Lecture # 4: Biochemical Classes and Elemental Considerations-II

1. Lecture # 4: Biochemical Classes and Elemental Considerations-II

2. Ocean POM Ocean Seds (C/N)a 10 20 30 40 0 Ocean DOM Bacteria Humics Plankton Reprise: Ways to examine / interpret Atomic ratios 1) Single dimension: or place on a continuum of “end-members”

3. 2.0 1.0  Degree of degredation Nutrient Potential 0 0.15 0.3 2) Multi-dimension: or “Property-Property Plots” Review eg #2- prop/ prop Energy Potential (reduction) H/C N/C

4. PART II: More focus on Basic Biochemical Classes • In general: each “compound class” has fairly distinct compositions: on structural, and thus also elemental scale. • This composition typically arises because of 1) major functional groups (and related function in cell).

5. Recall: Major Biota compositions Terrestrial: • Cellulose • Lignin (proteins, carbos, some lipids) Marine: • Proteins • Carbos * Some lipids

6. 1. Carbos Overall: ~ C6H10O5 • Carbohydrates: are the most abundant class of biochemical on Earth (~1/3 mass of plankton and ~1/2-3/4 mass of vascular plant tissues (woods are ~3/4 wt % polysaccharides). • Oxygen – Rich: O:C ~ 0.83 • H-C = medium. H:C ~ 1.67 • Relatively Few or No Hetero-Atoms- • N poor:N/C ~ 0 ( expressed as N/C as more common C/N = undefined)

7. Lipids I:Fatty Acids • . Largely storage and protective compounds Overall: ~ C10H20O 1) Largely storage and protective compounds • Super H-C- Rich! H:C ~ 1.6 • Oxygen – Poor:O:C ~ 0.1 • Also Relatively Few or No Hetero-Atoms- • N poor: N/C = 0

8. Proteins • Proteins: Major functional (enzymes) and structural component of cells. By weight, 50% or more of much marine plankton biomass (smaller cells, ie prokaryotes= even more…) • Amino Acids have great structural and chemical diversity, as do specific proteins (especially structural ones). However, as a bulk compound class, total “protein” has a very similar overall composition from widely diverse source types. • H-C: poorest H:C ~ 1.54 • Oxygen – medium: O:C ~ 0.38 • N-RICH!: C/N ~ 4-5 (N/C ~ 0.27)

9. HOCH 2 HC O HCOH H CO H CO 2 3 O H COH CH HC=O 2 O HC HCOH CH HOCH 2 HCOH CH CH OH HCOH H CO OCH OCH 3 3 3 OH H COH H CO H CO H CO H CO 2 3 3 3 O CH O HOCH OCH 2 H 3 HOH C C C=O O HCOH HC O 2 H CH H C 2 C=O H CO H CO CH HC 3 3 HOCH 2 HC CH CH HO 2 H COH 2 O CH CH O OCH 3 HC O OCH 3 O HOCH HOCH 2 H CO 2 3 HC O HC OCH 3 HCOH HC O HOCH HOCH H CO OCH 2 3 3 3 HC O CH O HCOH C=O H CO OCH 3 3 OH OH Schematic structural for spruce lignin (Adler, 1977) Lignins (and Tannins) -

10. Lignin ( Major terrestrial OC component) Overall: ~ C10H12O3 • Lignins: Major Structural Polymer for terrestrial biomass. Made up of Poly-Phenols- as such, very significant aromaticity ( fewer H-C), as well as C-O. • Relative to other classes, Poor in just about everything… • H-C: poorest H:C ~ 1.2 (recall 1:1 = totally aromatic) • Oxygen – Poorest: O:C ~ 0.3 • No Heteroatoms: N/C = 0

11. What about Humics (“Geomolecules?”)

12. What are Humics (Geomolecules)? Note: this “molecule” does not exist!! • Recall an “operational definition” • In terms of a structural class, or material such as “humics”- it means that there is no one actual structure, or even strictly speaking not even a “family” of structures (like amino acids, for example). • usually due to either complexity or analytical problems- it something defined instead by a set of properties or “operations.”

13. Humics / Geomolecules? Because of this, can VARY a lot- depending on 1) what environment it came from 2) how collected. However: still can make decent generalities: • Hallmarks: increasing condensation(= incr. In aromaticity) and lossof heteroatoms (loss of functionality)

14. Humics / Geomolecules? RESULT: Even “poorer” than lignins in some ratios! • H-C: Poor- poorest. 1 to < 1. • Oxygen – similar to lignin, or less: O:C ~ 0.3 • Hetero-atoms: poor, but not zero. C/N greatly depends on source. C/N ~ 30- 50 + ( N/C = 0.03- 0.02)

15. Elemental Ratios : OVERVIEW …Will be on web, I promise

16. PART III: Uses of Elemental Ratios in real samples • Basic diagnostic function: Given a sample of unknown OM in a given environmental compartment. What is it? * C/N most commonly used, however ALL major elemental ratios can be used.

17. #1: Sources ( Basic diagnostic Function) • Given a sample of unknown OM in a given environmental compartment. What is it? * C/N most commonly used, however ALL major elemental ratios can be used.

