Home MMiPeople Francesco Redi: scientist who tested spontaneous generation with rotting meat and maggot formation with an open container, sealed container, and gauze-covered container, and refuted spontaneous generation Needham: scientist who tested spontaneous generation with boiling chicken broth, sealing the container, and waiting a few days to assess for microbial growth, and supported spontaneous generation Spallanzani: scientist who tested spontaneous generation with further testing, Needham’s experiment, and tested with an open and closed container that was later opened, and refuted spontaneous generation Louis Pasteur: scientist who used swan-neck flasks in his experiment and definitively refuted spontaneous generation Anthony van Leeuwenhoek: scientist who was the first to observe eukaryotic microbes, calling them “wee animalcule” Robert Hooke: coined the term “cell” when looking at cork Matthias Schleiden: observed cells in plant tissue Theodor Schwann: observed cells in animal tissue Rudolf Virchow and Robert Remark: observed cells dividing to make new cells (not mitosis) Hippocrates: suggested disease has natural causes Thucydides: advocated for evidence-based analysis of cause and effect and suggested immunity after observing plague survivors didn't get sick again Marcus Terentius Varro: the first to propose that things we cannot see cause disease Ignaz Semmelweis: physician who observed the spread of disease among patients in different sides of the hospital and instituted hand washing between patients to reduce the spread of disease from patient to patient via healthcare workers Joseph Lister: surgeon who observed post-surgical infection and instituted hand washing and sterilization of medical equipment with 5% phenol solution for less disease Robert Koch: scientist who developed Koch’s postulates to determine the cause of disease and had a rivalry with Louis Pasteur John Snow: questioned the London cholera outbreak and asked questions to the people who had been infected about where they had been and what they had eaten or drank, and noticed that everyone who had cholera used one of two water pumps Classification of microbes What are the 2 domains that are composed of all microbes? Bacteria and Archaea What domain of life is composed only of some microbes? Eukarya What types of microbes do not fit into the domains of life? Viruses and Prions Prions: unicellular organisms in the domains Bacteria and Archaea with no nucleus and have cell walls Viruses: acellular and domainless (not alive) Eukaryotes: unicellular OR multicellular organisms, in domain Eukarya, have a nucleus, have membrane-bound organelles, and include fungi, algae, protazoa, and helminths How many times bigger are bacteria than viruses? 100x A cell is around how many times bigger than an individual bacteria? 10x Cell structures Know the function, general location, and whether they are shared with eukaryotes (if yes similarities/differences) of the following structures: 1. Nucleoid: contains chromosome(s) and nuclear-associated proteins that are usually haploid and circular near the center of the cell, which hold the DNA genetic information without a membrane Eukaryotes = have a nucleus, are diploid and linear Prokaryotes = have nucleoid, are haploid and circular 2. Ribosomes: work with mRNA protein synthesis, made up of proteins and RNA, found in cytoplasm Eukaryotes: 80S, 60 large, 40 small (18S sequencing) Prokaryotes: 70S, 50 large, 30 small (16S sequencing) 3. Cytoplasm: fluid inner layer 4. Fimbriae: short, bristle-like projections for attachment to surfaces 5. Endospores: not all bacteria have, protect bacteria in a dormant state/ harsh environment, found inside bacteria, sporulation = the process of becoming dormant, germination = process of becoming active 6. Plasma membrane: semipermeable, composed of lipids and proteins, controls transport into and out of cell, most inner layer before cytoplasm (ex: facilitated diffusion, active transport, diffusion, endocytosis (Eukaryotes), sterols (Eukaryotes), and cholesterol (Eukaryotes) Same for Eukaryotes 7. Cell wall: protects against harsh changing environments and osmotic stress, contains peptidoglycan in bacteria, contains Gram + and Gram - Steps of Gram stain: dye with crystal violet, iodine (mordant), alcohol (decolorizer), and safranin red If mycobacteria complete an acid-fast stain Gram + has LTA an TA and one membrane Gram - has LPS and 2 membranes 8. Capsule: protective protein shell, outermost layer 9. Pilus: medium projection, adheres to surfaces, does DNA gene transfer 10. Flagellum: long protein projections made of flagellin for movement (ex: 1= monotrichous, one at each end = amphitrichous, many at one end = lophotrichous, many flagella all over the cell = peritrichous 11. Plasmid: circular, double-stranded DNA not part of the chromosome, and can have 1-100 of the same or different plasmids to help with gene transfer, antibiotic resistance, and virulence factors, found anywhere in the cytoplasm Not part of Eukaryotes 12. Inclusion: not all bacteria have, helps with the storage of nutrients and other materials, has protein shell, and is found in cytoplasm (ex: lipid droplets store fats, volutin stores inorganic phosphates, sulfur inclusions store sulfur, gas bubbles store gas for buoyancy in water, magnetosomes store metals for movement) Not part of Eukaryotes; instead, they have vesicles for storage All cellular microbes have what four (4) components? Cell Membrane, Cytoplasm, Ribosomes, and DNA What is the only component of all cells that viruses have? Cytoplasm Know/ be able to identify the shapes of bacteria Round shape: coccus Rod shape: bacillus Vibrio: curved rod shape Short rods with combo of coccus and bacillus: coccobacillus Wavy spiral shape: Spirillum Coiled spiral shape: Spirochete Microbial growth Phases of growth Lag Phase: bacteria gear up for replication by increasing cell size, metabolism, and protein synthesis Log Phase: exponential growth phase, where bacteria actively replicate and are most susceptible to antibiotics Stationary Phase: growth curve flatlines bc bacteria are dying at same rate of growth, begin survival mode and sporulation, produce secondary metabolites, and produce virulence factors, and are low on space, nutrients, and oxygen Death Phase: bacteria die at exponential rate, increase amount of toxic waste, release spores, some spontaneously lyse to feed others, and persister cells refuse to die How do microbes replicate? Through binary fission, fragmentation, budding, and sexually What is a biofilm? Communities of bacteria (steps: colonization, attachment, replication, make EPS with antibiotic resistance, EPS kick bacteria out to replicate somewhere else) How does quorum sensing work? Bacteria want to work together, so they secrete autoinducers, and when you activate enough receptors, they activate a response Growth requirements – classifications and adaptations 1. Oxygen requirements Obligate Aerobes: need O2 to survive Obligate Anaerobes: die in presence of O2 Faculative: mostly