醫學系普通生物學注意事項 1. 作業在每周五中午 12:30 前, 由小老師依學號收齊繳給助教 ( 唯一例外 :10/7 日的作業在 10/13 日交 ) 2. 課輔時間為每周一晚間 6:00~8:00, 地點為第一醫學大樓十樓生醫系大教室三 ( 唯一例外 :10/27 日在十樓會議室 )

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1 醫學系普通生物學注意事項 1. 作業在每周五中午 12:30 前, 由小老師依學號收齊繳給助教 ( 唯一例外 :10/7 日的作業在 10/13 日交 ) 2. 課輔時間為每周一晚間 6:00~8:00, 地點為第一醫學大樓十樓生醫系大教室三 ( 唯一例外 :10/27 日在十樓會議室 ) 3. 期中考時間 : 11/18 早上 10:10~12:00 工學大樓六樓第二會議廳期末考時間 : 01/20 晚上 18:10~20:00 工學大樓六樓第二會議廳 4. 助教 : 林主祈聯絡方式 : 第一醫學大樓十樓生醫系邱健泰醫師實驗室 D @stmail.cgu.edu.tw 分機 :3494;3360( 至十月底 )

2 生物學教授大綱及教學目標生物醫學系羅時成老師 ext: 3295 陳嘉祥老師 ext.3812

3 Lectures by 羅時成老師 (week 1 to week 9) 1. What is life? Biology theme 2. Energy and Metabolism 3. What is gene? Central dogma 4. Origin and diversity of viruses 5. From prokaryotes to eukaryotes 6. Cell structure and function 7. Cell division and cell death 8. Cell development and cell fate 9. Mid-term exam

4 Lectures by 陳嘉祥老師 (week 10 to week 18) 10. The evolutionary view of life 11. Human evolution and migration 12. Population genetics 13. Sex in life and disease 14. Evolutionary view of disease: Why we get sick? 15. Evolutionary view of disease: Why we age? 16. Neurobiology of behavior 17. Ecology and human disease and health 18. Final exam

5 每週要撰寫反思日誌, 內容包括 : 1, 今天上課我學到了什麼? 2, 對於今天的上課內容我有什麼想法和感覺? 3, 分析一下, 自己為什麼會有以上的想法和感覺? 4, 對老師沒有說清楚或是應補充的建議 5, 對指定閱讀碰到或想到的問題

6 Home work: hand-in every Friday no later than 12:30PM (60 points) to TA Exam: Mid-term exam on the 9 th week and final on the 18th week (40 points) Office hour: 18:00-20:00PM 00PM every Monday at 10F classroom 3

7 觀念勝於細節思考重於記憶掌握來龍去脈加強延伸閱讀

8 Lecture 1: What is life? Biology theme 學習目標 : 1. To understand the philosophy of studying biology and to know why evolution is the central core of fbiology theme. 2. To know why bioinformatic is important Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

9 Lecture 1: What is life? Biology theme 1. The origin of life on the earth. 2. Examples of biology themes: gene is the unit of heredity and cell is the unit of life (reductionism vs. holism). 3. Evolution is the central theme of biology. 4. DNA technology, omic era and bioinformatics. Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

10 The origin of life on the earth

11 宇宙起始於大爆炸 ": 一個膨脹的宇宙

13 生命的起源? creation vs. evolution

14 單個細胞巨大分子 : 蛋白質核酸多醣

15 組成單元分子巨大分子單糖多醣胺基酸蛋白質核 X 核酸

16 生命產生的條件構成生命的物質從何而來? 在地球上自然形或來自太空的隕石! 原始大氣的組成 ( 水蒸氣氫甲烷氨等 ) 環境中的能量 ( 火山閃電地熱陽光宇宙射線 )

17 來自火星岩石上的生命痕跡?

18 Stanley Miller and origin of life Harold Urey 1950 建構生命的材料 ( 胺基酸糖分子等等 ) 可以由無機物 ( 建構生命的材料 ( 胺基酸糖分子等等 ) 可以由無機物 ( 水蒸氣氫氨等等 ) 在早期地球的環境中形成!

19 3 May 2008 eruption of the Chaiten volcano, Chile Science 322:404; 2008

20 尋找遠古 (35-38 億年前 ) 生命存在的痕跡

21 包埋在古老岩石中的生命痕跡與現今的單胞藻

22 這些不同生命形態的背後, 究竟具有那些共同的特質?

