Micro biology ch 8,7, 6 – Flashcards

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Metabolism
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Sum of all chemical reactions within a living organism
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Anabolism
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building of complex organic compounds from simplier compounds
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Catabolism
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breakdown of complex organic compounds into simpler compounds
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Anabolism
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- Biosynthesis
-Covalent bonds are formed
-Dehydration synthesis
-Endergonic: more energy consumed than produced (requires ATP)
Ex. Nucleotides are used to synthesize nucleic acids.
Amino acids are used in the synthesis of proteins.
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Endergonic
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more energy consumed than produced (requires ATP)
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Catabolism
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-Degradative
- Covalent bonds are broken
-Hydrolytic reaction
Exergonic: more energy produced than consumed (produces ATP)
-Drive anabolic reactions
Ex. Complex sugars ? monosaccharides
Sugar ? CO2 and H2O
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ATP
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-High energy molecule
-Last 2 phosphate bonds are unstable
-Energy is released when last phosphate bond is broken
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Metabolic Pathways
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-Usually, a single covalent bond is made/ broken in each reaction.
-Begins with a specific molecule and ends with a final product (endproduct)
-Many steps are needed
-Process is efficient!
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Collision Theory
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All atoms, ions, and molecules are continuously moving. When they collide, electrons aredisrupted and can form/break chemical bonds.
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Collision Theory
What factors determine if a reaction happens?
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Velocity
Activation energy
Chemical configuration
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Reaction Rate
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-Frequency of collisions containing enough energy to result in a reaction
-Dependent on # of reactant molecules at/above activation energy
Temperature
Pressure
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Enzymes
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-Proteins that catalyze/speed up biochemical reactions without being permanently altered
Some are RNA
-Characteristic 3D shape determines function
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substrate
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-substance acted on by an enzyme
-Specificity: act on only one substrate
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Active site:
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region of enzyme that interacts with substrate
“Induced fit” between the substrate and the active site
-Not a lock and key fit
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Enzyme Speed and Location
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Number of substrate molecules converted per individual enzyme per second
1,000 – several million molecules per second!
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How do enzymes work?
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-Catalyze reactions by increasing probability of reactions
-Lower activation energy
-Increase # of molecules that reach activation energy
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Ions: Fe2+,. Zn2+, Mg2+, Ca2+
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Form bridge between substrate and enzyme
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Coenzyme:
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organic cofactor
Remove a chemical group from one substrate and transfer/carry it to another
H+, CO2, amino groups, or electrons
Electron carriers (accept and donate electrons)
Niacin
NAD+ (catabolic rxns), NADP+ (anabolic rxns)
Other B vitamins
FAD, Coenzyme A (important in Krebs cycle)
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Electron carriers
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accept and donate electrons
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Factors Affecting Enzyme Activity
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Temperature
pH
Substrate Concentration
Presence of Inhibitors
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Temperature
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Increasing
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Denaturation
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Loss of protein structure
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Optimum temp
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- max enzyme activity
- 35-40oC for most pathogens
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pH Denaturation
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-Loss of protein structure

-H+ and OH- compete with ions
in ionic bonds
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Optimum PH
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pH at which enzyme activity is maximum
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Substrate Concentration
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Increases in substrate concentration increase
enzymatic activity until all of the active sites are full
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Saturation
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-All active sites are full
-Curve levels off
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Feedback inhibtion
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Common way to regulate metabolic pathways
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Oxidation
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loss of electrons
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Reduction
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gain of electrons
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Redox reaxtions
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Sometimes a electron is exchanged with a proton(H+)
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Metabolic Pathways
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-Series of connected chemical reactions within cell
-Enzymes at every step
-Store & release energy from organic compounds
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Carbohydrate catabolism
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-Common strategy for microbes to make ATP
-Carbs are easily oxidized (good fuels)
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Glucose C6 H12 06
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-Highly reduced molecule
-Lots of energy
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Cellular Respiration
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ATP-generating process in which molecules are oxidized and the final electron acceptor is an inorganic molecule
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Aerobic
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oxygen
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Anaerobic
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Anaerobic = not oxygen
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Glycolysis
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-sugar splitting
-1st stage of carb catabolism
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Glycolysis
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Used in most living cells
-Some bacteria have alt. pathways
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Glycolysis
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-Almost every step requires an
enzyme
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Glycolysis
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Splits 6C sugar into 2 3C molecules
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Glycolysis
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Oxidation & rearrangement to form
pyruvic acid
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Glucose
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2 pyruvic acid
(pyruvate is ionic form)
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Glycolysis
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Net gain = 2ATPs + 2NADH
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Glycolysis
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-Does not require oxygen
-Followed by respiration or
fermentation
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krebs cycle
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Gradually releases energy through e- transfer
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krebs cycle
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-E- transferred to carrier coenzymes