need O2 but can survive without it Microaerophiles: need O2 for survival but not atmospheric O2 (low levels) Aerotolerant: can survive with or without oxygen Capnophiles: like high CO2 and low O2 2. pH requirements Acidophiles: low pH (2-4), high H+ environments, efflux pumps to remove H+ ions, changes membrane composition to withstand low pH Neutrophiles: neutral pH (7), found within body Alkaliphiles: basic pH (9-10), modified lipid protein structures, modified electron transport system that use Na+ instead of H+, high OH- environment 3. temperature requirements Psychrophiles: like freezing temperatures a below 0-15 degrees, die at or above 20 degrees, found in cold lakes or the ocean floor, have hydrophobic proteins to increase flexibility, have decreased secondary stabilizing bonds Psychrotolerant: cold not ideal but wont kill them, live between 4-25 degrees (fridge temperature) Mesophiles: moderate temperatures, 20-40 degrees, grow in body Thermophiles: hot environments 50-80 degrees, hot springs, geothermal soil Hyperthermophiles: very hot environments 80-110 degrees, found in hydrothermal vents, increased saturation in membranes, increased stabilizing bonds, alter amino acids to prevent denaturation 4. osmolarity requirements Hypertonic: more water out Hypotonic: more water in Isotonic: equal water in and out Halotolerant: dont require salt but can grow in high salt environments Halophiles: love salt, found in ocean and salt lakes, have increased cytoplasmic glycerol, have efflux pumps for salt 5. barometric requirements Barophile: survive high atmospheric environments like the bottom of the ocean (something at top of mountain has low atmospheric pressure) Microbial Metabolism Means of generating energy (do the processes require oxygen?, which gives the most energy?) Glycolysis: does not require O2 bc it can be used during fermentation, used 2 ATP, makes 4 ATP, NET 2 ATP Kreb’s cycle: requires O2; NET after 1 round= 1ATP, 1 NADH, 1FADH2 (x2 for second round) Electron transport: requires O2, biggest payout of ATP with NET 34 ATP Photosynthesis: does not require O2 as it is a waste product, can do oxygenic and anoxygenic Microbial genetics DNA Replication – enzymes and functions DNA gyrase: unwinds DNA (enzyme) Helicase: unzips DNA (enzyme) Single-stranded binding proteins: bind to DNA so doesnt close back up (protein) Single-stranded binding proteins: bind to DNA so doesnt close back up (protein) DNA polymerase III: lay down new DNA nucleotides, synthesizes leading and lagging strands 5’ →3’(enzyme) DNA polymerase I: removes RNA primers (enzyme) DNA Ligase: seals RNA primers (enzyme) Topoisomerase 4: separates 2 circular chromosomes Transcription and translation – enzymes and function 1. RNA polymerase: turns DNA→ mRNA (transcription) 2. Ribosomes: 30S small, 50S large, 70S total 3. tRNA: A,P, and E sites, bacteria links transcription and translation bc no nucleus, has anticodon at opposite long 3’ end, high energy bond, same active translation process as Eukaryotes Be able to do DNA base pairing, transcription, and translation (given codon table) Also know differences between prokaryotic and eukaryotic Replication, transcription, and translation Genetic Diversity – how does this work? 1. Transformation: uptake of plasmid into different bacteria and is incorporated into its genetic material 2. Transduction: bacteriophage inserts its plasmid into a bacteria (virus that infects a bacteria) 3. Conjugation: like plasmid transfer (ex: rolling circle replication), “bacterial sex” 4

