BIO311c-Ch1-Introduction - Intro. Biol. Course Guide...

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Unformatted text preview: Intro. Biol. Course Guide Sathasivan, 2005 1. THE SCIENCE OF BIOLOGY Outline I. Why Study Biology II. Properties of Life III. Scientific Approaches in Biology IV. Classification System in Biology I. Why study biology? - Understanding life processes: The study of biology helps us understand the nature of life and the mechanisms underlying life processes. - Application of the knowledge: We can use the knowledge for survival, improvement of life, such as finding new cures for diseases and developing better plants for agriculture, or improving the environment. Why is biology increasingly important today? - The last few centuries were dominated by major discoveries in chemistry and physics. The 21st century will see a major impact by the explosion of information from researches in various disciplines of biological sciences merging with knowledge from other fields. - More than half a million papers are being published per year in biology alone. DNA, the secret code of life, was discovered only 5 decades ago, but we have sequenced the entire human genome already. Applications are rapidly increasing in various fields including medical, agricultural and veterinary sciences. Why study cellular and molecular biology? - The connecting basis of all life is at the cell and molecular level. DNA to RNA to protein and the cellular mechanisms form the fundamental basis of life. - Many biological phenomena are better understood at the biochemical and molecular level. - It provides an opportunity to genetically alter DNA, develop cures and diagnostics to improve life in a very fundamental and precise way. To study biology, we should start with the properties of living organisms, selected model systems and some broad approaches to study life. Chap. 1. 1 Introduction Intro. Biol. Course Guide Sathasivan, 2005 II. Properties of Life Life as we know is carbon based, organic in nature and contains water. The basic unit of life is the cell. The emergent properties of living organisms are as follows. Reproduction: Life comes only from another life. The genetic material in all living cells is made of DNA. Growth and development: All living organisms go through growth and developmental stages. Order and Structure: Living cells and organisms are highly ordered and structured. The structure correlates with function. Metabolism: Energy consumption and release happen constantly in a living organism. They consume organic foods, minerals and other nutrients. They can make and breakdown large molecules through various metabolic processes. Respiration: It is an essential process in this energy consumption and release. Living organisms breathe in oxygen and release carbon dioxide to generate energy. Response to environmental stimuli: The living organisms can sense (the surroundings) environmental cues and respond in an appropriate way. They can maintain internal conditions (homeostasis) in spite of changing surroundings. Adaptation and evolution: Living organisms adapt to their environment over short periods of their generation or over many generations. Over billions of years, life has adapted, changed and evolved to make new life forms. Autonomous movement: Living organisms such as bacteria, protists and animals can move autonomously. Fungi and plants normally grow towards sources of nutrition and/or light. 1. 2. 3. 4. 5. 6. 7. 8. III. Scientific Approaches in Biology Model systems: Since there are millions of living organisms, we can not study every one of them in a detailed manner. Hence we use selected organisms known as model systems to study the mechanism of life. A model system is a representative organism or a cell type used for conducting simple to complex biological experiments. Model systems are normally easy to grow, manipulate and study. A vast amount of genetic information is already available from published studies about them. Model Systems Prokaryotes: (unicellular and cells have no nucleus) E. coli (Escherichia coli) Salmonella (Salmonella typhimurium) Eukaryotes: (uni- & multicellular organisms with a Chap. 1. 