EXAM 1

Chapter I: The Microbial World and You

What is a Microorganism?
O Microbe or microorganism-microscopic living cells
O Microorganism- any living cell that is too small to seen by naked
eye. Ex. Need a microscope to view organism, some need electron
or different types.
O Group of Microorganisms- Are both prokaryotic and eukaryotic
O Prokaryotic- Bacteria, Archae
4 Only two groups -Bacteria and Archae
4 Archae- are separated from bacterial cells, they were called
archaebacteria
O Eukaryotic- Algae, Fungi, Parasitic, protozoa
4 Eukaryotic- have true nucleus
4 Prokaryotic- dont even have true nucleous, they have a
nucleoid.
O Virus- microscopic, or microorganism. They are neither eukaryotic
or prokaryotic. Not even considered to be cells sometimes. They are
classified as parasites or macromolecules.
4 Mad Cow Disease- caused by like a virus like molecule.
4 Border of living and non living
O Unicellular or Multi cellular- Microorganisms can be both.
4 Unicellular- Bacteria unicellular microbes
Multicellular- Fungi, Algae, Protozoa
Microbes and diseases
O Bacteria cause infections and food spoilage
4 Difference between infectious and disease
4 Infectious- pathogenic fungi, Influenza
Humans
Animals
Plants
4 Not Infectious- Alzheimer, Genetic or Immunology disorder
4 Food Spoilage
Cookie dough-salmonella
Meat products- e. coli
4 Microbes can cause food spoilage.
Many bacteria and fungi
O Pathogenicity- ability of microbe to cause disease
O Microbe- some are harmless, non pathogens
4 Ex. Flu Virus- some will suffer, some will not get sick, because
it is the same virus that is pathogenic to human beings,
because some get infected and some dont.
Depends on two factors:
Pathogenicity of Microbe
How Resistant you are to this Microorganism_-
(things can affect immune system- stress,
lifestyle etc. ).
O Immune- Innate(what were born with) and
Adaptive(environment)
O Etiological agent- cause of an infection. Pathogen that causes
infection
4 Ex. Salmonella- food poisioning
4 Ex. E-coli- diarrhea
Microbes and Human diseases
O 1. Biological Warfare:
4 Bacillus anthracis- causes anthrax
!roduces endospores that cannot be killed by boiling, uv
etc.
4 lostridium botulinum- causes food poisioning
!roduces very potent toxin, that causes botulism. Tip of
a needle amount of toxin, can make thousands of
people sick. Bioterrorism.
Botox- toxin from botulinum, acts on the nervous
system, getting rid of wrinkles. Amount of toxin is very
small so it is controllable.
O 2. Bacterial Resistance to antibiotics.
4 They were microbes that were resistant in the past, a lot of
competition among microbes , such as fungus secreting
penicillum by killing the bacteria, so it can use all the
enviroments nutrients for itself.
4 Antibiotics were produced by other microbes to survive in
nature, but some bacteria survived. Natural selection.
4 Different bacteria were becoming slowly resistant.
4 But because, we are overusing them now there is a resistant
bacteria now.
4 When immune system cannot control, thats when you need
the antibiotics. But if immune system down, its a lost cause.
O 3. Emerging Infectious Diseases- new diseases and diseases
increasing in incidence.
4 Swine Flu- Avian Influenza A: caused by Influenza A virus
4 MRSA: Meticillin-resistant $taphylococcus aureus
4 West Nile Encephalitis- caused by est Nile Virus
4 Bovine Spongiform Encephalopathy: caused by a prion
4 Escherichia coli 0157:H7 ( bad e. coli unlike digestive e. coli)
4 Ebola
4 Bird Flu
4 Some diseases remain restricted to areas, but because of
travel, diseases spread very easily.
4 Humans encroaching some of the areas that are for animals,
like forests, we are in contact with some of their diseases.
Microbes and Human Life
O 1. Recycling of chemical elements: N2 fixation
4 Bacteria recycle Nitrogen. Nitrogen present in air, cannot be
used by plants, it needs to be converted to other products
such as ammonia or nitrite. Bacteria convert original nitrogen
from air convert to ammonia and give it to plants.
Recycle Carbon, Sulfur etc.
O 2. Decomposition of organic matter: sewage treatment
4 Lots of different type of bacteria are used, water and sewage
are separated, and bacteria treat water to free toxins.
O 3. Bioremediation: clean up, remove pollution by using biological
cells.
4 Pseudomonas- microbe sprayed on oil spill. Uses as its own
food. This strain does not cause disease in aquatic life or
humans. But sometimes it can grow out of control, and it can
disturb the ecosystem. e have to control it when it is
degrading oil.
4 acillus
4 Ex. Bp oil spill. If oil spills on water, then chemicals are used,
but chemicals are toxic to aquatic life. And you cannot
remove them from water. So microorganisms are used to
remove oil. But spill was too big, so bioremediation was not
used.
O 4. Insect pest control: Biological Insecticides
4 DDT- pesticide to kill insects to save crops. Could also have
caused cancer in humans.
4 Bacteria can be used instead.
4 Bacillus thuringensis- good bacterium, does not cause
diseases in human and animals, but kills insects. Insects
cannot digest these bacterial proteins.
O 5. Food industry: vinegar, wine, beer, cheese, yogurt, bread,
pickles
4 ability of bacteria and fungi can ferment some food products.
4 Alcoholic beverages
4 Yeast- type of fungus, used for wine, beer, fermenting to
yeast cells. Wine
4 Bacteria also used in some breweries. Tequila
4 Product dependent on microbe.
4 Distinct flavor and taste.
O . Genetic Engineering: production of proteins, vaccines, enzymes,
growth hormones etc. eg. Insulin.
4 Blood sugar- diabetes need insulin, which used to come from
animals, get insulin from their pancreas. But we had to
sacrifice so many. Pancreatic cell has a gene which is
responsible to produce insulin. Take gene and put it in
bacteria, and when you grow them you get it to insulin.
4 Proteins, enzymes, hormones.
4 Human growth hormone gene is extracted and put into
bacteria.
O 7. Gene Therapy: use of viruses to carry replacement for defective
gene.
4 Mutation in gene can lead to certain disorders.
4 Take healthy form of gene and give to virus. Then virus goes
there. The defective gene is removed and the healthy gene is
given instead. Lot of challenges, but some are used.
O 8. Genomics: started with human genome project.
4 Genome of human cell has been mapped.
4 Genetic information of bacteria in database
4 Compare the genes from pathogenic bacteria to non-
pathogenic bacteria.
4 Good e. coli and bad e. coli
4 How to figure out which strains of bacteria or virus, if good or
bad.
How to properly write the scientific name of a microorganism
O Bacillus- genus
O anthracis-species
O Any given genus there can me multiple species
O Always capitalize first letter of genus.
O Either underline the text or italics or use.
O Bacillus anthracis: wrong...one continuous underline its, wrong, it
should be separated and underlined like Bacillus anthracis.
O You need to completely write the name before you start
abbreviation.
O Some bacterial names may be descriptive or honor a scientist.
A Brief History of Microbiology

