Aristotle (384–322 BC)

• Theory of Spontaneous Generation - The Greekphilosopher Aristotle (384–322 BC) published thetheory of spontaneous generation that theorizedhow some organisms could come into existencethrough non-living materials.

Spontaneous Generation is the theory that living things can come from non-living things!

Pneuma

• - Pneuma was theorized as the "spiritual essence" or "vital heat" that non-living material could possess in order to undergo spontaneous generation (non-living materials giving rise to living organisms!

Observations that lead to the Theory of Spontaneous

• There Were Observations that lead to the Theory of Spontaneous Generation -Without microscopes, it did APPEAR as though animals or insects were spontaneously appearing out of non-living things!

For example,

• fish would seemingly appear in a puddle water

• maggots would appear in rotting meats

• fleas would appear out of dust

• mice would appear out of piles of grain

• frogs appeared along river banks–

First Evidence Against Spontaneous Generation Francesco Redi – 1668

• Redi designed an experiment that disproved that maggots were able to spontaneously generate on rotting meat. His experiments also demonstrated that flies must have direct contact with the rotting meat in order for maggots to appear.

Louis Pasteur

• Louis Pasteurperformed a series ofexperiments thatpresentedoverwhelming evidenceagainst the theory ofspontaneousgeneration.

Swan-Necked Flasks

• Pasteur designed special flaskscontaining swan neck tubes thatprotruded from the top. The designallowed for air to pass through to thebroth, but prevented any microbesfrom passing through the air into thebroth.

• His experiment demonstrated thatexposure to air was not enough togrow microbes in broth. The broth hadto have exposure to microbes in the airto grow microbes in the broth.

Microscopes

•The discovery of cells and the development of cell theory due to the invention of high-powered microscopes in the 17th century.

Cell Theory

The Cell Theory states:

• The fundamental unitof life is the cell.

• All organisms containone or more cells.

• All cells come fromother cells.

Robert Hooke

• Robert Hooke discovered cells in 1665by looking at a piece of cork under amicroscope.

• Cork is made of dead plant cells.

• He only recognized plants as havingcells, not animals.

• Hooke named the structures he sawin cork "cells" after the Cells ofa Honeycomb

Discovery of Cells

Hooke described cells as structures resembling

• Honey Combs

• Small Boxes

• Bladders of Air

• Caverns

• Bubbles

Properties of Prokaryotes• Important Properties of Prokaryotic

Organisms

• rapid reproductive rate (usingbinary fission)

• ability to survive harsh conditions.

• some can produce endosporeswhich allow them to survivethrough long periods of unfavorableconditions

• Bacteria have been discovered insome of the most inhospitableenvironments on Earth.

• soil samples

• sulfurous underwater seavents

• acidic hot springs

• radioactive waste.

• They are, by far, the mostnumerous life form on Earth.

Properties of Prokaryotes

• They do nothave a nucleus

• They do nothave membrane-boundorganelles

Properties of Prokaryotes

• They do not have anucleus

• They do not havemembrane-boundorganelles

• Have a singlechromosome and asmall circularplasmid (DNA) as itsgenetic material.

Different Shapes of Bacteria

Configurations of Bacteria

More Configurations and Shapes of Bacteria

Taxonomy / Phylogeny

• All organisms are either eukaryoticor prokaryotic

• All prokaryotes are in either theBacteria or the Archaea domainsof life.

• Bacteria usually contain a cell wall.

• In 1977, Carl Woese recreatedtaxonomy so that it would containthe 3 current domains instead ofjust 2.

The phylogenic tree of taxonomy categorizes all organisms into 3 domains.

• Bacteria

• Archaea

• Eukaryota / Eukarya

• Eukaryotic organisms are made of (one or more) eukaryotic cells and belong to the Eukarya Domain.

