didn’t become important until after ~2.35 Ga when photosynthetic S-
       oxidizing bacteria had increased sulfate concentration in the oceans
       sufficiently for anaerobic S-reducing bacteria to evolve (photosynthesis
       preceded S-reduction which was followed by O respiration)
Stable Isotope Examples
• Stable isotopes can also tell you about
   biology
• Organisms take up light isotopes
   preferentially
• So, when an organism has higher
δ30Si, it means that it was feeding from a
   depleted nutrient pool
Stable Isotopes
Boron isotopes measured in forams used for paleo-pH
   δ11B depends on pH
   (Gary Hemming)

Nitrogen isotopes used for rapid temp. changes in ice cores
    δ15N depends on temp. gradient in firn
    (Jeff Severinghaus)

Stable isotopes are also used to study magmatic processes,
water-rock interactions, biological processes and anthropology
and various aspects of paleoclimate

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Elements in earth

  • 1. Formation of the Elements
  • 4. Chemical Equilibrium Exists when a system is in a state of minimum energy (G) - Often not completely attained in nature (e.g., photosynthesis leaves products out of chemical equilibrium) - A good approximation of real world -Gives direction in which changes can take place (in the absence of energy input.) -Systems, including biological systems, can only move toward equilibrium. -Gives a rough approximation for calculating rates of processes because, in general, the farther a system is from equilibrium, the more rapidly it will move toward equilibrium; however, it is generally not possible to calculate reaction rates from thermodynamic data.
  • 6. Acid-Base Equilibria Bronsted-Lowry definition: acid donates H+; base accepts H+ In aqueous systems, all acids stronger that H2O generate excess H+ ions (or H3O+); all bases stronger than H2O generate excess OH- 2 3 3 3
  • 7. Acid-Base Many reactions influence pH Photosynthesis and respiration are acid base reactions. aCO2(g) + bNO3- + cHPO42- + dSO42- + f Na+ + gCa2+ + hMg2+ iK+ + mH2O + (b + 2c + 2d -f -2g - 2h - i)H+<-----> {CaNbPcSdNafCagMghKiH2Om}biomass + (a + 2b)O2 Oxidation reactions often produce acidity. Reduction reactions consume acidity pH influences many processes -weathering (Fe and Al more soluble at lower pH) -cation exchange (leaching of base cations from soil due to acid rain) -sorption (influences surface charge on minerals and therefore what sticks to them)
  • 8. Acid-Base Alkalinity ≈ ANC Alkalinity = ∑(base cations) - ∑(strong acid anions) Any process that affects the balance between base cations and acid anions must affect alkalinity.
  • 9. Redox The oxidation state of an atom is defined with the following convention: •The oxidation state of an atom in an elemental form is 0. In O2, O is in the 0 oxidation state. •When bonded to something else, oxygen is in oxidation state -2 and hydrogen is in oxidation state of +1 (except for peroxide and superoxide). In CO32-, O is in -2 state, C is in +4 state. •The oxidation state of a single-atom ion is the charge on the ion. For Fe2+, Fe is in +2 oxidation state.
  • 10. Redox Redox reactions tend to be slow and are often out of thermodynamic equilibrium - but life exploits redox disequilibrium. Oxidation - lose electrons Reduction - gain electrons Fe was oxidized, Mn was reduced
  • 11. Why do we care about redox rxns? O Measure of oxidation-reduction potential gives us info about chemical species present and microbes we may find.
  • 14. QuickTime™ and a TIFF (Uncompressed) decompressor are needed to see this picture. Nitrification ammonia→ nitrite → nitrate Denitrification nitrate → nitrite → nitric oxide → nitrous oxide → N2 N Fixation N2 →ammonia
  • 15. What is an isotope? • Isotope- line of equal Z. It has the same # protons (ie. they are the same element) 14 N 15 N 12 C 13C 14 C but a diff. # of 10 B 11B neutrons.
  • 16. How did all this stuff get here? • 4 types of isotopes, based on how they formed: – Primordial (formed w/ the universe) – Cosmogenic (made in the atmosphere) – Anthropogenic (made in bombs, etc) – Radiogenic (formed as a decay product)
  • 17. Stable Isotopes Light isotopes are fractionated during chemical reactions, phase changes, and biological reactions, leading to geographical variations in their isotopic compositions FRACTIONATION: separation between isotopes on the basis of mass (usually), fractionation factor depends on temperature Bonds between heavier isotopes are harder to break
  • 18. Stable Isotope Examples • Rayleigh fractionation: light isotopes evaporate more easily, and heavy isotopes rain out more quickly δ = {(Rsample – Rstandard) / Rstandard} x 103
  • 19. Stable Isotope Examples ∀ δ18Ocarbonate in forams depends on δ18Oseawater as well as T, S ∀ δ18Oseawater depends on how much glacial ice there is – Glacial ice is isotopically light b/c of Rayleigh fract. – More ice means higher δ18Oseawater
  • 20. Stable Isotopes • C in organic matter, fossil fuels, and hydrocarbon gases is depleted in 13 C ==> photosynthesis – used as an indicator of their biogenic origin and as a sign for the existence of life in Early Archean time (~ 3.8 billion years ago) • N isotopic composition of groundwater strongly affected by isotope fractionation in soils plus agricultural activities (use of N-fertilizer and discharge of animal waste) • Particulate matter in ocean enriched in 15N by oxidative degradation as particles sink through water column – Used for mixing and sedimentation studies • S isotopes fractionated during reduction of SO42- to S2- by bacteria – didn’t become important until after ~2.35 Ga when photosynthetic S- oxidizing bacteria had increased sulfate concentration in the oceans sufficiently for anaerobic S-reducing bacteria to evolve (photosynthesis preceded S-reduction which was followed by O respiration)
  • 21. Stable Isotope Examples • Stable isotopes can also tell you about biology • Organisms take up light isotopes preferentially • So, when an organism has higher δ30Si, it means that it was feeding from a depleted nutrient pool
  • 22. Stable Isotopes Boron isotopes measured in forams used for paleo-pH δ11B depends on pH (Gary Hemming) Nitrogen isotopes used for rapid temp. changes in ice cores δ15N depends on temp. gradient in firn (Jeff Severinghaus) Stable isotopes are also used to study magmatic processes, water-rock interactions, biological processes and anthropology and various aspects of paleoclimate