MMiPeople Francesco Redi: scientist who tested spontaneous generation with rotting meat and maggot formation with an open container, sealed container, and gauze-covered container, and refuted spontaneous generation Needham: scientist who tested spontaneous generation with boiling chicken broth, sealing the container, and waiting a few days to assess for microbial growth, and supported spontaneous generation Spallanzani: scientist who tested spontaneous generation with further testing, Needham’s experiment, and tested with an open and closed container that was later opened, and refuted spontaneous generation Louis Pasteur: scientist who used swan-neck flasks in his experiment and definitively refuted spontaneous generation Anthony van Leeuwenhoek: scientist who was the first to observe eukaryotic microbes, calling them “wee animalcule” Robert Hooke: coined the term “cell” when looking at cork Matthias Schleiden: observed cells in plant tissue Theodor Schwann: observed cells in animal tissue Rudolf Virchow and Robert Remark: observed cells dividing to make new cells (not mitosis) Hippocrates: suggested disease has natural causes Thucydides: advocated for evidence-based analysis of cause and effect and suggested immunity after observing plague survivors didn't get sick again Marcus Terentius Varro: the first to propose that things we cannot see cause disease Ignaz Semmelweis: physician who observed the spread of disease among patients in different sides of the hospital and instituted hand washing between patients to reduce the spread of disease from patient to patient via healthcare workers Joseph Lister: surgeon who observed post-surgical infection and instituted hand washing and sterilization of medical equipment with 5% phenol solution for less disease Robert Koch: scientist who developed Koch’s postulates to determine the cause of disease and had a rivalry with Louis Pasteur John Snow: questioned the London cholera outbreak and asked questions to the people who had been infected about where they had been and what they had eaten or drank, and noticed that everyone who had cholera used one of two water pumps Classification of microbes What are the 2 domains that are composed of all microbes? Bacteria and Archaea What domain of life is composed only of some microbes? Eukarya What types of microbes do not fit into the domains of life? Viruses and Prions Prions: unicellular organisms in the domains Bacteria and Archaea with no nucleus and have cell walls Viruses: acellular and domainless (not alive) Eukaryotes: unicellular OR multicellular organisms, in domain Eukarya, have a nucleus, have membrane-bound organelles, and include fungi, algae, protazoa, and helminths How many times bigger are bacteria than viruses? 100x A cell is around how many times bigger than an individual bacteria? 10x Cell structures Know the function, general location, and whether they are shared with eukaryotes (if yes similarities/differences) of the following structures: 1. Nucleoid: contains chromosome(s) and nuclear-associated proteins that are usually haploid and circular near the center of the cell, which hold the DNA genetic information without a membrane Eukaryotes = have a nucleus, are diploid and linear Prokaryotes = have nucleoid, are haploid and circular 2. Ribosomes: work with mRNA protein synthesis, made up of proteins and RNA, found in cytoplasm Eukaryotes: 80S, 60 large, 40 small (18S sequencing) Prokaryotes: 70S, 50 large, 30 small (16S sequencing) 3. Cytoplasm: fluid inner layer 4. Fimbriae: short, bristle-like projections for attachment to surfaces 5. Endospores: not all bacteria have, protect bacteria in a dormant state/ harsh environment, found inside bacteria, sporulation = the process of becoming dormant, germination = process of becoming active 6. Plasma membrane: semipermeable, composed of lipids and proteins, controls transport into and out of cell, most inner layer before cytoplasm (ex: facilitated diffusion, active transport, diffusion, endocytosis (Eukaryotes), sterols (Eukaryotes), and cholesterol (Eukaryotes) Same for Eukaryotes 7. Cell wall: protects against harsh changing environments and osmotic stress, contains peptidoglycan in bacteria, contains Gram + and Gram - Steps of Gram stain: dye with crystal violet, iodine (mordant), alcohol (decolorizer), and safranin red If mycobacteria complete an acid-fast stain Gram + has LTA an TA and one membrane Gram - has LPS and 2 membranes 8. Capsule: protective protein shell, outermost layer 9. Pilus: medium projection, adheres to surfaces, does DNA gene transfer 10. Flagellum: long protein projections made of flagellin for movement (ex: 1= monotrichous, one at each end = amphitrichous, many at one end = lophotrichous, many flagella all over the cell = peritrichous 11. Plasmid: circular, double-stranded DNA not part of the chromosome, and can have 1-100 of the same or different plasmids to help with gene transfer, antibiotic resistance, and virulence factors, found anywhere in the cytoplasm Not part of Eukaryotes 12. Inclusion: not all bacteria have, helps with the storage of nutrients and other materials, has protein shell, and is found in cytoplasm (ex: lipid droplets store fats, volutin stores inorganic phosphates, sulfur inclusions store sulfur, gas bubbles store gas for