-NAD+ and FAD
(reduced to NADH and FADH2)
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krebs cycle
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Net 2 ATP + 6NADH + 2FADH2
*Per glucose molecule*
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krebs cycle
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Citric Acid Cycle
Tricarboxylic Acid Cycle
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Electron Transport Chain
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Several types of ETCs
- Even in same organism
-All function similarly
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Electron Transport Chain
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Location
-PM of bacteria
-Inner mitochondrial membrane of euk.
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Electron Transport Chain
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Carriers transfer e- energy into ATP
-Series of redox reactions
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proton motive force
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Energy drives H+ pumps creating
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chemiosmosis
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In the ETC H+ flow through ATP synthase
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ATP Synthase
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NADH3--->ATP
FADH2--->2ATP
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Prokaryotes
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38 ATPs from one glucose molecule
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Eukaryotes
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-36 ATPs
-Energy lost with transfer of NADH/FADH2 across membrane
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Anaerobic Respiration Summary
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-final e- acceptor = inorganic molecule (not O2)

- 2-36 ATPs / glucose
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Anaerobic Respiration
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2-36 ATPs / glucose
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Eukaryotes
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36 ATPs
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Fermentation
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Releases energy from sugar or other organic molecules
-Incomplete oxidation of carbohydrate
-Final e- acceptor is organic molecule
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Fermentation
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Final e- acceptor is organic molecule
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Fermentation
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-Oxygen not required (anaerobic)
-CAN occur in presence of O2
-2 ATPs made during glycolysis
- Krebs cycle and Electron transport not used
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Fermentation
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Glycolysis followed by pyruvate reduction
-NADH passes e-s to pyruvate instead of ETC
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Fermentation
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Endproducts depend on microbes, substrates, enzymes
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Alcohol Fermintation
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Ethanol produced
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Acid Fermintation
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Lactate
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Carbon
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50% dry weight of a bacterial cell
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Carbon
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obtain through energy sources (carbs,lipids,proteins)or Co2
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Carbon
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4 nutrional caegories
-Photoautotroph
-Chemoautotroph
-Photoheterotroph
-Chemoheterotroph
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Hydrogen
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-In all organic and most inorganic compounds
-Maintains pH, forms hydrogen bonds, source of free energy in redox reactions
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Hydrogen
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-Maintains pH, forms hydrogen bonds, source of free energy in redox reactions
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Hydrogen
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-In all organic and most inorganic compounds
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Nitrogen
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Needed for protein, nuceic acid, and ATP synthesis
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Nitrogen fixation
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conversion of N2(in air) into NH4
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Phosphorous (P)
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-DNA& RNA
-Phospholipids
-ATP
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Sulfur(S)
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Needed for protein (in Cys and Met)& vitamin synthesis (Biotin & Thiamine)
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Apoenzyme
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-protein portion
-inactive
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coenzyme
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cofactor
-non protein portion
-activator
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Holoenzyme
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-Whole enzyme
-active
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Ions
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Potassium, sodium, magnesium,calcium, sodium
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Essential organic molecules
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growth factors
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Aerobes require
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- O2 for aerobic respiration
- H+ (stripped from organic compounds) + O2(air) + electrons---->H2O
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Anaerobes
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-don't use 02 for energy production
-Anarobic respiration & fermentation
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radicals
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toxic products that oxygen is transferred into while it is being utilized
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Radicals are formed when
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- when o2 is used
-by ionizing radiation (H2O-->H+ (+) OH-)
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Oxygen radicals
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O2-:superoxide
H2O2:Hydrogen peroxide
OH-:hydroxyl ion
O2^2:Peroxide ion
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O2-
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superoxide
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H2O2
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Hydrogen peroxide
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OH-
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hydroxyl ion
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O2^2
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Peroxide ion
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Why are oxygen radicals toxic?
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- They are unstable
-Disrupts eletron arrangements around other molecules
-causes DNA or cell damage
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Detoxifaction
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-naturally occurring antioxidants
-Detoxifying enzymes
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Naturally occurring antioxidants
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-Tocopherol(vitamin E)
-Ascorbic acid (Vitamin C)
-Melatonin
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Detoxifying enzymes
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-Superoxide dismutase
-Catalase
-Peroxidase
