This document contains Chapters 1 to 2 PART I INTRODUCTION TO LIVING ANIMALS 1 Life: Biological Principles and the Science of Zoology 2 The Origin and Chemistry of Life 3 Cells as Units of Life 4 Cellular Metabolism CHAPTER 1 LIFE: BIOLOGICAL PRINCIPLES AND THE SCIENCE OF ZOOLOGY CHAPTER OUTLINE 1.1. The Uses of Principles A. Underlying Principles Central to Understanding Zoology 1. Laws of physics and chemistry underlie some zoology principles. 2. Principles of genetics and evolution guide much zoological study. 3. Principles learned from one animal group can be applied to others. 4. Some science methods specify how to conduct solid research. B. Zoology, the Study of Animal Life (Figure 1.1) 1. Zoologists studying many dimensions base research upon a long history of work. 2. Two central principles are evolution and the chromosomal theory of inheritance. 1.2. Fundamental Properties of Life A. Defining Properties of Life 1. Properties exhibited by life today are different from those at its origin. 2. Change over time, or evolution, has generated many unique living properties. 3. Definitions based on complex replicative processes would exclude non-life, but also early forms from which cellular life descended. 4. We do not force life into a simple definition, yet we can readily recognize life from a nonliving world. B. General Properties of Living Systems 1. Chemical Uniqueness (Figures 1.2, 2.15) a. Macromolecules in organisms are far more complex than molecules in nonliving matter. b. They obey the same physical laws as nonliving molecules but are more complex. c. Nucleic acids, proteins, carbohydrates and lipids are common molecules in life. d. Their general structure evolved early; thus the common amino acid subunits of proteins are found throughout life. e. They provide both a unity based on living ancestry and a potential for diversity. 2. Complexity and Hierarchical Organization (Figures 1.3, 1.4; Table 1.1) a. Life has an ascending order of complexity: macromolecules, cells, organisms, populations and species. b. Each of these levels has an internal structure: macromolecules form ribosomes and membranes, etc. and cells form tissues. c. However, each level has unique abilities and requirements; cells can replicate but are not independent in an organism. d. New characteristics that appear at the next level of organization are emergent properties. e. Because of the interactions of the components, we must study all levels directly as well as together. f. Diversity of emergent properties at higher levels is a result of evolution (i.e., lower levels without hearing cannot develop language). 3. Reproduction (Figure 1.5) a. Life comes from previous life but had to arise from nonliving matter at least once. b. Genes replicate genes, cells divide to produce new cells and organisms produce new organisms sexually or asexually. c. Reproduction is not necessary of individuals, but is necessary for a lineage to survive. d. Reproduction is a combination of contradictory processes of copying traits, but with variation. e. If heredity were perfect, life would never change; if it were wildly variable, life would lack stability. 4. Possession of a Genetic Program (Figure 1.6) a. Nucleic acids encode structures of protein molecules. b. DNA stores genetic information in animals. c. Sequences of nucleotide bases (A, C, G and T) code for the order of amino acids in a protein. d. The genetic code is correspondence between bases in DNA and sequence of amino acids. e. This genetic code was established early in evolution and has undergone little change. f. The genetic code in animal mitochondrial DNA is slightly different from nuclear and bacterial DNA. g. Changes in mitochondrial DNA (it contains fewer proteins) are less likely to disrupt cell functions. 5. Metabolism (Figure 1.7) a. Living organisms maintain themselves by acquiring nutrients from the environment. b. Breakdown of nutrients provides both energy and molecular components for cells. c. Metabolism is the range of essential chemical processes. d. Metabolism involves constructive (anabolic) and destructive (catabolic) reactions. e. Most metabolic pathways occur in specific cell organelles. f. The study of the performance of complex metabolic functions is physiology. 6. Development (Figure 1.8) a. Development describes characteristic changes an organism undergoes from origin to adult. b. It involves changes in size and shape, and differentiation within the organism. c. Some animals have uniquely different embryonic, juvenile and adult forms. d. The transformation from stage to stage is metamorphosis. e. Among animals, early stages of related organisms are more similar. 7. Environmental Interaction (Figure 1.9) a. Ecology is the study of an organism's interaction with the environment. b. Organisms respond to stimuli in the environment, a property called irritability. c. We cannot separate life and its evolutionary lineage from its environment. 8. Movement a. Energy extracted from environment permits living systems to initiate controlled movements that are essential for reproduction, growth, response to stimuli, and development. b. Animals are adapted for locomotion which has led to dispersal of entire populations from one geographic location to another over time. c. Movement of nonliving matter is controlled by external forces and thus is dissimilar to purposeful movements exhibited by living systems. C. Life Obeys Physical Laws 1. Vitalism is the belief that life requires more than basic laws of physics; biological research has found no basis for vitalism. 2. First Law of Thermodynamics (the law of conservation of energy) a. Energy cannot be created or destroyed; it can be transformed from one form to another. b. All aspects of life require energy. c. In animals, chemical energy in food is converted to chemical energy in cells and then converted to mechanical energy of muscle contraction. 3. Second Law of Thermodynamics a. Physical systems tend to proceed toward a state of greater disorder, or entropy. b. Energy obtained and stored by plants is released in many ways and eventually lost as heat. c. It takes a constant input of usable energy from food to keep an animal organized. d. The process of evolution does not violate the second law; complexity is achieved by perpetual use and dissipation of energy flowing into the biosphere from the sun. e. Physiologists study survival, growth, reproduction, etc. from an energetic perspective. 1.3. Zoology as a Part of Biology (Figure 1.10) A. Characteristics of Animals 1. Animals are a branch of the evolutionary tree of life. 2. Animals are part of a large limb of eukaryotes, organisms that include fungi and plants with nuclei in cells. 3. Animals are unique in nutrition; they eat other organisms and therefore need to capture food. 4. Animals lack photosynthesis; cell walls found in plants, and also lack absorptive hyphae of fungi. 5. Species of Euglena are examples of protists that combine properties of animals and plants. 1.4. Principles of Science A. Nature of Science 1. Science is a way of asking about the natural world to obtain precise answers. 2. Asking questions about nature is ancient; modern science is about 200 years old. 3. Science is separate from activities such as art and religion. 4. The trial over creation science provided a definition of science. a. Science is guided by natural law. b. Science has to be explanatory by reference to natural law. c. Science is testable against the observable world. d. Science conclusions are tentative; they are not necessarily the final word. e. Science is falsifiable. 5. Science is neutral regarding religion and does not favor one religious position over another. 6. The reappearance of “creation-science” in the guise of “intelligent-design theory” may force further defense of the teaching of science. B. Scientific Method (Figure 1.11) 1. Criteria for science form a hypothetico-deductive method. 2. Hypotheses are based on prior observations of nature or derived from theories based on nature. 3. The scientific method may be summarized in a series of steps: (1) Observation (2) Question (3) Hypothesis (4) Empirical test (5) Conclusions (6) Publication. 4. Testable predictions are made based on hypotheses. 5. A hypothesis powerful in explaining a wide variety of related phenomena becomes a theory. 6. Falsification of a specific hypothesis does not necessarily lead to rejection of a theory as a whole. 