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Ilana Kovach
Cell Structure
& Function
Chapter 3
Prokaryote EukaryoteDNA: In Cytoplasm
of cell
Organelles: Have
Ribosomes
Size & Organizations:
Single celled
Domains/ Kingdoms:
Archaea & Bacteria
DNA: In nucleus linear
chromosomes
Organelles: Membrane
Organelles
Size & Organizations:
Bigger more Organized
Domains & Kingdoms:
Eukarya
VirusesCannot Reproduce
Outside Cells
No Metabolism
outside Host cell
RNA or DNA never
Both
Debate living or non
living
Arrangement of Prokaryotic Cells
Cocci multiple Planes Bacilli single Planes
Coccus Diplococci Staphylococci
Streptococci Sarcina
Tetrad
Coccobacillus Bacilli
Diplobacilli Palisades
Streptobacilli
3 main Prokaryotic Cell shapes
Cocci
Spirals 1. Spirochetes Flexible
2. Spirillum Inflexible
Rods “Bacillis” Coccobacillus “Short Rod”
Vibrio “Curved Spiral”
Pleomorphic“Does not Have a shape”
External Structures of Bacterial Cells
Glycocalyx Made from Polysaccharides, polypeptides or Both*Function: protect cells from drying
Capsule firmly Attached
*Functions: Protection & Virulence Factor
Slime LayerLoosely attached (Water soluble)
*Functions: Protection & Aattachment Biofilms
Flagella
Structure
*Filament “Flagellin”rotate 360º
*Hook
*Basal Body
Arrangements*Amphitrichous “Axial Filament” Cork screw shapeVirulence Factor
*Peritrichous“Flagella everywhere”
*Monotrichous “Polar”
*Lophotrichous “Tuft”
FunctionRotate 360º “Boat propellers”
(H+) or (Na+) power “Counterclockwise or clockwise”
Runs (+)Tumbles (-)
Fimbriae & Pili
FimbriaeStiff vessels “Velcro” Virulence Factor helps attach
*think Fringe
Cranberry Juice E coli fimbriae can’t attach
Pili ˜Typically one-Few
*Regular ‘Pseudo Movement”*Conjugation= Process used to transfer from one DNA to another (Resistance to Antibiotic)
Bacterial Cell Walls
PeptidoglycanNAM (N-acetylmuramic acid)NAG (N- acetyl glucosamine)*attached by Tetrapeptide Cross Bridge
Gram Negative Thin Layer of Peptidoglycan + outer membrane
Periplasmic Space: Between inner & outer Membrane contains
peptidoglycan & periplasm
Outer Membrane (Envelope)
-Lipopolysaccharides/Endotoxin (Lipid + Sugar)
Lipid A
released from dead/damaged cells
may trigger fever, vasodilation, inflammation, shock,
(DIC)
-Porins
-other Proteins
Gram Positive Thick Layer of Peptidoglycan
Teichoic acids & lipoteichoic acids present
Acid Fast Cells Mycolic Acid “wax/hydrophobic”
Resistance
Special Staining Procedure
Gram Positive Gram Negative
Teichoic Acid
Lipoteichoic Acid
Peptidoglycan Layer (cell wall)
Cytoplasmic Membrane
Integral Protein
Peptidoglycan Layer of (cell wall)
Cytoplasmic Membrane
Outer Membrane of Cell
Porin Periplasmic Space
Lipopolysaccharide Layer(LPS) Containing Lipid A
Bacteria Without CELL
WALLs
Mycoplasma Sterols in Cell Membrane
Chlamydia Cell membrane + outer membrane (no
Peptidoglycan)
Bacterial Cytoplasmic Membrane
2 Main
Components:
1. Hydrocarbon Tails
“Hydrophobic”
2. Phosphate Heads
“Hydrophilic”
3 Main Functions:
1. Selectively Permeable
2. Energy Production (PMF)
3. Photosynthesis
(Photosynthetic Prokaryotes
Passive
Transport*Diffusion
*Facilitated Diffusion
*Osmosis
Active
Transport *Requires the cell to expend
ATP
*Active Transport
*Group Translocation
Cytoplasm in Bacteria
Cytosol Inclusions“Pockets of Chemicals”
Ribosomes“Protein Sythesis”
Prokaryotes 70s (Subunits made of 50s & 30s)
*S= Svedberg unit
Eukaryotes 80s
Cytoskeleton “Framework”
Membrane Bound Organelles in Eukaryotes
Nucleus, Endoplasmic
Reticulum
Golgi Bodies
Lysosomes
Peroxisomes
vacuoles
Vesicles
Mitochondria
Chloroplasts
Mitochondria &
Chloroplast in common
with Prokaryotes?