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Obligate Aeorobes
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only aerobic growth;oxygen required
-Medium:Growth occurs only where high concentrations of oxygen have diffused into the medium
-Presence of enzymes catalase and superoxide dismutase (SOD) allows toxic forms of oxygen to be neutralized;can use oxygen
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Facultative Anaerobes
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-Both aerobic and anaerobic growth; greater growth in presence of oxygen
-Medium:Growth is best where most oxygen is present, but occurs throughout tube
-Lacks enzymes to neutralize harmful forms of oxygen; cannot tolerate oxygen
-Presence of enzymes catalase and SOD allows toxic forms of oxygen to be neutralized;can use oxygen
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obligate anaerobes
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-organisms that survive in habitats without oxygen
-only anaerobic growth; ceases in presence of oxygen
Medium:Growth occurs only where there is no oxygen
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Aerotolerant Anaerobes
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-Medium:growth occurs evenly; oxygen has no effect
Presence of one enzyme, SOD, allows harmful forms of oxygen to be partially neutralized; tolerates oxygen
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Microaerophiles
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-Only aerobic growth; oxygen required in low concentration
-Medium:Growth occurs only where a low concentration of oxygen has diffused into medium
-Produce lethal amounts of toxic forms of oxygen if exposed to normal atmospheric oxygen
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In aerobic respiration carbohydrates are ultimately broken down into
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CO2
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chemiosmosis
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Most ATP produced in aerobic respiration occurs in the process of
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pyruvate
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In glycolysis the most reduced compound formed is
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ATP
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In glycolysis, the activation of glucose is accomplished by:
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oxygen
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The final electron acceptor in aerobic respiration is
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glycolysis
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Which stage of aerobic respiration requires ATP
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none
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. Which stage of aerobic respiration requires CO2?
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ATP synthase
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As protons flow through the ______, energy is released and exploited to combine ADP and inorganic phosphate to form ATP.
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ATP synthase
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is an enzyme, a molecular motor, an ion pump, and another molecular motor all wrapped together in one amazing nanoscale machine. It plays an indispensable role in our cells, building most of the ATP that powers our cellular processes
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-Prokaryotes
38 ATPs from one glucose molecule
-Eukaryotes get 36 ATPs
Energy lost with transfer of NADH/FADH2 across membrane
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Summary of Aerobic Respiration
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Anaerobic Respiration
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-final e- acceptor = inorganic molecule (not O2)
- 2-36 ATPs / glucose
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Fermentation
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-Releases energy from sugar or other organic molecules
-Incomplete oxidation of carbohydrate
-Final e- acceptor is organic molecule
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Fermentation
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-Oxygen not required (anaerobic)
-CAN occur in presence of O2
- 2 ATPs made during glycolysis
- Krebs cycle and Electron transport not used
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Fermentation
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-Glycolysis followed by pyruvate reduction
-NADH passes e-s to pyruvate instead of ETC
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Fermentation
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Endproducts depend on microbes, substrates, enzymes
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True
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Fermentation can occur in the presence of oxygen
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50% of dry weight of a typical bacterial cell
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Carbon
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Carbon
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Obtain through energy sources (carbs, lipids, proteins) or CO2
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Carbon
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4 Nutritional categories
Photoautotroph
Chemoautotroph
Photoheterotroph
Chemoheterotroph
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Photoautotroph
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are organisms that carry out photosynthesis. Using energy from sunlight, carbon dioxide and water are converted into organic materials to be used in cellular functions such as biosynthesis and respiration.
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Chemoautotroph
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Chemoautotrophs are organisms that obtain their energy from a chemical reaction (chemotrophs) but their source of carbon is the most oxidized form of carbon, carbon dioxide (CO2).
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Photoheterotroph
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Photoheterotrophs depend on light for their source of energy and mostly organic compounds from the environment for their source of carbon.
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Chemoheterotroph
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are unable to fix carbon to form their own organic compounds
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Hydrogen
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In all organic and most inorganic compounds
Maintains pH, forms hydrogen bonds, source of free energy in redox reactions
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Nitrogen
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Needed for protein, nucleic acid, and ATP synthesis
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Nitrogen fixation
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conversion of N2 (in air) into NH4+
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Phosphorous (P)
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is an essential element in the formation of phospholipids, a class of lipids that are a major component of all cell membranes, as they can form lipid bilayers, which keep ions, proteins, and other molecules where they are needed for cell function, and prevent them from diffusing into areas where they should not be. Phosphate groups are also an essential component of the backbone of nucleic acids and are required to form ATP – the main molecule used as energy powering the cell in all living creatures.
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Sulfur
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Needed for protein (in Cys & Met) & vitamin synthesis (Biotin & thiamine
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Ions:
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Potassium, sodium, magnesium, calcium, sodium
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Aerobes
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-require O2 for aerobic respiration