7. The most useful theories explain the largest array of different natural phenomena. 8. Scientific meaning of “theory” is not the same as common usage of theory as “mere speculation.” 9. Powerful theories that guide extensive research are called paradigms. 10. Replacement of paradigms is a process known as a scientific revolution; the evolutionary paradigm has guided biology research for over 150 years. C. Experimental Versus Evolutionary Sciences 1. Hypotheses can be divided into those that seek to understand proximate versus ultimate causes. 2. Studies that explore proximate causes are experimental sciences using experimental methods that: a. Predict the results of a disturbance based on tentative explanation. b. If the explanation is correct, then the predicted outcome should occur. c. If a different result occurs, our explanation is incorrect or incomplete. 3. Controls are repetitions of an experiment that lack disturbance or treatment. 4. The sub-fields of molecular biology, cell biology, endocrinology, developmental biology and community ecology rely heavily on experimental scientific methods. 5. Ultimate causes are addressed by questions involving long-term time spans. a. Evolutionary sciences address ultimate causes. b. Evolutionary questions are often explored using a comparative method. c. Patterns of modern similarities are used to establish hypotheses on evolutionary origins. d. Sub-fields include comparative biochemistry, molecular evolution, comparative cell biology, comparative anatomy, comparative physiology and phylogenetic systematics. 1.5. Theories of Evolution and Heredity (Figure 1.12) A. Darwin’s Theory of Evolution 1. Ernst Mayr describes five central theories of “Darwinism.” a. Perpetual change: changes across generations are a fact documented in the fossil record. b. Common descent: branching lineages form a phylogeny that is confirmed by expanding research on morphological and molecular similarities. (Figure 1.13) c. Multiplication of species: splitting and transforming species produces new species. d. Gradualism: small incremental changes over long periods of time cause gradual evolution, but current research is still studying if this explains all changes. (Figure 1.14) e. Natural selection: based on variability in a population, the inheritance of that variation, and different survival of those variants, explains adaptation. (Figure 1.15) 2. Darwin lacked a correct theory of heredity and assumed the current theory of blending inheritance was correct; Mendel’s theory of particulate inheritance became well known only in the very early 1900s. 3. Darwin’s theory as modified by incorporation of genetics is called “neo-Darwinism.” B. Mendelian Heredity and the Chromosomal Theory of Inheritance (Figure 1.16) 1. Chromosomal inheritance is the foundation for genetics and evolution, as laid down by Mendel. 2. Genetic Approach (Figure 1.17) a. Mendel’s technique involved crossing true-breeding populations. b. Production of F1 hybrids and F2 generations showed lack of blending, and masking of recessive traits by dominant traits. c. Traits assorted independently unless on the same chromosome. d. Expanded research, especially with fruit flies, clarified genetic mechanisms. 3. Contributions of Cell Biology (Figures 1.18, 1.19) a. Improvements in microscopes allowed observation of sperm and location of germ cell line. b. Discovery of chromosome pairs in body cells and single sets in germ cells clarified mode of heredity. Lecture Enrichment 1. From the Australian outback to interior New Guinea, all cultures regardless of science education level distinguish living from nonliving substances. Although this is the first day of classes and students may not have had an opportunity to read the assigned text, they can be led through a query of “what is life?” They will usually offer: growth, reproduction, response to the environment, metabolism, etc. Ask whether any one of these aspects alone distinguishes a living organism from nonliving organism. Note that it is not necessary for an individual organism to reproduce, and indeed most animals hatched or born do not survive to reproduce. 2. Clay is an example of self-replicating molecular assemblages that do not have the potential variety or the metabolism to be called living. Quartz is a molecule that can “grow,” “reproduce” and “respond” to light. Tardigrades can completely suspend metabolism for a century and dehydrate to ten percent of their living water content. These examples will appropriately muddle the definition of life. Nevertheless, it is critical in deciding that if we find life on Mars–would we recognize it? We continue attempts to confirm whether life has ever existed on Mars. What phenomena would we look for? 3. Levels of organization can seem rather abstract. Read job descriptions for biologists (e.g., histologist, population geneticist, community ecologist, etc.). Ask students what level of organization the scientist studies. 4. Virtually continuously throughout this course, students can be asked to design an experiment to test a particular hypothesis being discussed. 5. Ask students for examples of the scientific method in their everyday lives, such as fixing dinner, determining how to dress for the day’s weather and activities, or handling problems with a car that doesn’t work. 6. Students can search local newspapers for examples using the scientific method (e.g., testing consumer products, recalls, reports on medical research, jury decisions based on forensic evidence, etc.). Bring in a tabloid newspaper making fabulous claims and ask why it does not meet science standards. 7. Discuss the difference between scientific observations of the natural world and superstitions such as those associated with Friday the thirteenth and black cats. Examples involving Bigfoot, the Loch Ness Monster, spontaneous human combustion, living dinosaurs in remote areas, and other modern misbeliefs related to animals are given in the Skeptic and Skeptical Inquirer magazines. 8. Discuss why it is possible to prove a hypothesis or theory false but not prove it true. Be careful not to fall into the postmodernist or constructivist view of science knowledge being merely a mental construct, no better or worse than tribal beliefs, etc. or being tentative to the point of merely awaiting falsification. 9. Most students believe the world is spherical. Only students who have flown in the Concorde jetliner have direct observational evidence for this. Yet they believe the photos by astronauts, and phoning a person in China awakes them in a time zone 12 hours different from us. Such indirect evidence fortifies the model of a spherical earth. This illustrates science relies on reasoning to make sense of observational data. Commentary/Lesson Plan Background: Professors that are new to a college or university may consult with veteran professors about the state’s high school biology and other science requirements. In addition, the proportion of students that come from farm or urban backgrounds will provide a major indicator of student experiences. Most high school science texts discuss the “scientific method” as a very cookbook or lock-step method. And most college undergraduates do not have genuine experience with open-ended and purposeful science research, nor the breadth of experience to place limited research experience in a full perspective. Misconceptions: Many students see science as a body of encyclopedic knowledge and authority, and do not recognize an underlying scientific attitude or process. Some students have been told that science is only process, and have no appreciation for the role of the general public recognizing germ theory, for instance. Most citizens view science practiced only by scientists and do not consider the trouble-shooting performed by a medical doctor or mechanic to be in any way “scientific.” Most consider scientists always “open minded” and do not recognize that experiments often close the door to hypotheses that don’t work out. In many states, physics classes are not commonly taken in high school; this may be their first exposure to physics and many students will misunderstand the laws of physics as preventing evolution. A large portion of college students believe that dinosaurs and humans were on earth at the same time, and a similar proportion question the validity of the theory of evolution without much depth of knowledge about it. A large