Chapter 1 (1) Biology-I PDF

BIOC100 (Biology-I) The science of Biology Chapter 1 Dr. Mohammad Tauqeer Alam Department of Biology UAE University, Al-Ain  Textbook Biology Brooker, Fifth edition Mc Graw Hill. 2014 BIOC100 (Biology-I)  What is Biology? Biology is the study of life Millions o...

BIOC100 (Biology-I) The science of Biology Chapter 1 Dr. Mohammad Tauqeer Alam Department of Biology UAE University, Al-Ain  Textbook Biology Brooker, Fifth edition Mc Graw Hill. 2014 BIOC100 (Biology-I)  What is Biology? Biology is the study of life Millions of species on earth Forms of life: 1. Bacteria 2. Archaea 3. Eukaryota BIOC100 (Biology-I)  Biology as an interdisciplinary subject Biological systems work on principles from various fields: Physics Chemistry Mathematics Statistics and probability Business, trades and economics BIOC100 (Biology-I)  Why we study Biology? 1. Understanding the concept of life for the big picture 2. Discoveries for health and medical benefits 3. Understanding diseases 4. Economic benefits 5. Environment 6. Ecology to save the environment BIOC100 (Biology-I)  1. Understanding the concept of life for the big picture How and when the life originated? 13 billion years ago. Big-bang theory Are there planets where life is possible? Favorable environments to sustain life Why and how people die? Either disease, accident or old age BIOC100 (Biology-I)  2. Discoveries for health and medical reasons Diseases such as cancer, diabetes etc. Infections by other organisms such as covid-19, Tuberculosis etc. Drugs/Antibiotics for curing diseases/infections. Streptomycin Antibiotic derived from Streptomyces griseus used to treat a number of bacterial infections: Tuberculosis, Mycobacterium avium complex, Endocarditis, Bucellosis, Burkholderia infection, Plague, Tularemia. https://pubchem.ncbi.nlm.nih.gov/compound/Streptomycin BIOC100 (Biology-I)  The bark of the White Willow tree Aspirin (acetylsalicylic acid) - Salicylic acid used to reduce pain, fever, or - Used as a powerful pain relief inflammation remedy https://pubchem.ncbi.nlm.nih.gov/compound/asprin BIOC100 (Biology-I)  Pacific yew tree and cancer treatment Crystal Jelly fish Arrowhead and GFP Viper and discovery inhibitors of high blood pressure Streptomyces griseus soil bacteria and streptomycin BIOLOGY IS COOL! White willow tree and aspirin  3. Understanding diseases For a proper cure it is important to understand disease. Where the infection is? What kind of infection it is? How it started? How it is spreading? How to control the spread and cure the infections? BIOC100 (Biology-I)  Diabetes A chronic health condition. After food is broken into sugar, it is released into bloodstream. When the level of sugar in blood goes up, it sends signals. Then insulin is released which helps in releasing blood sugar to the body cells. In diabetic patients, body either can not make enough insulin or can’t properly. Therefore, too much blood sugar stays in bloodstream which causes serious health issues, such as heart disease, vision loss, and kidney disease. BIOC100 (Biology-I)  Cancer Cancer cells grow uncontrollably It can invade and infect other surrounding cells/ tissue/ organs. It can start anywhere in the body. In a normal healthy body cells grow and divide to generate new cells. When cells grow old, they die, and the newly produced cells overtake. In cancer, however, cell death is affected. Cells become old and abnormal and still remain alive. Moreover, new cells continue to be made although it is not needed which leads to abnormal growth called tumor. BIOC100 (Biology-I)  4. Economic benefits Agriculture production of food Medicine Pharmaceutical drug discoveries and production Industry biodegradable plastics, vegetable oil, biofuels, chemicals, detergents, paper and pulp and textiles. Technology advancement BIOC100 (Biology-I)  5. Ecology to save the environment Global warming and climate change Cleaning up environmental wastes Protect freshwater resources. Promote soils formation and protection. Provide for nutrient storage and recycling. These are only a few examples. There are so many examples for understanding how studying biological science is useful BIOC100 (Biology-I)  Properties of life Living vs non-living How about microorganisms Is bacteria alive? How about Viruses? BIOC100 (Biology-I)  Common characteristics of living organisms 1. Cell theory and organization 2. Energy use and metabolism 3. Response to environmental change 4. Regulation and homeostasis 5. Growth and development 6. Reproduction 7. Biological evolution BIOC100 (Biology-I)  1. Cell theory and organization Organisms maintain an order Simplest unit of organization is CELL Cell theory: All organisms are made of cells Cells are the simplest unit of life Cells come from pre-existing cells via cell division Unicellular and multicellular organisms Plants and animal cells have internal order Bacterial cell Animal cell https://commons.wikimedia.org/wiki/ BIOC100 (Biology-I) File:Simple_diagram_of_bacterium_(blank).svg  2. Energy use and metabolism Energy is needed to function