EXAM 1
Ch. 4 Functional Anatomy of Prokaryotic cells

Prokaryotic and Eukaryotic Cells
O Prokaryote- comes from greek word, for prenucleus
O Eukaryote- comes from greek word, for true nucleus.
Prokaryote and Eukaryote
O Prokaryote
4 Circular chromosome, not in membrane
4 No histone
4 No organelles
4 Peptidoglycan cell wall
4 Binary fission
O Eukaryote
4 Paired chromosomes in nuclear membrane
4 Histones present
4 Organelles
4 Polysaccharide cells walls
4 Mitosis
Basic Shapes/Morphology
O Rod shaped-
O Single-Bacillus
O plural-Bacilli
O
O Single bacteria- a bacterium
O Spherical- Coccus
4 Single-cocci
4 Two-diplococci
4
O Spiral
4 Spirillum- more like wave structure
4
4 Vibrio- sausage shaped structure, like a curved rod
4
4 Spirochete- cork screwed shaped structure
4
Unusual Shapes of Bacteria
O Star-shaped
O Rectangle
O Hyphal /Filamentous bacteria- shaped like fungus
Bacteria Arrangement
O Pairs: Diplococci, diplobacilli
4 Two bacteria together, right next to each other
4
O Chains: Streptococci, streptobacilli
4 Cocci and bacilli in a chain
4 Ex. Strep throat, caused by a streptococci.
4
O Clusters: Staphylococci
4 Remain in clusters
4 Only for cocci
4
4 Coccus can be divided into any parts, has many different axis.
But rod shaped only have two axis.
4 Tetrads- packet of four
4 Sarchinae- packet of 8
4 More than 8 bacteria in a cluster- staphylo
Monomorphic vs. Pleomorphic
O Monomorphic
O Pleomorphic- multiplie morphologies throughout lifetime
4 Rhizobium(rod, curved, comma, shape like letter Y)
4 Corynebacterium
4 Bacteria change shaped based on environmental conditions.
Significance of Size
O Typical size of prokaryote vs. typical eukaryote
4 1-2 um vs. 10-100 um
4 1 um= 10e-6 m
O Largest bacterium known
4 pulopiscium sp. As big as paramecium
O Need microscope to observe single microscope but can see a colony
of bacteria with the naked eye.
O Advantage of small size.
Functional Anatomy of Prokaryotic Cells
A. Glycocalyx
O Slimy
O Outside cell wall
O Usually sticky
O Composition
O Lots of sugars
O Two types of Glycocalyx: Capsule vs. Slime Layer
O rigid structure very organized- capsule(outside) like time capsule
outside is hard and organized
O slimy structure, very loosely cover- slime layer( inside time capsule,
everything will be mushy)
O Functions of Glycocalyx:
4 Slime layer allows cells to attach( everything is stuck
togethere inside.yucky)
4 Biofilm formation: slime from one bacteria attaches, other
bacteria with/without slime layer attaches, all microbes than
attach causing problems
4 Capsules prevent phagocytosis
If bacterium or virus enters yours body, your body will
deploy white blood cells so they can eat the virus, called
phagocytosis.
Capture these microbes and eat them.
Made from polysaccharides(sticky sugars), when
bacteria start starving they use capsules or slime layer
as source of energy.
B. Cell wall
O 1. Function: prevents osmotic lysis, rigidity, shape.
O Not involved in transport of nutrients(wall against letting shit go
through)
O 2. Composition and Structure
4 Peptidoglycan (PG)- found in bacterial cell walls
4 PARENTS(PG) CELL WALL, THEY ARE STRICT
Peptidoglycan (PG)
O 1. Made of Disaccharide polymer (NAG and NAM)- 2 different types
of sugars.
4 Put in a row in a alternate fashion
4 From each NAM there is a hanging chain, and that is called
tetrapeptide side chains.
O 2. Tetrapeptide side chains.
O 3. Peptide cross bridges- blue color, connect hanging chains, put
rows 1 and 2 together. Form between 2 different rows, not on same
row.
O Hanging chains- NAM
O
O
4 Penicillin- destroys cell wall, by breaking down cross bridges.
Two Types of Cell Walls in Prokaryotes.
O Differentiation based on amount of PG and other components.
O Gram is the scientist who introduced a staining procedure for
bacteria, called gram staining.
O Some become purple
O Some become pink
O Color depends on amount of peptidoglycan present.
1) Gram-positive (Gm+) cell walls.
O A. Thick layers of PG, multiple (10-12 layers)