buoyancy in water, magnetosomes store metals for movement) Not part of Eukaryotes; instead, they have vesicles for storage All cellular microbes have what four (4) components? Cell Membrane, Cytoplasm, Ribosomes, and DNA What is the only component of all cells that viruses have? Cytoplasm Know/ be able to identify the shapes of bacteria Round shape: coccus Rod shape: bacillus Vibrio: curved rod shape Short rods with combo of coccus and bacillus: coccobacillus Wavy spiral shape: Spirillum Coiled spiral shape: Spirochete Microbial growth Phases of growth Lag Phase: bacteria gear up for replication by increasing cell size, metabolism, and protein synthesis Log Phase: exponential growth phase, where bacteria actively replicate and are most susceptible to antibiotics Stationary Phase: growth curve flatlines bc bacteria are dying at same rate of growth, begin survival mode and sporulation, produce secondary metabolites, and produce virulence factors, and are low on space, nutrients, and oxygen Death Phase: bacteria die at exponential rate, increase amount of toxic waste, release spores, some spontaneously lyse to feed others, and persister cells refuse to die How do microbes replicate? Through binary fission, fragmentation, budding, and sexually What is a biofilm? Communities of bacteria (steps: colonization, attachment, replication, make EPS with antibiotic resistance, EPS kick bacteria out to replicate somewhere else) How does quorum sensing work? Bacteria want to work together, so they secrete autoinducers, and when you activate enough receptors, they activate a response Growth requirements – classifications and adaptations 1. Oxygen requirements Obligate Aerobes: need O2 to survive Obligate Anaerobes: die in presence of O2 Faculative: mostly need O2 but can survive without it Microaerophiles: need O2 for survival but not atmospheric O2 (low levels) Aerotolerant: can survive with or without oxygen Capnophiles: like high CO2 and low O2 2. pH requirements Acidophiles: low pH (2-4), high H+ environments, efflux pumps to remove H+ ions, changes membrane composition to withstand low pH Neutrophiles: neutral pH (7), found within body Alkaliphiles: basic pH (9-10), modified lipid protein structures, modified electron transport system that use Na+ instead of H+, high OH- environment 3. temperature requirements Psychrophiles: like freezing temperatures a below 0-15 degrees, die at or above 20 degrees, found in cold lakes or the ocean floor, have hydrophobic proteins to increase flexibility, have decreased secondary stabilizing bonds Psychrotolerant: cold not ideal but wont kill them, live between 4-25 degrees (fridge temperature) Mesophiles: moderate temperatures, 20-40 degrees, grow in body Thermophiles: hot environments 50-80 degrees, hot springs, geothermal soil Hyperthermophiles: very hot environments 80-110 degrees, found in hydrothermal vents, increased saturation in membranes, increased stabilizing bonds, alter amino acids to prevent denaturation 4. osmolarity requirements Hypertonic: more water out Hypotonic: more water in Isotonic: equal water in and out Halotolerant: dont require salt but can grow in high salt environments Halophiles: love salt, found in ocean and salt lakes, have increased cytoplasmic glycerol, have efflux pumps for salt 5. barometric requirements Barophile: survive high atmospheric environments like the bottom of the ocean (something at top of mountain has low atmospheric pressure) Microbial Metabolism Means of generating energy (do the processes require oxygen?, which gives the most energy?) Glycolysis: does not require O2 bc it can be used during fermentation, used 2 ATP, makes 4 ATP, NET 2 ATP Kreb’s cycle: requires O2; NET after 1 round= 1ATP, 1 NADH, 1FADH2 (x2 for second round) Electron transport: requires O2, biggest payout of ATP with NET 34 ATP Photosynthesis: does not require O2 as it is a waste product, can do oxygenic and anoxygenic Microbial genetics DNA Replication – enzymes and functions DNA gyrase: unwinds DNA (enzyme) Helicase: unzips DNA (enzyme) Single-stranded binding proteins: bind to DNA so doesnt close back up (protein) Single-stranded binding proteins: bind to DNA so doesnt close back up (protein) DNA polymerase III: lay down new DNA nucleotides, synthesizes leading and lagging strands 5’ →3’(enzyme) DNA polymerase I: removes RNA primers (enzyme) DNA Ligase: seals RNA primers (enzyme) Topoisomerase 4: separates 2 circular chromosomes Transcription and translation – enzymes and function 1. RNA polymerase: turns DNA→ mRNA (transcription) 2. Ribosomes: 30S small, 50S large, 70S total 3. tRNA: A,P, and E sites, bacteria links transcription and translation bc no nucleus, has anticodon at opposite long 3’ end, high energy bond, same active translation process as Eukaryotes Be able to do DNA base pairing, transcription, and translation (given codon table) Also know differences between prokaryotic and eukaryotic Replication, transcription, and translation Genetic Diversity – how does this work? 1. Transformation: uptake of plasmid into different bacteria and is incorporated into its genetic material 2. Transduction: bacteriophage inserts its plasmid into a bacteria (virus that infects a bacteria) 3. Conjugation: like plasmid transfer (ex: rolling circle replication), “bacterial sex” 4

