Download Title

CHAPTER 9
THE BIOSPHERE: HOW THE REVOLUTION IN BIOLOGY
RELATES TO GREEN CHEMISTRY
From Green Chemistry and the Ten Commandments of
Sustainability, Stanley E. Manahan, ChemChar Research,
Inc., 2006
[email protected]
9.1. GREEN CHEMISTRY AND THE BIOSPHERE
The biosphere consists of all living organisms and the materials and
structures produced by living organisms.
The biosphere and green chemistry
• Living organisms produce a wide range of materials that are used
by humans for a variety of purposes.
• Large quantities of substances including pesticides and fertilizers
are generated in the anthrosphere for use to control pests and
enhance the growth and health of organisms in the biosphere.
• Reduction of the use and generation of toxic substances in the
anthrosphere is designed to prevent harm to humans and other
organisms in the biosphere.
• Environmental conditions largely determined by anthrospheric
activities strongly affect organisms in the biosphere.
Organisms and Green Chemistry
Organisms applied to green chemistry
• Carry out chemical processes under mild conditions
• Cannot tolerate highly toxic substances
• Biological ecosystems
Sustainable operation of biological ecosystems
9.2. BIOLOGY AND THE BIOSPHERE
Biology is the science of life and the organisms that comprise life
Recall biological materials from Chapter 5
• Proteins • Carbohydrates • Nucleic acids • Lipids
Hierarchical organization
• Molecule < Organelles < Cells < Tissues < Organs < Organism
< Population < Community < Ecosystem < Biosphere
Metabolism
Metabolism is what occurs when organisms mediate chemical
(biochemical) processes to get energy, make raw materials required
for tissues in organisms or modify raw materials for this purpose,
and reproduce.
• Photosynthesis
• Cellular respiration in which glucose is oxidized to provide
energy
• Importance of adenosine triphosphate, ATP (below):
NH2
C
N
C
N
C H
H
C
C
N
N
Adenine
O
O
O
H
O P *O P *O P* O C H
O
O
O
O
C H H C
Ribose
C C H
* High-energy bonds
HO OH
Adenosine group
Organisms in the Biosphere
Organisms comprising the biosphere belong to six kingdoms.
• Archaebacteria and Eubacteria are generally single-celled
organisms without distinct, defined nuclei.
• Protists are generally single-celled organisms that have cell nuclei
and may exhibit rather intricate structures
• Plantae (plants) • Animalia (animals) • Fungi
Organisms comprising the biosphere belong to six kingdoms.
• Classified according to their food, energy, and oxygen
• Autotrophs make food and biomass from simple inorganic
substances, usually using solar energy to perform photosynthesis
• Chemautotrophs mediate inorganic chemical reactions for their
energy
• Heterotrophs, including humans, derive their energy and biomass
from the metabolism of organic matter, usually biomass from
plants.
• Aerobic
• Anaerobic
• Facultative
9.3. CELLS: BASIC UNITS OF LIFE
Prokaryotic cells
Eukaryotic cells
Golgi bodies
Plasma membrane
Lysosome
Ribosomes
Ribosomes
Nucleoid
Cell wall
Plasma
membrane
Cytoplasm
Prokaryotic cell
Chloroplast
Starch granule
Vacuole
Vacuole
Cytoplasm
Endoplamic
reticulum
Mitochondria
Cell wall
Eukaryotic animal cell
Nucleus
Eukaryotic plant cell
Photosynthesis
Photosynthesis
6CO2 + 6H2O (light energy, h)  C6H12O6 (glucose) + 6O2
Important role of cyanobacteria in past eons.
Iron oxide deposits formed by reaction of soluble Fe2+ with O2
produced by cyanobacteria in past times
4Fe2+ + O2 + 4H2O  2Fe2O3 + 8H+
9.4. METABOLISM AND CONTROL IN ORGANISMS
Respiration
C6H12O6 (glucose) + 6O2  6CO2 + 6H2O + energy (9..1)
Enzymes in Metabolism
Enzymes are proteins that act as biological catalysts
Enzyme
+ s ubs trate
enzyme/s ubstrate complex
products
+
enzyme
Enzyme action. The enzyme recognizes the substrate upon which it
acts because of the complementary shapes of the enzyme and the
substrate. The double arrows indicate that the processes are
reversible.
