Transcript Trace Metal Biogeochemistry 12.755

Marine Bioinorganic Chemistry
(Trace Metal Biogeochemistry)
12.741
MIT-WHOI Joint Program Graduate Course - Lecture 1
Mak Saito, Marine Chemistry and Geochemistry Department
Course websites: www.whoi.edu/sites/12.741
MIT Stellar account online for schedule
Outline:
1. Introductions, comments on course schedule, structure,
approach, assignments
2. Introduction to Trace Metal Biogeochemistry: an evolving field
3. Classifications of TM profiles
4. Metal Speciation lecture
Logistics
Schedule will be available at MIT stellar site for 12.741
Class readings will be available at www.whoi.edu/sites/12.741
Occasional Thursday classes to be scheduled
A great challenge of our field today:
Connecting the Global to the Molecular
Class Topics
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Introduction to trace metal biogeochemistry, broad categories
Metal Speciation
Free ion model
Algal uptake kinetics
The Droop model and colimitations
Mercury Biogeochemistry (Lamborg as guest lecturer)
Iron biogeochemistry (limitation, light colimitation, redox, speciation,
uptake mechanism, colloids, and policy)
Trace elements and the ancient ocean
Metalloenzymes
Analytical approaches (in silico and proteomic/mass spec)
Specific elemental biogeochemistries (Mn, Al, Pb, Co, Zn, Cd, Cu)
Vitamins and cofactors
Events
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Lecture/Discussion of Mercury policy (Carl Lamborg)
Lecture on Particulate metals (Phoebe Lam)
Bioinformatics module working with genomic resources
Phone conference with Bill Sunda, expert trace metal phytoplankton
interactions (if time allows)
• Discussion of iron fertilization
• Readings on ideas in science for discussion throughout semester
Inorganic components are (also) required by life
Trace Metal
Biogeochemistry
Marine and
Environmental
Bioinorganic
Chemistry
Bioinorganic
Chemistry
Metals in Biology Gordon Research Conference
Metals play many important roles in biological systems, from essential
functional or structural cofactors in proteins, to environmental toxins. The
Metals in Biology Gordon Research Conference is one of the longestrunning GRCs (starting in 1962). It brings together researchers that span
expertise from physical methods and synthetic chemistry through biology
and biomedicine. The strength of this multidisciplinary group is reflected
in the number of other GRCs that have "spun off" from Metals in Biology.
Inorganic biochemistry continues to be an active and vibrant area,
resulting in a perennial oversubscription to this GRC. To provide graduate
students in this area with the possibility to participate, our community
started the first Gordon Research Seminar (in Bioinorganic Chemistry),
which has overlapped and met after the Metals in Biology GRC for over
10 years.
Cell Biology of Metals Gordon Research Conference
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The 2013 Cell Biology of Metals Gordon Research Conference provides a highly interactive and
collegial forum for junior and senior investigators alike to learn of the latest advances in our
understanding of metal homeostasis, metabolism, and utilization in cells and organisms. The cell
biology of metals is an emerging field of active research and this conference is the key venue for
exciting unpublished work on nutrient metals (primarily iron, copper, zinc, and manganese), with
presentations of research in humans and mice as well as plants, nematodes, and single-celled
organisms. The meeting will bring together an outstanding and diverse group of molecular and
structural biologists, biochemists, geneticists, cell biologists, and clinicians to bridge the gap
between basic and applied research. Highlights include discussions of how dysregulation of metal
homeostasis and utilization underscores human disease and how bacterial pathogens work to
exploit host metal supplies to enhance their virulence in humans. Other sessions will address
metalloproteomics and metallogenomics, intracellular metal trafficking, metal cofactor assembly,
and metallosensor proteins and the regulation of gene expression. Oral presentations will be given
by both new investigators and established leaders in the field and will be complemented by
several poster sessions; some speakers will be selected from submitted poster abstracts. The
broad and integrated coverage of topics will allow for extensive "cross-fertilization" of ideas among
researchers studying metal nutrients from a multi-disciplinary perspective.