O B. Presence of Teichoic acids- give negative to charge to bacterial
cell wall to attract cations, like Na+ etc. ( alcohol, glycerol plus
phosphate)
4 May regulate movement of cations
4 Provide antigenic variation
O
2) Gram-negative (Gm-) cell walls
O a. Thin layer of PG+ outer membrane (2-3 layers)
O b. No teichoic acids
O c. Outer membrane- still part of cell wall.
4 Made up of lipopolysaccharides (LPS) layer,
4 LPS= O polysaccharide+ Lipid A
4 Lipid A- endotoxin, it is crucial, it is considered to be toxic.
Infections caused in humans are by gram negative bacteria
because of lipid A. When these bacteria are killed, Lipid A is
released. How our body responds to Lipid A it makes it toxic.
Body produces lots of inflammation.
O
How Penicillin affects bacterial cell wall
O Outer membrane cannot be destroyed
O Penicillin destroys cell wall by breaking down cross bridges
O Very effective on gram positive
O Cant kill gram negative because of outer membrane.
Atypical Cell Walls
O Three types- Gram positive, gram negative, acid fast
O A. Acid Fast cell wall
4 No outer membrane
4 Has peptidoglycan
4 Has waxy lipid (mycolic acid) which is not present in the other
grams, and they bind to peptidoglycan in acid-fast cell walls.
4 Easier to kill gram negative but still cant kill acid fast cell
walls.
4 More resistanat- Acid Fast>Gram negative>Gram positive
4 Mycobacterium Nocardia (Acid Fast)- causes tuberculosis,
leprosy
4
O B. Mycoplasmas
4 Group of bacteria, genus,
4 Lack cell walls, usually a problem
4 Filter sterilization- remove all virus etc. from liquid part.
4 Mycoplasmas, can twist and squeeze themselves through that
filter.
4 And now product is contaminated, and cannot use gram
staining because they have no cell wall.
4 Sterols in plasma membrane
O C. Archaea
4 Are not bacteria, but they are type Prokaryote cell
4 In their cells walls, they have pseudomurein (fake
peptidoglycan) (lack NAM and D-amino acids)
C. The Plasma Membrane or Cytoplasmic Membrane
O Membrane is viscous structure, like olive oil.
4 1. Phospholipid bilayer and Proteins
4
4 2. Fluid Mosaic Model
some proteins are fixed, some are moving around. They
are receptors.
4 3. Functions of plasma membrane
selective permeability allows passage of some
molecules.
Membrane decides if molecule decides to go in or not,
by size, shape and electrical charge.
Bacteria do not have mitochondria.
Maximum ATP production is by enzymes in plasma
membrane. Enzymes=mitochondria.
Some bacteria are photosynthetic, their chlorophyll are
located in plasma membrane.
Damage to the membrane by alcohols, quaternatry
ammonium(detergents), and polymyxin antibiotics
causes leakage of cell contents. Some bacteria attack
cell membrane.
4. Movement Across Plasma Membrane
O 1. Passive Transport- takes place along concentration gradient,
from high to low. Dont really use extra energy to bring molecules
inside.
4 a. Simple diffusion: CO2, O2,
4 b. Facilitaed diffusion: Glycerol
4 c. Osmosis: water
4
O 2. Active Transport- move from low to high, requires energy. Takes
place against gradient.
4 A. Active Transport
4 B. Grooup Translocation
Passive Transport:
O A. Simple diffusion: movement of a solute from an area of high
concentration to an area of low concentration. Through lipid bilayer.
O2 and Co2.
O B. Facilitated diffusion: solute combines with a transporte protein in
membrane, cannot just enter through lipid bilayer, need a protein
to go through membrane. For ex. Glycerol uses facilitated diffusion.
O
O C. Osmosis: movement of water across a selectively
O permeable membrane from an area of high water to an area of
lower water concentration.
4 Always moves where it tries to dilute the highly concentrated.
4
Osmolarity of the solution outside bacterial cells and its significance.
O Bacteria always have to face different conditions of solute
concentrations.
O Isotonic conditions-
O Hypotonic conditions-
O Hypertonic conditions