Enzymes
Enzymes are named for where they act and what they do, such as
gastric proteinase that acts in the stomach to hydrolyze proteins
A number of factors can affect enzyme action
Temperature
• Around 37˚C optimum for mammals
• Most destroyed above about 60˚C
• Potentially useful enzymes from thermal sources
Acidity
Adverse effects of toxic substances on enzymes
• Binding of “nerve gas” with acetylcholinesterase
Enzymes in green chemistry
• Toxicity of some chemicals to enzymes
• Mild conditions under which enzymes act
Nutrients
Nutrients are the raw materials that organisms require for their
metabolism.
• Macronutrients including plant fertilizers
• Micronutrients, such as boron, chlorine, copper, iron, zinc
Control in Organisms
Nervous system
• Nerve impulses
• Central nervous system
• Peripheral neuropathy (sometimes caused by toxic substances)
Molecular messengers
• Hormones
• Receptor proteins bond with hormones
H3C
H
C
H
C
H3C
H Ethylene
H
Plant hormone
associated with
ripening of fruit, other
processes
OH
Tes tos terone
O
Male animal sex
hormone
Regulation by Hormones
Animal regulatory hormones released by endocrine glands
• Anterior pituitary gland releases human growth hormone
• Parathyroid gland releases a hormone to stimulate uptake of
calcium into the blood from bones and the digestive tract
• Pancreas releases insulin to stimulate glucose uptake from blood
Toxic substances may interfere with the function of endocrine
glands.
• Toxic substances may mimic the action of hormones
• Estrogen-mimicking substances.
9.5. REPRODUCTION AND INHERITED TRAITS
Asexual reproduction
Sexual reproduction
Reproduction is directed by genes
• Alteration may cause mutations
• Control of production and exposure to mutagens is a major thrust
of green chemistry
9.6. STABILITY AND EQUILIBRIUM OF THE BIOSPHERE
Homeostasis (“same status”) is a state of stability and equilibrium of
an organism with its environment
A major objective of environmental science, including the practice
of green chemistry, is to maintain and enhance conditions of
homeostasis in the biosphere.
Ecology describes the interaction of organisms with their
surroundings and each other.
An ecosystem is a segment of the environment and the organisms in
it with all of the interactions and relationships that implies.
• Means of capturing energy
• Food chain or more complicated food webs
Biomagnification of poorly degradable organic chemicals that are
soluble in lipid (fat) tissue concentrated in lipid tissue at the top of
the food chain
The surroundings over a relatively large geographic area in which a
group of organisms live constitute a biome such as a tropical rain
forest.
Response of Life Systems to Stress
The ability of a community of organisms to resist alteration and
damage from threats such as drought is called inertia
Inertia depends upon
• Productivity
• Diversity
• Constancy
• Resilience
Relationships Among Organisms
In most ecosystems there is a dominant plant species that provides
a large fraction of the biomass anchoring the food chain in the
ecosystem.
Much of agricultural chemistry is devoted to trying to regulate the
competition of weeds with crop plants
In an undisturbed ecosystem the principle of competitive exclusion
applies in which two or more potential competitors exist in ways that
minimize competition for nutrients, space, and other factors required
for growth.
Symbiotic relationships between organisms which exist together to
their mutual advantage
• Lichen consisting of algae and fungi growing together on rocks
• Nitrogen-fixing bacteria growing in nodules on leguminous plant
roots
9.7. DNA AND THE HUMAN GENOME
Deoxyribonucleic acid, DNA
Action of ribonucleic acid, RNA
Representation of the double helix structure of DNA
(right). Hydrogen bonds between complementary
bases on the two strands are shown by dashed lines.
DNA in units associated with protein molecules called
chromosomes
• 23 pairs of chromosomes in humans
The strands of DNA in chromosomes are divided into
sequences of nucleotides each distinguished by the
nitrogen-containing base in it
Specific groups of nucleotides compose genes, each
of which has a specific function.
Human Genome Project to map the genes in the
human genome
Representation of Nucleosides
Continuation
of strand A
Hydrogen bonds between
bas es on adjacent strands
marked with asterices
O
O P O
O
H C
H C H O
C
H
H
C
N
H
C
H
C
H
CH3
C C
C
O
H
O* H
N H*
Thymine bas e
Continuation
of strand B
N
C
N
H
C N
C
C
N
H
CH
N C
Adenine bas e
H
O
C
H
C
H
O
H
C
H C H
O
O P O
O
-
Representation of two nucleosides in two adjacent
strands of DNA showing hydrogen bonding between
Continuation the bases thymine and adenine. These two bases
bonded together by hydrogen bonds constitute a
of strand A
base pair.
