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Nature of Living Things

Tillery et al. Chapter 20Prof. Geller

HNRS 227 Fall 2007

Outline of Chapter

• Characteristics of life• Cell theory• Cell membranes• Organelles• Respiration and photosynthesis• Prokaryotes• Eukaryotes

Characteristics of Life

• Biology – “study of living things”• Defining living things

– By characteristics• Metabolic processes• Generative processes• Responsive processes• Control processes• Structural similarities

Metabolic Processes

Generative Processes iClicker Question

• Which one of the following represents a generative process?

• A enzymes• B individual adaptation• C nutrient uptake• D cell division

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Responsive Processes Control Processes

iClicker Question

The overarching meaning of Homeostasis is• A contributor and provider• B expand• C same or constant• D receiver

iClicker QuestionIn response to a bacterial infection my body's

thermostat is raised. I start to shiver and produce more body heat. When my body temperature reaches 101 degrees, I stop shivering and my body temperature stops going up. This is an example of:

A) Negative feedbackB) A malfunctioning control systemC) Positive feedbackD) A negative impact

iClicker QuestionWhich of the following is an example of a positive

feedback?A) Shivering to warm up in a cold winter stormB) A cruise control set on your car applies more

gas when going up a hillC) You sweat on a hot summer's day and the

blood vessels in your skin vasodilateD) You get cut and platelets form a clot. This in

turn activates the fibrin clotting system andmore blood forms clots

Structural Similarities and Hierarchy

CommunityPopulation

OrganismOrgan

TissueCell

OrganellesMacromolecules

Atoms

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Cell TheoryThe Structure and Function of Cells

• 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.)

– Most common basic structure of all living organisms

• Cell Theory– Ubiquitous nature of cells– All cells come from previous cells

Cell Infrastructure

iClicker Question

• What is a cell?– A) The largest living units within our bodies.– B) Enzymes that "eat" bacteria– C) Microscopic fundamental units of all living

things.– D) All of the above.

Continuity of Life and Information

• 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

• Instructions/inheritance based on the precise, sequential order of nucleotides (ATCG)– Example: RAT versus TAR versus ART

Open Systems• All living organisms are open systems,

allowing organisms to interact with their environment– Processing stimuli– Responding to stimuli

• “Open” versus a “closed” system• Examples

– Orientation of leaves to sun– Eyes– Microbes and single cell organisms (e.g.,

amoeba)

Examples of Open Systems

26-580Figure 26.41

Eye

Sun-Tracking Plants

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Regulatory Systems

• Interplay of organisms with the environment requires a well balanced regulatory system

• Outcome: homeostasis– Set point, effectors, control centers and

sensors• Analogy: thermostat for heat control• Examples

– Enzymes in cells (lab exercise this week)– Thermostatic control of body temperature– pH of the cell

Regulatory Systems: Cybernetics

• Feedbacks (+ and -), homeostasis and cybernetics

Control Center/Sensor

Set Point Effector

PositiveFeedback

NegativeFeedback

Universality of Reproduction

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

• Methods– Sexual – Asexual (microbes; cell

division/mitosis)

• Ancillary but important function: creating new variants

• Examples– Siblings– Geranium plants– Dolly (the sheep)

Energy Utilization

• Three related activities: acquisition, utilization, and storage

• Energy Acquisition– Energy capture (autotrophs; heterotrophs)

• Energy utilization– Laws of Thermodynamics (1st and 2nd laws)– ATP (adenosine triphosphate) and ADP (adenosine

diphosphate• Energy storage

– Chemical bonds (C-C covalent bonds)– Starch, glycogen and lipids

Energy Utilization

Catabolism Biosynthesis/Anabolism

ADP

ATP

iClicker Question

• A useful chemical bond form of energy used in all cells is

• A DNA• B ATP• C proteins• D centrioles

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iClicker Question

• The ultimate energy source for most life on Earth is

• A ATP• B radiant energy from the Sun• C biochemicals• D DNA

Two Sides of a Coin: Diversity and Similarity

• Diversity is a hallmark of living systems– 1.5 M known species of plants, animals and microbes– 100 M+ thought to exist

• 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)

– Examples• Biochemistry• Structure and morphology• DNA

• DNA phylogeny lab (December)

What is Life? “Nuts and Bolts”

• Introduction to life• Themes/characteristics of all living

organisms• Cardinal structural and functional

characters

Structural and Functional Characters

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

Cells

• Smallest living unit• Most are microscopic

Discovery of Cells• Robert Hooke (mid-1600s)