Ed Stiefel and Francois Morel
Bringing fields together
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Metals in Biology and its Progeny
In the early 1970s, as an assistant professor at the State University of New York at Stony Brook, I started attending both the Inorganic Chemistry
Gordon Conference and the Metals in Biology (MIB) Conference. I had only a faint awareness of the diverse and critical roles that metal ions play in
biological systems. Attending the MIB Conference convinced me of the area’s enormous potential, and I committed myself to the nascent field of
bioinorganic chemistry.
Three specific results came from my early attendance at MIB. First I became aware of the ignorance about critically important molybdenum enzymes,
such as nitrogenase, nitrate reductase, and xanthine oxidase, and decided to focus on this area of research. Second, on the request of Steve Lippard
(then at Columbia University and editor of Progress in Inorganic Chemistry) with whom I drove to the conference, I wrote a review called “The
Bioinorganic and Coordination Chemistry of Molybdenum” that became a citation classic with over eight hundred citations. Third, an invitation to attend a
seminar from Bill Newton of the Charles F. Research Kettering Laboratory, who I met on the tennis court during the MIB Conference, led to my joining
the Nitrogen Fixation Mission at Kettering. Clearly, MIB had a tremendous influence on my early career and research.
In 1980, while still attending MIB, I moved to Exxon Corporate Research, and I persuaded the company to provide some support for MIB for many years.
In 1993 I chaired MIB, and, as Doug Rees presented the first nitrogenase crystal structure, I realized how far the field had come but how much was still
unknown. MIB continued to meet on a yearly basis in California, but there were always good-natured complaints that only one session, at most, was
spent on a particular subfield. This opened the door to new Gordon Conferences, such as the Nitrogen Fixation Conference, chaired by Doug Rees and
Bill Orme-Johnson, that first met in 1994 and at which I gave the opening talk, called “Chemistry of Nitrogen Fixation.” It was great to have a Gordon
Conference focused on the molecular aspects of nitrogenase.
At the Nitrogen Fixation Conference I first realized that a GRC on other molybdenum enzymes would attract a large audience. A few years later Russ
Hille, of Ohio State University, and I proposed a new Gordon Conference called Molybdenum and Tungsten Enzymes. Together we chaired the
inaugural conference held in New Hampshire in 1999, with eighty attendees. Two years later one hundred attendees met at Oxford University. This
specialized subject attracted bioinorganic chemists, crystallographers, biophysical chemists, molecular biologists, microbiologists, botanists, and
physicians. The resulting cross-fertilization was remarkable, and the conference continues to meet on a two-year cycle.
In 1998 my group at Exxon joined researchers from Princeton University, Rutgers University, and the University of California campuses to form the
Center for Environmental Bioinorganic Chemistry (CEBIC), directed by François Morel and funded by the National Science Foundation and the
Department of Energy. Many interactions among CEBIC researchers were first forged at Gordon Conferences. CEBIC was such a wonderful experience
that in 2001 I moved to Princeton University with appointments in the chemistry department and the Princeton Environmental Institute (which houses
CEBIC). At Princeton I have been fortunate to teach a freshman seminar called Elements of Life, which has convinced me that bioinorganic chemistry is
a splendid vehicle for teaching chemistry and its relation to biology, geology, astrobiology, and environmental science. Meanwhile, CEBIC continued to
thrive, and each year our summer workshop at Princeton drew more people from outside CEBIC. This success led François Morel and me to propose
the Environmental Bioinorganic Chemistry (EBIC) Gordon Conference, and in 2002 François and I chaired its inaugural conference, with 125 attendees
from a remarkable range of disciplines. The conference now meets regularly on a two-year cycle.