23 Philosophy related to study life science (biology) Believe what you believe To see is to believe ( 眼見為信 ) Your belief lead to your decision Decision and fate ( 決擇與命運 ) Make decision for your own and for other people p

24 Philosophy related to study life science (biology) Creation vs. Evolution Vitalism vs. Mechanism Reductionism vs. Holism

25 The Power and Limitations of Reductionism Reductionism is the reduction of complex systems to simpler components that are more manageable to study For example, the molecular structure of DNA An understanding of biology balances reductionism with the study of emergent properties For example, new understanding comes from studying the interactions of DNA with other molecules Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

26 Unit 單位 Searching for the smallest unit Atom and Cell Quantity and Quality

27 Origin 源頭 Origin of life Origin of eye Oi Origin i of flanguage

28 Modern biology is a great intellectual adventure that tries to understand the molecular underpinnings of life. What living organisms are made of, how they operate, how they get their energy, how they reproduce and of course how they have evolved from primitive forms to the astounding modern diversity of forms and function.

29 Overview: Inquiring About the World of Life Biology is the scientific study of life Biologists ask questions such as: How a single cell develops into an organism How the human mind works How living i things interact t in communities Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

30 Fig. 1-3 Order Evolutionary adaptation Response to the environment Regulation Energy processing Reproduction Growth and development

31 Concept 1.1: Themes connect the concepts of fbiology Biology consists of more than memorizing factual details Themes help to organize biological information Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

32 Evolution, the Overarching Theme of Biology Evolution makes sense of everything we know about living organisms Organisms living on Earth are modified d descendents d of common ancestors Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

33 Fig. 1-4a The biosphere Ecosystems Communities Populations Organisms

34 Fig. 1-4b Organs and organ systems 10 µm Cells Cell Organelles Tissues 50 µm 1µm Molecules Atoms

35 Theme 1: New properties emerge at each level in the ebiological og hierarchy Life can be studied at different levels from molecules to the entire living planet The study of life can be divided into different levels l of biological i l organization Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

36 Emergent Properties Emergent properties result from the arrangement and interaction of parts within a system Emergent properties characterize nonbiological entities as well For example, a functioning i bicycle emerges only when all of the necessary parts connect in the correct way Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

37 Systems Biology A system is a combination of components that function together Systems biology constructs t models for the dynamic behavior of whole biological systems The systems approach poses questions such as: How does a drug for blood pressure affect other organs? How does increasing CO 2 alter the biosphere? Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

38 Theme 2: Organisms interact with their environments, e ts,exchanging gmatter and denergye Every organism interacts with its environment, including nonliving factors and other organisms Both organisms and their environments are affected by the interactions between them For example, a tree takes up water and minerals from the soil and carbon dioxide from the air; the tree releases oxygen to the air and roots help form soil Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

39 Ecosystem Dynamics The dynamics of an ecosystem include two major processes: Cycling of nutrients, in which materials acquired by plants eventually return to the soil The flow of energy from sunlight to producers to consumers Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

40 Fig. 1-5 Sunlight Ecosystem Cycling of chemical nutrients Producers (plants and other photosynthetic organisms) Chemical energy Heat Consumers (such as animals) Heat

41 Energy Conversion Work requires a source of energy Energy can be stored in different forms, for example, light, chemical, kinetic, or thermal The energy exchange between an organism and its environment often involves energy transformations ti Energy flows through an ecosystem, usually entering as light and exiting as heat Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

42 Theme 3: Structure and function are correlated at all levels of biological og organization at o Structure and function of living organisms are closely related For example, a leaf is thin and flat, maximizing the capture of light by chloroplasts l Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

43 Fig. 1-6 (a) Wings (b) Bones Infoldings of membrane Mitochondrion (c) Neurons 100 µm (d) Mitochondria 0.5 µm

44 Theme 4: Cells are an organism s basic units of structure and function The cell is the lowest level of organization that can perform all activities required for life All cells: Are enclosed by a membrane Use DNA as their genetic information The ability of cells to divide is the basis of all reproduction, growth, and repair of multicellular organisms Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

45 Fig. 1-8 Eukaryotic cell Membrane Cytoplasm Prokaryotic cell DNA (no nucleus) Membrane Organelles Nucleus (contains DNA) 1 µm

