MIC 102 Final Exam

What happens in high salt concentrations?

High osmotic pressure places two stresses on microbes: - Decreases activity of water and its ability to cells (dries them out). - Decreases turgor pressure -> water will leave the microbe. - To maintain turgor pressure, cells will increase solute concentration in cell membrane. - Proteins will become inactivated.

Prokaryote vs eukaryote

Prokaryotes: - No true nucleus, lack true membrane-bound organelles, circular DNA contained in nucleoid that lacks a membrane. Eukaryotes: - Contains several types of membrane-bound organelles, linear DNA. - Both have DNA, ribosomes, cell membranes.

Differentiation

- Adaptive response of the cells to their environment. - Majority of the time, the change will occur in its structure and functional attributes.

Pili

- Aids in motility, adherence, transfer of nutrients, protein, and genetic material, aid in reproduction in some species. - Can act has grappling hooks. - Extend and retract via polymerization and depolymerization. - Proteins facilitate adhesion at tips of pilus.

Metabolomics

- All metabolic intermediates.

Proteomics

- All the proteins present in an environmental sample. - Extract proteins during cultivation.

Lactose (+), glucose (-)

- Allolactose to prevent lacI to bind to operator, sequence is open for RNAP to bind. - cAMP is produced, CAP is active -> they bring RNAP to the promoter sequence and associate. - Lac operon is transcribed in increasing amounts. - OPERON ON

Porin

- Allows different molecules to cross passively. - Lets things larger than glucose in but size matters. - Hydrophobic or large hydrophilic molecules require dedicated transporters.

Allosteric site

- Allows effectors to bind to the protein, resulting in conformational change.

Barophilic

- Also known as piezophiles. - Prefers environments with high pressure. - > 1 atm

Aerobic respiration

- ATP yield = ~30 mol of ATP, max 38 mol - Terminal electron acceptor = Oxygen - O₂ requirement = Yes

Viral latency

- Ability of virus to persist in host cell without proliferating and causing damage. - Can be established via episome or integrate into the host genome.

Energy and carbon sources

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Microbes defending against adaptive immunity

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Protein elongation

- 15 amino acid residues in nascent chain per second. - Entry in A site: EF-Tu-GTP elongation factor loads A site with aminoacyl-tRNA using GTP hydrolysis. - The factor is released and is recharged with GTP from another elongation factor (EF-Tu cycle). - Peptide bond formation (P site): Amino group of amino acid is close to the terminal acid group of growing peptide. - Catalyzed by segment of 32S RNA of 50S subunit. Peptide attached to tRNA at A site. - Translocation (E site): Another elongation factor TF-G-GTP binds to A site and transfers it to P site. - Pushes the tRNA in P site to the E site. - Translocation requires hydrolysis of GTP. - Uncharged tRNA enters the E site and exits.

Ion-coupled transport

- Active transport - Coupled to another ionic gradient (proton, sodium) set up by ATP. - Transport can go in either direction.

Protein initiation

- 30S subunit + IF1 and IF3 bind to Shine-Dalgarno sequence. - IF2-GTP loads initiator tRNA onto the start codon and IF3 is removed. - GTP hydrolysis occurs to load 50S subunits and remove IF units. - 50S requires AUG start codon on mRNA -> fMet - Requires IF2-GTP to hydrolyze and eject initiation factors to dock the 50S.

Spo0A phosphorelay system

- 5 sensory kinases start off the phosphorelay system. - Triggers: Cell density and starvation. - At low levels, Spo0A cannot prevent synthesis of a repressor that turns off the expression of several genes. - When spo0A levels are high, represses the synthesis of AbrB, genes coding for proteins needed for sporulation are expressed. - Cell is now committed to sporulation.

Microbes defending against innate immunity

- <any bacterial pathogens can modify the molecular structure of their PAMPs/have capsules to mask PAMPs, thereby avoiding immune detection through stealth and evasion. - The capsule of the bacterium can also prevent detection and phagocytosis. - Pathogens can also subvert innate immune responses by expressing protein effectors, which directly interfere with Toll-like receptor signalling pathways. - Mimic host by also having sialic acid.

Murein

- A peptidoglycan polymer consisting of sugars and amino acids. - Forms a mesh-like layer outside the plasma membrane of most bacteria, which forms the cell wall.

Endospore

- A resistant asexual spore that develops in some bacterial cells in the Firmicutes phylum. - Spore/seed-like form but not a true spore (they are just agents of survival). - Resists extreme environmental stressors. - Germination upon nutrient availability and become vegetative cells again.

Vaccines

- A sight exposure to an agent or its antigens that starts a primary response that generates T and B lymphocytes. - Immune system retains a memory of the agent. - Some B lymphocytes turn into memory cells that will reactivate a quicker response (secondary response) next time the virus occurs.

ATP binding cassette

- ABC - Binding proteins bring solutes to membrane protein complex using ATP. - ATP hydrolysis used to open channels and bring in solutes.

Fueling products

- ATP and reducing power NADPH - From organic, inorganic, photochemical redox reactions.

What is anaerobic respiration?

- ATP synthesis using sulfate, nitrate, sulfur, etc. - Used in low-oxygen environments.

Anaerobic respiration

- ATP yield = 2 mol of ATP - Terminal electron acceptor = Nitrate, nitrite, sulfite, etc. - O₂ requirement = No

Fermentation

- ATP yield = 2-4 mol of ATP - Terminal electron acceptor = Pyruvate - O₂ requirement = No

Entner-Doudoroff pathway

- Alternative link between pentose phosphate pathway (metabolic pathway parallel to glycolysis) and glycolysis. - Pentose phosphate pathway generates: NADPH and pentoses, ribose 5-phosphate (precursor for nucleotides) - In gram-negative bacteria. - Uses glucose and catabolized into pyruvate.