Both have double membranes and their own DNA Both
reproduce by Binary Fusion (which is also how bacteria
reproduces) It is theorized that those are the two
organelles that took part in the
endosymbiotic theory.
This is because they both have their own DNA, divide
separately from the cell, and look very similar to
bacteria's. According to the theory, they were once free
living organisms that started a mutualism with an early
eukaryotic cell, and they've been inseparable ever since
Arrangement of Prokaryotic Cells
Cocci multiple Planes Bacilli single Planes
Coccus Diplococci Staphylococci
Streptococci Sarcina
Tetrad
Coccobacillus Bacilli
Diplobacilli Palisades
Streptobacilli
Endospore FormationStep 1: DNA replicated
Step 2: DNA aligns Cells long Axis
Step 3: Cytoplasm Membrane Invaginates to form forespore
Step 4: Cytoplasmic Membrane Grows and Engulfs Forespore within a second membrane. Vegetative cell’s
DNA disintegrates
Step 5: A cortex of calcium & dipliconic acid is deposited between the membranes
Step 6: Spore Coat Forms around the endospore
Step 7: Maturation of endospore; completion of spore coat & increase in resistance to heat and chemicals by
unknown processes
Step 8: Endospore Released from original cell
Endospores (Bacillus & Clostridium)
Outer Spore Coat (Exosporium)
Outer Spore Coat
(Exosporium)
Spore Coat
Outer
Membrane
Cortex
Spore Core
Inner
Membrane
Prokaryotes
Reproduction
1) Binary Fission
Step 1: Cell Replicates its DNA
Step 2: Cytoplasmic Membrane Elongates Seperating DNA molecules
Step 3: Cross wall forms Membrane Invaginates
Step 4: Cross Wall forms completely
Step 5: Daughter Cells
2) Snapping Division Palisades (V-shapes)
Rules for Naming Bacteria
Genus + Species
Italicize or underline
1st name Capital Letter
Microbial
Metabolism
Chapter 5
Cellular Respiration
Pathway ATP produced
ATP Used
NADH produced
FADH2
Glycolysis 4 2 2 0Synthesis of Acetyl-CoA & Krebs Cycle
2 0 8 2
Electron Transport Chain
34 0 0 0
Total 40 2Net Total 38
Alternative Pathways
ATP produced
Electron Carriers
Products
Pentose Phosphate
1 ATP 2 NADPH 5 Carbon Precursor metabolites
Entner-Doudoroff
1 ATP 2 NADPH Other precursor metabolites
Alternate pathway’s
Kreb Cycle
Cellular Respiration
Glucose
C02
Pyruvic Acid
Acetyl CoA
Glycolysis
22
2
22
NADHFADH2
C02
Electron Transport
Chain
4
62
2
Ubiquinone's Cytochromes
Metal containing Proteins Flavinones
e-
Proton GradientATP
synthase 34
Final Electron Acceptor
Fumarate
Nitrate
Sulfate
Oxygen
Fermentation
NADH
NAD+
Ethanol
C02
+
Lactic Acid
Acetic Acid
Decarboxylation
Goes TO
oxidized
Main PURPOSE
Anaerobic
Aerobic
H+
Energy From e-Transfer Pumps & H+ across Membrane
Protons re-enter through channel
5. DHAP rearrange to form G3P
Energy Investment Stage
C C C C C CGlucose
C C C C C CGlucose 6- Phosphate
P
CP PC C C C CFructose 1, 6- Bisphosphate
ADP
ADP
Lysis Stage
Fructose 1, 6- Bisphosphate
P PC C C C C C
CCC
Dihydroxyacetone Phosphate (DHAP)