Intro/History

People

Francesco Redi: scientist who tested spontaneous generation with rotting meat and maggot formation with an open container, sealed container, and gauze-covered container, and refuted spontaneous generation
Needham: scientist who tested spontaneous generation with boiling chicken broth, sealing the container, and waiting a few days to assess for microbial growth, and supported spontaneous generation
Spallanzani: scientist who tested spontaneous generation with further testing, Needham’s experiment, and tested with an open and closed container that was later opened, and refuted spontaneous generation
Louis Pasteur: scientist who used swan-neck flasks in his experiment and definitively refuted spontaneous generation
Anthony van Leeuwenhoek: scientist who was the first to observe eukaryotic microbes, calling them “wee animalcule”
Robert Hooke: coined the term “cell” when looking at cork
Matthias Schleiden: observed cells in plant tissue
Theodor Schwann: observed cells in animal tissue
Rudolf Virchow and Robert Remark: observed cells dividing to make new cells (not mitosis)
Hippocrates: suggested disease has natural causes
Thucydides: advocated for evidence-based analysis of cause and effect and suggested immunity after observing plague survivors didn't get sick again
Marcus Terentius Varro: the first to propose that things we cannot see cause disease
Ignaz Semmelweis: physician who observed the spread of disease among patients in different sides of the hospital and instituted hand washing between patients to reduce the spread of disease from patient to patient via healthcare workers
Joseph Lister: surgeon who observed post-surgical infection and instituted hand washing and sterilization of medical equipment with 5% phenol solution for less disease
Robert Koch: scientist who developed Koch’s postulates to determine the cause of disease and had a rivalry with Louis Pasteur
John Snow: questioned the London cholera outbreak and asked questions to the people who had been infected about where they had been and what they had eaten or drank, and noticed that everyone who had cholera used one of two water pumps

Classification of microbes

What are the 2 domains that are composed of all microbes? Bacteria and Archaea
What domain of life is composed only of some microbes? Eukarya
What types of microbes do not fit into the domains of life? Viruses and Prions
Prions: unicellular organisms in the domains Bacteria and Archaea with no nucleus and have cell walls
Viruses: acellular and domainless (not alive)
Eukaryotes: unicellular OR multicellular organisms, in domain Eukarya, have a nucleus, have membrane-bound organelles, and include fungi, algae, protazoa, and helminths
How many times bigger are bacteria than viruses? 100x
A cell is around how many times bigger than an individual bacteria? 10x

Cell structures

Know the function, general location, and whether they are shared with eukaryotes (if yes similarities/differences) of the following structures:

1. Nucleoid: contains chromosome(s) and nuclear-associated proteins that are usually haploid and circular near the center of the cell, which hold the DNA genetic information without a membrane

Eukaryotes = have a nucleus, are diploid and linear
Prokaryotes = have nucleoid, are haploid and circular

2. Ribosomes: work with mRNA protein synthesis, made up of proteins and RNA, found in cytoplasm

Eukaryotes: 80S, 60 large, 40 small (18S sequencing)
Prokaryotes: 70S, 50 large, 30 small (16S sequencing)

3. Cytoplasm: fluid inner layer

4. Fimbriae: short, bristle-like projections for attachment to surfaces

5. Endospores: not all bacteria have, protect bacteria in a dormant state/ harsh environment, found inside bacteria, sporulation = the process of becoming dormant, germination = process of becoming active

6. Plasma membrane: semipermeable, composed of lipids and proteins, controls transport into and out of cell, most inner layer before cytoplasm (ex: facilitated diffusion, active transport, diffusion, endocytosis (Eukaryotes), sterols (Eukaryotes), and cholesterol (Eukaryotes)

Same for Eukaryotes

7. Cell wall: protects against harsh changing environments and osmotic stress, contains peptidoglycan in bacteria, contains Gram + and Gram -

Steps of Gram stain: dye with crystal violet, iodine (mordant), alcohol (decolorizer), and safranin red
- If mycobacteria complete an acid-fast stain

Gram + has LTA an TA and one membrane
Gram - has LPS and 2 membranes

8. Capsule: protective protein shell, outermost layer

9. Pilus: medium projection, adheres to surfaces, does DNA gene transfer

10. Flagellum: long protein projections made of flagellin for movement (ex: 1= monotrichous, one at each end = amphitrichous, many at one end = lophotrichous, many flagella all over the cell = peritrichous