Domain Eukarya

Eukaryotic Organisms

• Plantae• Animalia• Fungi• Algae

• Prokaryoticorganisms arecomposed of a singleprokaryotic cell andbelong to either theBacteria Domain orthe Archaea Domain.

The Bacteria Domain is separated into 5 PHYLA

• proteobacteria

• chlamydia

• spirochetes

• cyanobacteria

• gram-positivebacteria

5 Classes of Proteobacteria

• Alpha proteobacteria

• Beta proteobacteria

• Gammaproteobacteria

• Delta proteobacteria

• Epsilonproteobacteria

• Alpha proteobacteria• Beta proteobacteria• Gamma proteobacteria• Delta proteobacteria• Epsilon proteobacteria

In the phylogenic/taxonomic classification system, the Proteobacteria

Phylum (plural; Phyla) is broken down into 5

major groups call classes.

Alpha Proteobacteria

• Gram-negative

• Oligotrophic• Oligotrophic means that

they can survive inhabitats that providelittle nutrients.

• Extremophiles / Live inExtreme Environments• sediments deep in the

ocean

• soil deep below theEarth's surface

• inside of glacial ice.

• Alpha proteobacteria• Beta proteobacteria• Gamma proteobacteria• Delta proteobacteria• Epsilon proteobacteria

CLASSES of PROTEOBACTERIA

PHYLA of BACTERIA

Properties of Alpha Proteobacteria

Beta Proteobacteria

• Eutrophs (copiotrophs)• Eutrophs (copiotrophs)

require a lot (copiousamounts) of organicnutrients to survive.

• Alpha proteobacteria• Beta proteobacteria• Gamma proteobacteria• Delta proteobacteria• Epsilon proteobacteria

CLASSES of PROTEOBACTERIA

PHYLA of BACTERIA

Properties of Beta Proteobacteria

Gamma Proteobacteria• highly motile

• aerobic

• nonfermenting

• resistant to many antibiotics• Alpha proteobacteria• Beta proteobacteria• Gamma proteobacteria• Delta proteobacteria• Epsilon proteobacteria

CLASSES of PROTEOBACTERIA

PHYLA of BACTERIA

Properties of Gamma Proteobacteria

Delta Proteobacteria

• gram-negative

• sulfate-reducing bacteria

• Alpha proteobacteria• Beta proteobacteria• Gamma proteobacteria• Delta proteobacteria• Epsilon proteobacteria

CLASSES of PROTEOBACTERIA

PHYLA of BACTERIA

Properties of Delta Proteobacteria

• Epsilon Proteobacteria

• Live in the digestive system of the humanbody.

• One of these, H. Pylori is the bacteriaresponsible for stomach ulcers.

• Alpha proteobacteria• Beta proteobacteria• Gamma proteobacteria• Delta proteobacteria• Epsilon proteobacteria

CLASSES of PROTEOBACTERIA

PHYLA of BACTERIA

Properties of Epsilon Proteobacteria

Another way to categorize bacteria

is based on how they react to the

Gram Stain Procedure.

Gram Stain Procedure

Cresyl Violet is the Primary Stain

(Purple/Blue Color)

Decolorization Step

Safranin is the Counter Stain

(Red/Pink Color)

Gram Staining Results in Different Types of Bacteria

Gram-Positive BacteriaAppear purple/blue because these bacteria retain the

Cresyl Violet Primary Stain even after the decolorization step. The primary stain blocks the pink/red safranin

counterstain from view because the blue/purple is darker and therefore more dominant.

Gram-Negative BacteriaAppear Pink/Red due to Safranin Counterstain. They

do not retain the blue/purple Cresyl Violet Stain after the decolorization step.

Atypical BacteriaRemains colorless, because these bacteria do not have a cell wall. These bacteria do

not retain the Cresyl violet primary stain or the counter stain, safranin.

Prokaryotes fall into one of the following categories based upon how or if they stain with the Gram stain.

• Gram-Positive

• Gram-Negative

• Atypical

GRAM-NEGATIVE BACTERIA

• These bacteria live on theskin and mucousmembranes.

