Attributes of LifeAttributes of Life16 and 21 November16 and 21 November

Introduction to lifeIntroduction to lifeThemes/characteristics of living organismsThemes/characteristics of living organismsStructural and functional charactersStructural and functional characters

IntroductionIntroduction

What defines life?What defines life?________________________________________________________________________________________________

ThemesThemes

Hierarchy theory and emergent propertiesHierarchy theory and emergent propertiesStructure: “it is the cell”Structure: “it is the cell”Continuity of life: function of “information”Continuity of life: function of “information”Openness of biological systemsOpenness of biological systemsRegulatory capacity of living systemsRegulatory capacity of living systemsCapacity to reproduceCapacity to reproduceCapacity to acquire, utilize, and store energyCapacity to acquire, utilize, and store energyDiversity and similarity of living systemsDiversity and similarity of living systems

Hierarchical Nature of Living Hierarchical Nature of Living SystemsSystems

CommunityCommunityPopulationPopulation

OrganismOrganismOrganOrgan

TissueTissue

CellCellOrganellesOrganelles

MacroMacromoleculesmoleculesAtomsAtoms

InfrastructureInfrastructure

Cell: Structure and FunctionCell: Structure and Function

Organism’s basic unit of structure and functionOrganism’s basic unit of structure and functionLowest level of structure capable of performing life’s Lowest level of structure capable of performing life’s activities (e.g., irritability, reproduce, grow, develop, activities (e.g., irritability, reproduce, grow, develop, etc.)etc.)Most common basic structure of all living organisms Most common basic structure of all living organisms

Cell TheoryCell TheoryUbiquitous nature of cellsUbiquitous nature of cellsAll cells come from previous cellsAll cells come from previous cells

General Cell StructuresGeneral Cell Structures

Continuity of Life and InformationContinuity of Life and Information

Order in any system originates from instructions Order in any system originates from instructions serving as a template for organization (e.g., serving as a template for organization (e.g., Constitution, Bill of Rights)Constitution, Bill of Rights)In living systems, instructions codified in the In living systems, instructions codified in the DNADNAInstructions/inheritance based on the precise, Instructions/inheritance based on the precise, sequential order of nucleotides (ATCG)sequential order of nucleotides (ATCG)

Example: RAT versus TAR versus ARTExample: RAT versus TAR versus ART

Open SystemsOpen Systems

All living organisms are open systems, allowing living organisms are open systems, allowing organisms to interact with their environmentorganisms to interact with their environment

Processing stimuliProcessing stimuliResponding to stimuliResponding to stimuli

“Open” versus a “closed” system“Open” versus a “closed” systemExamplesExamples

Orientation of leaves to sunOrientation of leaves to sunEyesEyesMicrobes and single cell organisms (e.g., amoeba)Microbes and single cell organisms (e.g., amoeba)

Examples of Open Systems

26-580Figure 26.41

Eye

Sun-Tracking Plants

Regulatory SystemsRegulatory Systems

Interplay of organisms with the environment Interplay of organisms with the environment requires a well balanced regulatory systemrequires a well balanced regulatory systemOutcome: Outcome: homeostasishomeostasis

Set point, effectors, control centers and sensorsSet point, effectors, control centers and sensorsAnalogy: thermostat for heat controlAnalogy: thermostat for heat controlExamplesExamples

Enzymes in cells (lab exercise this week)Enzymes in cells (lab exercise this week)Thermostatic control of body temperatureThermostatic control of body temperaturepH of the cellpH of the cell

Regulatory Systems: CyberneticsRegulatory Systems: Cybernetics

Feedbacks (+ and Feedbacks (+ and --), homeostasis and cybernetics), homeostasis and cybernetics

Control Center/Sensor

Set Point Effector

PositiveFeedback

NegativeFeedback

Universality of ReproductionUniversality of Reproduction

Reproduction: regenerative process of Reproduction: regenerative process of making new organisms (not necessarily making new organisms (not necessarily copies)copies)MethodsMethods

Sexual Sexual Asexual (microbes; cell division/mitosis)Asexual (microbes; cell division/mitosis)

Ancillary but important function: Ancillary but important function: creating new variantscreating new variantsExamplesExamples

SiblingsSiblingsGeranium plantsGeranium plantsDolly (the sheep)Dolly (the sheep)