proportion view evolution as “survival of the fittest” without recognizing that survival is only useful if it promotes reproduction. Schedule: Students may lack the book assignment the first day of class, but this is the point where an instructor establishes the ground rules of quizzes, testing, whether notes will be given in outline form, etc. If you use in-class questioning, beginning with “What is Life?” as in Lecture Enrichment #1 above, which can set the pace. HOUR 1 1.1. The Uses of Principles A. Underlying Principles Central to Understanding Zoology B. Zoology, the Study of Animal Life 1.2. Fundamental Properties of Life A. Defining Properties of Life B. General Properties of Living Systems C. Life Obeys Physical Laws 1.3. Zoology as a Part of Biology A. Characteristics of Animals HOUR 2 1.4. Principles of Science A. Nature of Science B. Scientific Method C. Experimental Versus Evolutionary Sciences 1.5. Theories of Evolution and Heredity A. Darwin’s Theory of Evolution B. Mendelian Heredity and the Chromosomal Theory of Inheritance ADVANCED CLASS QUESTIONS: Recent satellite probes as well as meteorite discoveries have been used to search for the possibility of life on Mars. What properties would scientists look for in currently living life forms? If life once existed but became extinct, what evidence would still exist that life once existed? Answer: To answer the question, scientists would look for specific properties in currently living life forms on Mars, as well as evidence of past life that may now be extinct. Properties of currently living life forms on Mars that scientists would look for include: 1. Presence of Water: Life, as we know it, requires water. Therefore, scientists would search for evidence of liquid water or water ice on Mars, as it could indicate the presence of living organisms. 2. Organic Molecules: Scientists would look for organic molecules such as amino acids, nucleic acids, and lipids, which are the building blocks of life as we know it. 3. Metabolism: Detection of metabolic activity, such as the production of gases like oxygen or methane, could indicate the presence of living organisms. 4. Structures Resembling Cells: Microscopic examination of Martian soil or rock samples may reveal structures resembling cells, indicating the presence of living organisms. 5. Adaptations for Survival: Scientists would look for adaptations that enable organisms to survive in Mars' harsh environment, such as resistance to radiation or extreme temperatures. Evidence of past life that may still exist on Mars, even if the life forms themselves are extinct, includes: 1. Fossils: Fossilized remains of ancient organisms, such as microorganisms or multicellular organisms, would provide evidence of past life on Mars. 2. Biological Markers: Chemical signatures left behind by living organisms, such as certain isotopic ratios or distinctive organic molecules, could indicate the past presence of life. 3. Microbial Mats: Layers of microbial communities, known as microbial mats, could leave behind distinctive patterns or structures in Martian rocks. 4. Biofilms: Biofilms, which are communities of microorganisms encased in a matrix of extracellular polymeric substances, could leave behind distinctive traces in Martian rocks. By searching for these properties and evidence, scientists hope to determine whether life currently exists on Mars or if it existed in the past. Scientists use the scientific method to gather information about the natural world. Can this include the past? Does how a forensics expert reconstructs a crime scene differ in substance from how an evolutionary biologist reconstructs ancient ecology from fossil evidence? Answer: Yes, the scientific method can be used to gather information about the past. Both forensics experts and evolutionary biologists use similar principles and methods to reconstruct events from the past, although the specific techniques and tools they use may differ. Forensics experts reconstruct a crime scene by gathering and analyzing physical evidence such as fingerprints, DNA, and other trace evidence. They use this evidence to piece together what happened during the crime. Similarly, evolutionary biologists reconstruct ancient ecology from fossil evidence. They gather and analyze fossils, as well as other geological and biological evidence, to understand the environments and organisms that existed in the past. While the specific techniques and tools may vary, both forensics experts and evolutionary biologists rely on observation, evidence collection, analysis, and hypothesis testing to reconstruct events from the past. When utilizing the scientific method, hypotheses can be proven false, but not true. Does this mean all science is conjecture until disproven? Can anyone explain the “uncertainty principle” and the ability of scientists to calculate the tolerance limits of their knowledge? Answer: When utilizing the scientific method, hypotheses can indeed be proven false through empirical testing, but they cannot be proven true with absolute certainty. However, this does not mean that all science is merely conjecture until disproven. The uncertainty principle in science acknowledges the inherent limitations of human knowledge and measurement. It states that there is a fundamental limit to the precision with which certain pairs of physical properties of a particle, such as position and momentum, can be known simultaneously. In the context of scientific inquiry, this principle reminds us that all scientific knowledge is provisional and subject to revision based on new evidence or more precise measurements. Scientists can calculate the tolerance limits of their knowledge by quantifying the uncertainty associated with their measurements and conclusions. This involves statistical analysis and considering factors such as experimental error, variability in data, and the limitations of measurement techniques. Therefore, while scientific hypotheses cannot be proven true with absolute certainty, they can be supported by a preponderance of evidence and withstand repeated testing and scrutiny. Science is a process of continually refining and improving our understanding of the natural world based on empirical evidence and logical reasoning. What evidence exists that all living things evolved from a common ancestor? How does this concept explain the unity of life forms? Answer: The evidence supporting the idea that all living things evolved from a common ancestor comes from multiple fields of study, including comparative anatomy, molecular biology, embryology, and the fossil record. 1. Comparative Anatomy: Comparative anatomy shows similarities in the structures of organisms that suggest a common ancestry. For example, the pentadactyl limb (limb with five digits) is found in mammals, birds, reptiles, and amphibians, indicating a shared evolutionary history. 2. Molecular Biology: Molecular evidence, particularly DNA and protein sequences, also supports the theory of common descent. Similarities in the genetic code and sequences of genes among different species suggest a common ancestry. 3. Embryology: Comparative embryology reveals similarities in the early developmental stages of different species, suggesting a common evolutionary origin. For instance, during embryonic development, vertebrates such as fish, birds, and mammals show similarities in the pharyngeal pouches, tail structures, and limb buds. 4. Fossil Record: The fossil record provides evidence of transitional forms, or organisms that share characteristics of both ancestral and descendant groups. Fossils of transitional forms, such as Tiktaalik (a transitional form between fish and tetrapods), provide evidence of the evolutionary transitions between major groups of organisms. The concept of common descent explains the unity of life forms by suggesting that all living organisms are related through a shared evolutionary history. According to this concept, all organisms share a common ancestor, and the diversity of life on Earth arose through a process of descent with modification. Over time, organisms diversified and adapted to different environments, leading to the wide array of life forms observed today. The unity of life forms is explained by the presence of shared characteristics and genetic similarities among different species, reflecting their common ancestry. 