Meanwhile MIB is thriving, despite the heavy attendance draw (one thousand participants) of the International Conference on Biological Inorganic
Chemistry. Without losing momentum, MIB continues to spawn new conferences such as the 2002 Metals in Medicine (chaired by Nick Farrell) and the
2005 Cell Biology of Metals (chaired by Nigel Robinson and Dennis Winge). MIB is far from finished as it continues to stimulate interdisciplinary crossfertilization of ideas in an intimate setting with a wonderfully paced program that only GRC can provide.
Molecular: Metalloenzymes and Marine Biochemistry
• ~25% of all proteins now believed to require a metal for
functionality (Waldron and Robinson, 2009; Andreini et al., 2004)
• Metals allow proteins to have:
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Site(s) for catalytic activity
Redox reaction capability
Structural features (e.g. “zinc finger” loops)
• Most marine biogeochemical reactions involve metalloenzymes
– Photosynthesis (Fe, Mn, Cu, Zn, Co, Cd)
– N2 fixation, denitrification, nitrification, NH3 oxidation, urea use (Fe,
Cu, Mo, Ni)
– Carbon remineralization (Zn, Co)
– Organic phosphate utilization (Zn)
– Superoxide dismutation (Cu, Zn, Fe, Ni)
Trace metal biogeochemistry
Driven originally by analytical chemistry
• Initial measurements of many metals far too high due to
contamination
Biological or “Bioinorganic” component has grown in:
• Bioactive metals: Fe, Co, Cd, Zn, Cu, Ni, Mn, Mo etc.
• Iron limitation discovered
• The Role Complexation on Bioavailability
• Metalloenzymes
• Other limitations and colimitations
• Future roles for genomics, metagenomics, proteomics
10 mg/L ~= 10mM for Fe, Ni, Mn, Cu, Zn
“uniformly distributed” and “random nature”
Global: GEOTRACES
Science Plan
A 10-12 year international
program to map the
chemistry of the oceans
focusing on trace metals
and isotopes.
Started ~2010
http://www.geotraces.org/
Iron as a limiting nutrient in HNLC regions
(Review of Iron Fertilization Experiments Boyd et al., 2007, Science)
Purposeful (white crosses) and natural (red crosses) Fe enrichment studies
have shown Fe limitation of phytoplankton growth.
GEOTRACES Goal: making WOCE-like
sections for Trace Elements and Isotopes
Meridional Pacific, Hiscock, Measures and Landing, GBC 2008
Four Categories of Trace Metal Profiles in 2D
1. Conservative distributions
- Residence time greater than 100000 years
- Much greater than the residence time of the oceans
- Molybdenum, tungsten, antimony, rubidium: are
involved in particle cycling, but the quantities are
insignificant relative to their large seawater inventory
- Concentrations of some are quite high: Mo = 105nM
- Don’t increase with thermohaline circulation
- Searching for the kink in Molybdenum due to
nitrogen fixation
Four Categories of Trace Metal Profiles in 2D
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Nutrient-type distributions:
– Significantly involved with internal cycles of
biologically derived particulate material
– Distributions are dominated by phytoplankton
uptake in surface waters followed by export of some
of this material below the surface layer and
subsequent remineralization and release to
intermediate and deep waters
– Have a low level of scavenging in intermediate and
deep waters
– (N, P, Si) Zinc, Cadmium, Barium, Silver, Nickel
– Increase in concentration with thermohaline
circulation
– Can be used as paleoproxies for P (Cd) or Si (Zn) in
foram tests and diatom opal.
Four Categories of Trace Metal Profiles in 2D
3. Scavenged-type distributions
- Strong interactions with particles
- Short residence times (~100-1000y)
- Increased concentration near sources
- Decreased concentrations away from sources
- Decreased concentrations along flow path due to
continual scavenging
- Aluminum, lead, manganese
- Nonmenclature tangent: Aluminium (British and Aussies) and
Aluminum (Elsewhere)
Four Categories of Trace Metal Profiles in 2D
4. Hybrid-Type Metals
- Strongly influenced by both micronutrient use and
remineralization and scavenging processes.