Energy UtilizationEnergy Utilization

Three related activities: acquisition, utilization, and Three related activities: acquisition, utilization, and storagestorageEnergy AcquisitionEnergy Acquisition

Energy capture (autotrophs; heterotrophs)Energy capture (autotrophs; heterotrophs)Energy utilizationEnergy utilization

Laws of Thermodynamics (1Laws of Thermodynamics (1stst and 2and 2ndnd laws)laws)ATPATP (adenosine triphosphate) and (adenosine triphosphate) and ADPADP (adenosine (adenosine diphosphatediphosphate

Energy storageEnergy storageChemical bonds (CChemical bonds (C--C covalent bonds)C covalent bonds)Starch, glycogen and lipidsStarch, glycogen and lipids

Energy UtilizationEnergy Utilization

Catabolism Biosynthesis/Anabolism

ADP

ATP

Two Sides of a Coin: Two Sides of a Coin: Diversity and SimilarityDiversity and Similarity

DiversityDiversity is a hallmark of living systemsis a hallmark of living systems1.5 M known species of plants, animals and microbes1.5 M known species of plants, animals and microbes100 M+ thought to exist100 M+ thought to exist

SimilaritySimilarity is a hallmark of living systemsis a hallmark of living systemsStriking similarity at the molecular level (DNA): kinship to Striking similarity at the molecular level (DNA): kinship to worms, squirrels, birds and pigs (you DNA is ~90% pig)worms, squirrels, birds and pigs (you DNA is ~90% pig)ExamplesExamples

BiochemistryBiochemistryStructure and morphologyStructure and morphologyDNADNA

DNA phylogeny lab (December)DNA phylogeny lab (December)

What is Life? “Nuts and Bolts”What is Life? “Nuts and Bolts”

Introduction to lifeIntroduction to lifeThemes/characteristics of all living Themes/characteristics of all living organismsorganismsCardinal structural and functional Cardinal structural and functional characterscharacters

Structural and Functional CharactersStructural and Functional Characters

Cells as the physical infrastructureCells as the physical infrastructureBiological catalysis: enzymesBiological catalysis: enzymesCell membranesCell membranesWater as the medium of lifeWater as the medium of lifePolymers (CPolymers (C--based polymers)based polymers)Compartmentation Compartmentation viavia organellesorganellesMajor types of cellsMajor types of cells

Cells as the Physical InfrastructureCells as the Physical Infrastructure

Cell theoryCell theoryAll organisms composed of cellsAll organisms composed of cellsCells as smallest unit of organization exhibiting characteristicCells as smallest unit of organization exhibiting characteristics s of lifeof life

StructureStructure

Cell Membrane

Nucleus

Cytoplasm

General Features of a CellGeneral Features of a Cell

Size correlated with functionSize correlated with functionUpper limit: 0.00001 m (1 x 10Upper limit: 0.00001 m (1 x 10--55 m)m)Relationship of volume to distanceRelationship of volume to distanceAnything over 1 x 10Anything over 1 x 10--55 m is nonfunctionalm is nonfunctional

Efficacy of transport/diffusionEfficacy of transport/diffusion

Diffusion

23-479Figure 23.5

1 . 10-5 m

EnzymesEnzymes

IntroductionIntroductionReactions are very slow (not sufficient to sustain life)Reactions are very slow (not sufficient to sustain life)Mechanisms to accelerate specific reactions Mechanisms to accelerate specific reactions preferentiallypreferentially

Accelerants = Catalysts = EnzymesAccelerants = Catalysts = EnzymesProteins (relate to information brokers)Proteins (relate to information brokers)Change rate of reactionsChange rate of reactionsHigh degree of specificityHigh degree of specificityRegeneratedRegenerated

Energy Needed

ReactantsProducts

“Hill”

Base case for Base case for reactions to occurreactions to occur

Reactants Reactants Products Products

Energy analysis Energy analysis (thermodynamics)(thermodynamics)

Energy to cause Energy to cause reaction to occur reaction to occur (over the “hill”)(over the “hill”)

Enzymes: How They WorkEnzymes: How They Work

How Enzymes WorkHow Enzymes Work

Efficacy of enzymes: “Hill” heightEfficacy of enzymes: “Hill” heightMechanismMechanism

Lower the height of the “hill”Lower the height of the “hill”Selectivity/specificitySelectivity/specificity