properly and to maintain internal order Cell perform chemical reactions in order to break nutrients, called respiration Chemical reactions involving breakdown and synthesis of compounds called metabolism Plants, Algae can directly use sunlight to produce their nutrients by photosynthesis. BIOC100 (Biology-I)  3. Response to environmental change Response to environmental change is important for survival Living organisms generate a response to the environment changes Phototropism: plants lean towards light Blowfish become larger and extends its spikes when it is threatened by a predator Hibernation Bacteria can detect the shortage of nutrients in the environment Bacteria when threatened by other pathogens releases antibiotics as a safety mechanism BIOC100 (Biology-I)  4. Regulation and homeostasis Organisms regulate their cells and body to maintain stable condition. Example: Most mammals maintain a stable body temperature. Human Cells work efficiently at 37 degree C. Shivering in cold and sweating in hot weather Life in Thermophilic, extreme environments Maintaining pH. Different organs have different pH and they need to be maintained. Calcium level, blood pressure etc. Regulate cellular metabolism so that nutrients are used at an appropriate rate. Generate new cellular components when needed BIOC100 (Biology-I)  5. Growth and development Growth produces more and larger cells Development is a series of changes in the state of a cell, tissue, organ or organism. Development produces organisms with a defined set of characters. In unicellular organisms, new cells are small and they grow by synthesizing additional components In multicellular organisms, life begin at single-cells level and then undergo multiple cell division to develop into a complete organism. Growth and development may have defects BIOC100 (Biology-I)  6. Reproduction Organisms reproduce new organisms Offspring usually have same characteristics as their ancestors Organisms have genetic material (DNA) which contains the blue print of the organization, development and function of life. In reproduction the genetic material is transferred from parent(s) to offspring BIOC100 (Biology-I)  7. Biological evolution Due to continuous change in environment organisms evolve Population changes from generation to generation Better adapted to the environment BIOC100 (Biology-I)  Levels of Organization 1. Atoms 2. Molecules and macromolecules 3. Cells 4. Tissues 5. Organs 6. Organism 7. Population 8. Community 9. Ecosystem 10.Biosphere 24  Levels of Organization 1. Atoms are the smallest unit of matter. 2. Molecules are a group of atoms bonded with each other. Macromolecules are formed when many molecules bond together to form a polymer (carbohydrates, DNA, RNA etc.). 3. The cell is the smallest unit of biological organization that biologists consider alive. Molecules and macromolecules associate with each other to form larger structures such as membranes. Cells are surrounded by a plasma membrane, carry out complex chemical reactions, and are at least potentially capable of self reproduction. Cells come in a wide variety of shapes and sizes. Not all cells have a nucleus, but again all true cells have genetic material in the form of DNA. 4. Tissue is a group of similar cells that associate with each other to carry out a specific set of functions. For example:. Muscle tissue is for contraction.. Connective tissue is tissue consisting of cells surrounded by a large amount of non living material.. Nerve tissue is for the conduction of nerve impulses and secretion of specialized chemicals called neurotransmitters. 5. Organs are groups of two or more types of tissues organized together to carry out a particular set of functions. Organs typically have several kinds of tissue. The heart is composed of several type of tissues, including muscle, nervous and connective tissue.  Levels of Organization 6. The organism or individual is that level of biological organization that has its own distinct existence as a complex, self reproducing unit. All living things can be called organisms. We are multicellular organisms in that we are made of many highly specialized cells which cannot exist independently of other cells in the organism. Many organisms are unicellular, that is consist of a single independent cell. Organisms are classifies as belonging to a particular species, which is a related group of organims. The members of the same species are closely related genetically. 7. Population is group of freely interacting and breeding individuals of the same species that occupies the same environment. 8. Community is all the populations of different species living and interacting together in a distinct area. (e.g: all the species in a prairie). The type of species that are found in a community are determined by the environment and by the interactions of species with each other. 9. Ecosystem is formed by interactions of a community of organisms with their physical (non living) environment. 