- Does not accumulate with thermohaline circulation
- Can depend on geographic location: high dust input can obscure
surface drawdown signal
- “Hybrid-Type” is a relatively new descriptor
- Bruland and Lohan (assigned reading this week): Iron, copper
- Although not included, Cobalt is undoubtedly a hybrid-type metal
- Mn could be one as well, but only at high latitudes, where
nutrient-like drawdown occurs
These four geochemical categories of metals in seawater
are a direct result of their (bio)chemical properties:
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Solubility
Inorganic speciation
Organic Speciation
Redox chemistry
Bioactive
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Distributions affected by biota, often
presumed biological function
Does not necessarily require use by
biota, since there appear to be nonbiological elements with nutrient-like
profiles
Definitions
• Ligand – an atom, ion, or
molecule that donates/shares
electrons with one or more
central atoms or ions. Metalligand bonds (inner sphere) are
covalent.
• Chelate – (from Greek chelos =
crab, with two binding claws) two
or more donor atoms from a
single ligand to the central metal
atom
• Coordination environment or
chemistry: number of ligands that
a metal can have. Most metals
have a # of 6, forming octahedral
complexes
Vraspir and Butler 2009
Atomic Orbitals: building-up principle
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Ground state electron configurations:
1s 2s 2p 3s 3p 4s 3d 4p …
s subshell accommodates 2 e-, p subshell 6 e-, d subshell 10 e-, f 14 e-
Properties of Metal Atoms and Ions
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Metallic Radius of an element: half the distance from nearest neighbor atoms in the solid metal
Ionic Radius – the distance between centers of the cation and anion
There is a general decrease in metallic and ionic radius across a period. Due to increase in
nuclear charge while electrons are added to the orbitals of the same shell (excluding d-block
metals). The result is a more compact atom.
Lanthanide contraction: where the f-block is filled prior to the d block, those orbitals have poor
shielding properties and fail to compensate for the increasing nuclear charge, resulting in a more
compact atom
This effect also occurs in the d-block, due to poor shielding by d electrons (e.g. between Sc and
Ni)
Valence, Ionization Energy, and Hardness-Softness
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Metal chemistry strongly influenced by the removal of electrons from a
neutral atom
Valence electrons are the outermost electrons surrounding a closed shell
Main group elements: outer electron shells are s and p orbitals (Li, Na, K)
– React violently with water (e.g. pure sodium to NaOH, +1 ions)
Transition group elements (metals): have incomplete d electron shell
Most transition metals have variable valence, a major component of their
chemistry (Fe: +2, +3, Mn: +2, +3, +4, +6, +7)
Ionization energy is the minimum needed to remove an electron from a
gas phase atom
Hardness is the difference between the ionization energy of the neutral
atom and its anion.
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Related to ability to remove electrons
Soft: large and relatively polarizable
Hard: small and less easily polarized
Characteristics of Metal Ion Binding to Ligands
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Soft vs Hard
– Soft: Ions are large
and easily polarizable
– Hard: Small and less
easily polarizable
Soft metals tend to “like”
soft ligands
Hard metals tend to “like”
hard ligands
Examples:
Hard: Fe3+, Co3+ and OHSoft: Cd2+, Cu+, Hg2+ and
sulfide groups
Characteristics of Metal Ion Binding to Ligands
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Soft vs Hard
– Soft: Ions are large
and easily polarizable
– Hard: Small and less
easily polarizable
Soft metals tend to “like”
soft ligands
Hard metals tend to “like”
hard ligands
Examples:
Hard: Fe3+, Co3+ and OHSoft: Cd2+, Cu+, Hg2+ and
sulfide groups
The Irving-Willliams Series
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Observations that complex stability for each ligand have a tendancy to rank:
Mn2+ < Fe2+ < Co2+ < Ni2+ < Cu2+ > Zn2+
Caused by decreases in ionic radius across series and resultant ligand field
stabilization effects
Many implications both for ligands “L’s” in seawater and for protein binding
of metals inside cells, area for much future research
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For example it is hard to find any cobalt(II) ligand that is stronger than a nickel(II) ligand
Complexation Environment
• “Free ions” is really a misnomer
• Cu2+ is actually Cu(H2O)62+, if not bound by other inorganic species
• Water is a ligand, ligand-exchange rxn constants indicative of rate of
reactivity, or the kinetics
• Dissociation of water molecules dependent on size and inversely to
the size of the metal cation
Water loss exchange rates
Aquatic Chemistry of Trace Elements:
A marine water column context
Solubility Products: Example for Fe(OH)3(s)
Ksp= [Fe][OH]3 = 1042.7
Stability constants for metal complexes (where L is ligand, M is Metal):
K = [ML]/[M][L]
Ligands can include inorganic chemical species:
In oxic systems: OH-, CO32-,SO42-, Cl-, PO43-,
In anoxic systems add: HS-,, S2Ligands can also include organic chemical species:
EDTA, DTPA, NTA, Citrate, Tris, siderophores, cobalophores,
DFB, TETA, and the famous unknown ligand(s) “L”
Aquatic Chemistry of Trace Elements:
A marine water column context
Detailed balancing: Principle of Microscopic Reversibility
kf
Mn+ + LML
kb
d[ML]/dt = kf [M+] [L-]
-d[M+]/dt = -d[L-]/dt = kb [ML]
At steady state:
kf [M+] [L-] = kb [ML]
kf / kb = [ML]/([M+][L-]) = K
Aquatic Chemistry of Trace Elements:
A marine water column context
However, there can be Non-Ideal effects (Morel and Hering 76-82):
- The effects of other solutes on the free energy of ion(s) of interest
- Solubility product and stability constants need to be corrected, or
better, determined to/at the appropriate ionic strength.
- The activity of the metal is: {Mn+} = [Mn+]gMn+
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The activity coefficient, gMn+, can be estimated by the Debye-Huckel
correction or the Davies expression (modified Debye-Huckel)
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I (ionic strength) = ½ S(mi x Zi2) (m=conc, Z = charge for each ion i)
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Seawater I = 0.72 mol kg-1
Z=charge, A = 1.17 M-1/2, B=0.3M-1/2
Thermodynamic databases (Martell and Smith) will provide the ionic
strength experimental conditions for each constant (e.g. 0.1M)
Quasi constant value between I=0.3-0.7
From Morel and Hering, 1993, p77
Average Major Seawater Ions (mM)
(Morel and Hering, p291)
HCO3SO42ClCa2+
Mg2+
Na+
K+
2.38
28.2
0.545
0.0102
0.0532
0.468
0.0102
Average Major Seawater Ions (mM)
(Morel and Hering, p291)
HCO3SO42ClCa2+
Mg2+
Na+
K+
2.38
28.2
0.0532
0.0102
Abundance (or lack there of) is our friend
Seawater constituents:
• Major ions (the salt) – millimolar and higher
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– Na+
– Cl– Mg2+
– Ca2+
– HCO3-
Organic ligands/chelators - nanomolar
– “L”
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Trace metals/elements – picomolar to nanomolar
– Mn+
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With major ions, everything depends on everything (and must be
considered simultaneously
With trace elements, we can consider one element at a time, independently
of other constituents
Preview: Software for Metal Speciation
• Mineql – Westall et al. a program made for calculating aqueous
speciation and solubility at low temperature geochemical conditions
• Critical.exe – Smith and Martell volumes built into a DOS baseddatabase.
• Paper and pencil calculations to understand, verify results, and
cross-check assumptions with computer-assisted calculations.
Morel and Hering 1993
Vraspir and Butler, 2009
Readings – available on website
www.whoi.edu/sites/12.755
• Bruland and Lohan -Treatise on Geochemistry Chapter
• Morel and Hering, Principles of Aquatic Chemistry
Chapter 6
• Background: Lippard and Berg Bioinorganic Chemistry
chapter 2
• Goldberg Biography