– Observed sliver of cork– Saw “row of empty boxes”– Coined the term cell

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Cell theory

• (1839)Theodor Schwann & Matthias Schleiden“ all living things are made of cells”

• (50 yrs. later) Rudolf Virchow“all cells come from cells”

Principles of Cell Theory

• All living things are made of cells

• Smallest living unit of structure and function of all organisms is the cell

• All cells arise from preexisting cells(this principle discarded the idea of spontaneous generation)

Cell Size Cells Have Large Surface Area-to-Volume Ratio

Characteristics of All Cells

• A surrounding membrane• Protoplasm – cell contents in thick fluid• Organelles – structures for cell function• Control center with DNA

Molecule Movement & Cells

• Passive Transport

• Active Transport

• Endocytosis (phagocytosis & pinocytosis)

• Exocytosis

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Passive Transport

• No energy required

• Move due to gradient– differences in concentration, pressure, charge

• Move to equalize gradient– High moves toward low

Types of Passive Transport

1. Diffusion

2. Osmosis

3. Facilitated diffusion

Diffusion

• Molecules move to equalize concentration

Osmosis

• Special form of diffusion

• Fluid flows from lower solute concentration

• Often involves movement of water– Into cell– Out of cell

Solution Differences & Cells• solvent + solute = solution• Hypotonic

– Solutes in cell more than outside– Outside solvent will flow into cell

• Isotonic– Solutes equal inside & out of cell

• Hypertonic– Solutes greater outside cell– Fluid will flow out of cell

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Facilitated Diffusion

• Differentially permeable membrane

• Channels (are specific) help molecule or ions enter or leave the cell

• Channels usually are transport proteins (aquaporins facilitate the movement of water)

• No energy is used

Process of Facilitated Transport

• Protein binds with molecule• Shape of protein changes• Molecule moves across membrane

Active Transport• Molecular movement• Requires energy (against gradient)• Example is sodium-potassium pump

Endocytosis

• Movement of large material– Particles– Organisms – Large molecules

• Movement is into cells• Types of endocytosis

– bulk-phase (nonspecific)– receptor-mediated (specific)

Process of Endocytosis• Plasma membrane surrounds material• Edges of membrane meet• Membranes fuse to form vesicle

Forms of Endocytosis• Phagocytosis – cell eating• Pinocytosis – cell drinking

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Exocytosis• Reverse of endocytosis• Cell discharges material

Exocytosis• Vesicle moves to cell surface• Membrane of vesicle fuses • Materials expelled

iClicker Question

In which decade were you born?• A 1990s• B 1980s• C 1970s• D 1960s• E 1950s

iClicker Question

In which year was Geller’s first peer-reviewed paper published?

• A 1964• B 1974• C 1984• D 1994• E 2004

iClicker Question

• In which journal was Geller’s first pee-reviewed paper published?

• A Astrophysical Journal• B Astronomical Journal• C Journal of Chromatography• D Journal of Physics• E The Physics Teacher

ENERGY, ENZYMES, & METABOLISM

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Remember ENERGY

• Energy is the capacity to do work• Energy exists in multiple forms

– Light– Heat– Electricity– Chemical bond energy– Etc.

• These various types of energy can be places into two groups– Kinetic energy– Potential energy

KINETIC ENERGY• “Energy of motion”• Anything that moves possesses kinetic

energy– e.g., Heat, light, balls on a pool table, flowing

water, flowing electrons, etc.

POTENTIAL ENERGY• “Energy of location or structure”• “Stored energy”• Resting objects may still possess

energy– e.g., A rock at the top of a hill, chemical

bond energy

THERMODYNAMICSFirst Law of Thermodynamics• (The Law of Conservation of Energy)

“Energy cannot be created or destroyed”

“The total amount of energy in the universe is constant”

• Gee, does this still sound pretty boring?

THERMODYNAMICS• Energy cannot be created or destroyed• However, it can be converted from

one form to another• What energy transformations are

taking place here?

THERMODYNAMICS

• If energy cannot be created or destroyed, why do we humans need continual inputs of energy?

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THERMODYNAMICSThe Second Law of Thermodynamic Consequences

“Every energy transformation makes the universe more disordered”

– Entropy is a measure of this disorder or randomness“Every energy transformation increases the

entropy of the universe”“When energy is converted from one form to

another, some fraction of the potentially usable energy is lost”

– Not destroyed, but converted to entropy

THERMODYNAMICS

• I weighed over eight pounds at birth• I weigh more than eight pounds now• I have increased in order and complexity

• Is this counter to the Second Law of Thermodynamics?

