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

Francesco Redi

Scientist who tested spontaneous generation with rotting meat and maggot formation, refuting spontaneous generation.

Needham

Scientist who supported spontaneous generation through boiling chicken broth and sealing the container.

Spallanzani

Scientist who refuted spontaneous generation with further tests involving open and closed containers.

Louis Pasteur

Scientist who used swan-neck flasks to definitively refute spontaneous generation.

Anthony van Leeuwenhoek

First to observe eukaryotic microbes, calling them 'wee animalcule'.

Robert Hooke

Coined the term 'cell' when examining cork.

Matthias Schleiden

Observed cells in plant tissues.

Theodor Schwann

Observed cells in animal tissues.

Rudolf Virchow

Observed cells dividing to make new cells.

Hippocrates

Suggested that disease has natural causes.

Thucydides

Advocated for evidence-based analysis of cause and effect, suggesting immunity after plague observation.

Marcus Terentius Varro

The first to propose that unseen things cause disease.

Ignaz Semmelweis

Observed disease spread among patients and instituted hand washing to reduce infection.

Joseph Lister

Surgeon who implemented hand washing and sterilization of equipment to minimize post-surgical infections.

Robert Koch

Developed Koch’s postulates to determine the cause of disease.

John Snow

Investigated the London cholera outbreak and identified contaminated water pumps as the source.

Bacteria

Microbial domain composed of unicellular organisms without a nucleus.

Archaea

Domain of life with unicellular organisms that are prokaryotic and often extremophiles.

Eukarya

Domain of life that includes organisms with a nucleus, which can be unicellular or multicellular.

Viruses

Acellular entities that cannot replicate independently and do not fit into traditional domains of life.

Prions

Infectious agents composed solely of protein and can cause disease.

Ribosomes

Cellular structures responsible for protein synthesis, differing in size between prokaryotes and eukaryotes.

Nucleoid

Region in prokaryotic cells containing genetic material, lacking a surrounding membrane.

Cell wall

Protective structure in bacteria composed of peptidoglycan, varying between Gram-positive and Gram-negative.

Capsule

A protective protein shell found on the outside of some bacterial cells.

Fimbriae

Short, bristle-like projections in bacteria for attachment.

Flagellum

Long, whip-like structure for bacterial motility, made of flagellin.

Plasmid

Circular DNA molecule found in bacteria that can carry genes for antibiotic resistance.

Biofilm

Community of bacteria that adhere to surfaces and encase themselves in a protective matrix.

Lag Phase

Initial phase of bacterial growth where cells prepare for replication.

Log Phase

Exponential growth phase of bacteria where they are most vulnerable to antibiotics.

Stationary Phase

Growth phase where the rate of cell growth equals the rate of cell death.

Death Phase

Final phase in bacterial growth where cells die at an exponential rate.

Binary Fission

A method of asexual reproduction in bacteria where a single cell divides into two.

Autoinducers

Molecules secreted by bacteria during quorum sensing to communicate and coordinate group behavior.

Obligate Aerobes

Bacteria that need oxygen for survival.

Obligate Anaerobes

Bacteria that are killed by oxygen.

Facultative Anaerobes

Bacteria that can grow with or without oxygen.

Acidophiles

Organisms that thrive in acidic environments (pH 2-4).

Thermophiles

Organisms that thrive in hot environments (50-80 degrees Celsius).

Hyperthermophiles

Organisms that thrive in extremely hot environments (80-110 degrees Celsius).

Psychrophiles

Organisms that prefer very cold temperatures (below 15 degrees Celsius).

Glycolysis

Metabolic pathway that converts glucose into pyruvate, yielding 2 ATP without requiring oxygen.

Kreb’s Cycle

Aerobic process that produces 1 ATP, 1 NADH, and 1 FADH2 per round, requires oxygen.

Electron Transport Chain

Final stage of cellular respiration that generates the bulk of ATP and requires oxygen.

Transformation

Uptake of foreign DNA by bacteria from their surroundings.

Transduction

Transfer of genetic material from one bacterium to another via a bacteriophage.

Conjugation

Direct transfer of plasmid DNA from one bacterial cell to another through a pilus.

DNA gyrase

Enzyme that unwinds DNA ahead of the replication fork.

Helicase

Enzyme that unzips the DNA double helix during replication.

RNA polymerase

Enzyme responsible for synthesizing mRNA from a DNA template during transcription.

Operon

A functional unit of DNA containing a cluster of genes under the control of a single promoter.

Virus Lifecycle

The sequence of events a virus goes through to enter a cell, replicate, and exit the host.

Baltimore Classification

Classification of viruses based on their type of genome and method of replication.