GLOSSARY
March 3, 2012 LACSSP teacher workshop
Photosynthesis and Chemosynthesis
OXYDATION REDUCTION (REDOX): oxidation is the loss of electrons and
reduction is the gain of electrons.
PHOTOSYNTHETIC PIGMENTS:
(http://www.ucmp.berkeley.edu/glossary/gloss3/pigments.html)
Pigments are colorful compounds.
Pigments are chemical compounds which reflect only certain wavelengths of visible
light. This makes them appear "colorful". Flowers, corals, and even animal skin contain
pigments which give them their colors. More important than their reflection of light is the
ability of pigments to absorb certain wavelengths.
Because they interact with light to absorb only certain wavelengths, pigments are useful
to plants and other autotrophs --organisms which make their own food using
photosynthesis. In plants, algae, and cyanobacteria, pigments are the means by which the
energy of sunlight is captured for photosynthesis. However, since each pigment reacts
with only a narrow range of the spectrum, there is usually a need to produce several kinds
of pigments, each of a different color, to capture more of the sun's energy.
There are three basic classes of pigments.
Chlorophylls are greenish pigments which contain a porphyrin ring. This is a stable
ring-shaped molecule around which electrons are free to migrate. Because the electrons
move freely, the ring has the potential to gain or lose electrons easily, and thus the
potential to provide energized electrons to other molecules. This is the fundamental
process by which chlorophyll "captures" the energy of sunlight.
There are several kinds of chlorophyll, the most important being chlorophyll "a". This is
the molecule which makes photosynthesis possible, by passing its energized electrons on
to molecules which will manufacture sugars. All plants, algae, and cyanobacteria which
photosynthesize contain chlorophyll "a". A second kind of chlorophyll is chlorophyll "b",
which occurs only in "green algae" and in the plants. A third form of chlorophyll which is
common is (not surprisingly) called chlorophyll "c", and is found only in the
photosynthetic members of the Chromista as well as the dinoflagellates. The differences
between the chlorophylls of these major groups was one of the first clues that they were
not as closely related as previously thought.
Carotenoids are usually red, orange, or yellow pigments, and include the familiar
compound carotene, which gives carrots their color. These compounds are composed of
two small six-carbon rings connected by a "chain" of carbon atoms. As a result, they do
not dissolve in water, and must be attached to membranes within the cell. Carotenoids
cannot transfer sunlight energy directly to the photosynthetic pathway, but must pass
their absorbed energy to chlorophyll. For this reason, they are called accessory
pigments. One very visible accessory pigment is fucoxanthin the brown pigment which
colors kelps and other brown algae as well as the diatoms.
Phycobilins are water-soluble pigments, and are therefore found in the
cytoplasm, or in the stroma of the chloroplast. They occur only in Cyanobacteria and
Rhodophyta.
The picture at the right shows the two classes of phycobilins which may be extracted
from these "algae". The vial on the left contains the bluish pigment phycocyanin, which
gives the Cyanobacteria their name. The vial on the right contains the reddish pigment
phycoerythrin, which gives the red algae their common name.
Phycobilins are not only useful to the organisms which use them for soaking up light
energy; they have also found use as research tools. Both pycocyanin and phycoerythrin
fluoresce at a particular wavelength. That is, when they are exposed to strong light, they
absorb the light energy, and release it by emitting light of a very narrow range of
wavelengths. The light produced by this fluorescence is so distinctive and reliable, that
phycobilins may be used as chemical "tags". The pigments are chemically bonded to
antibodies, which are then put into a solution of cells. When the solution is sprayed as a
stream of fine droplets past a laser and computer sensor, a machine can identify whether
the cells in the droplets have been "tagged" by the antibodies. This has found extensive
use in cancer research, for "tagging" tumor cells.
LIGHT-DEPENDENT REACTIONS: From Wikipedia, the free encyclopedia
Light-dependent reactions of photosynthesis at the thylakoid membrane
See also: Light-independent reactions
The 'light-dependent reactions', or photosynthesis, is the first stage of photosynthesis,
the process by which plants capture and store energy from sunlight. In this process, light
energy is converted into chemical energy, in the form of the energy-carrying molecules
ATP and NADPH. In the light-independent reactions, the formed NADPH and ATP
drive the reduction of CO2 to more useful organic compounds, such as glucose. However,
although light-independent reactions are, by convention, also called dark reactions, they
are not independent of the need of light, for they are driven by ATP and NADPH,
products of light. They are often called the Calvin Cycle or C3 Cycle.