O .85% is the osmolarity inside cell
O osmotic lysis- under hypotonic conditions
O plasmolysis- under hypertonic conditions
Active Transport
O a. Using either PMF(proton motive force) or ATP to go against
concentration gradient.
O b. Group translocation- occurs only in bacteria, only belongs to
prokaryotic world.
O Bacteria cannot perform exocytosis and endocytosis
O C. Endocytosis- eukaryotic cells take substance inside
O D. Exocytosis-
Group Translocation
O Molecule goes through this and enters cell.
O Phosphate group attaches to molecule.
O Molecule that is transported is attached to phosphate, is chemically
modified.
O
D. Flagella
O 1. Movement or locomotion is function
O 2. Made up of 3 parts
4 a. filament: flagellin
4 b. attached to a protein hook
4
4 c. anchored to the wall and membrane through basal body
4 body recognizes flagella on bacteria, flagellin protein
recognized as foreign molecule by our cells.
4 Flagella protein are H antigens (e. coli 0157:H7)
O 3. Flagellar arrangement on a bacterial cell surface.
4 A. monotrichous
4 B. amphitrichous
4 C. lophotrichous- group of flagella present at one end.
4 D. peritrichous-flagella all over bacterial cell
O 4. Run and tumble
4 rotate flagella- run
4 unrotate flagella- tumble.
O 5. Chemotaxis- move toward nutrients, or away from chemical
4 Phototaxis- move where light is
O 6. Helicobacter pylori- responsible for causing ulcers
E. Fimbriae and Pili
O 1. Who has them?
4 When flagella are absent, some of them will
4 Gram negative bacteria
O 2. Fimbriae
4 bacteria use this to attach intestinal tract. Pathogenic(fucker
wont leave)
O 3. Pilli
4 facilitate transfer of DNA from one cell to one another
(transfer pills)
4 gliding motility
4 twitching motility
F. Cytoplasm
O No cytoskeleton
O No membrane bound organelles
O Do no exist in bacteria
G. Nucleoid
O 1. Bacterial chromosome characteristics
4 no nuclear membrane in prokaryotes
4 nucleus freely suspended in cytoplasm
4 no histones
4 circular DNA
4 haploid, only one copy of gene
O 2. Size and packaging: supercoiling
H. Plasmids
O 1. What are they?
4 Only few bacteria will have plasmid DNA
4 Not associated with nucleoid chromosomal DNA
4 Completely independent DNA molecules
4 Do not depend on chromosomal DNA
4 Plasmid outside nucleoid
4 Carry genes for antibiotic resistant genes
4
O 2. Advantages to bacteria
O 3. Transfer
I. Ribosomes
O 1. Function
O 2. Compositon/structure
4 small subunit (30s) + large subunit (50s)= complete 70s
ribosome, humans have 80s
4
O 3. Antibiotic effect on ribosomes
J. inclusions/storage granules
O 1. Metachromatic/volutin/polyphosphate granules
4 diagnostic use: Corynebacterium diphtheriae- bacteria
causing diphtheria
4 used in diagnostic purpose
O 2. Polysaccharide Granules: storage site when they are present in
abundance and use them when they are starving.
O 3. Lipid Inclusions- most common found granules
4 PHB: poly-B-hydroxybutyric acid
4 Granules are for energy
4 Humans take these lipids from bacteria and synthesize
plastic4
O 4. Sulfur Granules
4 only bacteria that use sulfur use these granules
4
K. Endospores
O 1. Who produces?
4 Made by gram positive bacteria
4 Needs some 200 plus genes to make endospores.
4 Bacterial endospores are necessary for survival.
O 2. NOT reproductive! Resting structures
O 3. When are they produced?
O 4. How long can they survive?
4 Can survive form a week to millions of years
O Bacterial cell always dies when it releases endospores
O
O 5. Structure of a free endospore (DPA)
4 spore coat- dipicolinic acid
O 6. Germination
O 7. Importance of endospores medically and in food processing.
4 When you are performing surgery, make sure everything is
aseptic.
4 If endospores survive when canning procedure occurs, they
can germinate and give rise to bacteria.
O 8. Destroying endospores
4 a. John Tyndall and tyndallization
boiling and incubating, to kill endospores.
4 b. autoclave and pressure cooker
cook something under pressure to create sterilization