2 Introduction Intro. Biol. Course Guide Sathasivan, 2005 Plants: Fungi: Animals: membrane bound nucleus in their cells) Arabidopsis (Arabidopsis thaliana) Corn (Zea mays) and Rice (Oryza sativa) Yeast (Saccharomyces cerevisea) Fruit fly (Drosophila melanogaster) Nematode (Caenorhabditis elegans) Mouse (Mus musculus) and Zebra fish (Danio rerio) Human cell lines. (He la cells) Broad Approaches to Study Life Based on whether an entire organism or part(s) of an organism is used in an experiment, we can call the studies as either holism or reductionism. Holism: An approach to study whole organisms for behavioral, physiological and nutritional studies. For example, rats are used as a model system to study the effect of various drugs on aging. Reductionism: An approach to study multicellular organisms at cellular or tissue levels. Whole organisms are not used. Cells or tissues derived from the organisms are used to conduct experiments. For example, various cell lines of humans and cell suspensions of higher plants are used for cellular, biochemical and molecular studies. Another way to describe a study is based on whether the experiment is done under living or non-living conditions. In vivo studies are used to study physiology, ecology of organisms under living conditions. Examples: rats, rabbits, plant tissue culture etc. These studies can be holistic or using cells or tissues. In vitro studies include experiments performed under nonliving (abiotic) conditions, i.e. in a test tube with known quantities of chemicals and enzymes added and incubated at a particular temperature, pH etc. Such systems are used to study biochemistry, cell biology and molecular biology. These studies are strictly reductionistic in approach. In situ studies refer to experiments conducted to determine the presence of certain molecules such as DNA, RNA or protein in a particular site (say within a cell or tissue). For example, Fluorescent in situ hybridization (FISH) is used to determine which chromosome contains a particular gene. These are normally in vitro studies based on reductionism. Scientific Reasoning A scientific process usually starts with a hypothesis (a prediction that can be properly tested) followed by experimentation with proper controls allowing conclusions Chap. 1. 3 Introduction Intro. Biol. Course Guide Sathasivan, 2005 to be drawn. The conclusions can be made using an inductive or deductive method. Inductive Method: Specific conclusions and observations are used to make generalization. For example, based on observing various species, Darwin was able to formulate a general concept of evolution. Deductive method: General concepts are used to deduce specific conclusions. For example, based on the fact that all birds have feathers, you can say that if “peacock” is a bird, it should have feathers. Hypotheses are formed based on observations and they must be testable. Experiments must be conducted in a controlled way with proper treatments and controls. The treatments may include positive (has been tested and shown to work) and negative (should not work) controls. For example, if you are conducting experiments on new antibiotics to kill E. coli then you will plate the bacteria in proper medium, each of them mixed with the different kinds of new antibiotics in separate plates. The positive control will have a known antibiotic and a negative control will be without any antibiotic. Once the results of an experiment are repeated by several scientists under various conditions, then they may be used to form a theory, if it is a unifying concept. If it is confirmed that they are proven true at all times, it may lead to a law. IV. Classification System in Biology Taxonomic Classification: A standard classification system is important to group and classify the millions of living organisms. This system is periodically modified based on the consensus of several scientists at an international level. The current classification system can be summarized as below and shown in a concept map below. Domains Bacteria Kingdoms Archaea Eukarya Protista Domain Family Fungi Plantae Animalia Kingdom Phylum Class Order Genus Species varieties or ecotypes Chap. 1. 4 Introduction Intro. Biol. Course Guide Sathasivan, 2005 Domains 1. Bacteria: Most diverse group of unicellular bacteria prokaryotic (prior to formation of nucleus). 2. Archaea: Archaebacteria. Part prokaryotic and part eukaryotic - survives in extreme conditions. 3. Eukarya: (with true nucleus) Eukaryotic Kingdoms: • Protista: Unicellular eukaryotes, heterotrophic, e.g. paramecium, and amoeba. • Fungi: Multicellular and some unicellular, heterotrophic, e.g. yeast. • Plantae: Monocots and dicot plants - photosynthetic. • Animalia: All animals. multicellular, heterotrophic. Biological Hierarchy The living world has a hierarchical order as shown below and we study them at different levels in different experiments. 1. Atoms (C, H, O, N, S etc.) 2. Molecules (CO2, O2, H2O, amino acids, sugars etc) 3. Macromolecules (proteins, carbohydrates, lipids) 4. Parts of cells (membrane, nucleus, mitochondria) 5. Cells (unicellular and unicellular organisms) 6. Tissues (bone, muscles, nerve cells) 7. Organs (heart, lungs, brain) 8. Organ systems (circulatory or reproductive systems) 9. Multicellular Organisms (plants, fungi and animals) 10. Population (Many individuals of same species) 11. Ecosystem (Collection of populations in a limited area) 12. Biomes (Desert, forest, tundra) 13. Biosphere (Living crust of the earth in air, land and water). Chap. 1. 5 Introduction ...
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