THERMODYNAMICS

The Second Law of Thermodynamics• Note that we have talked about the

universe as a whole, not each individual part of the universe– The universe as a “closed system”

• No energy enters or leaves• In a closed system, entropy increases

THERMODYNAMICS

The Second Law of Thermodynamics• You, as an individual, can increase in

order– You do so at the expense of your environment– Overall, the net change in you and in your

environment is an increase in disorder • You + environment = a closed system

THERMODYNAMICS• Certain events occur spontaneously, while others do not

– Spontaneous processes occur without outside help– e.g., Water flows downhill, not uphill

• How can we explain this?

THERMODYNAMICS

• When a spontaneous process occurs, the stability of the system increases– Entropy is increased in such a process– The tendency for entropy to increase drives

such processes• A process can occur spontaneously only if

it increases the entropy of the system• Free energy is released in such a process

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THERMODYNAMICS

• The free energy released in spontaneous processes can be harnessed to do work

THERMODYNAMICS1) Are energy transformations occurring here?

A) Yes B) No2) Where is the spontaneous process?

A) Left Picture B) Right Picture3) Is work being done in left picture?

A) Yes B) No4) Is work being done in right picture?

A) Yes B) No

THERMODYNAMICS1) Are energy transformations occurring here?

A) Yes B) No2) Is there a spontaneous process?

A) Yes B) No3) Is work being done here?

A) Yes B) No

CHEMICAL REACTIONS

• Some chemical reactions release free energy– Spontaneous reactions– Exergonic reaction

• Some chemical reactions require free energy in order to proceed– Nonspontaneous reactions– Endergonic reaction

• The energy released in exergonic reactions can be used to drive endergonic reactions

NEED FOR ENERGY

• The environment within a cell is highly organized and separate from the external environment– Maintaining this ordered

environment costs energy– Many processes within a cell

require energy– The requirement for energy is

a unifying feature of life• Many organisms extract energy from food via

aerobic cellular respiration

CELLULAR RESPIRATION

• Cellular respiration involves a series of chemical reactions that release free energy– Exergonic reactions

• This free energy is used for cellular work

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ATP

• ATP couples of energy-releasing (exergonic) reactions to energy-requiring (endergonic) reactions

ATP CYCLE

• ATP and ADP are readily interconverted– ATP ADP releases energy– ADP ATP requires energy

ATP CYCLE

• Energy-releasing reactions store energy as ATP– ADP ATP

• Energy-requiring reactions receive energy from ATP– ATP ADP

CHEMICAL REACTIONS

• The laws of thermodynamics define which reactions are spontaneous and which are not

• Some spontaneous chemical reactions occur at nearly imperceptibly slow rates– The rate of many metabolically important

chemical reactions is insufficient to sustain life• Enzymes can increase the rate of

chemical reactions

ENZYMES

• An enzyme is a biological catalyst– Biological because it is a protein– Catalyst because it speeds up a reaction without

being consumed or permanently altered in the process

• Note– All enzymes are proteins, but not all proteins are

enzymes– All enzymes are catalysts, but not all catalysts are

proteins

ACTIVATION ENERGY

• Every chemical reaction involves both breaking and forming chemical bonds– Breaking bonds requires energy– Forming new bonds releases energy– (Sometimes net release, sometimes net requirement)

• Even though a particular reaction may be spontaneous, a small amount of energy must be initially invested– “Activation energy”

• How do you earn interest at your bank?

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ACTIVATION ENERGY

• Free energy is required to break bonds– Activation energy

• Free energy is released when new bonds are formed

ENZYMES

• Enzymes speed up chemical reactions by lowering their activation energy– The net change in free energy remains

unchanged

SUBSTRATE

• The reactants in an enzyme-catalyzed reaction are termed “substrates”

Substrate product

Sucrose glucose & fructoseStarch sugars

Deoxynucleotide triphosphates DNAEtc.

ENZYME SPECIFICITY

• No single type of enzyme can catalyze all chemical reactions

• Enzymes display specificity as to what chemical reaction they catalyze– “Substrate specificity”

• Specific enzymes catalyze the following reactions– Sucrose glucose & fructose – Starch sugars– Deoxynucleotide triphosphates DNA

ENZYME STRUCTURE

• Enzymes are proteins with specific three-dimensional shapes– Defined by chemical bonds– 1o, 2o, 3o, & 4o structures

• The portion of an enzyme that binds to the substrate is the “active site”– Complementarity of fit– Lock-and-key fit– Induced fit (shaking hands)

CATALYTIC CYCLE

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REACTION RATE

• The rate of an enzyme-catalyzed reaction is dependent upon several factors– [Substrate]– [Enzyme]– Temperature– pH– Cofactors– Inhibitors