EXAM 1 10/13/2010 8:19:00 PM
Ch. 5 Microbial Metabolism Enzymes

Metabolism: sum of all chemical reactions within an organism.
Metabolism
O 1. Anabolism: make
O 2. Catabolism: break down
Metabolic Reactions
O A metabolic pathway is a sequence of enzymatically catalyzed
chemical reactions in a cell which are determined by enzymes
4 1. Exergonic- catabolic
4 2. Endergonic- anabolic
Enzymes:
O Biological catalysts
O Protein in nature( or RNA composition)
O Reaction runs 8-10 billion times faster
O Enzymes help reactions go faster
Energy Requirements of a Chemical Reaction
O Enzymes function by lowering Activation energy
O Allowing molecules with lower energy to interact
O Activation energy is the amount of energy needed for chemical
reaction to take place.
O
Enzyme Structure
Holoenzyme-complete structure of enzyme

O 1. Apoenzyme- protein part, major part, inactive
O 2. Cofactor- non protein part, activator
4 1. Coenzymes: NAD+, FAD, CoA------organic
4 2. Metal Ions------inorganic
Fe+2, Mg+2, Mn+2
4 Why do we eat vitamins from vegetables?
Many of these coenzymes are made from vitamins, if
you have vitamin deficiency, then cofactors not function
properly, enzyme doesnt work properly, metabolism
doesnt work.
Mechanism of Enzymatic Action
O Active sit of enzyme
O Enzyme- sustrate complex
O Specificity of active site
O
Relationship between Enzyme Structure And Function
O Primary,secondary, tertiary, quaternary structure of an enzyme
O Change of enzyme shape
O Change of active site-denaturation
O Active site is a 3 dimensional structure, not possible to form in
primary structure and secondary because it is a chain of amino
acids in primary structure.
O Denatured- loss of shape of active site
O As tertiary structure unfolds, enzymatic active site is not in proper
shape.
O Tertiary structure- hydrogen bonds are holding globular form.
Factors affecting enzymatic activity
O Temperature
O pH
O Substrate concentration
O Inhibitors
Effect of temperature on Enzyme Activity



Inhibitors
O Competitive Inhibition
O Non competitive inhibition
Enzyme Inhibitors: Competitive Inhibition
O Competitive inhibitor blocks active site, so substrate cannot bind.
O Target of sulfur cells do no exist in human enzymes. Only targets
bacteria and kills them.
O
Enzyme Inhibitors: Non Competitive Inhibition
O Allosteric
4 Inhibitor binds to location on enzyme, binds to allosteric site,
changing the shape of the active site.
O Metal Chelator
4 Many enzymes require cofactor. Chelator bind to metal ions
and take them away from enzymes, inhibiting the function of
enzymes.
4 Mercury is toxic because it can inhibit the activity of different
enzymes
O
EXAM 1 10/13/2010 8:19:00 PM
Oxidation-Reduction Reactions
1. Oxidation-lose e
2. Reduction- gain e
3. Redox/Coupled reactions- oxidation and reduction
4. Dehydrogenation- loss of H and proton.
Reduced compounds as source of energy

Metabolism: Source of Energy
O Phototrophs(need sunlight) vs. Chemotrophs (use chemicals as
energy)
4 Sunlight
4 Carbohydrates
4 Lipids
4 Proteins
4 Inorganic compounds.
Metabolism: Mechanisms
O Three Mechanisms to extract electrons and Energy from the
substrate:
4 Aerobic Respiration
4 Anaerobic Respiration
4 Fermentation- not the same as anaerobic respiration
I. Glucose Metabolism by Aerobic Respiration
to study glucose metabolism
O Uses oxygen to extract energy from the bonds contained in glucose
molecules
O
O If prokaryotes all energy from a glucose molecule is used 38 ATP
O If eukaryotes-> 36ATP
O 3 Stages
4 Glycolysis/EMP- common to respiration and fermentation
4 Krebs Cycle/TCA
4 Electron transport chain
4

