1. Attributes of Life (Chapter 19) Introduction to life Introduction to life Themes/Characteristics of all living organisms Themes/Characteristics of all living organisms Cardinal structural and functional “nuts and bolts” of all life Cardinal structural and functional “nuts and bolts” of all life

2. Introduction What defines life? What defines life? Irritability (particularly after a test!) Irritability (particularly after a test!) Grows spontaneously (as in first year of college and old age) Grows spontaneously (as in first year of college and old age) Reproduce Reproduce Some exceptions Some exceptions Ice grows Ice grows Mule (donkey x horse) but does not reproduce Mule (donkey x horse) but does not reproduce Defining life Defining life Multiple definitions all with multiple perspectives Multiple definitions all with multiple perspectives Best to focus on what are themes or general features Best to focus on what are themes or general features

3. What is Life? Chapter 23 Introduction to life Introduction to life Themes/Characteristics of all living organisms Themes/Characteristics of all living organisms Cardinal structural and functional “nuts and bolts” of all life Cardinal structural and functional “nuts and bolts” of all life

4. Themes/Characteristics Hierarchy theory and emergent properties Hierarchy theory and emergent properties Structure and function: “it is the cell, stupid” Structure and function: “it is the cell, stupid” Continuity of life based on information: “it is your genes, stupid” (not jeans) Continuity of life based on information: “it is your genes, stupid” (not jeans) Openness of biological systems Openness of biological systems Regulatory capacity of living systems Regulatory capacity of living systems Capacity to reproduce Capacity to reproduce Capacity to utilize energy Capacity to utilize energy Diversity and similarity of living systems Diversity and similarity of living systems Evolution of living systems Evolution of living systems

5. Take-Home Messages - Themes Hierarchical nature of the living world Hierarchical nature of the living world Emergent properties of living systems Emergent properties of living systems Cell as a basic unit of structure and function Cell as a basic unit of structure and function Continuity of life based on information Continuity of life based on information Openness of biological systems Openness of biological systems Regulatory capacity of living systems: homeostasis Regulatory capacity of living systems: homeostasis Capacity to reproduce Capacity to reproduce Capacity to utilize energy Capacity to utilize energy Two sides of the same coin: diversity and similarity of living systems Two sides of the same coin: diversity and similarity of living systems Evolution as the cornerstone of biology and living systems (explains diversity and similarity) Evolution as the cornerstone of biology and living systems (explains diversity and similarity)

6. Themes/Characteristics Hierarchy theory and emergent properties Hierarchy theory and emergent properties Structure and function: “it is your cells, stupid” Structure and function: “it is your cells, stupid” Continuity of life based on information: “it is your genes, stupid” Continuity of life based on information: “it is your genes, stupid” Openness of biological systems Openness of biological systems Regulatory capacity of living systems Regulatory capacity of living systems Capacity to reproduce Capacity to reproduce Capacity to utilize energy Capacity to utilize energy Diversity and similarity of living systems Diversity and similarity of living systems Evolution of living systems Evolution of living systems

7. Hierarchical Nature of Living Systems Community Population Population Organism Organism Organ Organ Tissue Tissue Cell Cell Organelles Organelles Macromolecules Macromolecules Atoms Atoms

8. Emergent Properties of Living Systems Consequence of hierarchy theory: emergent properties Consequence of hierarchy theory: emergent properties With each step up in the hierarchy, novel properties emerge that were not present at lower levels and were not predictable With each step up in the hierarchy, novel properties emerge that were not present at lower levels and were not predictable Example: cell composed of trillions of macromolecules arranged in very precise ways that result in highly ordered and complex machinery (sum far greater than the parts) Example: cell composed of trillions of macromolecules arranged in very precise ways that result in highly ordered and complex machinery (sum far greater than the parts)