Protein 3Protein 3--D structure (1, 2, 3, and 4 protein D structure (1, 2, 3, and 4 protein conformation)conformation)

ConclusionConclusionAbsence of enzyme: minutes to hours to Absence of enzyme: minutes to hours to days to yearsdays to yearsPresence of enzyme: 1,000 Presence of enzyme: 1,000 -- 10,000 10,000 reactions reactions per secondper secondIncrease in rate > 10Increase in rate > 1066 orders of magnitudeorders of magnitude

Membranes: StructureMembranes: Structure

Membranes: complex polymer, Membranes: complex polymer, with principal monomer (lipid) with principal monomer (lipid) being a fatty acid + glycerol (i.e., being a fatty acid + glycerol (i.e., phospholipids)phospholipids)Lipid bilayer at the molecular levelLipid bilayer at the molecular level

Phosphate/ Glycerol (Hydrophilic)

Fatty Acid (Hydrophobic)

Membranes: StructureMembranes: Structure

Lipid bilayer: “fluid membrane” with floating Lipid bilayer: “fluid membrane” with floating chunks of proteins and carbohydrates (i.e., chunks of proteins and carbohydrates (i.e., icebergs)icebergs)

Lipid Bilayer

Protein Chunk

Proteins in Lipid BilayerProteins in Lipid Bilayer

Membranes: FunctionsMembranes: Functions

Example of hierarchy theory and emergent Example of hierarchy theory and emergent propertiespropertiesSelective permeabilitySelective permeabilitySignaling: cellSignaling: cell--toto--cell communicationcell communication

Transport through Membrane: Transport through Membrane: Selective PermeabilitySelective Permeability

Signaling in/on MembranesSignaling in/on Membranes

Cystic fibrosis Vaccinations Allergies

Water: Medium for MetabolismWater: Medium for Metabolism

Liquid medium for metabolism and its importanceLiquid medium for metabolism and its importanceRole of water (HRole of water (H22O)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 HExquisite and unique properties of H22OO

Biological MacromoleculesBiological Macromolecules

Define polymer…..Define polymer…..Major biomacromolecules of carbonMajor 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 acidsAnalogy to an alphabetAnalogy to an alphabet

General Cell StructuresGeneral Cell Structures

Principle of CompartmentationPrinciple of Compartmentation

Cells are compartmentalizedCells are compartmentalizedElaborate and organized infrastructureElaborate and organized infrastructureAnalogy to a dormAnalogy to a dorm

Corridors as endoplasmic reticulumCorridors as endoplasmic reticulumRooms as organellesRooms as organelles

Consequence of not being compartmentalizedConsequence of not being compartmentalized

Compartmentation

23-494Figure 23.22

Cell TypesCell Types

ProkaryotesProkaryotesNo typical nucleusNo typical nucleusNo mitochondria, chloroplasts, No mitochondria, chloroplasts, Golgi, or endoplasmic reticulumGolgi, or endoplasmic reticulumDNA, enzymes, metabolize, etc.DNA, enzymes, metabolize, etc.Example: bacteriaExample: bacteria

EukaryotesEukaryotesTrue nucleus and all the organellesTrue nucleus and all the organellesPlant eukaryotesPlant eukaryotes

Chloroplast for photosynthesis Chloroplast for photosynthesis and cell walland cell wall

Animal eukaryotesAnimal eukaryotes

OmissionsOmissions

Cell cycle (pp. 478Cell cycle (pp. 478--482)482)Controlled methods transport (pp. 464Controlled methods transport (pp. 464--465)465)NonNon--membraneousmembraneous organelles (pp. 474organelles (pp. 474--475)475)Nuclear component (p. 475)Nuclear component (p. 475)

When you contract a fever, your body When you contract a fever, your body temperature is elevated. temperature is elevated.

Is fever and inadvertent consequence of the Is fever and inadvertent consequence of the infection or is it an example of homeostasis?infection or is it an example of homeostasis?

Each of you has been vaccinated for multiple Each of you has been vaccinated for multiple childhood diseases. You may or may not have childhood diseases. You may or may not have taken a flu vaccine.taken a flu vaccine.

Explain how membrane and information Explain how membrane and information attributes of living systems underpin the efficacy attributes of living systems underpin the efficacy of vaccinations.of vaccinations.