The light-dependent reactions take place on the thylakoid membrane inside a chloroplast.
The inside of the thylakoid membrane is called the lumen, and outside the thylakoid
membrane is the stroma, where the light-independent reactions take place. The thylakoid
membrane contains some integral membrane protein complexes that catalyze the light
reactions. There are four major protein complexes in the thylakoid membrane:
Photosystem I (PSI), Photosystem II (PSII), Cytochrome b6f complex, and ATP
synthase. These four complexes work together to ultimately create the products ATP and
NADPH.
The two photosystems absorb light energy through proteins containing pigments, such as
chlorophyll. (Makes the color of leaves and trees green.) The light-dependent reactions
begin in photosystem II. When a chlorophyll a molecule within the reaction center of
PSII absorbs a photon, an electron in this molecule attains a higher energy level. Because
this state of an electron is very unstable, the electron is transferred from one to another
molecule creating a chain of redox reactions, called an electron transport chain (ETC).
The electron flow goes from PSII to cytochrome b6f to PSI. In PSI, the electron gets the
energy from another photon. The final electron acceptor is NADP. In oxygenic
photosynthesis, the first electron donor is water, creating oxygen as a waste product. In
anoxygenic photosynthesis various electron donors are used.
Cytochrome b6f and ATP synthase work together to create ATP. This process is called
photophosphorylation, which occurs in two different ways. In non-cyclic
photophosphorylation, cytochrome b6f uses the energy of electrons from PSII to pump
protons from the stroma to the lumen. The proton gradient across the thylakoid
membrane creates a proton-motive force, used by ATP synthase to form ATP. In cyclic
photophosphorylation, cytochrome b6f uses the energy of electrons from not only PSII
but also PSI to create more ATP and to stop the production of NADPH. Cyclic
phosphorylation is important to create ATP and maintain NADPH in the right proportion
for the light-independent reactions.
The net-reaction of all light-dependent reactions in oxygenic photosynthesis is:
2H2O + 2NADP+ + 3ADP + 3Pi → O2 + 2NADPH + 3ATP
The two photosystems are protein complexes that absorb photons and are able to use this
energy to create an electron transport chain. Photosystem I and II are very similar in
structure and function. They use special proteins, called light-harvesting complexes, to
absorb the photons with very high effectiveness. If a special pigment molecule in a
photosynthetic reaction center absorbs a photon, an electron in this pigment attains the
excited state and then is transferred to another molecule in the reaction center. This
reaction, called photoinduced charge separation, is the start of the electron flow and is
unique because it transforms light energy into chemical forms.
DARK REACTION:
LIGHT INDEPENDENT REACTION: From Wikipedia, the free encyclopedia
The light-independent reactions of photosynthesis are chemical reactions that convert
carbon dioxide and other compounds into glucose. These reactions occur in the stroma,
the fluid-filled area of a chloroplast outside of the thylakoid membranes. These reactions
take the light-dependent reactions and perform further chemical processes on them. There
are three phases to the light-independent reactions, collectively called the Calvin cycle:
carbon fixation, reduction reactions, and ribulose 1,5-bisphosphate (RuBP) regeneration.
Despite its name, this process occurs only when light is available. Plants do not carry out
the Calvin cycle by night. They, instead, release sucrose into the phloem from their starch
reserves. This process happens when light is available independent of the kind of
photosynthesis (C3 carbon fixation, C4 carbon fixation, and Crassulacean Acid
Metabolism); CAM plants store malic acid in their vacuoles every night and release it by
day in order to make this process work.[1]
Light-independent reactions
The simplified internal structure of a chloroplast
Overview of the Calvin cycle and carbon fixation
CORRECT EQUATION FOR PHOTOSYNTHESIS—get from Nick is this correct?
The overall chemical reaction involved in photosynthesis is:
6CO2 (carbon dioxide) + 12H2O (water) --> C6H12O6 (glucose) +
6O2 (oxygen gas) + 6H2O (water)
CHROMOTOGRAPHY
Main article: History of chromatography
Thin layer chromatography is used to separate components of a plant extract, illustrating
the experiment with plant pigments that gave chromatography its name
Chromatography, literally "color writing", was first employed by Russian scientist
Michael Tsvet in 1900. He continued to work with chromatography in the first decade of
the 20th century, primarily for the separation of plant pigments such as chlorophyll,
carotenes, and xanthophylls. Since these components have different colors (green,
orange, and yellow, respectively) they gave the technique its name. New types of
chromatography developed during the 1930s and 1940s made the technique useful for
many separation processes.
