Ozone

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Effect of greenhouse gases on Earths IR emissions
300
280
atmospheric window (no absorbing gases)
near tropopause (coldest light)
saturated at center of band
for methane, some absorption, but not saturated
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atmospheric window
corresponds to 667 cm-1
Effect of CO2 is that much of the outgoing IR
centered around l 15 mm gets absorbed and
reradiated. The incremental effect is small for
each additional CO2, because much of that
outgoing radiation is already absorbed
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Effects of progressive CO2 addition to the
Earths IR emissions
No CO2
10 ppm CO2
1000 ppm CO2
100 ppm CO2
Response of IR emission to CO2 is not
linear instead it is logarithmic (incremental
decrease is proportional to the amount already
there)
-doubling of CO2 concentration, in any range,
decreases Iout by the same amount
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Atmosphere with no CO2
Addition of greenhouse gas (CO2)
Radiation balance reestablished by increasing
temperature on the ground
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Model-dependent temperature sensitivity to CO2
increase
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N2O

• A novel period in geological history
• the Anthropocene (P. Crutzen)
• accelerated use of fossil fuel resources
• with steeply rising emissions
• impact of human activities on carbon, nitrogen,
• and other biogeochemical cycles
• major changes in Earths surface cover
• deforestation, soil degradation, etc.

Data from IPCC4
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At T 288K, Iout 390 W/m2
LOSU assessed level of scientific understanding

• Radiative forcing imbalance in the energy
  equilibrium of Earth
• change in solar insolation rate
• change in IR absorption/reradiation (natural or
  anthropogenic)
• Requires then a reequilibration (fast in
  stratosphere generally slow in troposphere)

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Current rate of increase 1.9 ppm/yr
monthly mean

• CO2 levels have increased from 280 ppm to 387 ppm
  since 1860
• Seasonal variation less CO2 in summer (Northern
  hemisphere) because of
• fixation due to increased photosynthesis.
  Most land in Northern hemisphere.

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(Flux in GtC/yr)
1 GtC (gigaton carbon) 109 metric tons
1012 kg 1015 grams (1 petagram Pg) 1 Tg
(teragram) 1012 grams
Fast exchange (75 m.)
Permanent sink
(GtC)
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YIELD ENERGY
Biochemical intermediaries
CONSUME ENERGY

• Overall scheme of photosynthesis and the
  separation of light
• and carbon assimilation reactions CO2 H2O
  ? O2 (CH2O)
• Photosynthesis occurs in some bacteria, algae,
  vascular plants
• Light reactions 2H2O 2NADP ? 2 NADPH 2H
  O2
• (thermodynamically coupled to ADP Pi ? ATP
  (30.5 kJ/mol))

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• Photosynthesis takes place in chloroplasts
• Two membranes outer is porous, inner is not
• Inner compartment has an aqueous region
  (stroma)
• Stroma contains flattened vesicles
  (thylakoids), stacked in grana,
• containing membrane-associated ATP synthesis
  machinery
• Light reactions occur in thylakoid membrane
  dark reactions
• occur in stroma

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chloroplast
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Unique properties of water Very high boiling and
melting point High internal cohesive energy due
to hydrogen bonds 3D network of H-bonds Each
water can donate 2 H-bonds and also accept 2
H-bonds Solid water (ice) has an expanded,
open lattice, so water density increases upon
melting. Low density ice forms atop liquid water
in lakes below ice, life is protected in a
still-aqueous phase from very low atmospheric
temperatures
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Hydrophobic effect Enthalpy of dissolution for
hydrophobic compounds in water is negative
(favorable), but entropy is highly negative
(unfavorable) ?DG unfavorable The negative
entropy reflects increased ordering in the
water molecules surrounding the hydrophobic
solute This principle drives the formation of
natural clathrates, especially the methane
hydrates present in huge quantities under the
sea floor and in the Arctic tundra
Hydrophobic effect also drives the formation of
membranes in biological systems, where the
redox reactions essential to biogeochemical
cycles occur
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Hydrophobic membranes surround all cells (and
organelles inside eukaryotic cells). Primary
constituents are fatty acids and lipids such as
triacylglycerols
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Biological membranes are organized as lipid
bilayers
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General structure of amino acids Zwitterionic
form at pH 7.0 pKa of COO- is about 2.0
pKa of NH3 is about 9.5

• Example of an amino acid
• (alanine), where R is CH3
• The central carbon atom
• is bonded to 4 different
• substituents
• This is an example of a
• chiral center
• The L and D forms are
• called stereoisomers
• They are nonsuperimposable
• mirror images
• In nature, the amino acids found
• in proteins are L

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• Primary structure of a pentapeptide, with
  asymmetric ends.
• Note that the peptide bond is always identical
  between amino acids
• The R-groups of the amino acids are independent
  of the peptide link
• and they may occur in any order in the
  chain.
• This pentapapetide is Ser-Gly-Tyr-Ala-Leu
• The sequence of the pentapeptide is read from
  amino to carboxyl ends

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• Because there is no allowed rotation about the
  peptide bond, the
• four substituent atoms on the C-N must all be
  in the same plane
• However, rotation is allowed about N-Ca (F) and
  about Ca-C (?)
• Therefore a peptide still has considerable
  conformational freedom,
• but this is limited by steric clashes at some
  F-? angles