5. Animal ecology experiments can be classified in two general categories: Ecologists can bring an animal into the laboratory, isolate it in a chamber where they can determine all the environmental conditions affecting it and then alter one variable. Or, they can study the animal in the wild and attempt to determine why it occurs in certain natural habitats. Using terms given in the text for science methodology, explain the benefits of both systems. Answer: The two general categories of animal ecology experiments, laboratory-based experiments, and field-based studies offer distinct advantages: 1. Laboratory-based experiments: Controlled environment: In laboratory settings, ecologists can control and manipulate environmental variables precisely. They can isolate the animal in a controlled chamber where all environmental conditions are known and easily manipulated. Precision and repeatability: Experiments conducted in controlled laboratory environments allow for precise manipulation of variables and replication of experiments. This enhances the ability to identify cause-and-effect relationships between environmental factors and animal behavior or physiology. Reduction of confounding variables: By controlling environmental variables, researchers can reduce the influence of confounding variables, making it easier to identify the specific factors affecting the animal. 2. Field-based studies: Real-world relevance: Field studies allow ecologists to observe animals in their natural habitats, providing insights into their behavior, interactions, and ecology under natural conditions. Ecological validity: Studying animals in their natural environment provides ecological validity, ensuring that the results are applicable to real-world situations. Complexity of interactions: Field studies allow researchers to observe the complex interactions between animals and their environment, including interactions with other species, predation, competition, and resource availability. Long-term observations: Field studies often allow for long-term monitoring of animal populations, which is essential for understanding population dynamics, habitat use, and responses to environmental change over time. In summary, laboratory-based experiments offer precise control over environmental variables and allow for the identification of cause-and-effect relationships, while field-based studies provide ecological validity, allowing researchers to observe animals in their natural habitats and understand the complex interactions between animals and their environment. Both approaches are valuable and can complement each other, providing a more comprehensive understanding of animal ecology. CHAPTER 2 THE ORIGIN AND CHEMISTRY OF LIFE CHAPTER OUTLINE 2.1. Spontaneous Generation of Life? A. History 1. Spontaneous generation was a belief that frogs could arise from earth, mice from rotten matter, etc. 2. In 1861, Louis Pasteur demonstrated sterilized broth in flasks, even exposed to air, could not spontaneously ferment. 3. However, Oparin and Haldane independently proposed a long period of “abiotic molecular evolution” stating life did once arise from nonliving chemistry. (Figure 2.1) 2.2. Water and Life (Figure 2.2) 1. Life on earth depends on the properties of water. a. Water has a high specific heat capacity; this ability protects organisms from extreme thermal fluctuations. b. Water has a high heat of vaporization; this allows terrestrial organisms to cool themselves by removing excess heat. c. Water has a unique density behavior; ice is less dense than liquid water. (Figure 2.3) d. Water has a high surface tension that lends to its great cohesiveness. (Figure 2.4) e. Water has a low viscosity. f. Water is an excellent solvent. (Figure 2.5) 2.3 Organic Molecular Structure of Living Systems A. Carbon 1. Organic compounds contain carbon; most are produced in living systems. 2. Over one million carbon-based molecules have been identified. B. Carbohydrates: Nature’s Most Abundant Organic Substance 1. Carbohydrates contain carbon, hydrogen and oxygen, usually in ratio of 1C:2H:1O as H–C–OH. 2. Carbohydrates provide structural elements and store energy. 3. Glucose is commonly found in the blood of animals and is an important immediate energy source for cells. (Figure 2.6, 2.7) 4. Cellulose occurs in greater quantities than all other organic materials combined. 5. Carbohydrates, synthesized by plants by photosynthesis, are the starting point of food chains. 6. Monosaccharides a. Monosaccharides are simple sugars with a carbon backbone of four, five or six carbon atoms. b. Glucose, galactose and fructose all contain free sugar groups. (Figure 2.8) c. The hexose glucose is particularly important in life. 7. Disaccharides (Figures 2.9) a. Disaccharides contain two monosaccharides bonded together. b. Maltose is formed from binding two glucose molecules and removing one water molecule. c. Sucrose (table sugar) is a linkage of glucose to fructose. d. Lactose (milk sugar) is a linkage of glucose and galactose. 8. Polysaccharides a. Polysaccharides are chains of glucose molecules called polymers. b. Most have the formula (C6H10O5)n where n is the number of simple sugar subunits. c. Glycogen is a polymer of glucose; found in vertebrate liver and muscle cells, it is storage carbohydrate of animals. d. Cellulose is the principal structural carbohydrate of plants. C. Lipids: Fuel Storage and Building Material 1. Lipids are fats and fat-like substances. 2. Lipids have low polarity; therefore they are insoluble in water but soluble in organic solvents. 3. Triglycerides (Figure 2.10) a. Stored fats are derived directly or converted from carbohydrates; they are the major animal fuels. b. Triglycerides consist of glycerol and three molecules of fatty acids. c. Neutral fats are esters, combining alcohol and an acid. d. Fatty acids in triglycerides are usually 14–24 carbons long. e. When every carbon in a chain is bonded to two hydrogen atoms, it is saturated. f. Unsaturated fatty acids, common in plant oils, have two or more carbon atoms joined by double bonds. (Figure 2.11) 4. Phospholipids (Figure 2.12) a. Phospholipids have a structural role in molecular organization of tissues and membranes. b. They resemble triglycerides with one fatty acid replaced by phosphoric acid and an organic base. c. Lecithin is an important phospholipid of nerve membranes. d. The phosphate group is charged and therefore polar; the rest of the molecule is nonpolar, so phospholipids can bridge both environments. e. The term amphiphilic describes compounds, like phospholipids, that are polar and water-soluble on one end and non-polar on the other end. 5. Steroids (Figure 2.13) a. Steroids are complex alcohols with fat-like properties. b. They are biologically important. c. Steroids include cholesterol, vitamin D, adrenocortical hormones and sex hormones. D. Amino Acids and Proteins 1. Proteins are large molecules composed of 20 kinds of amino acids. (Figure 2.14) 2. Amino acids are joined by peptide bonds. 3. Two amino acids and a peptide bond form a dipeptide. 4. With one free amino group on one end and a free carboxyl on the other, additional amino acids can be joined to form a long chain of enormous variety. 5. Levels of Protein Structure (Figure 2.15) a. Primary structure is the sequence of amino acids in the polypeptide chain. b. Secondary structure comes from the bond angles of the sequence: alpha-helix and beta sheets. c. Bending and folding of secondary structures forms the tertiary structure, often stabilized by disulfide, hydrogen, ionic and hydrophobic bonds. d. Quaternary structure occurs when several polypeptide chains form subunits of a huge protein molecule, as in hemoglobin. 6. Proteins form much of the framework of the cytoplasm and organelles. 7. Proteins function as enzymes to catalyze most reactions; cell biology can be studied as protein biology. 8. Prions are infectious proteins that cause the host’s normal proteins to become contorted into abnormal 3-dimensional shapes. E. Nucleic Acids 1. Nucleic acids are complex polymeric molecules. 2. Sequence of nitrogenous bases encodes genetic information for inheritance. 3. They store directions for synthesis of enzymes and other proteins. 4. They are the only molecules that can replicate themselves. 5. DNA is deoxyribonucleic acid. 6. RNA is ribonucleic acid. 7. Both DNA and RNA are polymers of repeated units called nucleotides, each containing a sugar, a nitrogenous base and a phosphate group. 