9. Infrastructure of A Cell

10. Themes/Characteristics Hierarchy theory and emergent properties Hierarchy theory and emergent properties Structure and function: “it is cells, stupid” Structure and function: “it is cells, stupid” Continuity of life based on information: “it is your genes, stupid” Continuity of life based on information: “it is your genes, stupid” Structure correlated with function Structure correlated with function Openness of biological systems Openness of biological systems Regulatory capacity of living systems Regulatory capacity of living systems Capacity to reproduce Capacity to reproduce Capacity to utilize energy Capacity to utilize energy Diversity and similarity of living systems Diversity and similarity of living systems Evolution of living systems Evolution of living systems

11. Cell: Structure and Function Organism’s basic unit of structure and function Organism’s basic unit of structure and function Lowest level of structure capable of performing life’s activities Lowest level of structure capable of performing life’s activities Most common basic structure of all living organisms Most common basic structure of all living organisms Robert Hooke (1665) and Anton van Leewenhook Robert Hooke (1665) and Anton van Leewenhook Cell Theory Cell Theory Ubiquitous nature of cells Ubiquitous nature of cells All cells come from previous cells All cells come from previous cells

12. Hooke’s Cell (Cork)

13. General Cell Structures

14. Themes/Characteristics Hierarchy theory and emergent properties Hierarchy theory and emergent properties Structure and function: “it is cells, stupid” Structure and function: “it is cells, stupid” Continuity of life based on information: “it is your genes, stupid” Continuity of life based on information: “it is your genes, stupid” Openness of biological systems Openness of biological systems Regulatory capacity of living systems Regulatory capacity of living systems Capacity to reproduce Capacity to reproduce Capacity to utilize energy Capacity to utilize energy Diversity and similarity of living systems Diversity and similarity of living systems Evolution of living systems Evolution of living systems

15. Continuity of Life and Information Order in any system originates from information and instructions that serve as a template for organizing “parts” Order in any system originates from information and instructions that serve as a template for organizing “parts” In living systems, instructions are encoded/inherited in the DNA In living systems, instructions are encoded/inherited in the DNA Inheritance is based on the precise order of nucleotides (ATCG) Inheritance is based on the precise order of nucleotides (ATCG) Example: RAT versus TAR versus ART Example: RAT versus TAR versus ART Continuity of life is based on information that is: Continuity of life is based on information that is: Transferred from generation to generation over time Transferred from generation to generation over time Preserved/stores at the molecular level in DNA Preserved/stores at the molecular level in DNA

16. Infrastructure of A Cell

17. Themes/Characteristics Hierarchy theory and emergent properties Hierarchy theory and emergent properties Structure and function: “it is cells, stupid” Structure and function: “it is cells, stupid” Continuity of life based on information: “it is your genes, stupid” Continuity of life based on information: “it is your genes, stupid” Openness of biological systems Openness of biological systems Regulatory capacity of living systems Regulatory capacity of living systems Capacity to reproduce Capacity to reproduce Diversity and similarity of living systems Diversity and similarity of living systems Evolution of living systems Evolution of living systems

18. Themes/Characteristics Hierarchy theory and emergent properties Hierarchy theory and emergent properties Structure and function: “it is cells, stupid” Structure and function: “it is cells, stupid” Continuity of life based on information: “it is your genes, stupid” Continuity of life based on information: “it is your genes, stupid” Openness of biological systems Openness of biological systems Regulatory capacity of living systems Regulatory capacity of living systems Capacity to reproduce Capacity to reproduce Diversity and similarity of living systems Diversity and similarity of living systems Evolution of living systems Evolution of living systems

19. Open Systems All living organisms are open systems, allowing organisms to interact with their environment All living organisms are open systems, allowing organisms to interact with their environment Processing stimuli from the environment Processing stimuli from the environment Responding to stimuli in the environment Responding to stimuli in the environment Characterize an “open” versus a “closed” system Characterize an “open” versus a “closed” system Examples Examples Orientation of leaves to sun Orientation of leaves to sun Eyes Eyes Ears Ears Microbes and single cell organisms (e.g., amoeba) Microbes and single cell organisms (e.g., amoeba)