-H+ (stripped from organic cmpds) + O2 (air) + electrons? H2O
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Anaerobes
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don’t use O2 for energy production
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radicals
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As oxygen is utilized it is transformed into several toxic products
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Radicals are formed
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-when O2 is used
-by ionizing radiation (H2O ? H+ + OH-)
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-They are unstable
- Disrupt electron arrangements around other molecules
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Why are oxygen radicals toxic
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obligate anaeorobe
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Which of the following cannot survive in the presence of O2?
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Solute
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- substance dispersed within a solvent
-solid sometimes gas
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Solvent
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- dissolving medium (usually liquid)
-usually water, or a liquid
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Solution
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- mixture of substances that cannot be separated by filtration
-combinationation of substances that solvents are dissolved
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Concentration gradient
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Difference in concentration on two sides of a membrane
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Passive
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moves from high to low conc;
no energy/ATP required
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Active
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moves from low to high conc;
energy required
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Passive Processes
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Simple Diffusion

Facilitated Diffusion

Osmosis
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Simple Diffusion
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Net movement of solute molecules ---from high to low concentration
-Stops at equilibrium
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Facilitated Diffusion
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s the process of spontaneous passive transport of molecules or ions across a cell's membrane via specific transmembrane integral proteins.
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Osmosis
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Net movement of solvent (usually H2O) across selectively permeable membrane
Passive transport of solvent
Movement follows the CG for solvent
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simple diffusion
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once the molecules stop at equilibrium they dont stop moving
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small uncharged molecules
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what kind of molecules can easily go through simple diffusion
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Facilitated Diffusion
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charged molecules go from high to low. They cant cross the membrane on their own because they are charged so they need carrier proteins transport proteins and permeass to act as channels
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Osmossis
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-most instance water is the solvent
-water doesnt move easiliy or quickly because it has a partial charge
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Aquaporin
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allows more rapid, faster movement of water
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Isotonic
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-is equal, still has movement inside and outside
-rates of diffusion are equal in both directions
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Hypotonic
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less solute outside the cell compared to the inside
cell wall:the cell swells, the cell wall resists osmotic pressure prevents it from bursting
no cell wall: cell swells and may burst if no mechanism exists to remove water
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Hypertonic
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Higher concentration outside
Cell wall: water diffuses out of the cell and shrinks the cell membrane away from the cell wall
no cell wall: water diffuses out of the cell causes it to shrink and become distorted
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Gram +
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Which bacteria are more susceptible to osmotic lysis?
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Active Transport
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-Require ATP
-Usually move against CG
Can be with CG but at a faster rate

-Requires carrier protin
-Examples
*Ion pumps
*Group Translocation
Transport is coupled with alteration
Only in prokaryotes
*Endocytosis
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Group Translocation
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-Transport is coupled with alteration
-Only in prokaryotes
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Endocytosis
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is a form of active transport in which a cell transports molecules (such as proteins) into the cell (endo- + cytosis) by engulfing them in an energy-using process.
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Phagocytosis
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process by which certain living cells called phagocytes ingest or engulf other cells or particles. The phagocyte may be a free-living one-celled organism, such as an amoeba, or one of the body cells, such as a white blood cell.
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Pinocytosis
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the ingestion of liquid into a cell by the budding of small vesicles from the cell membrane.
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Receptor-mediated
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is a process by which cells absorb metabolites, hormones, other proteins -
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Acidophiles
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acid-tolerant microbes
Stomach pH = 1 (Helicobacter pylori)
Vagina pH = 3-5 (Lactobacillus)