• These Bacteria are found inthe Gastro-intestinal tract andthe urogentital tract.

GRAM-POSITIVE BACTERIA

GRAM-POSITIVE BACTERIA

• Has a cell wall composed of THICK peptidoglycan

• Has a cell wall composed of THIN peptidoglycan

GRAM-NEGATIVE BACTERIA

Another way to categorize bacteria is based on

Their Need for Oxygen

Aerobes - Prokaryotic organisms that require oxygen

Anaerobes - Anaerobes are microbes that do not require oxygen.• In fact, some types of anaerobes will die

when exposed to oxygen.• These types of bacteria are found in

portions of the human• mouth,• sinuses,• throat and• lower bowels.

DEEPLY-BRANCHING BACTERIA

• Deeply branching bacteria are special class of bacteria that are very ancient. These bacteria are thought to be the closest living organisms to the "universal common ancestor" that is defined as the first life-form to exist on Earth. These bacteria are remarkably resilient and can withstand the harshest, most inhospitable habitats on Earth!

• Some are extremophiles that prefer temperatures near the boiling point of water!

Cytophaga-Flavobacterium-Bacteroides (CFB) Bacteria

• CFB Bacteria -this phylum includes the

healthy bacteria of the

human digestive tract

Metabolism•Metabolism:

Metabolism is a general term for all of the chemical reactions and physical mechanisms of the cell needed to keep the cell alive.

Metabolism

•Anabolism: Smaller molecules are combined to form larger molecules by creating chemical bonds. This process requires energy in the form of ATP

• Catabolism: Larger molecules are broken apart into smaller molecules by breaking chemical bonds. This process releases energy in the form of ATP

ENZYMES

• Enzymes are very specific. They must fit together with the molecule(s) they are acting upon in a lock-and-key fashion.

ENZYMES

• Enzymes catalyze reactions by decreasing the activate energy needed for the reaction to proceed. In essence, the enzyme speeds up the reaction.

• Enzyme are not considered reactants or products in the chemical reaction.

• Enzymes are not consumed or altered when they catalyze a reaction. For this reason, they are also reusable.

ENZYMES

Factors that influence enzyme activity

• shape

• temperature

• Presence of inhibitor

The difference between competitive and noncompetitive inhibitors

• competitive inhibitors: binds to the same site as the substrate (active site)

• The substrate and the inhibitor will compete for the same binding site. This site is also called the active site.

• noncompetitive inhibitors: bind to a different site other than the active site

• This binding can result in allosteric inhibition by altering the shape (conformation) of the substrate binding site.

ATP - This is adenine triphosphate.• The phosphate groups

have bonds that contain a lot of stored energy. When the last phosphate bond is broken, energy is released and ATP becomes ADP.

ATP is made using 3 mechanisms.

• Substrate-Level Phosphorylation

• A Phosphate group is transferred from some molecule to ADP to create ATP.

• Oxidative Phosphorylation

• Phosphate is added to ADP through a series of REDOX reactions (an oxidation-reduction reactions) occurring during a respiratory pathway

• Photophosphorylation

• Phosphate group is added to ADP to make ATP using the energy collective from the sun.

There are 3 metabolic strategies

• Aerobic Cellular Respiration• Glycolysis• The Kreb's Cycle (Citric Acid Cycle)• The Electron Transport Chain (Oxidative Phosphorylation)

- Oxygen is the final electron acceptor- Oxygen is needed for this process

• Anaerobic Cellular Respiration• Glycolysis• The Kreb's Cycle (Citric Acid Cycle)• The Electron Transport Chain (Oxidative Phosphorylation)

• Another inorganic molecule BESIDES oxygen, is the final electron acceptor

• Oxygen is not needed for this process• Nitrates - Some prokaryotes can use nitrates as their electron acceptor.• Sulfates - Some prokaryotes can use sulfates as their electron acceptor.• Iron Compounds - Some prokaryotes can use iron compounds as their

electron acceptor.