P
1. Glucose (Substrate- Level Phosphorylation)
2. Glucose Molecules Rearranged for form fructose 6 phosphate
3. Fructose 6 phosphate Phosphorylated to form Fructose 1, 6-Biphosphate
4 . Fructose 1, 6-Biphosphate splits to form (DHAP & G3P)
Glyceraldehyde 3 Phosphate (G3P)
C C CP C C CP
Energy Conserving Stage Glyceraldehyde 3 Phosphate (G3P)
C CCP P C CC
P2NAD+2NADH2
C CCCCCP P P P
STEP 6: 2 Inorganic phosphates are added to (G3P) & 2 NAD+ are reduced to NADH
Two 1, Phosphoglyceric Acid
ADP
22
Two 3 Phosphoglyceric Acid
CCC P C C C P
STEP 7: 2 ATP are phosphorylated by substrate level to form 2 ATP
H202
C C C C C C
PP
Two Phosphoenolpyruvic Acid (PEP)
STEP 8 & 9: Remaining Phosphates moved to middle carbon & water removed from each substrate
ADP2
2
C C C C C C
STEP 10: 2 ATP are phosphorylated by substrate level to form 2 ATP
Two Pyruvic Acid
Formation of Acetyl-CoAC
C
C
Pyruvic Acid
OOH
C02
C
C H
Acetate
NADHNAD+
CoA
Acetyl-CoA
Decarboxylation
C
C
CoA
Fermentation
C
C
C
C02
Pyruvic Acid
Lactic Acid
NAD+
NADH
Acetaldehyde
NADH NAD+
Ethanol
Krebs Cycle
Acetyl-CoA
CoA
C
C
C
C
C
CC
C
C
OOH
OOH
OOH
Citric Acid
1 2
CoA
C
C
C
C OOH
OOH
OOH
C
IsoCitric Acid
NADH
NAD+
C02+3
C
C
C
C
C
OOH
OOHα-ketoglutaric Acid
NADH C02+C
C
C
C
CoA
Succinyl-CoA
OOH
ADP
GDP
Acetyl-CoA
CoA
CoA
FAD+
4
5
C
C
C
C OOH
OOH
Succinic Acid
6
C
C
C
CHOO
OOH
Fumaric Acid
FADH2
7
H20
8C
C
C
C
Malic Acid
OOH
OOH
C
C
C
C
OOH
OOHOxaloacetic Acid
NADH
Start Here
H20
Electron Transport Chain
Flavoproteins Ubiquinone
Cytochromes (b) Cytochromes (c)
NAD+
NADHFADH2
FAD+
H+
++
H+H+
e- e-
e-e-
e-e-
H+
H+
H+H+
H+H+
H+H++
+
+
+ +
+
+
+
+
-
-
-
-- -
-
-
-
-
𝟏
𝟐o
e- e-
ATP synthase
ADPP+
H+
H+
H+ H+
1
2
4
3
Microbial
Growth &
Nutrition
Chapter 6
Light (Photo-) Chemical Compounds (Chemo-)
Carbon Dioxide (Auto-)
Photoautotrophs
Plants Algae & Cyanobacteria use H20 to reduce CO2, Producing O2 as a by-product
Green sulfur Bacteria and Purple sulfur bacteria do not use H20 nor O2
Chemoautotrophs
Hydrogen, Sulfur and Nitrifying bacteria, some archaea
Organic Compounds (Hetero-)
Photoheterotrophs
Green Nonsulfur Bacteria and purple nonsulfure Bacteria, Some Archaea
Chemoheterotrophs
Aerobic Respiration: Most animals, fungi and protozoa and many bacteria
Anaerobic Respiration Some animals, Protozoa, Bacteria, and archaea
Fermentation; Some bacteria, Yeast and Archaea
Energy SourceC
arb
on
Sou
rce
Lag Stage
Log Stage Stationary Stage
Death Stage
Microbial Growth Curve
Toxic forms of Oxygen Neutralizing Toxic forms of
Oxygen
Singlet Oxygen Formed during photosynthesis as electrons are boosted to higher state
Photosynthesis organisms Contain Carotenoids
Superoxide
Anion
Produced by incomplete reduction of oxygen during respiration
Superoxide Dismutase (Enzyme)
Peroxide
Anion
Formed when superoxide anions are neutralized Peroxidase and/or Catalase (Enzymes)
Hydroxyl
Radical
Formed from ionizing radiation& incomplete reduction of hydrogen peroxide
