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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.

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From Green Chemistry and the Ten Commandments of Sustainability, Stanley E. Manahan, ChemChar Research, Inc., 2006

[email protected]

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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.

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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

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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

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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.


•Cellular respiration in which glucose is oxidized to provide energy

• Importance of adenosine triphosphate, ATP (below):

Adenosine group

* High-energy bonds

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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.


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Prokaryotic cellsEukaryotic cells

Prokaryotic cell

Eukaryotic animal cell

Eukaryotic plant cell

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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+

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C6H12O6 (glucose) + 6O2 6CO2 + 6H2O + energy (9..1)

Enzymes in Metabolism

Enzymes are proteins that act as biological catalysts

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.

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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


• Around 37˚C optimum for mammals

• Most destroyed above about 60˚C

• Potentially useful enzymes from thermal sources


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

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Nutrients are the raw materials that organisms require for their metabolism.

•Macronutrients including plant fertilizers

•Micronutrients, such as boron, chlorine, copper, iron, zinc

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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

Plant hormone associated with ripening of fruit, other processes

Male animal sex hormone

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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.

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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

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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.

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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

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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

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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

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Representation of Nucleosides

Representation of two nucleosides in two adjacent strands of DNA showing hydrogen bonding between the bases thymine and adenine. These two bases bonded together by hydrogen bonds constitute a base pair.

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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.

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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 protein-synthesizing 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.

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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

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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

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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

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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.

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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

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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

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Bioconcentration Factor

Concentration of xenobiotic in lipid

Bioconcentration factor =

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.

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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, SO42- for 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

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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

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Biodegradation of resistant compounds, such as 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

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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.

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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)

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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

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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 high-value crops where the costs can be justified.