• Fermentation• Glycolysis ONLY• An ORGANIC MOLECULE is the final electron acceptor• Oxygen is not needed for this process

There are 3 metabolic strategies

• Aerobic Respiration is the most efficient. It produces up to 38 ATP.

• Anaerobic Respiration produces between 2 and 36 ATP.

• Fermentation produces alcohols or other compounds and only produces 2 ATP.

Categories Based on How Energy is Obtained

• AUTOTROPHS - organisms that can synthesize their own food from inorganic sources. For example, some prokaryotes can use the carbon in carbon dioxide (CO2) from the air

• HETEROTROPHS - organisms that cannot synthesize their own food. These organisms must consume organic molecules (sugars, proteins or lipids).

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Summary of Organism

Classifications Based on

Energy (Electron)

Source

Summary of Organism

Classifications Based on

Energy (Electron)

Source

Chemoheterotrophs/Chemoorganotrophs

-Use organic chemical compounds as the electron source (Proteins, Lipids and Carbohydrates).

Summary of Organism

Classifications Based on

Energy (Electron)

Source

Chemoheterotrophs/Chemoorganotrophs

• The chemoheterotrophs that are able to use oxygen, will undergo Aerobic Cellular Respiration.

• These would be Aerobically RespiratingChemoorganitrophs

Summary of Organism

Classifications Based on

Energy (Electron)

Source

Chemoheterotrophs/Chemoorganotrophs

• The chemoheterotrophs that are NOT able to use oxygen, will undergo Anaerobic Cellular Respiration.

Summary of Organism

Classifications Based on

Energy (Electron)

Source

Chemoautotrophs/Chemolithotrophs

• Use Carbon Dioxide CO2 as Source of Carbon

• Use inorganic chemical compounds as the electron acceptor (sulfur, iron, carbon monoxide, and hydrogen).

Summary of Organism

Classifications Based on

Energy (Electron)

Source

Phototrophs

• Use Light as their Energy Source

Summary of Organism

Classifications Based on

Energy (Electron)

Source

Phototrophs that use organic compounds (proteins, lipids and carbohydrates) as a carbon source are

called PHOTOHETROTROPHS

Summary of Organism

Classifications Based on

Energy (Electron)

Source

Phototrophs that use the carbon dioxide (CO2) as a carbon source are called

PHOTOAUTOTROPHS

Summary of Organism

Classifications Based on

Energy (Electron)

Source Photoautotrophs that release oxygen as a waste product are called OXYGENIC

PHOTOSYNTHESIZERS

Summary of Organism

Classifications Based on

Energy (Electron)

Source

Photoautotrophs that DO NOT release

oxygen as a waste product are called

ANOXYGENIC PHOTOSYNTHESIZERS

Some Interesting Energy Sources

• Chemolithotroph ("litho" means rock) -prokaryotic organisms that use inorganic

chemical compounds as the electron source. Inorganic chemical compounds are as follows:

• Toluene - some prokaryotes can use toluene as their electron source.

• Ammonia - some prokaryotes can use ammonia as their electron source.

• Arsenic - some prokaryotes can use arsenic as their electron source.

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Summary Table

Cellular Respiration

• Cellular respiration has 3 processes and 1 vital transition reaction

1) Glycolysis2) The Transition Reaction3) The Kreb's Cycle / The Citric Acid Cycle4) The Electron Transport Chain / Oxidative Phosphorylation

Glycolysis

• Glycolysis is performed in all living organisms.

• Glycolysis always takes place in the cytoplasm of the cell.

• Glycolysis does not require oxygen and can be performed in both aerobic and anaerobic prokaryotes.