[SUBSTRATE]

• The rate at which an enzyme converts substrate into product can be increased by increasing substrate concentration– There is a limit

• At some substrate concentration all of the enzymes’ active sites are bound to substrate– The enzyme is “saturated”– Adding more substrate will not increase the rate– Adding more enzyme will increase the rate

TEMPERATURE & pH• An enzyme’s three-

dimensional shape is defined by various chemical bonds– Altering the temperature

or pH can interfere with these bonds

– Altered enzyme shape compromises activity

– “Denaturation”

COFACTORS

• Many enzymes require non-protein helpers for catalytic activity– “Cofactors”

• Cofactors may be organic or inorganic– Inorganic cofactors are typically metal ions– Organic cofactors (“coenzymes”) are typically

vitamins or are derived from vitamins• e.g., DNAse requires Mg2+ as a cofactor

– Removal of Mg2+ inactivates the enzyme

INHIBITORS• Certain chemicals can selectively

inhibit the activity of specific enzymes– May be reversible or irreversible– Generally weak vs. covalent bonds

• Competitive inhibitors– Compete for binding to active site– Increased [substrate] can overcome

• Noncompetitive inhibitors– Binding elsewhere alters shape,

alters active site

INHIBITORS

• Many poisons act by inhibiting enzymes– e.g., DDT inhibits key enzymes in the nervous

system– e.g., many antibiotics inhibit (penicillin, etc.)

key bacterial enzymes• Selective inhibition of key enzymes is an

essential mechanism of metabolic control

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FEEDBACK INHIBITION

• Anabolic biosynthetic pathways produce an end-product such as an amino acid

• This end-product should be produced only when needed

• In many cases, this end-product acts as an inhibitor of an enzyme functioning early in the biosynthetic pathway– “Feedback inhibition”

Energy Needed

ReactantsProducts

“Hill”

• Base case for reactions to occur– Reactants – Products

• Energy analysis (thermodynamics)– Energy to cause

reaction to occur (over the “hill”)

Enzymes: How They Work

How Enzymes Work• Efficacy of enzymes: “Hill” height• Mechanism

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

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

• Conclusion– Absence of enzyme: minutes to hours

to days to years– Presence of enzyme: 1,000 - 10,000

reactions per second– Increase in rate > 106 orders of

magnitude

Membranes: Structure• Membranes: complex polymer,

with principal monomer (lipid) being a fatty acid + glycerol (i.e., phospholipids)

• Lipid bilayer at the molecular level

Phosphate/ Glycerol (Hydrophilic)

Fatty Acid (Hydrophobic)

Membranes: Structure

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

Lipid Bilayer

Protein Chunk

Proteins in Lipid Bilayer

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Membranes: Functions

• Example of hierarchy theory and emergent properties

• Selective permeability• Signaling: cell-to-cell communication

Transport through Membrane: Selective Permeability Signaling in/on Membranes

Cystic fibrosis Vaccinations Allergies

Water: Medium for Metabolism

• Liquid medium for metabolism and its importance

• Role of water (H2O)– Physical properties (e.g., polarity, phases)– Chemical properties (e.g., pH, solution)

• Exquisite and unique properties of H2O

iClicker Question

Fatty acids and glycerols are part of • A Carbohydrates• B Proteins• C Nucleic Acids• D Lipids

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iClicker Question

• The monomer “monosaccharide” is what type of molecular polymer?

• A Carbohydrate• B Protein• C Nucleic Acid• D Lipid

iClicker Question

Amino acids are portions of• A Carbohydrates• B Proteins• C Nucleic Acids• D Lipids

iClicker Question

Nucleotides are portions of• A Carbohydrate• B Protein• C Nucleic Acid• D Lipid

General Cell Structures

Principle of Compartmentation

• Cells are compartmentalized– Elaborate and organized infrastructure– Analogy to a dorm

• Corridors as endoplasmic reticulum• Rooms as organelles

• Consequence of not being compartmentalized

Compartmentation

23-494Figure 23.22

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Cell Types

• Prokaryotes

• Eukaryotes

Prokaryotic Cells• First cell type on earth• Cell type of Bacteria and Archaea• No membrane bound nucleus• Nucleoid = region of DNA concentration• Organelles not bound by membranes

Eukaryotic Cells• Nucleus bound by membrane• Include fungi, protists, plant,

and animal cells• Possess many organelles

Protozoan

Omissions

• Cell cycle (pp. 478-482)• Controlled methods transport (pp. 464-

465)• Non-membraneous organelles (pp. 474-

475)• Nuclear component (p. 475)