20. The structure of the eye 26-580Figure 26.41

21. Themes/Characteristics Hierarchy theory and emergent properties Hierarchy theory and emergent properties Structure and function: “it is cells, stupid” Structure and function: “it is cells, stupid” Continuity of life based on information: “it is your genes, stupid” Continuity of life based on information: “it is your genes, stupid” Openness of biological systems Openness of biological systems Regulatory capacity of living systems Regulatory capacity of living systems Capacity to reproduce Capacity to reproduce Capacity to utilize energy Capacity to utilize energy Diversity and similarity of living systems Diversity and similarity of living systems Evolution of living systems Evolution of living systems

22. Regulatory Systems Constant interplay of organisms with the environment requires a well balanced regulatory system Constant interplay of organisms with the environment requires a well balanced regulatory system Consequence is homeostasis Consequence is homeostasis Set point, effectors, control centers and sensors Set point, effectors, control centers and sensors Analogy to thermostat for heat control Analogy to thermostat for heat control Examples Examples Enzymes in cells (lab exercise next week) Enzymes in cells (lab exercise next week) Thermostatic control of body temperature Thermostatic control of body temperature

23. Regulatory Systems: Cybernetics Feedbacks (+ and -), homeostasis and cybernetics Feedbacks (+ and -), homeostasis and cybernetics Control Center/ Sensor Set PointEffector Positive Feedback Negative Feedback

24. Themes/Characteristics Hierarchy theory and emergent properties Hierarchy theory and emergent properties Structure and function: “it is cells, stupid” Structure and function: “it is cells, stupid” Continuity of life based on information: “it is your genes, stupid” Continuity of life based on information: “it is your genes, stupid” Openness of biological systems Openness of biological systems Regulatory capacity of living systems Regulatory capacity of living systems Capacity to reproduce Capacity to reproduce Capacity to utilize energy Capacity to utilize energy Diversity and similarity of living systems Diversity and similarity of living systems Evolution of living systems Evolution of living systems

25. Universality of Reproduction Reproduction: regenerative process of making new organisms from previously existing organisms (not necessarily copies) Reproduction: regenerative process of making new organisms from previously existing organisms (not necessarily copies) Methods Methods Sexual Sexual Asexual (microbes; cell division/mitosis) Asexual (microbes; cell division/mitosis) Ancillary but important function: creating new variants Ancillary but important function: creating new variants Example: siblings Example: siblings

26. Themes/Characteristics Hierarchy theory and emergent properties Hierarchy theory and emergent properties Structure and function: “it is cells, stupid” Structure and function: “it is cells, stupid” Continuity of life based on information: “it is your genes, stupid” Continuity of life based on information: “it is your genes, stupid” Openness of biological systems Openness of biological systems Regulatory capacity of living systems Regulatory capacity of living systems Capacity to reproduce Capacity to reproduce Capacity to utilize energy Capacity to utilize energy Diversity and similarity of living systems Diversity and similarity of living systems Evolution of living systems Evolution of living systems

27. Energy Utilization Why is energy use an important theme? Why is energy use an important theme? Energy transduction Energy transduction Thermodynamics (1 st and 2 nd laws) Thermodynamics (1 st and 2 nd laws) Energy source is ________ Energy source is ________ Energy capture Energy capture Autotrophs (energy from sun “directly” via phoptosynthesis) Autotrophs (energy from sun “directly” via phoptosynthesis) Heterotrophs (energy from other organisms) Heterotrophs (energy from other organisms) Energy storage Energy storage Chemical bonds (C-C bonds, which are _____ bonds) Chemical bonds (C-C bonds, which are _____ bonds) ATP (adenosine triphosphate and ADP (adenosine diphosphate) ATP (adenosine triphosphate and ADP (adenosine diphosphate) Energy dissipation Energy dissipation 2 nd Law of Thermodynamicvs 2 nd Law of Thermodynamicvs