Aerobic Respiration to study glucose metabolism
O Uses oxygen to extract energy from the bonds contained in glucose
molecules
O If all energy from a glucose molecule is used 38 ATP
O 3 Stages
4 Glycolysis/EMP
4 Krebs Cycle
4 Electron transport chain
O
1. Glycolysis "splitting glucose
O Break down glucose into pyruvates (pyruvic acids - 2 molecules)
O Embden Meyerhof Parnas Pathway - EMP - named after them
O Does not require oxygen, but can occur in the presence or the
absence of oxygen
O This is used to begin the breakdown of glucose - it is a stepwise
breakdown, but is called "incomplete
O Incomplete - because there is further oxidation required in order to
release all the energy in the molecule
O Produces:
4 2 Pyruvic Acid
4 2 ATP - by substrate level phosphorylation
4 2 NADH (the reducing agent to be used later)
O Substrate level phosphorylation
NOTE: Basic principle of metabolism - whenever a substance is oxidized, as
a result of the lost of electrons, the chemical bonds in glucose become
unstable, they then break down and the energy in the h=chemical bonds is
released (oxidation of glucose = degradation of glucose)
O
The Role of ATP
O Currency of energy - energy is held within the phosphate bonds
O Structure of ATP
4 Adenine
4 Ribose
4 Phosphate groups (inorganic)
4
Synthesis of ATP
O Substrate level - energy from an exergonic reaction
4 ex. glycolysis
O Oxidative level - energy from proton motive force
4 ex. Electron transport chain
O Photophosphorylation - when sunlight is involved
4 ex. Photosynthesis
O
Electron Carriers
O NAD+, NADP+, FAD
4 In their oxidized forms
O NADH, NADPH, FADH2
4 In their reduced form, they carry electrons to the ETC
O
Alternate Pathways
Why? Based on the enzymes that the bacteria contain
O Entner-Doudoroff Pathway (ED)
4 Converts glucose to 2 pyruvic acid molecules producing 1 ATP
The ATP yield is less
Bacteria using this beginning step as the initial step for
glucose breakdown will grow a little slowly -- there is a
relation between ATP release and bacterial growth - will
take long to appear as colonies on the Petri dish
O Why? Based on the enzymes that the bacteria contain
O Ex. !seudomonas
Pentose Phosphate Pathway (PPP)
O Break down glucose, pentose sugars
O Yield is 1 ATP
O Why do bacteria that have enzymes to do EMP do this?
4 Amphibolic pathway - it can contribute to both catabolism
and anabolism
Ribose-5-phosphate Nucleic acids (anabolic)
Erythrose phosphate (catabolic)
2. Krebs Cycle/Tricarboxylic Acid Cycle (TCA)
O Further oxidizing the pyruvate (pyruvic acid)
4 A. Transition step/Bridge Step - Carboxylation
2 Pyruvate 2 Acetyl CoA + 2NADH + 2CO2
4 B. Krebs Cycle/TCA
4
4 Produces:
6 CO2 (4 CO2 + 2 CO2 from carboxylation)
2 ATP (converted from 2 GTP) substrate level
phosphorylation
6 NADH
2 FADH2
4 Complete breakdown of glucose occurs here
If glucose is completely broken down, why does aerobic
respiration need to continue to electron transport chain?
To generate ATP and to recycle NAD+ and FAD

3. Electron Transport Chain
Molecules donate their electrons to the ETC
O NADH, NADPH, FADH2 NAD+, NADP+, FAD
O 1. Located in prokaryotic plasma membrane (same also takes place
in eukaryotic mitochondria - intermembrane space)
4 Prokaryotes dont have mitochodria occurs in plasma
membrane
*RECALL: Second function of plasma membrane participate in the
production of ATP in the ETC
O 2. 3 Classes of electron carriers
4 Ubiquinone ex. Coenzyme Q
4 Flavoproteins ex flavin mononucleotide
4 Cytochromes ex. b, c1 a1, a3 etc.
O 3. Diverse nature of ETC
4 Even though you see these protein complexes in a certain
sequence here, but they can differ depending on the organism
that you are observing
4 BUT they all serve the same purpose
O 4. In EUKARYOTES Oxygen is ALWAYS the final electron acceptor
O In BACTERIA Oxygen is only the final electron acceptor in
AEROBIC conditions
O
Peter Mitchell
O Introduced the concept of chemiosmosis
O Chemiosmotic model explains link between electron transport and
ATP generation
Chemiosmotic model of ATP generation

