1. Attributes of Life 16 and 21 November Introduction to life Introduction to life Themes/characteristics of living organisms Themes/characteristics of living organisms Structural and functional characters Structural and functional characters

2. Introduction What defines life? What defines life? ________________ ________________

3. Themes Hierarchy theory and emergent properties Hierarchy theory and emergent properties Structure: “it is the cell” Structure: “it is the cell” Continuity of life: function of “information” Continuity of life: function of “information” 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 acquire, utilize, and store energy Capacity to acquire, utilize, and store energy Diversity and similarity of living systems Diversity and similarity of living systems

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

5. Infrastructure

6. 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 (e.g., irritability, reproduce, grow, develop, etc.) Lowest level of structure capable of performing life’s activities (e.g., irritability, reproduce, grow, develop, etc.) Most common basic structure of all living organisms Most common basic structure of all living organisms Cell Theory Cell Theory Ubiquitous nature of cells Ubiquitous nature of cells All cells come from previous cells All cells come from previous cells

7. General Cell Structures

8. Continuity of Life and Information Order in any system originates from instructions serving as a template for organization (e.g., Constitution, Bill of Rights) Order in any system originates from instructions serving as a template for organization (e.g., Constitution, Bill of Rights) In living systems, instructions codified in the DNA In living systems, instructions codified in the DNA Instructions/inheritance based on the precise, sequential order of nucleotides (ATCG) Instructions/inheritance based on the precise, sequential order of nucleotides (ATCG) Example: RAT versus TAR versus ART Example: RAT versus TAR versus ART

9. Open Systems 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 Processing stimuli Responding to stimuli Responding to stimuli “Open” versus a “closed” system “Open” versus a “closed” system Examples Examples Orientation of leaves to sun Orientation of leaves to sun Eyes Eyes Microbes and single cell organisms (e.g., amoeba) Microbes and single cell organisms (e.g., amoeba)

10. Examples of Open Systems 26-580Figure 26.41 Eye Sun-Tracking Plants

11. Regulatory Systems Interplay of organisms with the environment requires a well balanced regulatory system Interplay of organisms with the environment requires a well balanced regulatory system Outcome: homeostasis Outcome: homeostasis Set point, effectors, control centers and sensors Set point, effectors, control centers and sensors Analogy: thermostat for heat control Analogy: thermostat for heat control Examples Examples Enzymes in cells (lab exercise this week) Enzymes in cells (lab exercise this week) Thermostatic control of body temperature Thermostatic control of body temperature pH of the cell pH of the cell

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

13. Universality of Reproduction Reproduction: regenerative process of making new organisms (not necessarily copies) Reproduction: regenerative process of making new 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 Examples Examples Siblings Siblings Geranium plants Geranium plants Dolly (the sheep) Dolly (the sheep)

14. Energy Utilization Three related activities: acquisition, utilization, and storage Three related activities: acquisition, utilization, and storage Energy Acquisition Energy Acquisition Energy capture (autotrophs; heterotrophs) Energy capture (autotrophs; heterotrophs) Energy utilization Energy utilization Laws of Thermodynamics (1 st and 2 nd laws) Laws of Thermodynamics (1 st and 2 nd laws) ATP (adenosine triphosphate) and ADP (adenosine diphosphate ATP (adenosine triphosphate) and ADP (adenosine diphosphate Energy storage Energy storage Chemical bonds (C-C covalent bonds) Chemical bonds (C-C covalent bonds) Starch, glycogen and lipids Starch, glycogen and lipids

15. Energy Utilization Catabolism Biosynthesis/ Anabolism ADP ATP

16. 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): kinship to worms, squirrels, birds and pigs (you DNA is ~90% pig) Striking similarity at the molecular level (DNA): kinship to worms, squirrels, birds and pigs (you DNA is ~90% pig) Examples Examples Biochemistry Biochemistry Structure and morphology Structure and morphology DNA DNA DNA phylogeny lab (December) DNA phylogeny lab (December)

17. What is Life? “Nuts and Bolts” Introduction to life Introduction to life Themes/characteristics of all living organisms Themes/characteristics of all living organisms Cardinal structural and functional characters Cardinal structural and functional characters

18. Structural and Functional Characters Cells as the physical infrastructure Cells as the physical infrastructure Biological catalysis: enzymes Biological catalysis: enzymes Cell membranes Cell membranes Water as the medium of life Water as the medium of life Polymers (C-based polymers) Polymers (C-based polymers) Compartmentation via organelles Compartmentation via organelles Major types of cells Major types of cells

19. Cells as the Physical Infrastructure Cell theory Cell theory All organisms composed of cells All organisms composed of cells Cells as smallest unit of organization exhibiting characteristics of life Cells as smallest unit of organization exhibiting characteristics of life Structure Structure Cell Membrane Nucleus Cytoplasm

20. General Features of a Cell Size correlated with function Size correlated with function Upper limit: 0.00001 m (1 x 10 -5 m) Upper limit: 0.00001 m (1 x 10 -5 m) Relationship of volume to distance Relationship of volume to distance Anything over 1 x 10 -5 m is nonfunctional Anything over 1 x 10 -5 m is nonfunctional Efficacy of transport/diffusion Efficacy of transport/diffusion