2.4. Chemical Evolution A. Oparin-Haldane Hypothesis 1. Aleksander Oparin and J.B.S. Haldane independently proposed a hypothesis of chemical evolution. 2. They proposed the early atmosphere consisted of simple compounds: water, carbon dioxide, hydrogen gas, methane and ammonia, but lacked oxygen. 3. The compounds necessary for life are not synthesized outside cells nor are they stable in the presence of oxygen. 4. Rock evidence indicates virtually no atmospheric oxygen at earliest times; this provided a reducing atmosphere. 5. Both methane (CH4) and ammonia (NH3) are fully reduced compounds. 6. Such an atmosphere, with variations in heat and high radiation, was conducive to prebiotic synthesis but unsuited to modern life forms. 7. Many chemicals would not react without a continuous source of free energy to produce a reaction. 8. Electrical discharges in lightning today produce a large amount of organic matter. 9. Alternative to the “hot dilute soup” scenario is the hydrothermal vent hypothesis, which places these extreme events underwater. B. Prebiotic Synthesis of Small Organic Molecules (Figure 2.16) 1. In 1953, Stanley Miller and Harold Urey tested the Oparin-Haldane hypothesis. 2. A mixture of methane, hydrogen, ammonia, and water was circulated past an electric spark, boiled, and condensed; after a week of continuous sparking, approximately 15% of the carbon had been converted to organic compounds. 3. Many compounds related to life were formed, including four of the amino acids, urea and several simple fatty acids. 4. Critics contend that the early earth atmosphere may have been different from Miller’s test. 5. Omitting ammonia and methane resulted in smaller amounts of compounds and required longer time periods. 6. More recent experiments have clarified the sequences leading through formaldehyde, hydrogen cyanide, cyanoacetylene, etc. that react with water and ammonia or nitrogen to produce a wider array of organic compounds. 7. The finding of amino acids in meteorites provides additional evidence for their natural abiotic synthesis. C. Formation of Polymers 1. The next state required condensation of amino acids, nitrogenous bases and sugars. 2. These polymerizations are condensation (dehydration) reactions 3. Water tends to drive reactions toward decomposition by hydrolysis. 4. In living systems, condensation reactions occur in aqueous (cellular) environments with enzymes. 5. Without enzymes and ATP energy, macromolecules soon decompose. 6. The strongest hypothesis for prebiotic assembly of biologically important polymers is that they occurred within the boundaries of semi-permeable membranes formed from small amphiphilic molecules. 7. Amphiphiles extracted from the Murchison meteoriteform membranous vesicles in aqueous solutions (Figure 2.17); fatty acids and long-chained alcohols from meteorites may be possible components of prebiotic membranes. 2.5. Origin of Living Systems A. Self-replicating Systems 1. Fossils date to 3.8 billion years ago; earliest life form probably originated 4 billion years ago. 2. Protocells would have been autonomous, membrane-bound units with functional organization that permitted self-reproduction. 3. On top of previous chemical evolution, nucleic acids were needed as simple genetic systems. 4. This causes a biological paradox. a. How could nucleic acids appear without the enzymes to synthesize them? b. How could enzymes evolve without nucleic acids to direct their synthesis? 5. Their RNA, not protein content, catalyzes translation of mRNA by ribosomes. 6. Therefore, earliest enzymes could have been RNA, which would have been the earliest self-replicating molecules; thus it would have been an “RNA world.” 7. Proteins are better catalysts and DNA is more stable; thus they would eventually be selected. 8. Before this stage, only environmental conditions and chemistry shaped biogenesis. 9. After this stage, the system responds to natural selection and evolves. B. Origin of Metabolism (Figure 2.18) 1. History of the evolution of complex metabolism is yet to be understood; a model is proposed here. 2. Autotrophs synthesize their own food; heterotrophs must obtain food from the environment. 3. Earliest microorganisms are considered primary heterotrophs; they were probably anaerobic and similar to Clostridium bacteria. 4. They could survive as long as the nutrient soup was abundant; protocells that converted inorganic precursors to a required nutrient would have a selective advantage as nutrients were depleted. 5. Evolution of autotrophic organisms required gaining enzymes to catalyze conversion of inorganic molecules to more complex ones. C. Appearance of Photosynthesis and Oxidative Metabolism 1. Autotrophy evolves with photosynthesis. 2. Modern photosynthesis involves carbon dioxide and water to form sugar and oxygen. 3. Early photosynthesis probably used hydrogen sulfide or other hydrogen sources. 4. Production of oxygen began building an atmosphere; at 1% of its current level, oxygen begins to form an ozone shield and restrict UV radiation reaching the surface. 5. Then photosynthetic organisms spread across land and water, increasing oxygen production. 6. Oxidative (aerobic) metabolism appeared using oxygen as the terminal receptor and completely oxidizing glucose to carbon dioxide and water. 7. Cyanobacteria, eukaryotic algae and plants have generated our current atmosphere of 21% oxygen. 2.6. Precambrian Life A. Cambrian Explosion 1. Pre-Cambrian covers time before Cambrian began nearly 600 million years ago. 2. Most animal phyla appear within a few million years at the beginning of Cambrian: the “Cambrian explosion.” 3. This likely represents the absence of fossilization rather than abrupt emergence. B. Prokaryotes and the Age of Cyanobacteria (Blue-Green Algae) 1. Primitive Structures of Prokaryotes a. A single DNA molecule, lacking histones, is in a nucleoid but not bound by nuclear membranes. b. They lack mitochondria, plastids, Golgi apparatus and endoplasmic reticulum. c. During division, the nucleoid divides and replicates but does not go through organized mitosis. d. Cyanobacteria peaked in abundance one billion years ago; they were dominant for two-thirds of life’s history. 2. They are classified in kingdom Monera by some taxonomists, and kingdom Eubacteria by others. 3. Prokaryotes comprise two lineages of very distinct organisms. a. Most bacteria are in the kingdom Eubacteria. b. Archaebacteria have a unique cellular metabolism, different cell wall chemistry and unique ribosomal RNA. C. Appearance of Eukaryotes (Figure 2.19) 1. Advanced Structures of Eukaryotes a. A membrane nucleus contains chromosomes composed of chromatin. b. There is more DNA, and eukaryotic chromatin contains histones and RNA. c. Cellular division usually is an organized process called mitosis. d. In the cytoplasm are many membrane-bound organelles. 2. Fossils suggest eukaryotes arose 1.5 million years ago. (Figure 2.20) 3. Lynn Margulis and others proposed eukaryotes are a symbiosis of multiple bacteria. (Figure 2.21) a. Mitochondria and plastids contain their own DNA. b. Nuclear, plastid and mitochondrial ribosomal RNAs show distinct evolutionary lineages. c. Plastid and mitochondrial ribosomal DNA is closer to bacterial DNA. d. Plastids are closest to cyanobacteria in structure and function. e. A host cell that could incorporate plastids or mitochondria with their enzymatic abilities would be at a great advantage. 4. Endosymbiotic theory proposes that pre-eukaryotes arose from anaerobic bacteria that served as a host with aerobic bacteria. (Figure 2.22) a. The nucleus and other organelles were derived from infoldings of the cell membrane. b. Aerobic bacteria were ingested or parasitized and came to reside in the cytoplasm. c. A permanent mutualistic relationship developed whereby the aerobic bacteria living in its host would have metabolized toxic oxygen and the host anaerobic bacteria provided food and protection. d. Scientists have collected data and tested this theory and found that it is a reasonable. 5. Eukaryotes may have originated many times. 6. Heterotrophs that cropped cyanobacteria provided ecological space for other types of organisms. 7. Food chains of producers, herbivores and carnivores accompanied a burst of evolutionary activity that may have been permitted by atmospheric changes. 