Acids from fermentation preserve foods

Microbial wastes are acidic
Use buffers in media
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Hypotonic Solutions
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If concentrations of dissolved solutes are less outside the cell than inside, the concentration of water outside is correspondingly greater. When a cell is exposed to such hypotonic conditions, there is net water movement into the cell. Cells without walls will swell and may burst (lyse) if excess water is not removed from the cell. Cells with walls often benefit from the turgor pressure that develops in hypotonic environments.
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Reducing media
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contains ingredients that deplete O2
Ex. Thioglycollate medium (liquid)
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Anaerobic jars
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Used for plate cultures
Colony growth
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Capnophiles
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Require CO2 & some O2
-Intestines, respiratory tract, body tissues
- CO2 incubator or candle jar
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Biofilms
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Benefits
-Share nutrients
-Shelter
?-opportunity for genetic exchange
Cooperative activity
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Quorum sensing
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Communication via chemical cues
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Bacterial Growth
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Most reproduce by binary fission
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Budding
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Outgrowth of cell that grows and
separates from parent
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External Spores (conidiospores)
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- Filamentous bacteria
- Spores develop into new cells
-More common for fungi
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Fragmentation
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New cells grow from fragments
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Bacterial Growth
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Most culturable bacteria reproduce by binary fission
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Generation Time
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Time required for cell number to double
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Lag Phase
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-cell number not increasing
-metabolic activity is still going on
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Log Phase
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-Increase in population of bacteria cells
-Exponential growth
-shortest generation time
-Greatest Growth
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Stationary Phase
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-Nutrient depletion
-slows growth
-cell division=cell death
-waste product
-period of equilibrium
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Death Phase
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-still cell division is occurring
-death is occurring faster rate than growth
-now death out weighs growth
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lag phase
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In lab, you are asked to inoculate a Phenol Red broth with E. coli. You immediately place the tube in the 37?C incubator. In which phase of the bacterial growth curve is your culture?
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death phase
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You leave your culture in the 37?C incubator for five days. In which phase is the culture most likely in when you remove it?
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Direct measurement
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-Technique that involves some counting
- Count small sample & determine total population
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Indirect measurement
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-Estimation of cell numbers without counting cells
- Turbidity, Mass, Spectrophotometry
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Plate Counts
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Direct count

-Estimates live cells by counting colonies
-30-300 CFU/plate
-Pour plate method or spread plate method
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Filtration Method
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-Volume passed through membrane (bacteria trapped)
- Transfer to plate and grow
-Count colonies and divide
by number of ml filtered (CFU/ml)
-Good when bacteria # is small
Can’t count 1CFU/ml
Ex. Water samples
(coliform bacteria)
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Direct Microscopic Count
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Count number of cells spread over grid using a microscope

-Advantages: quick (no incubation required)
counts all cells (live and dead)
-Disadvantage: difficult to count motile bacteria
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Turbidity
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-Indirect
-Uses spectrophotometer
Measures amount of light
passing through a sample
% transmittance
Absorbance
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Turbidity
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-Advantage: quick and easy

-Disadvantages:
must be read during log phase
needs to be correlated to direct measurement
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Turbidity Method
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-Indirect method of measurement
-Degree of cloudiness, turbidity, reflects the relative population size
-Advantage: quick and easy
-Disadvantages:
must be read during log phase
needs to be correlated to direct measurement
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Direct microscopic count
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You are part of the Quality Control team that measures the microbial growth of Horizon milk. You are expected to deliver same-day results before the milk is shipped. Which of the following techniques do you most likely use for your job?
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Hypertonic Solutions
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If concentrations of dissolved solutes are greater outside the cell, the concentration of water outside is correspondingly lower. As a result, water inside the cell will flow outwards to attain equilibrium, causing the cell to shrink. As cells lose water, they lose the ability to function or divide. Hypertonic environments such as concentrated brines or syrups have been used since antiquity for food preservation because microbial cells that would otherwise cause spoilage are dehydrated in these very hypertonic environments and are unable to function.
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General Characteristics of Viruses
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-Not all have spikes
-Not all cause disease
-Requires electron Microspy
-All Acellular
-Either DNA or RNA genome
-Have to have a host cell
-Small amounts of DNA or RNA
-All have a protein capsid
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Virion
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-fully developed virus particle, infectious
-if feature is missing it is not a virion
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Virus Genome
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SS DNA