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Protein secondary structure the alpha helix, is
a local conformation of The peptide backbone
stabilized by hydrogen bonds between N-H and
carbonyl groups along the spiraling peptide chain.
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N
N
C
C
C
N
C
N
N
N
C
C
Another major feature of protein secondary
structure that is stabilized by hydrogen
bonding is the beta sheet. The beta sheet is
formed by parallel or antiparallel (N?C
directions) chains hydrogen-bonding by means of
N-H and carbonyl oxygen contacts. The peptide
segments in a beta sheet do not have to be
directly continuous in the protein chain
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Proteins are embedded in the lipid bilayer. The
peptide sections that traverse the bilayer can
form globular folds inside the bilayer
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If there is a complex fold in the membrane,
formed by helices or sheets, then often
hydrophilic residues are on the inside, because
the protein is dissolved in a hydrophobic
membrane.
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Light-harvesting complex from plants
chromophores are bound to protein and are in a
fixed geometric orientation an LHC trimer
has 36 chlorophylls
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Thylakoid membranes are functionally arranged
into photosystems with 50-200 chromophores per
system Light is transduced to chemical energy
only in the photochemical reaction center a
special pair of two chlorophyll a
molecules The function of most of the
chromophores in a photosystem is to harvest
light photons and to transfer, by exciton
transfer, the energy successively to the
reaction center.
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• Structure of purple bacterium photosynthetic
• reaction center together with rapid reaction
• kinetics allows assignment of the
• sequence of events in electron transfer
• Light excites the special Chl2 pair
• The electron is rapidly passed to pheophytin
• The electron rapidly moves to quinone A
• There is a slow transfer, through nonheme
• iron, to quinone B, which is diffusible
• The electron hole in Chl2 is filled by
• transfer from a heme of cytochrome c,
• after cycling through cytochrome bc1
• The Chl2 pair is an excellent electron
  donor
• (E -1.0 V) reactions are highly
  favored
• thermodynamically fixing of chromophore
• geometry by protein ensures efficiency

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no carbon fixation
CO2 fixation is possible
H2S?S
ADP Pi ? ATP
H2S?S
anoxygenic photoheterotroph
anoxygenic photoautotroph
There are several classes of photosynthetic
reaction centers I. Single reaction centers are
the Type I Fe-S (green sulfur bacteria) and the
Type II Pheophytin-Quinone (purple bacteria) II.
Double reaction centers (as in plants, combine
the 2 single reaction centers, to form the
Z-scheme)
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YIELD ENERGY
Biochemical intermediaries
CONSUME ENERGY

• Overall scheme of photosynthesis and the
  separation of light
• and carbon assimilation reactions CO2 H2O
  ? O2 (CH2O)
• Light reactions 2H2O 2NADP ? 2 NADPH 2H
  O2
• (thermodynamically coupled to ADP Pi ? ATP
  (30.5 kJ/mol))
• NADPH synthesis allows CO2 fixation into
  carbohydrate

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• In plant chloroplasts, photosynthesis
• requires two reaction centers
• The overall Z scheme is not cyclic
• H2O is oxidized and NADP
• is ultimately reduced to NADPH
• Two photon absorptions are needed
• to drive the reduction, in PSI/PSII
• Oxygen is evolved in a specific
• complex (water-splitting complex)
• A proton gradient drives
• ATP synthesis

Each arrow represents a protein-mediated redox
reaction (e- transfer)
Overall Z-scheme -- 2 H2O 2 NADP 8 hv ? O2
2 NADPH 2 H One electron transferred per 2
photons absorbed (one each in PSI and
PSII) Forming one O2 requires 4 electron
transfers (8 photons)
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Ribulose bisphosphate carboxylase/oxygenase (RUBIS
CO)

• Carbon assimilation requires three separate
  stages
• The overall process is cyclical Calvin cycle
• 1. CO2 is condensed with a five-carbon sugar
  (R15BP) to yield two 3C sugars
• 2. ATP and NADPH are used to reduce 3PG to G3P
• 3. Six 3C sugars (G3P) are rearranged to three
  5C sugars
• (regeneration of R15BP) while one G3P is the
  net yield from 3 CO2

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(Flux in GtC/yr)
1 GtC (gigaton carbon) 109 metric tons
1012 kg 1015 grams (1 petagram Pg) 1 Tg
(teragram) 1012 grams
Fast exchange (75 m.)
Permanent sink
(GtC)
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Anthropogenic sources -fossil fuels cement 6.3
GtC/yr -permanent deforestation 1.6
GtC/yr
CO2 fixation
Fast exchange
Permanent sink
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Anthropogenic sources -fossil fuels cement 6.3
GtC/yr -permanent deforestation 1.6
GtC/yr Fate of anthropogenic CO2 42 stays in
air longer than 1 yr 29 absorbed by ocean
surface 29 Northern Hemisphere land
CO2 fixation
Fast exchange
Permanent sink
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• Residence time (yr) steady-state concentration
  (ppm)/ input rate (ppm/yr)
• Can also be defined with respect to output rate
• Can be well-defined if there is a known removal
  mechanism
• (example CH4 is removed by reaction with
  hydroxyl radical in the
• troposphere in a reaction with established
  kinetics)
• For CO2, the removal mechanisms are complex
• (i) photosynthesis cycle terrestrial biosphere
  absorption (fast)
• (ii) dissolution in oceans (hundreds of years)
• (iii) reactions in ocean to equilibrate with
  CaCO3 (thousands of yrs)
• (iv) weathering reactions (hundreds of thousands
  of years)
• After 1000 years 15-30 of CO2 remains in the
  atmosphere
• After 100,000 years 7 of CO2 remains in the
  atmosphere

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Long-term fate of atmospheric CO2 following a
large release from fossil fuel burning
today
Climatic Change 90, 283-297 (2008)