21. Diffusion 23-479Figure 23.5 1. 10 -5 m

22. Enzymes Introduction Introduction Reactions are very slow (not sufficient to sustain life) Reactions are very slow (not sufficient to sustain life) Mechanisms to accelerate specific reactions preferentially Mechanisms to accelerate specific reactions preferentially Accelerants = Catalysts = Enzymes Accelerants = Catalysts = Enzymes Proteins (relate to information brokers) Proteins (relate to information brokers) Change rate of reactions Change rate of reactions High degree of specificity High degree of specificity Regenerated Regenerated

23. Energy Needed Reactants Products “Hill” Base case for reactions to occur Base case for reactions to occur Reactants Reactants Products Products Energy analysis (thermodynamics) Energy analysis (thermodynamics) Energy to cause reaction to occur (over the “hill”) Energy to cause reaction to occur (over the “hill”) Enzymes: How They Work

24. How Enzymes Work Efficacy of enzymes: “Hill” height Efficacy of enzymes: “Hill” height Mechanism Mechanism Lower the height of the “hill” Lower the height of the “hill” Selectivity/specificity Selectivity/specificity Protein 3-D structure (1, 2, 3, and 4 protein conformation) Protein 3-D structure (1, 2, 3, and 4 protein conformation) Conclusion Conclusion Absence of enzyme: minutes to hours to days to years Absence of enzyme: minutes to hours to days to years Presence of enzyme: 1,000 - 10,000 reactions per second Presence of enzyme: 1,000 - 10,000 reactions per second Increase in rate > 10 6 orders of magnitude Increase in rate > 10 6 orders of magnitude

25. Membranes: Structure Membranes: complex polymer, with principal monomer (lipid) being a fatty acid + glycerol (i.e., phospholipids) Membranes: complex polymer, with principal monomer (lipid) being a fatty acid + glycerol (i.e., phospholipids) Lipid bilayer at the molecular level Lipid bilayer at the molecular level Phosphate/ Glycerol (Hydrophilic) Fatty Acid (Hydrophobic)

26. Membranes: Structure Lipid bilayer: “fluid membrane” with floating chunks of proteins and carbohydrates (i.e., icebergs) Lipid bilayer: “fluid membrane” with floating chunks of proteins and carbohydrates (i.e., icebergs) Lipid Bilayer Protein Chunk

27. Proteins in Lipid Bilayer

29. Membranes: Functions Example of hierarchy theory and emergent properties Example of hierarchy theory and emergent properties Selective permeability Selective permeability Signaling: cell-to-cell communication Signaling: cell-to-cell communication

30. Transport through Membrane: Selective Permeability

31. Signaling in/on Membranes Cystic fibrosis Vaccinations Allergies

32. Water: Medium for Metabolism Liquid medium for metabolism and its importance Liquid medium for metabolism and its importance Role of water (H 2 O) Role of water (H 2 O) Physical properties (e.g., polarity, phases) Physical properties (e.g., polarity, phases) Chemical properties (e.g., pH, solution) Chemical properties (e.g., pH, solution) Exquisite and unique properties of H 2 O Exquisite and unique properties of H 2 O

33. Biological Macromolecules Define polymer….. Define polymer….. Major biomacromolecules of carbon Major biomacromolecules of carbon Carbohydrates (monomer is ______) Carbohydrates (monomer is ______) Lipids (monomer is _______ + _______) Lipids (monomer is _______ + _______) Proteins (monomer is ____________) Proteins (monomer is ____________) Nucleic acids (monomer is __________) Nucleic acids (monomer is __________) “Information brokers”, particularly for nucleic acids “Information brokers”, particularly for nucleic acids Analogy to an alphabet Analogy to an alphabet

34. General Cell Structures

35. Principle of Compartmentation Cells are compartmentalized Cells are compartmentalized Elaborate and organized infrastructure Elaborate and organized infrastructure Analogy to a dorm Analogy to a dorm Corridors as endoplasmic reticulum Corridors as endoplasmic reticulum Rooms as organelles Rooms as organelles Consequence of not being compartmentalized Consequence of not being compartmentalized

36. Compartmentation 23-494Figure 23.22

37. Cell Types Prokaryotes Prokaryotes No typical nucleus No typical nucleus No mitochondria, chloroplasts, Golgi, or endoplasmic reticulum No mitochondria, chloroplasts, Golgi, or endoplasmic reticulum DNA, enzymes, metabolize, etc. DNA, enzymes, metabolize, etc. Example: bacteria Example: bacteria Eukaryotes Eukaryotes True nucleus and all the organelles True nucleus and all the organelles Plant eukaryotes Plant eukaryotes Chloroplast for photosynthesis and cell wall Chloroplast for photosynthesis and cell wall Animal eukaryotes Animal eukaryotes

38. Omissions Cell cycle (pp. 478-482) Cell cycle (pp. 478-482) Controlled methods transport (pp. 464-465) Controlled methods transport (pp. 464-465) Non-membraneous organelles (pp. 474-475) Non-membraneous organelles (pp. 474-475) Nuclear component (p. 475) Nuclear component (p. 475)

39. When you contract a fever, your body temperature is elevated. Is fever and inadvertent consequence of the infection or is it an example of homeostasis?

40. Each of you has been vaccinated for multiple childhood diseases. You may or may not have taken a flu vaccine. Explain how membrane and information attributes of living systems underpin the efficacy of vaccinations.