8. The merging of disparate organisms to produce evolutionary novel forms is called symbiogenesis. Lecture Enrichment 1. Some substances have macroscopic images (e.g., sugar, lipids, protein in meat) and the large size of an albumin molecule is apparent in the thick viscosity of egg white, but it is difficult to image something that is primarily nucleic acid, etc. without lab work. 2. Note how different molecules such as nucleic acids and proteins may appear different in various life forms but still have the same basic structure to perform the same kind of job. Why are some molecules essentially the same in bacteria and humans and very different in others? 3. Draw, use transparencies, slides or video to illustrate the different isomeric forms of the hexose sugars glucose, fructose, and galactose, and reasons for their different characteristics. Show how the structures fit into enzymes and why different enzymes would be needed to interact with different isomers. 4. Speculate what would happen if genetic engineering gave humans the ability to directly digest cellulose. Would this be useful or not? Ask students to consider the structure of our digestive tracts and the current use of cellulose as roughage. 5. Describe how denaturation affects the different levels of a protein’s structure. Which levels would be most affected by denaturation? Contrast denaturation caused by heat (cooking food) as opposed to mild denaturation caused by reversible pH changes. 6. Compare the bonds that link the carbohydrates, lipids, proteins and nucleic acids. Consider the size of the final molecules and which ones are branched and unbranched. Prepare students for the link between the information in DNA, RNA and proteins that will be discussed later. 7. Early researchers probing the possibility of life on other planets speculated that it might be based on another atom besides carbon—perhaps silicon. Ask students to consider the chemical properties of silicon compared to carbon and speculate on how this might make life different or impossible as we know it. Commentary/Lesson Plan Background: There is substantial chemical knowledge assumed in this chapter, including references to rather remote properties of clay soil and microspheres. Most discussion of basic carbohydrates, lipids and proteins should constitute review from previous biology coursework in high school and college. Misconceptions: Students may assume that most major breakthroughs are made by the U.S. science establishment; both J.B.S. Haldane (British) and Aleksander Oparin (Russian) were not Americans. How we view the world determines what we believe and what we believe determines how we view the world; thus anti-evolutionists focus on detecting contradictions and paradoxes in evolutionary theory, but the ribozyme/RNA world discovery demonstrates how some logical dilemmas resolve themselves. Students often only relate “polymer” with plastic, but the monomer-polymer concept for cellulose, chitin, etc. is equivalent. Many students will find it “intuitive” that the first cells had to be autotrophic. Schedule: The speed of coverage of this chapter will vary considerably depending on the general chemistry background of students. Some understanding of basic chemistry is critical to appreciating the roles of organelles in the next chapter.
HOUR 1 2.1. Spontaneous Generation of Life A. History 2.2. Organic Molecular Structure of Living Systems A. Carbon B. Carbohydrates C. Lipids D. Amino Acids and Proteins E. Nucleic Acids
HOUR 2 2.3. Chemical Evolution A. Oparin-Haldane Hypothesis B. Prebiotic Synthesis of Small Organic Molecules C. Formation of Polymers 2.4. Origin of Living Systems A. Self-replicating Systems B. Origin of Metabolism C. Appearance of Photosynthesis and Oxidative Metabolism 2.5. Precambrian Life A. Cambrian Explosion B. Prokaryotes and the Age of Cyanobacteria (Blue-Green Algae) Appearance of the Eukaryotes
2.6. A. Symbiogenesis ADVANCED CLASS QUESTIONS: The atoms and bonds within a molecule determine its chemical and physical properties. Compare fats that contain mostly saturated fatty acids with oils that contain mostly unsaturated fatty acids to demonstrate this concept. Answer: The difference in chemical and physical properties between fats containing mostly saturated fatty acids and oils containing mostly unsaturated fatty acids is primarily due to the difference in the arrangement of atoms and bonds within the molecules. Saturated Fats: • Chemical Structure: Saturated fats contain fatty acid molecules in which the carbon atoms are bonded to as many hydrogen atoms as possible, resulting in a straight, "saturated" carbon chain. • Physical Properties: • Solid at room temperature. • Higher melting point. • Pack closely together, leading to a solid, dense structure. • Examples: Animal fats such as butter, lard, and fat in red meat. Unsaturated Oils: • Chemical Structure: Unsaturated oils contain fatty acid molecules with one or more double bonds between carbon atoms, resulting in kinks or bends in the carbon chain. • Physical Properties: • Liquid at room temperature. • Lower melting point. • Cannot pack as closely together due to the kinks or bends in the carbon chain, resulting in a less dense structure. • Examples: Vegetable oils such as olive oil, sunflower oil, and canola oil. Comparison: • Physical State: Saturated fats are solid at room temperature, while unsaturated oils are liquid. • Melting Point: Saturated fats have a higher melting point compared to unsaturated oils. • Packing Density: Saturated fats can pack closely together due to their straight carbon chains, leading to a solid, dense structure. Unsaturated oils cannot pack as closely together due to the kinks or bends in their carbon chains, resulting in a less dense structure. These differences in physical properties are directly related to the arrangement of atoms and bonds within the molecules, illustrating how the atoms and bonds within a molecule determine its chemical and physical properties. The properties of a molecule determine the role that the molecule plays in the cells or the body of an organism. Why are phospholipids useful in membranes? Answer: Phospholipids are useful in membranes because of their unique structure and properties: 1. Amphipathic Nature: Phospholipids have a hydrophilic (water-attracting) "head" and hydrophobic (water-repelling) "tails." This amphipathic nature allows phospholipids to spontaneously form bilayers in aqueous environments, such as cell membranes. 2. Formation of Bilayers: In an aqueous environment, phospholipids arrange themselves into a bilayer with the hydrophilic heads facing outward towards the water and the hydrophobic tails facing inward, away from the water. This bilayer structure forms the basis of cell membranes, providing a barrier between the cell's internal environment and the external environment. 3. Selective Permeability: The phospholipid bilayer is selectively permeable, allowing certain molecules to pass through while restricting the movement of others. This selective permeability is essential for regulating the passage of ions and molecules in and out of the cell, maintaining cellular homeostasis. 4. Fluidity: Phospholipids give cell membranes a fluid nature, allowing them to change shape and allowing the movement of proteins and other molecules within the membrane. This fluidity is crucial for various cellular processes such as cell signaling, membrane trafficking, and cell division. 5. Protein Anchoring: Phospholipids also serve as anchor points for membrane proteins, which play essential roles in cell signaling, transport, and structure. In summary, phospholipids are useful in membranes because their unique structure allows them to form the lipid bilayer, which serves as a flexible, selectively permeable barrier that separates the cell from its environment and plays a crucial role in maintaining cellular function and homeostasis. Ask why life is based on carbon. Note the characteristics of carbon that could be responsible for this usage. Ask students to speculate why silicon, with four electrons in its outer shell, would function as the basis of life. Answer: Life is based on carbon due to several unique characteristics of carbon atoms: 1. Versatility: Carbon has the ability to form four covalent bonds with other atoms, allowing it to create a wide variety of complex and stable molecules. This versatility enables carbon to form the long chains and complex three-dimensional structures necessary for life. 2. Tetravalency: Carbon has four valence electrons, allowing it to readily form covalent bonds with other atoms, including itself. This property enables carbon atoms to bond together to form chains, rings, and branched structures, giving rise to a diverse array of organic molecules. 