Peroxidase and/or Catalase Antioxidants
Direct MethodsViable Plate count: Lot of Bacteria; Dilute low enough to count serial Dilutions ~ (30-300); Live Only
Membrane Filtration: Bacteria cannot go through filter; therefore filter retain cells ~Live Only
Microscopic Count: special slide & coulter counter; Does not distinguish Dead or alive
Indirect MethodsMetabolic Activity: nutrient consumption & Waste Production (Color change); Live only
Dry Weight: Desiccated (dried) waste weighed; does not distinguish dead or alive
Turbidity: More turbid; Use spectrophotometer to measure absorbance of more bacteria; Does
not distinguish alive or dead
Obligate (Strict) Aerobes
Requires O2
Undergo Aerobic Respiration Oxygen final Electron Acceptor
Microaerophil Require lower O2 levels (2-10%)
Undergo Aerobic Respiration Limited ability to detoxify hydrogen peroxide and superoxide Radicals
Facultative (Facultative Anaerobes)
Can Live either Presence OR absence of O2 (Prefer Oxygen)
Aerobic Respiration Anaerobic Respiration Fermentation
Aerotolerant Can live in either Presence or Absence of Oxygen (Doesn’t Prefer Oxygen)
Never use Aerobic metabolism Have enzymes that neutralize toxic oxygen
Obligate (Strict) Anaerobes
O2 is Deadly
Use anaerobic Metabolism Lack Enzymes to neutralize toxic oxygen
Oxygen Requirements
PsychrophilesCold ~ (-5- 20º); optimal: 10º
MesophilesModerate ~ (15º-45º); optimal: 37º
ThermophilesHot ~ (Low 40’s – 80’s)
Hyperthermophiles HOT!! (60’s and Above)
Osmotic Pressure (Isotonic, Hypertonic, Hypotonic)
Hypertonic Solution: No Cell Wall Crenate
Cell Wall Plasmolyzed
Hypotonic Solution: No Cell Wall Bursts or Lyses
Cell Wall Rigid Enough to Hold
*Salt Meat, Sugar Jelly, Pickles never Spoil
Required for Metabolism
Two physical effects of water: Hydrostatic & Osmotic Pressure
Hydrostatic Pressure Barophils (Extremophile) - Organisms that live under Extreme pressure
Membranes & Enzymes depend on Pressure to maintain their 3-D
functional Shape
Classification Factors
Other Classification Factors
Salt Concentration Halophiles-able to live in High salt concentrations; Dead Sea
Obligate Halophiles – Require Salt up to 30% concentrations
Halotolerant- Able to tolerate high salt concentration; Sweat on skin
pH Neutrophils (6.5-7.5) Most Microbes
Acidophils (Acidic habitats)
Alkalinophils (Alkaline Habitats up to 11.5)
Capnophils – Thrive in presence in areas of high concentration of CO2
Microbial
Genetics
Chapter 7
DNA Replication DNA RNA1. Phosphate2. Deoxyribose Sugar3. Nitrogen Base
1. Phosphate2. Ribose Sugar3. Nitrogen Base
4 Bases: (A) adenine (T) thymine (G) guanine (C) Cytosine 4 Bases: (A) adenine (U) Uracil (G) guanine (C) Cytosine
Hydrogen Bond Adenine & Thymine (2 bonds) Guanine & Cytosine (3 bonds)
Single Stranded!!!
Transcription Translation
Plasmids
Fertility Plasmids:
Pili Conjugation
Plasmids are small molecules of DNA that replicate
independently of the chromosome.