DS DNA-our genome

SS RNA

DS RNA-never seen in our genome unless infected by a virus
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capsid
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protect nucleic acids
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Envelope
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-not all viruses have a envelope
- around capsid
-came from host cell usually the PM from the host
-it has a envelope because it is most likely to dry out
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Influenza
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-8 segmented genome
-Hemaglutin is the attachment
-Affect Respiratory system
- an RNA virus
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RNA Viruses
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Go through Antigentic drift
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capsomeres
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Virus Protein coat is made of
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nucleocapsid
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-Protects nucleic acid
-Capsid + nucleic acid =
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Icosahedral or helical shape
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Virus structure
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Viral structure:Enzymes
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All viruses use some host machinery
Ribosomes
DNA polymerases
Drugs that interfere with these enzymes disrupt viral AND host cell function
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All RNA viruses need an RNA polymerase
We can target these with drugs!
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Some Viruses package their own (viral) enzymes which is
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Enveloped viruses
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-Phospholipid membrane around capsid
From host plasma or nuclear membrane

-Must stay moist during spread from host to host
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-Viral proteins and sugars bind host receptors
-Attachment factors on virion surface
Naked viruses
Enveloped viruses
-Determine host range of virus
Ex. Influenza & HIV
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Viral Attachment Factors
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-viruses dont have a cell structure
-No domains
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Why aren’t viruses classified according to the same taxonomic system as prokaryotic and eukaryotic microbes?
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Determines how it gets copied
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Virus Strategy for replication
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Obligate intracellular parasites

Host-specific

Can be cultured only inside living cells
Bacteria
Living animals
Chicken egg
Cultured cells
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Growth of Viruses
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bacteriophage
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Which of the following is a virus that infects bacteria?
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Virion
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infective form
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Lytic cycle
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multiplication in host cell in which host cell is disrupted to release virions
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Lysogenic cycle or latent phase
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Dormant stage when virus is not undergoing “active” replication; host cell is not killed
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Lytic cycle
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Which type of viral life cycle causes the host cell to die?
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lysozyme
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Which of the following enzymes is necessary for T4 phage entry into and exit from a host bacterial cell like E. coli?
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Attachment
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Bacteriophage:Tail fibers attach to cekk wall proteins

Animal virus:Attachment sites are plasma proteins and glycoproteins
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Penetration
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Bacteriophage:viral DNA injected into host cell

Animal virus:CApsid enters by endocytosis or fusion
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Uncoating
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Bacteriophage:not required

Animal virus:Enzymatic removal of capsid proteins
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Biosynthesis
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Bacteriophage:in cytoplasm

Animal virus:In nucleus (DNA viruses) or cytoplasm (RNA viruses)
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Chronic Infection
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Bacteriophage:Lysogeny

Animal virus:Latency; slow viral infections; cancer
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Release
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Bacteriophage:Host cell lysed

Animal virus:Enveloped viruses bud out; nonenveloped viruses rupture plasma membrane
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Influenza Virus
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-Enveloped RNA Virus
- Hemaglutinin and neuraminidase determine Influenza strains
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Antigenic Shift
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Pigs susceptible to avian and human flu strains
Segmented genome allows mixing in pigs (intermediate host)
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-RNA remains in the cytoplasm
-All RNA viruses make an RNA-dependent RNA polymerase
Copies RNA strand
(+ sense / - sense strands)
-Translation by host
-Virus Assembly
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Animal Viral Biosynthesis: RNA Genomes
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-Viral DNA moves to the nucleus
-DNA is transcribed
-Translation by host ribosomes
-DNA is replicated in nucleus
-Virus assembles
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Animal Viral Biosynthesis: DNA Genomes
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