3. Compatibility with Water: Carbon-based molecules are generally hydrophobic, meaning they do not readily dissolve in water. This property is crucial for forming biological membranes and compartments within cells. 4. Stability: Carbon-carbon bonds are relatively stable, allowing carbon-based molecules to persist over long periods, essential for the stability and longevity of biological structures. 5. Isomerism: Carbon-based molecules can exist as structural isomers, molecules with the same chemical formula but different structural arrangements. This property increases the diversity of organic molecules and allows for the specific functions required for life processes. Regarding silicon, while it also has four valence electrons and can form four covalent bonds, there are several reasons why silicon is not suitable as the basis for life: 1. Bond Strength: Silicon-oxygen bonds are stronger than carbon-oxygen bonds, making silicon-based molecules more stable. However, this also makes silicon-based molecules less reactive than their carbon-based counterparts, hindering the ability to participate in the dynamic chemical reactions necessary for life processes. 2. Limited Diversity: While silicon can form a variety of complex structures, it is not as versatile as carbon. Silicon-based molecules are more limited in the types of bonds and structures they can form compared to carbon-based molecules, reducing the diversity of potential biological molecules. 3. Solubility: Silicon-based molecules tend to be more soluble in water than carbon-based molecules, making them less suitable for forming the hydrophobic barriers necessary for cell membranes and compartments. 4. Chemical Reactivity: Silicon-based molecules are less reactive than carbon-based molecules, making them less suitable for participating in the diverse range of chemical reactions required for life processes. Overall, while silicon shares some similarities with carbon, its properties make it less suitable as the basis for life compared to carbon. Carbon's unique combination of versatility, compatibility with water, stability, and reactivity make it uniquely suited to form the complex molecules necessary for life. Query how the amount of ATP used in one day can exceed by many times the amount of ATP in the human body. Answer: The amount of ATP used in one day can exceed by many times the amount of ATP stored in the human body due to the continuous turnover of ATP molecules. ATP (adenosine triphosphate) is the primary energy currency of the cell. While the human body contains only a small amount of ATP at any given time (approximately 50 grams), it is constantly being synthesized and hydrolyzed to provide energy for various cellular processes. The average adult human uses around 40 kg (or 88 pounds) of ATP per day. This far exceeds the total amount of ATP stored in the body. However, ATP is rapidly recycled through cellular respiration, a process that continuously generates ATP from the breakdown of carbohydrates, fats, and proteins. During cellular respiration, glucose and other organic molecules are oxidized to produce ATP through a series of biochemical reactions. Each molecule of glucose can generate up to 36-38 molecules of ATP through aerobic respiration (in the presence of oxygen). Furthermore, ATP is also regenerated through processes such as substrate-level phosphorylation and oxidative phosphorylation, which occur during glycolysis, the citric acid cycle, and the electron transport chain. In summary, while the total amount of ATP stored in the human body is relatively small, the continuous turnover and regeneration of ATP through cellular respiration and other metabolic processes allow the body to use and regenerate ATP far in excess of the amount stored at any given time. Ask if condensation and hydrolysis reactions would be exact opposites of each other. Point out that these reactions are not generally one-step processes, but require several steps and several enzymes to carry out the complete reaction. Answer: Condensation and hydrolysis reactions are not exact opposites of each other, although they are related. Condensation Reaction : • In a condensation reaction, two molecules combine to form a larger molecule, with the elimination of a small molecule such as water. • For example, in the synthesis of a peptide bond between two amino acids to form a dipeptide, a condensation reaction occurs, releasing a molecule of water. Hydrolysis Reaction : • In a hydrolysis reaction, a larger molecule is broken down into smaller molecules with the addition of a water molecule. • For example, the breakdown of a dipeptide into two amino acids involves a hydrolysis reaction, where a water molecule is added to break the peptide bond. While condensation and hydrolysis reactions are conceptually opposite, they are not generally one-step processes. Instead, they typically require several steps and several enzymes to carry out the complete reaction. For example : • In the synthesis of a peptide bond (condensation reaction), several steps are involved, including the activation of the carboxyl group of one amino acid and the nucleophilic attack of the amino group of another amino acid. This process requires enzymes such as aminoacyl-tRNA synthetases. • In the hydrolysis of a peptide bond, enzymes called peptidases catalyze the breaking of the bond, but again, it's not a one-step process. It involves several steps to complete the hydrolysis reaction. In summary, while condensation and hydrolysis reactions are conceptually opposite, they are not simple, one-step processes. They often require several steps and specific enzymes to carry out the complete reaction. Discovery of liquid water under the frozen surface of a distant moon in our solar system has caused scientists to speculate on the possibility of life on that moon. Researchers hold little hope of any familiar life form existing on any planet or moon in the absence of water. Why? Answer: Water is considered essential for life as we know it, and there are several reasons why researchers hold little hope of any familiar life form existing on any planet or moon in the absence of water: 1. Universal Solvent : Water is known as the "universal solvent" because it can dissolve a wide range of substances, including salts, sugars, acids, and gases. This ability allows water to transport essential nutrients and molecules within living organisms, facilitating biochemical reactions necessary for life. 2. Medium for Chemical Reactions : Water serves as a medium for biochemical reactions, providing an environment where molecules can interact and react. Many important biological reactions, such as photosynthesis and cellular respiration, occur in aqueous solutions. 3. Maintaining Temperature : Water has a high specific heat capacity, meaning it can absorb and store a large amount of heat with only a slight change in temperature. This property helps to stabilize temperatures on Earth and within living organisms, preventing rapid fluctuations that could be harmful to life. 4. Maintaining pH Balance : Water can act as a buffer, helping to maintain a relatively constant pH within living organisms. This is essential for the proper functioning of enzymes and other biological molecules. 5. Structural Component : Water is a major component of cells and tissues, making up a large portion of the human body and the bodies of other living organisms. It provides structural support and helps maintain the shape of cells and tissues. 