11. Plasmid: circular, double-stranded DNA not part of the chromosome, and can have 1-100 of the same or different plasmids to help with gene transfer, antibiotic resistance, and virulence factors, found anywhere in the cytoplasm

Not part of Eukaryotes

12. Inclusion: not all bacteria have, helps with the storage of nutrients and other materials, has protein shell, and is found in cytoplasm (ex: lipid droplets store fats, volutin stores inorganic phosphates, sulfur inclusions store sulfur, gas bubbles store gas for buoyancy in water, magnetosomes store metals for movement)

Not part of Eukaryotes; instead, they have vesicles for storage

All cellular microbes have what four (4) components? Cell Membrane, Cytoplasm, Ribosomes, and DNA
What is the only component of all cells that viruses have? Cytoplasm

Know/ be able to identify the shapes of bacteria

Round shape: coccus
Rod shape: bacillus
Vibrio: curved rod shape
Short rods with combo of coccus and bacillus: coccobacillus
Wavy spiral shape: Spirillum
Coiled spiral shape: Spirochete

Microbial growth

Phases of growth

Lag Phase: bacteria gear up for replication by increasing cell size, metabolism, and protein synthesis
Log Phase: exponential growth phase, where bacteria actively replicate and are most susceptible to antibiotics
Stationary Phase: growth curve flatlines bc bacteria are dying at same rate of growth, begin survival mode and sporulation, produce secondary metabolites, and produce virulence factors, and are low on space, nutrients, and oxygen
Death Phase: bacteria die at exponential rate, increase amount of toxic waste, release spores, some spontaneously lyse to feed others, and persister cells refuse to die

How do microbes replicate? Through binary fission, fragmentation, budding, and sexually

What is a biofilm? Communities of bacteria (steps: colonization, attachment, replication, make EPS with antibiotic resistance, EPS kick bacteria out to replicate somewhere else)

How does quorum sensing work? Bacteria want to work together, so they secrete autoinducers, and when you activate enough receptors, they activate a response

Growth requirements – classifications and adaptations

1. Oxygen requirements

Obligate Aerobes: need O2 to survive
Obligate Anaerobes: die in presence of O2
Faculative: mostly need O2 but can survive without it
Microaerophiles: need O2 for survival but not atmospheric O2 (low levels)
Aerotolerant: can survive with or without oxygen
Capnophiles: like high CO2 and low O2

2. pH requirements

Acidophiles: low pH (2-4), high H+ environments, efflux pumps to remove H+ ions, changes membrane composition to withstand low pH
Neutrophiles: neutral pH (7), found within body
Alkaliphiles: basic pH (9-10), modified lipid protein structures, modified electron transport system that use Na+ instead of H+, high OH- environment

3. temperature requirements

Psychrophiles: like freezing temperatures a below 0-15 degrees, die at or above 20 degrees, found in cold lakes or the ocean floor, have hydrophobic proteins to increase flexibility, have decreased secondary stabilizing bonds
Psychrotolerant: cold not ideal but wont kill them, live between 4-25 degrees (fridge temperature)
Mesophiles: moderate temperatures, 20-40 degrees, grow in body
Thermophiles: hot environments 50-80 degrees, hot springs, geothermal soil
Hyperthermophiles: very hot environments 80-110 degrees, found in hydrothermal vents, increased saturation in membranes, increased stabilizing bonds, alter amino acids to prevent denaturation

4. osmolarity requirements

Hypertonic: more water out
Hypotonic: more water in
Isotonic: equal water in and out
Halotolerant: dont require salt but can grow in high salt environments
Halophiles: love salt, found in ocean and salt lakes, have increased cytoplasmic glycerol, have efflux pumps for salt

5. barometric requirements

Barophile: survive high atmospheric environments like the bottom of the ocean (something at top of mountain has low atmospheric pressure)

Microbial Metabolism

Means of generating energy (do the processes require oxygen?, which gives the most energy?)