Continuation
of strand B
Protein Synthesis
To make a protein
• DNA produces a nucleic acid segment designated mRNA, which
goes out into the cell and causes the protein to be formed through a
process called transcription and translation
• The gene is said to be expressed
Proteins are the biological molecules that make up much of the
structure of cells and that perform most of the key functions of living
organisms.
Protein Synthesis (Cont.)
Proteins are made according to directions provided by cellular DNA:
1. The DNA in a gene that is specific for a particular protein
transfers information for the protein synthesis to RNA.
2. The RNA links with a cell ribosome, which is the proteinsynthesizing entity of the cell.
3. Using directions provided by the RNA, the ribosome assembles
amino acids into a protein.
4. The protein performs the function for which it is designed in the
organism; for example, it may function as an enzyme to carry out
metabolic processes.
Genome Sequencing and Green Chemistry
A key goal of green chemistry is to use chemicals that have
maximum effectiveness for their stated purpose with minimum side
effects.
• Applies to pharmaceuticals in which a knowledge of the human
genome may enable development of drugs that do exactly what
they are supposed to do without affecting nontarget systems
• Drugs can be made very efficiently with little waste material.
DNA sequencing as it relates to green chemistry applied to
organisms other than humans
Possible to deal with organisms on a highly scientific basis in areas
such as pest control and the biosynthesis of raw materials
Synthesis of precisely targeted insecticides which kill target pests
without affecting other organisms
• Effective at very low doses, thus minimizing the amount of
insecticide that has to be synthesized and applied
Manipulating Genes
Exact knowledge of organism’s genomes is extremely helpful in the
practice of genetic engineering in which genes are transferred
between species to enable production of desired proteins and to give
organisms desirable characteristics, such as pest resistance.
A number of medically useful proteins and polypeptides are now
produced by genetically engineered microorganisms, most
commonly genetically modified Escherichia coli bacteria
• Biosynthesis of human insulin consisting of only 51 amino acids,
which requires two genes
• Human growth hormone
• Tissue plasmogen activator that dissolves blood clots formed in
heart attacks and strokes
• Vaccine proteins to inoculate against diseases such as meningitis,
hepatitis B, and influenza
9.8. GENETIC ENGINEERING
Domestication of wild species followed by genetic modification of
crops and animals has occurred through selection over thousands of
years
• Breeding has been a slow process
• Provided properties, such as higher yield, heat and drought
tolerance, cold resistance, and resistance to microbial or insect
pests
• During the 1900s, increased understanding of genetics greatly
accelerated the process of breeding different varieties
• High yielding dwarf varieties of wheat and rice leading to the
“green revolution” of the 1950s
• Hydrids from crossing of two distinct lines of the same crop,
dating in a practical sense from the mid-1900s
Traditional breeding requires traits from the same species that is
being bred
Transgenic Technology
Transgenic technology to transfer genes from one organism to an
entirely different kind
• Transgenic technology can be used beneficially in plant breeding to
increase tolerance to stress, increase yield, enhance the value of the
end product by enriching it in desired biochemicals such as
essential amino acids, and otherwise make plants more useful.
Transgenic technology is possible because a gene in DNA will make
the protein for which it is designed in an organism quite different
from the one in which the gene originated
• In some cases a gene transferred from one organism to another as a
segment of DNA will often perform the function for which it was
developed in the recipient organism
• Enzymes are used in the process, with restriction enzymes cutting
out desired regions of DNA and ligase enzymes joining the ends of
DNA together and enzymes are used to further manipulate and
amplify the DNA.
Transgenic Technology (Cont.)
After a specific gene is isolated, it is cloned by insertion into a
bacterium, which reproduces the gene many times.