O Protons are pumped outside of the cell (by proton pumps) with
successive electron transfers, creating an electrochemical gradient
4 gradient like this stores a lot of energy
4 Proton electrochemical gradient =PMF (Proton motive force)
4
O Require the enzyme ATP synthase or ATP ase
O Protons will flow down their concentration gradient with the help of
protein channels called ATPsynthase or ATP ase
O This exergonic process fuels the phosphorylation of ADP to
synthesize ATP
O When ATP is synthesized by using the energy of the ETC oxidative
phosphorylation
O
O Total ATP generation = 38 ATP per glucose
How many if glucose is turned into CO2 and water? 38
O How many if glucose is turned into CO2? 4 (NO WATER!)
O Only up to Krebs Cycle
Eukaryotic cells molecules must cross the mitochondrial membrane , which
loses energy in the process, this doesnt need to happen in prokaryotic cells
O
Anaerobic Respiration
O 1. Glycolysis
O 2. Krebs Cycle/TCA
O 3. Electron transport Chain : FINAL ELECTRON ACCEPTOR IS NOT
OXYGEN
4 BUT RATHER IT IS AN INORGANIC COMPOUND
ex. Nitrate, sulfate, carbonate
O ATP production is less than 38
4 Range is 2-37
4 Why?
Because the final electron acceptor is different and
there is a difference in the red-ox potential
O
O Bacterial Respiration
4 Sequence of reactions that involved Glycolysis, Krebs and
Electron Transport Chain
4 This definition is NOT correct, there is another type of
respiration that can occur!!!
O
O
Bacterial Anaerobic Respiration is not the same as:
O Fermentation - Two stages
O 1. Glycolysis
O 2. Pyruvic Acid Metabolism
O
NOTE: DOES NOT INVOLVE KREBS CYCLE OR ELECTRON TRANSPORT CHAIN
O
O End products?
4 Not fixed
4 Different bacteria produce different end products
4 Completely dependant on the organism
4 Lactic Acid $treptococcus, Lactobacillus, Bacillus
Yogurt products
4 Ethanol and CO2 $acchromyces
Though ethanol is not the only alcohol produced by
fermentation
Many different alcoholic compounds can be produced by
fermentation
4 Propionic acid, acetic acid, CO2, H2 !ropionibacterium
Gives swiss cheese its unique taste, smell and size of
the holes
NOTE: Products produced by second half of fermentation are not useful for
bacteria!
O They only need what is produced by the first step, ATP is only
produced in the first step, Glycolysis.
O In fact, they can harm the bacteria, if lactic acid builds up, they can
die while sitting in it
O
So why is pyruvic acid metabolism necessary for bacteria?
O In AEROBIC Respiration, the NADH that was produced in glycolysis
would be taken to the ETC, we need to turn it back into NAD+
O This step is achieved by the fermentation of pyruvic acid
O
Fermentation is not a metabolically efficient process, slower growth
compared to aerobic respiration and anerobic respiration
O You can judge the growth of bacteria by the turgidity of the tube
they are growing in
O In a petri dish, there will be more colonies in the aerobic respiration
plate
O If you continue, the colony size will be larger in Aerobic plate
O
When Humans are exercising rigorously, and the muscles do not have
enough oxygen, it leads to fermentation lactic acid achy, sore muscles
O ACTUALLY the protons that come from Lactic acid
O
O Only glycolysis is common between aerobic respiration and
fermentation
O
Metabolism using other sources of energy
Lipids
O Become glycerol or fatty acids (via lipase)
O Then enter the cell and then are modified
O Glycerol to Glyceraldehyde-3-phosphate Glyc Pyruvic acid
O Fatty acids become acetyl CoA via beta-oxidation
O
Proteins
O Proteins become amino acids via extracellular proteases
O Amino acids become organic acids vai deamination,
decarboxylation, dehydrogenation, desulfurylation
O Then they enter the Krebs Cycle
O

When bacteria respire using inorganic acids, they do not use Glycolysis or
the Krebs Cycle they use the Electron transport chain

Bacterial Respiration does not always consist of Glycolysis, Krebs Cycle, and
ETC.

Chemolithotrophs
O No other living cell in the world that can use inorganic compounds
for energy
O They can use aerobic respiration as well as anerobic respiration,
processes are a little different though
O They grow very slowly, because they do not obtain a lot of energy
from the electron transport chain
O NH4+ ----- e- -----> NAD+ NADH ETC
O Fermentation is NOT respiration because it does not use the ETC
4 Types
O Hydrogen bacteria
O Sulfur bacteria
4 Live in sulfur springs
4 Live in sewage - polluted waters
4 Ex. Beggiatoa, Thiobacillus
4 Bioleaching leaching the bacteria away
O Iron bacteria
O Nitrifying bacteria
4 Ammonia oxidizers convert ammonia to nitrite
(Nitrosomonas)
4 Nitrite oxidizers convert nitrite to nitrate (ex. Nitrobacter)

III. Glucose Metabolism by Fermentation
O 1. Glycolysis
4 same as before.
4 ATP produced by substrate level phosphorylation only in
glycolysis
O 2. Pyruvic Acid Metabolism
4 begins with pyruvic acid
4 pyruvic acid will be converted to different compounds
4 some bacteria will convert pyruvic acid to ethanol, lactic acid,
propionic acid etc.
4 Know the examples of different products
4 As bacteria are converting different end products, are they
useful for these?
Absolutely no value for these end products
4 Second Half, no ATP produced
O 3. No Krebs Cycle or Electron Transport Chain
What is the need for pyruvic acid metabolism for bacteria?
O Regeneration of NAD+
O NADH need to be reoxidized to NAD+
O When respiration is happening, bacteria usually regenerate ATP
with ETC, but fermentation does not have ETC, so pyruvic acid
metabolism is used for NAD+ regeneration
Anaerobic- involves ETC
Fermentation- no TCA or ETC
O 3. ATP produced only during Glycolysis by substrate level
phosphorylation
O 4. Regeneration of NAD+
O 5. Final Electron acceptor: organic molecules such as pyruvate or its
derivative.
O Total ATP= 2 ATP
Fermentation generates yields least amount of ATP