Glycolysis

• Glycolysis can be broken down into 2 phases;An energy investment

phase - In the energy investment phase of glycolysis, 2 ATP molecules are used

• An energy payoff phase - In the energy payoff phase, 4 ATP molecules, are produced, for a net gain of 2 ATP molecules

Energy Investment

Energy Payoff

ATP is produced by substrate-level phosphorylation.

Glycolysis

• Glycolysis Begins with 1 Glucose Molecule.

• Glycolysis Produces 2 ATP (net).

• Glycolysis produces NADH which carries electron to the ETC.

• The end product of glycolysis is 2 pyruvate molecules.

GLUCOSE

2 Pyruvate Molecules

There are 3 Glycolysis PathwaysEmbden-Meyerhof-Parnas

(EMP) pathway.Entner-Doudoroff (ED)

pathwayPentose Phosphate

Pathway (PPP)Also known as....

The Phosphogluconate Pathway orThe Hexose Monophosphate Shunt.

The glycolytic pathway used by most microorganisms

is the Embden-Meyerhof-Parnas (EMP) pathway.

The ED glycolysis pathway is the only form of glycolysis used by the gram-negative

pathogen Pseudomonas aeruginosa. Pseudomonas aeruginosa is a common

bacteria known for antibiotic resistance. This pathogen

causes many of the hospital-acquired infections.

E. coli, also use the ED form of glycolysis, but they also have the ability to use

EMP pathway.

The PPP glycolysis pathway, creates building blocks (or precursors) for

amino acids and nucleotides.

This form of glycolysis will take place in the cell when

amino acids and nucleotides are needed to form proteins

and nucleic acids, respectively (RNA or DNA).

The Transition Reaction

• Before the pyruvate molecules can enter the Kreb's cycle, they must first undergo a transition reaction.

• After glycolysis, each of the pyruvate molecules will be transformed into Acetyl CoA.

• NADH is also produced in the transition reaction , but no ATP is produced.

CO2

The Kreb's Cycle(The Citric Acid Cycle)

After the transition step, Acetyl CoA enters the Krebs cycle.

• NADH and FADH2 are produced.

• One ATP is produced by substrate-level phosphorylation.

• 2 CO2 molecules are released.

Keep in mind that one glucose molecule will take two

turns of the Krebs cycle to process.

The Electron Transport Chain (ETC)• The ATP formed in the Electron Transport Chain is formed using

oxidative phosphorylation.

• The enzyme needed for making ATP using oxidative phosphorylation is ATP synthase. ATP synthase creates ATP.

• The electron transport chain (ETC) exists in the plasma membrane in prokaryotic cells.

• You may recall that this process occurs in the mitochondria in eukaryotic cells.

The Electron Transport Chain (ETC)STEPS OF THE ETC PROCESS

• NADH and FADH2 transport the electrons (in the form of hydrogen) from the processes of glycolysis, the transition reaction and the citric acid cycle

to the electron transport chain.

• The H from NADH and FADH2 goes to the first complex of the electron transport chain.

The Electron Transport Chain (ETC)

STEPS OF THE ETC PROCESS

• Hydrogen is made up on one proton and one electron.

• The electron gets pulled off of the hydrogen molecule and travels through the different complexes of the electron Transport chain.

The Electron Transport Chain (ETC)

STEPS OF THE ETC PROCESS

• The hydrogen becomes a hydrogen ion (H+) once it looses its electron, Since hydrogen is made up of only one electron and one proton, the hydrogen ion (H+) is simply a single proton.

HYDROGEN ION

Electron Transport Chain

• The protons are pumped out of the membrane using a proton pump which creates a concentration (or electrochemical) gradient. The proton pump move the protons (H+) from inside the cell to outside of the cell membrane, between the cell wall and the cell membrane.

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The Electron Transport Chain (ETC)STEPS OF THE ETC PROCESS (cont.)

•The protons (H+) want to get back into the cell due to its electrochemical gradient. •This forces the protons to travel through the ATP synthase in order to get back into the cell.