10. Biosphere is the region on (land), below (water), and above (air) the Earth's surface where life exists. Living things can be found well into the atmosphere, the deepest parts of the ocean, and at least in some areas, microbes live in rock several kilometers below the surface of the earth. The levels of Biological Organization 27  Unity and diversity of Life Unity: All modern life has a common set of characteristics They all are based on evolution Diversity: Earth has diverse environment (Cold, extreme cold, extreme hot, acidic, alkali, desert, rain forest etc) Life exists in all these diverse environment due to evolution BIOC100 (Biology-I)  Modification due to biological evolution BIOC100 (Biology-I) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.  Evolutionary mechanisms: Number of years 1. Vertical descent with mutation 2. Horizontal gene transfer Single generation BIOC100 (Biology-I)  1. Vertical descent with mutation This is a traditional view of evolution Involves a progression of changes in a series of ancestors - called lineage. New species evolve from pre-existing species through a series of mutations. Mutation occurs randomly in the genome. If it helps for better survival and reproduction then those mutations are retained. BIOC100 (Biology-I) Natural selection Natural selection: When a mutation causes a beneficial change the frequency of mutation may change in population from one generation to another. However, mutation some time may be neutral and sometime harmful Horse evolution 0 Hippidium and Equus other genera 5 Styohipparion Nannippus Evolution of 10 Hipparion Neohipparion Pliohippus Sinohippus Megahippus modern horse Archaeohippus Calippus through a 20 Anchitherium Hypohippus Merychippus Millions of years ago (mya) series of mutations in the ancestors Parahippus Miohippus Mesohippus 40 Paleotherium Epihippus Propalaeotherium Pachynolophus Orohippus 55 Hyracotherium Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. BIOC100 (Biology-I)  2. Horizontal gene transfer (HGT) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Lateral gene transfer (LGT) Antibiotic- resistance Genes transferred from gene from DNA E. coli organism to organism DNA Can happen between members of different species Example: Resistance to Horizontal antibiotics happen due to gene transfer to acquiring of antibiotic resistant Antibiotic- another genes by bacteria. resistance species gene HGT mechanisms: Bacterial species such as Bacterial species such as Escherichia coli Streptococcus pneumoniae transformation, transduction and conjugation, BIOC100 (Biology-I)  Tree of life Web of life Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. Bacteria Archaea Eukarya Fungi Animals Plants Protists KEY Vertical evolution Horizontal gene transfer Common ancestral community of primitive cells BIOC100 (Biology-I)  Classification of Living Organisms Taxonomy is the grouping of species based on common ancestry. All forms of life can be placed into three large categories or DOMAINS:. Bacteria- unicellular prokaryote. Archaea- unicellular prokaryote (bacteria-like organisms that live in extreme aquatic environments.. Eucarya- unicellular to multicellular eukaryotes Organisms in domain eucarya are subdivided into 4 KINGDOMS:. Protista. Fungi. Plantae 36. Animalia Classification of Living Organisms Living organism Prokaryotic Eukaryotic Nucleu cell cell s? Bacter Archa Domai ia ea Eukarya n Protis Plant Anima Fun Kingdo ts s ls gi m  Classification of living organisms Earth has 10-100 million different species 8.7 million estimate excluding bacteria Organisms with recent common ancestors are grouped together Grouping of organisms is called taxonomy, based on Vertical descent Three main categories Prokaryotic; or Microorganism domain 1. Bacteria Eukaryotic; Larger cell 2. Archaea 3. Eukarya BIOC100 (Biology-I)  1. Prokaryotic Prokaryotes do not have membrane-bound structures 0.1-5 μm in diameter prokaryotes do not have mitochondria 1. Bacteria Mostly unicellular organism Simple cell structure 2. Archaea Unicellular Live in extreme environments Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. BIOC100 (Biology-I)  2. Eukaryotic Larger cells (around 10-100 μm) Internal compartments for specific functions Protists Plants Cell nucleus containing genetic material Mitochondria organelles enclosed Fungi Animals by a plasma Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display. membrane BIOC100 (Biology-I)  Taxonomic Clown Approximate time Approximate Examples Classification group anemonefish when the common number of is found in ancestor for this modern species group arose in this group Domain Eukarya 2,000 mya > 5,000,000 Grouping of species Kingdom Animalia 600 mya > 1,000,000 into smaller groups based on Phylum Chordata 525 mya 50,000 evolutionary relationship Class Actinopterygii 420 mya 30,000 Order Perciformes 80 mya 7,000 Emphasizes the Family Pomacentridae ~ 40 mya 360 unity and diversity of Genus Amphiprion ~ 9 mya 28 different species Species ocellaris > 3 mya 1 Example: Clownfish BIOC100 (Biology-I) Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.  