Why do some bacteria choose Fermentation over Anaerobic Respiration?
O Final electron acceptor such as nitrate is not present, they cannot
perform anaerobic respiration, so they opt for fermentation
O Some bacteria also do not have ETC. which is the most important
part.
O
Lactic acid buildup in Eukaryotes.
O Pre-lect quiz: All the bacteria in the prokaryotic world have ability
to either respire or ferment but no bacteria will have the ability to
perform both these metabolic processes.
4 False
EXAM 1 10/13/2010 8:19:00 PM
Ch. 6 Microbial Growth
Principles of Bacterial Growth
O 1. Definition: Bacterial growth is defined as an increase in cell
number leading to an increase in size of a population.
4 It is not growing in size in bacterial growth
4 It is increase in the number of bacteria.
4 Bacteria will start using nutrients from petri dish.
4 Multiply into millions
O 2. Process: Bacteria generally multiply by the process of binary
fission
4 Bacterial Reproduction- binary fission
Binary Fission


Generation Time
O 1. The time it takes for a bacterial cell to double in number is
Generation time.
O Doubling time
O 2. The environmental and nutritional factors affect the generation
time.
4 Ex. E. coli growing in test tube, incubate at 37 degrees
Celsius with nutrients.
4 Ex. In Olentangy river, E. coli will taken longer to grow.
Environmental Factors
O 1. Temperature
4 given bacterium always has range of temp, where it will grow.
Certain bacteria grow well in rt., 37 degrees Celsius,
O 2. Oxygen
O 3. pH
O 4. Water avaiilablity
Temperature
O 1. Temperature range: ex. Bacterium requires 20-50 degrees
Celsius, within this range, there is temp minimum, is lowest, temp
maximum highest. If you cross either of these limits, bacteria will
not grow.
4 Temp. minimum
4 Temp. optimum- most ideal growth for bacteria, gives
maximum amount of growth. Usually 10 degrees Celsius less
than temp maximum.
4 Temp. maximum
O 2. It depends on the availability of enzymes, for ex. Some enzymes
work at high or low temp.
Typical growth Rates and Temperature

O Microbiology- refer to temperature in degrees Celsius
Temperature based groups of Prokaryotes
O Psychrophiles (-10, 12, 18)( capable of growth in freezing
condition)
4 Psychorotrops and Psychrophiles can grow in 4 degrees
Celsius, but psychrophiles grow best in refrigerator)
4 Psychrophiles are not responsible for food spoilage, they are
not found in your food, because they are usually found in
extremely cold, such as glaciers, arctic region.
O Psychrotrophs (0, 23, 30)
4 Psychorotrops and Psychrophiles can grow in 4 degrees
4 Psychorotrophs are responsible for food spoilage in your
fridge
O Mesophiles (10, 37, 50)
45 degrees Celsius- enzymes dentaure
O Thermophiles (40-72)
O Hyperthermophiles
Know the temp numbers, for each group, maximum, minimum
optimum

Temperature based groups of prokaryotes
O 3. Thermophiles
4 optimal: above 45
O 4. Extreme thermophiles
4 optimal: 70 or higher
Prokaryotic groups based on oxygen requirement
O 1. Obligate aerobes
4 must have oxygen to grow
O 2. Obligate anaerobes
4 they cannot stand oxygen, and they dont use them, they will
die with oxygen
O 3. Facultative Anaerobes
4 can grow in O2, or can grow without O2. Ex. Given a choice,
e. coli will always grow the best in oxygen.
O 4. Microaerophiles
4 do require O2 to grow, micro suffix, means require only small
amounts of O2, if too much O2, they will not grow as well.
O 5. Aerotolerant anaerobles
4 when exposed to O2, they dont die like obligate anaerobes,
they can tolerate O2.
Toxic Derivatives of Oxygen

O toxic byproducts can destroy bacterial cell
O need enzymes to get rid of toxic by products
O enzyme- superoxide dismutase acts and destroys H202.
O SOD and catalase take care of toxic derivatives of oxygen
O Peroxidase also gets rid of toxic derviavatives of oxygen
O Two enzymes that are needed to tolerate oxygen. Obligate aerobe
O Obligate anaerobe do not have these enzymes.
O Facultative will have both enzymes.
O 4 and 5 both have SOD but they dont have much of catalase.
Anaerobic Jar, and Anaerobic Chamber

pH
O 1. Neutrophiles:
4 optimal pH 5-8
O 2. Acidophiles
4 Thiobacillus in acid mine drainage
4 Grow in acidic conditions
4 Produces sulfuric acid

O 3. Alkalophiles
4 some Bacillus species
4 prefer alkaline pH
why does pH change when bacteria grow, because the bacteria produce acid,
so people add buffers so bacteria are growing in that pH range.

Water Availability
O - Osmotic pressure
O 1. Hypertonic (plasmolysis- bacteria will not grow)
4 Food preservation
4 Bacteria will not grow because there is not enough water
4 Have to have isotonic conditions to grow happy
O 2. Osmotolerant (Facultative Halophiles)
4 able to grow in high salt conc.
4 Tolerate the present
O 3. Halophiles
4 must have large quantities of salt in order to grow.
4 Salt Lake, Utah

Format Of Exam
O 40 multiple choice questions
O 2 points each
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