28. Energy Flow Catabolism Biosynthesis ADP ATP

29. Themes/Characteristics Hierarchy theory and emergent properties Hierarchy theory and emergent properties Structure and function: “it is cells, stupid” Structure and function: “it is cells, stupid” Continuity of life based on information: “it is your genes, stupid” Continuity of life based on information: “it is your genes, stupid” Openness of biological systems Openness of biological systems Regulatory capacity of living systems Regulatory capacity of living systems Capacity to reproduce Capacity to reproduce Capacity to utilize energy Capacity to utilize energy Diversity and similarity of living systems Diversity and similarity of living systems Evolution of living systems Evolution of living systems

30. Two Sides of a Coin: Diversity and Similarity Diversity is a hallmark of living systems Diversity is a hallmark of living systems 1.5 M known species of plants, animals and microbes 1.5 M known species of plants, animals and microbes 100 M+ thought to exist 100 M+ thought to exist Similarity is a hallmark of living systems Similarity is a hallmark of living systems Striking similarity at the molecular level (DNA) so you are more akin to worms, squirrels, birds and pigs (~90%!) than you think Striking similarity at the molecular level (DNA) so you are more akin to worms, squirrels, birds and pigs (~90%!) than you think Examples Examples Biochemistry Biochemistry Structure and morphology Structure and morphology DNA DNA Conclusion: two sides of the same coin Conclusion: two sides of the same coin

31. Themes/Characteristics Hierarchy theory and emergent properties Hierarchy theory and emergent properties Structure and function: “it is cells, stupid” Structure and function: “it is cells, stupid” Continuity of life based on information: “it is your genes, stupid” Continuity of life based on information: “it is your genes, stupid” Openness of biological systems Openness of biological systems Regulatory capacity of living systems Regulatory capacity of living systems Capacity to reproduce Capacity to reproduce Capacity to utilize energy Capacity to utilize energy Diversity and similarity of living systems Diversity and similarity of living systems Evolution and adaptation of living systems Evolution and adaptation of living systems

32. Evolution and Adaptation Define “evolution” Define “evolution” Define “adaptation” Define “adaptation” Why is “evolution” and “adaptation” important in living systems Why is “evolution” and “adaptation” important in living systems Examples of evolution Examples of evolution Macroscale: origin of species Macroscale: origin of species Microscale: Microscale: Microbes resistant to antibiotics Microbes resistant to antibiotics Moths resistant to air pollution Moths resistant to air pollution Examples of adaptation Examples of adaptation Articulation of the joints in animals Articulation of the joints in animals Planar structure of leaves Planar structure of leaves

33. Evolution and Adaptation Cornerstone theory of biology (relate to hypothesis) Cornerstone theory of biology (relate to hypothesis) Explains diversity of life Explains diversity of life Explains similarity of life Explains similarity of life Theories in biology are difficult to have stood the test of time and even more difficult to address very divergent features of living systems Theories in biology are difficult to have stood the test of time and even more difficult to address very divergent features of living systems Evolution is one of the long-standing theories that has the fascinating and unusual feature of explaining not only the diversity of life but at the same time the striking similarity among all living organisms Evolution is one of the long-standing theories that has the fascinating and unusual feature of explaining not only the diversity of life but at the same time the striking similarity among all living organisms Charles Darwin (1859): Origin of Species Charles Darwin (1859): Origin of Species

34. Take-Home Messages - Themes Hierarchical nature of the living world Hierarchical nature of the living world Emergent properties of living systems Emergent properties of living systems Cell as a basic unit of structure and function Cell as a basic unit of structure and function Continuity of life based on information Continuity of life based on information Openness of biological systems Openness of biological systems Regulatory capacity of living systems: homeostasis Regulatory capacity of living systems: homeostasis Capacity to reproduce Capacity to reproduce Capacity to utilize energy Capacity to utilize energy Two sides of the same coin: diversity and similarity of living systems Two sides of the same coin: diversity and similarity of living systems Evolution as the cornerstone of biology (explains diversity and similarity) Evolution as the cornerstone of biology (explains diversity and similarity)