6. Hydration : Water plays a crucial role in hydration, allowing for the transport of nutrients, removal of waste products, and regulation of osmotic pressure within cells. In summary, water is essential for life as we know it because of its unique properties that support biochemical reactions, maintain temperature and pH balance, provide structural support, and facilitate the transport of nutrients and waste products within living organisms. Therefore, the discovery of liquid water on a distant moon in our solar system increases the possibility of life existing there, as it provides a potential habitat where life, as we understand it, could potentially thrive. Life has a chemical and physical basis. Give an example from your knowledge of nutrition, medicine or the environment to show that this concept has everyday applications. Answer: An example demonstrating that life has a chemical and physical basis can be found in the field of nutrition, specifically in the process of digestion. Example: Digestion of Carbohydrates • Chemical Basis : Carbohydrates are macromolecules composed of carbon, hydrogen, and oxygen atoms. The chemical bonds within carbohydrates store energy that can be released during digestion. • Physical Basis : Digestion begins in the mouth, where mechanical processes such as chewing break down food into smaller particles, increasing its surface area. This facilitates the action of digestive enzymes. • Everyday Application : When you eat a piece of bread, the physical act of chewing breaks down the bread into smaller particles, exposing a larger surface area for enzymatic action. Enzymes in saliva, such as amylase, start breaking down the carbohydrates in the bread into smaller molecules such as maltose. This process represents the physical and chemical basis of life, where the chemical composition of the food (carbohydrates) is broken down by both mechanical (chewing) and chemical (enzymatic digestion) processes to release energy that can be utilized by the body. This example illustrates how the chemical composition of food (carbohydrates) undergoes both physical and chemical processes during digestion to provide energy for life processes. It demonstrates the everyday application of the concept that life has a chemical and physical basis. Atomic structure involves electronic energy levels. Show that living things are dependent upon the energy relationships of electrons. Answer: Living things are highly dependent upon the energy relationships of electrons, which are governed by atomic structure and electronic energy levels. Several key processes in living organisms rely on these energy relationships: 1. Chemical Bonding : • Atoms form chemical bonds by either sharing or transferring electrons to achieve a stable electron configuration. For example, in the formation of covalent bonds, atoms share electrons to fill their outer electron shells, resulting in stable molecules. • Biological molecules such as carbohydrates, lipids, proteins, and nucleic acids are formed through various types of chemical bonds, all of which involve the interactions of electrons. 2. Metabolism and Energy Production : • Cellular respiration, the process by which cells generate ATP (adenosine triphosphate) for energy, relies on the transfer of electrons between molecules. • During cellular respiration, electrons are transferred through a series of redox (oxidation-reduction) reactions, releasing energy that is used to synthesize ATP. • The electron transport chain, located in the inner mitochondrial membrane, is a series of protein complexes and electron carriers that transfer electrons, ultimately leading to the production of ATP. 3. Photosynthesis : • In photosynthesis, plants and some bacteria use the energy from sunlight to convert carbon dioxide and water into glucose and oxygen. • This process involves the absorption of light energy by chlorophyll molecules, which causes the excitation of electrons. • Excited electrons are transferred through a series of redox reactions, ultimately leading to the production of ATP and NADPH, which are used to synthesize glucose. 4. Electron Transport in Membranes : • Electron transport chains are also involved in other cellular processes, such as oxidative phosphorylation and photosynthesis. • These chains are located in cell membranes and are responsible for transferring electrons between molecules, generating energy that is used to power various cellular processes. In summary, the energy relationships of electrons, governed by atomic structure and electronic energy levels, are essential for the formation of chemical bonds, metabolism, energy production, and various other cellular processes. Living things are highly dependent upon these energy relationships for their survival and function. So far, for every molecule that life forms can put together, such as cellulose or chitin, there are bacteria that can digest them into sugar and other smaller molecules. What would happen if a tree or insect could build a complex molecule that no organism or natural process could decompose? Answer: If a tree or insect could build a complex molecule that no organism or natural process could decompose, it could have several implications: 1. Accumulation of Waste : If the complex molecule cannot be decomposed, it would accumulate over time, leading to the buildup of waste products in the environment. This could potentially disrupt ecosystems and harm organisms that rely on the environment for food and habitat. 2. Resource Limitation : The accumulation of non-decomposable molecules could limit the availability of essential nutrients and resources for other organisms. This could have cascading effects throughout the ecosystem, affecting the abundance and distribution of species. 3. Loss of Nutrient Cycling : Decomposition is an essential part of nutrient cycling in ecosystems. If certain molecules cannot be decomposed, it could disrupt the balance of nutrients in the ecosystem, leading to nutrient imbalances and reduced soil fertility. 4. Ecological Imbalance : The inability to decompose certain molecules could lead to ecological imbalances, potentially favoring certain species over others and altering the structure and function of ecosystems. 5. Long-Term Environmental Impact : The accumulation of non-decomposable molecules could have long-term environmental impacts, potentially affecting ecosystem stability and resilience to environmental changes. Overall, if organisms were able to produce complex molecules that could not be decomposed by any organism or natural process, it could have significant consequences for ecosystem functioning and biodiversity. It is important for ecosystems to have mechanisms in place to break down and recycle organic matter, ensuring the sustainable functioning of the ecosystem. 10. Many insects feed exclusively on one type of food such as plant sap (primarily sugar), blood proteins or starch. Yet these organisms are themselves made of a wide range of molecules. Where does this molecular diversity come from? Answer: The molecular diversity found in organisms that feed exclusively on one type of food, such as plant sap, blood proteins, or starch, comes from their ability to synthesize a wide range of molecules from the basic building blocks provided by their food source. 1. Metabolic Pathways : Organisms have evolved complex metabolic pathways that allow them to convert simple molecules from their food into a wide variety of complex molecules necessary for their growth, development, and survival. 2. Anabolism : Through anabolic processes, organisms can synthesize a diverse array of molecules, including carbohydrates, lipids, proteins, and nucleic acids, from simpler precursors obtained from their food. 3. Assimilation of Nutrients : After feeding on a specific food source, organisms break down the molecules present in that food and absorb the basic building blocks. These building blocks are then used as precursors for the synthesis of a wide range of molecules. 4. Nutrient Recycling : Organisms are also capable of recycling and repurposing molecules within their bodies. For example, proteins obtained from the diet can be broken down into amino acids, which can then be used to synthesize new proteins or other nitrogen-containing molecules. 5. Specialized Enzymes : Many organisms have evolved specialized enzymes and metabolic pathways that allow them to efficiently convert specific types of molecules into other types of molecules. These enzymes catalyze specific chemical reactions, allowing for the synthesis of a diverse array of molecules. In summary, the molecular diversity found in organisms that feed exclusively on one type of food comes from their ability to synthesize a wide range of molecules from the basic building blocks provided by their food source. Through complex metabolic pathways, organisms can convert simple molecules into the complex molecules necessary for their survival and function. Instructor Manual for Integrated Principles of Zoology Cleveland Hickman, Jr., Susan Keen, Allan Larson, David Eisenhour, Helen I'Anson, Larry Roberts 9780073524214