46 Theme 4: The continuity of life is based on heritable e information o in the form of DNA Chromosomes contain most of a cell s genetic material in the form of DNA (deoxyribonucleic acid) DNA is the substance of genes Genes are the units of inheritance that transmit information from parents to offspring Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

47 DNA Structure and Function Each chromosome has one long DNA molecule with hundreds or thousands of genes DNA is inherited by offspring from their parents DNA controls the development and maintenance of organisms Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

48 Fig. 1-9 Sperm cell Nuclei containing DNA Fertilized egg Embryo s cells with with DNA from copies of inherited DNA Egg cell both parents Offspring with traits inherited from both parents

49 Fig Nucleus DNA Nucleotide Cell (a) DNA double helix (b) Single strand of DNA

50 Genes control protein production indirectly DNA is transcribed into RNA then translated into a protein An organism s genome is its entire set of genetic instructions Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

51 Systems Biology at the Levels of Cells and Molecules The human genome and those of many other organisms have been sequenced using DNA-sequencing machines Knowledge of a cell s genes and proteins can be integrated using a systems approach Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

52 Fig. 1-11

53 Fig Outer membrane and cell surface Cytoplasm Nucleus

54 Advances in systems biology at the cellular and molecular level depend on High-throughput h t technology, which h yields enormous amounts of data Bioinformatics, which is the use of computational tools to process a large volume of data Interdisciplinary research teams Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

55 Theme 5: Feedback mechanisms regulate biological systems s Feedback mechanisms allow biological processes to self-regulate l Negative feedback means that as more of a product accumulates, the process that creates it slows and less of the product is produced Positive feedback means that as more of a product accumulates, the process that creates it speeds up and more of the product is produced Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

56 Fig Negative feedback A Enzyme 1 B Excess D blocks a step D D D C Enzyme 2 Enzyme 3 D (a) Negative feedback W Enzyme 4 Positive feedback + X Enzyme 5 Excess Z stimulates a step Z Z Z Y Enzyme 6 Z (b) Positive feedback

57 Fig. 1-13a Negative feedback A Enzyme 1 B Excess D D Enzyme 2 blocks a step D D C Enzyme 3 D (a) Negative feedback

58 Fig. 1-13b W Enzyme 4 Positive feedback + X Enzyme 5 Excess Z stimulates a step Z Z Z Y Enzyme 6 Z (b) Positive feedback

59 Concept 1.2: The Core Theme: Evolution accounts for the unity and diversity of life Nothing in biology makes sense except in the light of evolution Theodosius Dobzhansky Evolution unifies biology at different scales of size throughout h t the history of life on Earth Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

60 Organizing the Diversity of Life Approximately 1.8 million species have been identified and named to date, and thousands more are identified each year Estimates t of the total t number of species that actually exist range from 10 million to over 100 million Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

61 Grouping Species: The Basic Idea Taxonomy is the branch of biology that names and classifies species into groups of increasing breadth Domains, followed by kingdoms, are the broadest units of classification Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

62 Fig Species Genus Family Order Class Phylum Kingdom Domain Ursus americanus (American black bear) Ursus Ursidae Carnivora Mammalia Chordata Animalia Eukarya

63 The Three Domains of Life The three-domain system is currently used, and replaces the old five-kingdom system Domain Bacteria and domain Archaea comprise the prokaryotes Domain Eukarya includes all eukaryotic organisms Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

64 Fig (a) DOMAIN BACTERIA (b) DOMAIN ARCHAEA (c) DOMAIN EUKARYA Protists Kingdom Plantae Kingdom Fungi Kingdom Animalia

65 The domain Eukarya includes three multicellular kingdoms: Plantae Fungi Animalia Other eukaryotic organisms were formerly grouped dinto a kingdom called dprotista, though h these are now often grouped into many separate kingdoms Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

66 Unity in the Diversity of Life A striking unity underlies the diversity of life; for example: DNA is the universal genetic language common to all organisms Unity is evident in many features of cell structure Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

67 Fig µm 5 µm Cilia of Paramecium 0.1 µm Cross section of a cilium, as viewed with an electron microscope Cilia of windpipe cells

68 Charles Darwin and the Theory of Natural Selection ect Fossils and other evidence document the evolution of life on Earth over billions of years Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

69 Charles Darwin published On the Origin of Species by Means of Natural Selection in 1859 Darwin made two main points: Species showed evidence of descent with modification from common ancestors Natural selection is the mechanism behind descent with modification Darwin s theory explained the duality of unity and diversity Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

70 Fig. 1-19

71 Darwin observed that: Individuals in a population have traits that vary Many of these traits are heritable (passed from parents to offspring) More offspring are produced than survive Competition is inevitable Species generally suit their environment Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

72 Darwin inferred that: Individuals that are best suited to their environment are more likely l to survive and reproduce Over time, more individuals in a population will have the advantageous traits In other words, the natural environment selects for beneficial traits Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

73 Fig Population with varied inherited traits. 2 Elimination of individuals with certain traits. 3 Reproduction of survivors. 4 Increasing frequency of traits that enhance survival and reproductive success.