Glycolysis: does not require O2 bc it can be used during fermentation, used 2 ATP, makes 4 ATP, NET 2 ATP
Kreb’s cycle: requires O2; NET after 1 round= 1ATP, 1 NADH, 1FADH2 (x2 for second round)
Electron transport: requires O2, biggest payout of ATP with NET 34 ATP
Photosynthesis: does not require O2 as it is a waste product, can do oxygenic and anoxygenic

Microbial genetics

DNA Replication – enzymes and functions

DNA gyrase: unwinds DNA (enzyme)
Helicase: unzips DNA (enzyme)
Single-stranded binding proteins: bind to DNA so doesnt close back up (protein)
Single-stranded binding proteins: bind to DNA so doesnt close back up (protein)
DNA polymerase III: lay down new DNA nucleotides, synthesizes leading and lagging strands 5’ →3’(enzyme)
DNA polymerase I: removes RNA primers (enzyme)
DNA Ligase: seals RNA primers (enzyme)
Topoisomerase 4: separates 2 circular chromosomes

Transcription and translation – enzymes and function

1. RNA polymerase: turns DNA→ mRNA (transcription)

2. Ribosomes: 30S small, 50S large, 70S total

3. tRNA: A,P, and E sites, bacteria links transcription and translation bc no nucleus, has anticodon at opposite long 3’ end, high energy bond, same active translation process as Eukaryotes

Be able to do DNA base pairing, transcription, and translation (given codon table)

Also know differences between prokaryotic and eukaryotic Replication, transcription, and translation

Genetic Diversity – how does this work?

1. Transformation: uptake of plasmid into different bacteria and is incorporated into its genetic material

2. Transduction: bacteriophage inserts its plasmid into a bacteria (virus that infects a bacteria)

3. Conjugation: like plasmid transfer (ex: rolling circle replication), “bacterial sex”

4. Transposons: “jumping genes”, transposons will cut out transposon gene into different part of DNA, normally disrupts gene

What are the components of an operon, and what do they do?

Regulatory gene: transcription factor
Promoter: where transcription factor binds
Operator: where repressors bind
Genes: get transcribed together
mRNA: polysistronic (all at once)
Polyprotein: all separate (ex: covid)
Parts of Operon: promoter, operator, and genes

Ch 8: Virology

Know steps of the virus lifecycle

Virus particle binds to the host receptor
Virus is brought into host cell and begins to uncoat
Virus does early gene expression (makes proteins required for replication)
Genoe replication
Late gene expression (makes more virus particles)
Assembly of virus
Leave host cell→ lyse/kill host cell OR non-lytic where viruses are released by a secretory pathway

Baltimore classification

Do they use viral polymerase, or can they use the host polymerases?
What is required to make proteins? Can they translate directly once inside the cell?
- dsDNA: uses host polymerase and ribosomes, cannot translate directly
- ssDNA: uses host polymerase and ribosomes, cannot translate directly
- dsRNA: uses own pol (RdRp), uses host ribosomes, cannot directly translate
- +ssRNA: uses own polymerase, can translate directly
- -ssRNA: uses own pol (RdRp), uses host ribosomes, cannot directly translate
- ssRNA + RT: use own polymerase but when they enter the host cell they use the host polymerase, cannot translate directly
- dsRNA + RT: use own polymerase but when they enter the host cell they use the host polymerase, cannot translate directly
May ask you about specific viruses from the disease chapter related to what we know/can infer based on their Baltimore classification
- Infuenza Virus: -ssRNA, uses own polymerase, cannot translate directly
- Sars COV2: +ssRNA, uses own polymerase, can translate directly
- Herpes Simplex 1 and 2: dsDNA, uses host polymerase, cannot translate directly
- Human Papillomavirus: dsDNA, uses host polymerase, cannot translate directly
- Norovirus: -ssRNA, uses own polymerase, cannot translate directly
- Ebola Virus: -ssRNA, uses own polymerase, cannot translate directly
- HIV: ssRNA + RT, uses own polymerase but when it enters host it uses their polymerase
- Rabies Virus: -ssRNA, uses own polymerase, cannot translate directly
- Polio Virus: +ssRNA, uses own polymerase, can translate directly