In order for a gene to generate a desired protein at the appropriate
time and location in a plant, a promoter must be added that
functions as a switch
• The easiest promoter to use is a constitutive promoter that causes
the gene to be expressed in most of the plant’s tissues and
throughout its lifetime—cauliflower mosaic virus
Genes may be inserted with a gene gun that uses a very small
projectile to literally shoot genetic information into cells
Genes may also be inserted through the action of Agrobacterium
tumafaciens bacteria
After insertion of genes, a viable plant must be developed
9.9. BIOLOGICAL INTERACTION WITH
ENVIRONMENTAL CHEMICALS
Bioaccumulation is the term given to the uptake and concentration
of xenobiotic materials by living organisms from water in streams or
bodies of water, sediments in bodies of water, drinking water, soil,
food, or even the atmosphere
Biomagnification in which xenobiotic substances become
successively more concentrated in the tissues of organisms higher in
the food chain
• Usually with poorly degradable, lipid-soluble organic compounds
Loss of xenobiotics back to water by depuration
The most straightforward case of bioaccumulation is
bioconcentration, which occurs when a substance dissolved in
water enters the body of a fish or other aquatic organism by passive
processes (basically, just “dissolves” in the organism), and is carried
to bodies of lipid in the organism in the blood flow
• Hydrophobicity model
Bioconcentration Factor
Bioconcentration factor =
Concentration of xenobiotic in lipid
Concentration of xenobiotic in water
Typical bioconcentration factors for PCBs and hexachlorobenzene in
sunfish, trout, and minnows range from somewhat more than 1,000
to around 50,000, reflecting the high lipid solubility of these
compounds.
9.10. Biodegradation
Environmental biodegradation of xenobiotic compounds by bacteria,
fungi, and protozoa
• Xenobiotic utilized for food and energy
• Xenobiotic subjected to cometabolism in which the organism’s
enzymes act upon the substances as a “side-line” of their normal
metabolic processes
• Cometabolism by Phanerochaete chrysosporium (white rot) fungus
of organochlorine compounds, including PCBs and dioxins
• Small changes, such as addition, deletion, or modification of a
functional group
• Complete biodegradation to simple inorganic species—CO2 for
carbon, NH4+ or NO3- for nitrogen, HPO42- for phosphorus, SO42for sulfur— the process of mineralization
Detoxication refers to biological conversion of a toxic substance to
non-toxic or less toxic substance without necessarily undergoing
biodegradation
Factors in Biodegradation
A number of factors are involved in determining the effectiveness
and rate of biodegradation
• The compound has to be biodegradable
• Physical properties, such as water solubility
• Chemical characteristics including the presence of functional
groups amenable to microbial attack
H
H C H
H
H C H H C H
H H
H
H C C C C
H H
H
H C H
H
H
H
C C C H
H
H
H C H
H
Highly branched, poorly
biodegradable compound
H H H H H H H H H O
H C C C C C C C C C C OH
H H H H H H H H H
Highly biodegradable compound with a
s traight hydrocarbon chain and a functional group amenable to biological attack
Biodegradability
Biodegradation of resistant compounds, such as phenol
OH Phenol
Biodegradability of compounds is an important consideration in
green chemistry
• Especially true of “consumable” materials, such as detergents, that
are dissipated to the environment
9.11. THE ANTHROSPHERE IN SUPPORT OF THE
BIOSPHERE
The most direct interface between the biosphere and technology
occurs in agriculture.
The production of biomass per unit area of land has increased in a
spectacular fashion in recent decades with the use of fertilizers,
herbicides, insecticides, and sophisticated means of cultivation and
harvesting.
Now the application of recombinant DNA technology to agriculture
promises even greater advances.
Anthrosphere and Biosphere
Growing realization of the important information that nature can
provide in maintaining agricultural productivity
• In prevention of water erosion, terraces constructed on land are
designed to funnel excess water runoff onto grassed waterways that
can be seeded with a tough, erosion-resistant sod that stands up
under the punishment of occasional deluges of runoff water while
surviving intermittent severe droughts
• May be possible to reseed prairie areas to tough native grasses and
allow bison to feed upon the grass as a source of meat (less fat and
more healthy than beef from cattle)
Restoration Ecology
Restoration ecology to restore and develop “natural” areas such as
farmland that is too marginal to support profitable agricultural
operations. The example of restoring native grasslands was
mentioned above
• Much of the rocky, hilly, unproductive farmland in New England is
now reverting to forests
• Construction machinery with the capacity to move enormous
quantities of dirt have proven useful, for example, levelling large
areas for the construction of wetlands
• Restoration ecology to recover populations of game animals
Anthrosphere in Support of the Biosphere
Sophisticated chemical analysis techniques can now be used to find
and eliminate the sources of chemical hazards to wildlife
• Used to locate problems with insecticidal DDT, biomagnified
through the food chain
• Analysis of mercury in fish
Dealing with projected effects of global warming
• Genetically engineering plant varieties that can withstand the heat
and drought resulting from global warming
• Plants that can grow in saltwater
• Using renewable solar and wind energy, vast water desalination
projects will be developed to provide fresh water to irrigate highvalue crops where the costs can be justified.