74 The Tree of Life Unity in diversity arises from descent with modification For example, the forelimb of the bat, human, horse and the whale flipper all share a common skeletal architecture Fossils provide additional evidence of anatomical unity from descent with modification Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

75 Darwin proposed that natural selection could cause an ancestral species to give rise to two or more descendent species For example, the finch species of the Galápagos Islands Evolutionary relationships are often illustrated with tree-like diagrams that show ancestors and dtheir descendentsd Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

76 Fig COMMON ANCESTOR Warbler finc ches Insect-eat ters Seed-eater Bud d-eater Green warbler finch Certhidea olivacea Gray warbler finch Certhidea fusca Sharp-beaked ground finch Geospiza difficilis Vegetarian finch Platyspiza crassirostris Mangrove finch Cactospiza heliobates T ree finches In nsect-eaters Woodpecker finch Cactospiza pallida Medium tree finch Camarhynchus pauper Large agetee tree finch Camarhynchus psittacula Small tree finch Camarhynchus parvulus Ground finches Seed- -eaters Ca actus-flower- eaters Large cactus ground finch Geospiza conirostris Cactus ground finch Geospiza scandens Small ground finch Geospiza fuliginosa Medium ground finch Geospiza fortis Large ground finch Geospiza magnirostris

77 Scientists use two main forms of inquiry in their study of nature The word Science is derived from Latin and means to know Inquiry is the search for information and explanation There are two main types of scientific inquiry: discovery science and hypothesis-based science Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

78 Discovery Science Discovery science describes natural structures and processes This approach is based on observation and the analysis of data Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

79 Types of Data Data are recorded observations or items of information Data fall into two categories Qualitative, or descriptions rather than measurements Quantitative, or recorded measurements, which are sometimes organized into tables and graphs Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

80 Fig. 1-23

81 Induction in Discovery Science Inductive reasoning draws da conclusions through the logical process of induction Repeat specific observations can lead to important generalizations For example, the sun always rises in the east Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

82 Deduction: The If Then Logic of Hypothesis Based Science Deductive reasoning uses general premises to make specific predictions For example, if organisms are made of cells (premise 1), and humans are organisms (premise 2), then humans are composed of cells (deductive prediction) Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

83 The Myth of the Scientific Method The scientific method is an idealized process of inquiry Hypothesis-based science is based on the textbook scientific method but rarely follows all the ordered steps Discovery science has made important t contributions with very little dependence on the so-called scientific method Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

84 Limitations of Science In science, observations and experimental results must be repeatable Science cannot support or falsify supernatural explanations, which h are outside the bounds of science Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

85 Model Building in Science Models are representations of natural phenomena and can take the form of: Diagrams Three-dimensional objects Computer programs Mathematical equations Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

86 Science, Technology, and Society The goal of science is to understand natural phenomena The goal of technology is to apply scientific knowledge for some specific purpose Science and technology are interdependent Biology is marked by discoveries, while technology is marked by inventions Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

87 The combination of science and technology has dramatic effects on society For example, the discovery of DNA by James Watson and Francis Crick allowed for advances in DNA technology such as testing ti for hereditary diseases Ethical issues can arise from new technology, but have as much to do with politics, economics, and cultural values as with science and technology Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

88 DNA technology Recombinant DNA PCR DNA sequencing (NGS, next generation sequencing, deep sequencing) micro-array (gene chip)

89 OMIC era Gene genome (whole DNA) Transcripts transcriptome (whole RNA) Proteins proteom (whole protein) Metabolite metabolome, Nucleolus l nucelome

Introduction: Themes in the Study of Life

Chapter 1 Introduction: Themes in the Study of Life Edited by Shawn Lester PowerPoint Lecture Presentations for Biology Eighth Edition Neil Campbell and Jane Reece Lectures by Chris Romero, updated by