Chromatography technique developed substantially as a result of the work of Archer John
Porter Martin and Richard Laurence Millington Synge during the 1940s and 1950s. They
established the principles and basic techniques of partition chromatography, and their
work encouraged the rapid development of several chromatographic methods: paper
chromatography, gas chromatography, and what would become known as high
performance liquid chromatography. Since then, the technology has advanced rapidly.
Researchers found that the main principles of Tsvet's chromatography could be applied in
many different ways, resulting in the different varieties of chromatography described
below. Advances are continually improving the technical performance of
chromatography, allowing the separation of increasingly similar molecules.
CHEMOSYNTHESIS:
http://www.pmel.noaa.gov/vents/nemo/explorer/concepts/chemosynthesis.html
Chemosynthesis is the process by which certain microbes
create energy by mediating chemical reactions.
From Wikipedia, the free encyclopedia
http://en.wikipedia.org/wiki/Chemosynthesis
In biochemistry, chemosynthesis is the biological conversion of one or more carbon molecules (usually
carbon dioxide or methane) and nutrients into organic matter using the oxidation of inorganic molecules
(e.g. hydrogen gas, hydrogen sulfide) or methane as a source of energy, rather than sunlight, as in
photosynthesis. Chemoautotrophs, organisms that obtain carbon through chemosynthesis, are
phylogenetically diverse, but groups that include conspicuous or biogeochemically-important taxa include
the sulfur-oxidizing gamma and epsilon proteobacteria, the Aquificaeles, the Methanogenic archaea and the
neutrophilic iron-oxidizing bacteria.
Many microorganisms in dark regions of the oceans also use chemosynthesis to produce biomass from
single carbon molecules. Two categories can be distinguished. In the rare sites at which hydrogen
molecules (H2) are available, the energy available from the reaction between CO 2 and H2 (leading to
production of methane, CH4) can be large enough to drive the production of biomass. Alternatively, in most
oceanic environments, energy for chemosynthesis derives from reactions in which substances such as
hydrogen sulfide or ammonia are oxidized. This may occur with or without the presence of oxygen.
Many chemosynthetic microorganisms are consumed by other organisms in the ocean, and symbiotic
associations between chemosynthesizers and respiring heterotrophs are quite common. Large populations
of animals can be supported by chemosynthetic secondary production at hydrothermal vents, methane
clathrates, cold seeps, and whale falls.
It has been hypothesized that chemosynthesis may support life below the surface of Mars, Jupiter's moon
Europa, and other planets.[1]
Giant tube worms use bacteria in their trophosome to react hydrogen sulfide with oxygen as a source of
energy.
Some reactions produce sulfur, such as:
Hydrogen sulfide chemosynthesis: CO2 + O2 + 4H2S → CH2O + 4S + 3H2O
(CH2O is used to mean carbohydrate, not formaldehyde.)
Instead of releasing oxygen gas as in photosynthesis, solid globules of sulfur are produced. In bacteria that
can do this, such as purple sulfur bacteria, yellow globules of sulfur are present and visible in the
cytoplasm.
Discovery
In 1890, Sergei Nikolaevich Vinogradskii (or Winogradsky) proposed a novel life process called
chemosynthesis. His discovery suggested that some microbes could live solely on inorganic matter and
emerged during his physiological research in the 1880s in Strassburg and Zurich on sulfur, iron, and
nitrogen bacteria.
This was confirmed nearly 90 years later, when hydrothermal ocean vents were predicted to exist in 1970s.
The hot springs and strange creatures were discovered by Alvin, the world's first deep-sea submersible, in
1977 at the Galapagos Rift. At about the same time, Harvard graduate student Colleen Cavanaugh proposed
chemosynthetic bacteria that oxidize sulfides or elemental sulfur as a mechanism by which tube worms
could survive near hydrothermal vents. Cavanaugh later managed to confirm that this was indeed the
method by which the worms could thrive, and is generally credited with the discovery of
chemosynthesis.[citation needed]
A 2004 television series hosted by Bill Nye named chemosynthesis as one of the 100 greatest scientific
discoveries of all time.[2]