The Electron Transport Chain (ETC)STEPS OF THE ETC PROCESS (cont.)

•As the H+ travels through ATP synthase, this gives off the energy needed for ATP synthase to make ATP.

The Electron Transport

Chain (ETC)

• In aerobic respiration, oxygen is the final electron acceptor in the terminal step of cellular respiration.

• A single oxygen molecule is going to catch 2 electrons that are coming off the end of the electron transport chain.

• The oxygen molecule is also going to pick up 2 protons from the surrounding intracellular fluid.

• This means oxygen is adding 2 hydrogen molecules to become water H2O.

The Electron Transport

Chain (ETC)

• In anaerobic respiration, another inorganic molecule (such nitrates or nitrites) will be used as the final electron acceptor in the terminal step of the electron transport chain.

• Obligate anaerobes will use anaerobic respiration.

The Cell Also Catabolizes Proteins

and Lipids. These Other Pathways

Merge with Cellular Respiration.

What About Fermentation?

• Glycolysis Aerobic Cellular Respiration = 36-38 ATP

• Glycolysis Anaerobic Cellular Respiration = 2-36 ATP

• Glycolysis Fermentation = 2 ATP

Obligate Aerobes

•Obligate Aerobes -Prokaryotes that require oxygen (O2) for metabolism (aerobic respiration). Humans are an example of obligate aerobes since we absolutely depend upon the presence of oxygen.

Obligate Anaerobes

• Obligate Anaerobes -Prokaryotes that do not need oxygen (or cannot be exposed to oxygen) only undergo anaerobic metabolism (anaerobic respiration) and are classified as obligate anaerobes. • For example, C.

botulinum, the bacterium that causes botulism, is able to grow inside of canned food in the absence of oxygen.

Facultative Anaerobes

• Prokaryotes that exhibit metabolic flexibility.

• These microbes have metabolic pathways for when oxygen is present and another set of metabolic pathways for when oxygen is unavailable.

For example, the bacteria responsible for staph

infections and strep throat are facultative anaerobes.

Alcoholic Fermentation• Many organisms that do

not require oxygen, will undergo a process of fermentation.

• Fermentation takes place in the absence of oxygen and uses an organic molecule (such as pyruvate) as a final electron acceptor.

• Fermenting organisms produce only 2 ATP molecules per glucose molecule.

The Yeast, Saccharomyces cerevisiae

• The microbe commonly used for alcoholic fermentation, baking and even biofeul production is the yeast Saccharomyces cerevisiae. • Yeast are single-celled

fungi that belong to the Fungi Kingdom in the Eukarya Domain.

LACTIC ACID FERMENTATION

• Fermentation by some bacteria, like those in yogurt and other soured food products, and by animals in muscles during oxygen depletion, is lactic acid fermentation.

LACTIC ACID BACTERIA

• Bacteria that are known to use lactic acid fermentation are called lactic acid bacteria (LAB).

• ,Many LAB are gram-negative and are used in food production.

• Some types of yogurt

• cheeses

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Heterolactic Fermentation• Some bacteria can do

heterolacticfermentation, that produces more than one fermentation product.

• They may produces a mixture of lactic acid, ethanol and/or acetic acid, and CO2.

• These bacteria types are used to make pickles!

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Carbon Dioxide Gas

• The bubbles in champagne and the holes in your bread and cakes are due to the carbon dioxide released as a waste product of the fermentation process!

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Triglycerides - Enzymes called lipases function to break down glycerol into its smaller fatty acid subunits.

Phospholipids - Enzymes called phospholipases, break apart the phospholipid molecule into its individual fatty acids and phosphorylated head units.

Fatty acids - A process called β-oxidation removes acetyl groups from the ends of fatty acid chains.

Proteins - Enzymes called proteases break up large proteins into smaller amino acids chains called peptides.

• Have you ever noticed that the chemical equation for aerobic cellular respiration and photosynthesis are basically the same equation in reverse??