18. Ocean POM Ocean Seds (C/N)a 10 20 30 40 0 Ocean DOM Bacteria Humics Plankton Recall our ocean example:

19. Example from Nature:C/N Continuum of Amazon River vs Ocean Recall our “operational” C-Cycle boxes: Major Sources for OM in river: Soils Fresh leaves Major operational River OM pools: Fine POM Coarse POM DOM

20. Sketched model.. SOIL Operational OM boxes in river: POC-LARGE POC-small RIVER DOC humics

21. Questions: what are linkages? ?? SOIL ?? ?? ?? Operational OM boxes in river: POC-LARGE POC-small RIVER DOC humics

22. Amazon DOM Mainstem Amazon Soil OM Amazon Fine POM Amazon coarse POM Rio Negro DOM Fresh Leaves (source!) 50 – 60 ! 10 20 30 40 0 Ocean DOM Bacteria Marine Humics Ocean Seds Plankton Ocean POM C/N Continuum: Amazon River vs Ocean Amazon Basin Ocean)

23. Question to Ponder: if you were to start constructing a C-cycle box model (of Amazon to Ocean) based on these values, How strong (or definitive) would the information you have be?

24. #2) Elemental Ratios to track Transformations • Biological Degredative Transformations • Abiotic Transformations

25. Individual Proxies: C/N proxy = % AA-N %Amino Acid -N as a Diagenetic Indicator 0 70 10 20 30 40 50 60 30 Sediment Trap UDOM Coast Surf Sed. Coast Deep Sed. Reduced Turbidite Oxidized Turbidite

26. Humics Major biochemical sources on “bio” plot- vs. ‘std’ humics Energy Potential (reduction)  Degree of degredation Nutrient Potential

27. Question: would transformations be the same for biotic & abitiotic changes? Marine biota Leaf Humus Energy Potential (reduction)  Degree of degradation Nutrient Potential

28. Geomolecules: Van Krevlyn- type Plots Maturity (Armomaticity) Energy Potential (reduction)

29. Ancient History: OM in rocks.. Maturity (Armomaticity) Energy Potential (reduction)

30. A Final Note: practical problems with C:H, C:O • C/N most commonly used, b/c 1: lots of information, but ALSO relatively easy to measure. Why? You measure N0x  Not much N contamination. 2) BUT for H and O, you measure H2O Contamination? • Gigantic sources: 1) Air. (Ever try to get MS line clear of water signal?) 2) worse: many materials are Hydroscopic. ever try to get something really dry? Both clays and many biochemicals absorb water to “beat the band”.

31. Oceanographic Spin: The Redfield Ratio Bulk OM: Unlike on Land, We Know ~ what it starts at! Ratios relative to Redfield: 1. Tell you about its degradation history. 2.Tells you about likely reactivity.  Hold implications regarding geochemical fate: (concommitant use of other elements.)

32. RKR Notes 1) RKR is a giant “average” number  In real life, RKR is actually not constant, and as a consequence, actually NOT accurate in many locations. ie: Varies with nutrient availablity & plankton type. Eg: RKR C:N ~ 8.6, but in temperate waters, C/N of 7 is closer to reality, and for example for bacteria/small cells, C/N of 6 or even 5 is closer.. Eg II: some growth experiments:

33. RKR is based on “bulk” OM techniques. But is it right? Recall statements about P –controlling OM? Do such ratios hold in real world? 1: reality check on stoichiometries: theoretical and actual mean stiochiometries for material remineralization from different oceans ( Geosecs data, Takahashi et al., J GRes. 90, 6907-6924, 1985): NOTE: Consistently more O2 (~175 moles) is actually required to respire sinking planktonic remains than is calculated from the RKR ratio (138 moles O2)!!

34. This sort of observation can have BIG PICTURE implications for understanding large cycles: for example, consider remineralization of Carbos vs Lipids Þ ¬ CH O + O CO + H O (carbohydrate - Like 1 mol O2) 2 2 2 2

35. END

36. 2007 Amazon example Ideas: 1) Focus on C-Cycle box-style model even more directly (earlier?). Sketch boxes on board- but focus on unknown arrows that C/N data WILL help FILL IN. (Eg focus even more directly on QUESITONS- where does POM come from? Direct from trees? Residence time in soils? Both? Where does DOM Come from? ADD Pictures? Think it would be cool to make this a mini- env. Example ! Bunch of cool pictures, and maybe some basin photos, with more background RE the QUESTION- Make connnection between Amazon river to ocean system coupling.

37. RE: Shrag’s talk: The Final Question: 1) IF we know key ratios do 1) vary over SPACE today- and 2) depart from theory • What variation in key ratios (eg C:P in shrag case) might have occurred over TIME on million year time scales? For purposes of his model, seemed Shrag was assuming: a) none. (none significant) b) OM burial is only 20% of total C burial, so who cares.

38. WHY?  Difference is likely due to a greater concentration of H in actual sinking organic particles than in the RKR model material (which is essentially like carbohydrate.

39. Hedges Paper (on web): if you use 13C NMR to look at biochemical compositions, do bulk elemental Redfield values still hold up? • NO… maybe not. • Problem: appears to be in Oxygen! • Suggests major issue with water..somewhere in protocol.

40. UDOM Unfractionated Pacific Avg. DOC/DON (Seattle 1992 workshop). Example 1-D: C/N Continuum Typing DOM from ocean 10 20 30 40 0 Bacteria Marine Humics Plankton Sed Trap OM 2007: did not use this slide- seemed too redundant Amazon river example gives same ideas.