Binomial nomenclature Two part description for unique scientific name of each species First part is Genus Second part is species descriptor Genus is capitalized Species descriptor is not capitalized Both names are italicized Amphiprion ocellaris = Clownfish BIOC100 (Biology-I)  Genome and Proteome connection of evolution Genome genome Genome is the complete genetic makeup of the cell Gene Gene Gene C A B Stores information for the organism’s characteristics Genome is passed from generation to generation Act as a tool for evolutionary change mRNA Genome sequence can be used to illustrate the evolutionary relationship among organisms Study of genome is genomics Proteome Proteome Overall proteins of the cell/organism Genes make proteins Responsible for the structure and function of the cell Study of proteome is proteomics BIOC100 (Biology-I)  Biology as a scientific discipline Science in biology – observation, identification, experimental investigation, and theoretical explanation of natural phenomena Studied at different levels - from molecular levels to the population level BIOC100 (Biology-I) Investigate life at different levels Different branches of biology study life at different levels using a variety of tools. As new tools become available, they allow scientists to ask new questions 45  Scientific method or Hypothesis testing Make Report results ▶ observation ▶ ▶ Ask a question conclusion s Prior knowledge ▶ ▶ Prior knowledge Form a hypothesis experimen ts ▶ BIOC100 (Biology-I)  Scientific method 1. Observation 3. Experiment 96% of things are unobservable Testing the hypothesis Acquisition of information or data collection Set experiment well from a primary source Do proper analysis and observation can also involve the perception and recording of data via the use of interpretation scientific instruments 4. Conclusion 2. Hypothesis Support the hypothesis - Failed to Educated guess - or a proposed reject the hypothesis explanation for a phenomenon reject the hypothesis: If a Based on observation. hypothesis is incorrect it should be More knowledge leads to better hypothesis falsifiable, which means it can be Scientific hypothesis has to be testable shown to be incorrect BIOC100 (Biology-I)  Progression of Scientific method Hypothesis Educated guess based on observation Theory More thoroughly tested and widely accepted hypothesis Best explanation that we have among all possible explanations Evolution, Cell theory Principle More concrete concept Natural selection, mutation, gene flow Law Clear concept of how things work Law of thermodynamics, gravity, Inheritance BIOC100 (Biology-I)  Experimental design Careful planning of an experiment – before the experiment Describe participants allocation to experimental groups, most often random selection or randomized block design where participants are divided into homogeneous blocks (for example, age groups) Minimize confounding variables Should be able to differentiate dependent variable vs independent variable Reduce variability BIOC100 (Biology-I)  Lady tasting tea devised by Ronald Fisher The test used was Fisher's exact test. 8 randomly ordered cups of tea – 4 prepared by first pouring the tea, then adding milk, 4 prepared by first pouring the milk, then adding the tea. The null hypothesis is that the subject has no ability to distinguish the teas there was no alternative hypothesis BIOC100 (Biology-I)  Variables in experimental design Sample size - Representative of the population and diversity Variable selection – changeable element of the experiment a good experiment only has two changing variables: the independent variable and dependent variable – outcome/result. Let’s say you are testing to see how the amount of light received affects plant growth: The independent variable, in this case the amount of light, is changed by you, the researcher. As you change the independent variable, you watch what happens to the dependent variable. In this case you see how much the plants grow.A control variable is another factor in an experiment; it must be held constant. In the plant growth experiment, this may be factors like water and fertilizer levels. If control variables aren’t kept constant, they could ruin your experiment. For example, you may conclude that plants grow optimally at 4 hours of light a day. However, if your plants are receiving different fertilizer levels, your experiment becomes invalid. Procedure should be standard and constant for all BIOC100 (Biology-I)  Discovery based science The collection and analysis of data without a preconceived hypothesis is called discovery-based science. Outcome of discovery-based science may lead to new hypothesis Helps in understanding of basic concept Example: discovery of new gene without knowing its function Lead to hypothesis testing BIOC100 (Biology-I)  Points to consider in research and experiment Critical thinking Self critical Confident Experts opinion Think about the big picture Ask more and more questions. Answering one question lead to several questions. Having good scientific questions is key in research field. BIOC100 (Biology-I)