Resistance Plasmids: Penicillin, Antibiotics
Cryptic Plasmid:
I don’t know Virulence Plasmids:
Toxin, Attachment Protein
(Cause disease)
Bacteriocin Plasmids:
Antagonistic kill other
Bacteria
Horizontal Gene Transfer
Conjugation in genetics: method of horizontal gene transfer in which a bacterium containing a fertility plasmid forms a conjugation pilus that attaches and transfers plasmid genes to a recipient; in reproduction of ciliates: coupling of mating cells
Transformation Method of horizontal gene transfer in which a recipient cell takes up DNA from the environment. (Dead Organisms) Griffiths with Streptococcus Pneumoniae
Transduction Method of horizontal gene transfer in which DNA is transferred from one cell to another via a replicating virus.
Horizontal Gene Transfer: Process in which a donor cell contributes part of its genome to a
recipient cell, which may be a different species or genus from the donor.
F+1. Donor cell attaches to a recipient cell with its Pilus 2. Pilus may draw cells together 3. One strand of F plasmid DNA transfers to the recipient 4. The recipient synthesizes a complementary strand to become F+ Cell
with a pilus; the donor synthesizes the complementary strand, restoring its complete plasmid.
Hfr1. F plasmid integrates into chromosome by recombination 2. Cell joins via a pilus 3. Portion of F plasmid partially moves into recipient cell trailing a strand
of donor’s DNA 4. Conjugation ends with pieces of F plasmid and donor DNA in recipient
cells; Cells synthesize complementary DNA strands 5. Donor DNA and Recipient DNA recombine, making a recombinant
F - cells
Griffiths Experiment
Discovered transformation
Strain S (Capsulated) Killed Mice
Strain S (Heat treated) did not harm mice
Strain R (No capsule) did not harm mice
Strain R + Heat treated strain S Killed Mice
After a virus called bacteriophage (phage)
attaches to a host cell, it injects its genome
into the cell and directs the cell to
synthesize new phages. During assembly
of new phages some host DNA may be
incorporated, forming transducing
phages, which subsequently carry donor
DNA to a recipient cell.
1. Phage injects its DNA2. Phage enzymes degrade host DNA 3. Cell synthesizes new phages that incorporate phage DNA
and mistakenly some host DNA 4. Transducing Phage injects Donor DNA 5. Donor DNA is incorporated into recipients chromosome
by recombination
Operons
Inducible: are not usually transcribed and must be activated by inducers such as quorum sensing polypeptides
Operon: A series of genes, a promoter, and often a
sequence controlled by one regulatory gene. The operon
model explains gene regulation in prokaryotes.
Lac operon Repressed
3’
Promotor & Regulatory GenePromotor
1 2 3
Lactose Catabolism Genes
5’ Template DNA strand
Repressor mRNA
Translation
Transcription
Repressor
RNA polymerase Can’t bind
Operator (Blocked)
Lac Operon
Lac operon Induced
3’
Repressor
3’5’
321Template DNA strand5’
Repressor cannot bind
Inducer (Allolactose from lactose)
TranscriptionProceeds
RNA for lactose Catabolism
Type of Metabolic Pathway
regulated: Catabolic pathways
production of virulence proteins
Regulating Condition: Presence
of substrate of pathway, quorum
sensing polypeptides
Trp
Trp
Repressible: operates in reverse fashion they are transcribed continually until deactivated by repressors
which bind to the operator and inhibit transcription trp Operon Active
OperatorPromotor
Trp Operon with five genes
Regulatory Genes
Inactive Repressor
Transcription
Template DNA strand
mRNA coding multiple polypeptides
Trp
Enzymes of tryptophan biosynthetic pathway
5’
5’
5’
3’
3’
3’
trp Operon Repressed
3’
Trp
Trp
Trp
Tryptophan(Corepressor)
Activated Repressor Trp
Operator blocked
Inactivate Repressor
RNA polymerase Ceases
5’
21 3 4 5
5 432 1
Type of Metabolic
Pathway regulated: Anabolic
pathways
Regulating Condition: Presence
of product of pathway, quorum
sensing polypeptides
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