Anammox

- Anaerobic conversion of ammonia and nitrite to N₂ (gas). - Microbes that perform this process were unable to be cultivated. - 1/3 or more of dinitrogen production in oceans is derived from anammox.

Genomic

- Analysis of an entire genome. - Extra DNA during cultivation.

Stationary phase and stress

- Any stressor or combination of stressors can lead to the same general outcome. - sRNA is used as first step to integrate multiple inputs into a single response. - RpoS (sigma factors) is the main convergence point. - Changes transcriptional factors, gene expression goes up or down depending on response.

Biased random walks

- Approaches goal through focusing behavior by adjusting frequency of runs and tumbles.

Technology and knowledge of environmental samples

- As our techniques have gotten better and our sequencing got cheaper, we can use better markers. - Not just one locus or rRNA, but confirm it with with a couple more. - Leads to more accuracy due to longer sequences. - Cultivation-independent identification

Ammonia assimilation

- Assimilated to make glutamate using reducing power of NADPH. - 2-oxoglutarate incorporates ammonia and synthesizes glutamate. - Glutamine and 2-oxoglutarate synthesizes glutamate. - Glutamate incorporates another ammonia and makes glutamine with ATP.

Stages of viral lifestyle

- Attachment: Bind to host cell receptors, sugars, or proteins. - Penetration: Eject DNA into host cell. - Biosynthesis: makes copies of its viral genome, nucleic acid, and proteins. - Shut down or slow bacterial synthesis. - Maturation: assemble new virions; capsid filled w/ DNA/RNA genome. - Release: Cell lysis

When attractant is sensed

- Attractant binds to MCP. - MCP binding causes MCPs to inhibit CheA's autophosphorylation. - No active CheA -> no active CheY -> counterclockwise flagellar motion -> RUNNNNN - CheR can methylate the MCP and reactivating CheA. - More attractant is needed to change conformation again before it could inhibit CheA. - Therefore it will alternate. - Repellent binds. - Stimulates cheA autophosphoryolation -> more tumbling - Higher activity CheA also phosphorylates CheB, which removes the methyl groups from MCP. - MCP will sense smaller quantities of repellent in order to prevent cell from habituating.

Sickle cell gene

- Autosomal genetic disorder that is a missense mutation in Hb. - Heterozygous HbS carriers are protected against malaria. - Occurs in regions most affected by malaria -> co-evolutionary response. - Sickle cell phenotype offers the individual resistance to plasmodia infection by making RBCs less hospitable for trophozoites and schizonts.

Auxiliary pathway

- Auxiliary pathways are alternative ways to make precursor metabolites to avoid certain products accumulating.

B lymphocytes

- B cells - Each produce a different antibody. - Can clone themselves when dormant to increase response when it is needed. - Reproduces many antibodies at a time. - Responsible for antibody formation.

Bacterial cell walls

- Bacteria have a cell wall for cell support and protection against mechanical stress or damage. - Made of peptidoglycan or murein.

Twitching motility

- Bacteria that attach to the surface of host cells or to inanimate surfaces. - The cells move in a jerky fashion on solid surfaces. - Uses pili to grab onto surfaces and translocate across the surface.

Transduction

- Bacterial DNA is transferred from viruses. - Bacteriophages make mistakes when packing DNA during assembly and accidentally carry DNA from host to a new one. - Transducing particles: The virions carrying the host DNA. - Generalized transduction and specialized transduction.

Death phase

- Bacterial culture growth phase where population decreases exponentially. - Could be due to lack of nutrients, environmental temperatures above or below tolerance band for species, or other conditions.

Stationary phase

- Bacterial culture phase where population growth will begin to decline due to depleted nutrient supply and waste products accumulating. - Cell growth reaches a plateau, no overall population growth. - Bacteria that form spores produce endospores (help with adapting to conditions).

Exponential phase

- Bacterial culture stage where cell growth rate is at max. - Cells are dividing via binary fission, metabolic activity is high. - Antibiotics most effective during this period.

Bacterial versus archaeal cell envelope

- Bacterial phospholipid bilayer has glycerol di-ESTERS (fatty acid chain). - Archaeal phospholipid bilayers and monolayers have glycerol di-ETHERS (isoprenoids).

Photosynthesis

- Bacterial phototrophs use light sensitive pigments (bacteriophylls). - Lights hits the pigments and electrons are photoexcited. - Electrons are moved to electron transport chain. - ETC uses proton motive force, H+ ions enter ATP synthase, producing ATP. - ATP and NADPH generated and used to fix sources of carbon to produce precursor metabolites required for the biosynthesis of macromolecules.

Prokaryotic cell division

- Binary fission. - Most gram-negative bacteria: Divide by a constriction in the middle. - Some gram-positive bacteria: Do not divide with constriction.

SeqA

- Binds to unmethylated DNA and blocks DnaA from initiating in those spots. - SeqA will dissociate when the cell methylates.

Supercoils

- Lowers energy required to separate 2 strands of DNA double helix. - Topoisomerase and gyrase are use to maintain supercoiling.

What kinds of viral genomes require macromolecular synthesis before protein production?

- Both single stranded and double stranded DNA viruses require macromolecular synthesis, they both need to make mRNA before protein. - Double stranded RNA also requires macromolecular synthesis, they need to make mRNA. - Only ss+RNA can synthesize protein directly.

Glycolysis

- Breakdown of glucose by enzymes, releasing energy and pyruvate. - Glucose -> 2 pyruvate + 2 NADH + 2 ATP - (2 ATP investments to get 4 out).

Building blocks

- Building blocks from environment are not readily available. - Blocks are made from 13 precursor metabolites. - Building blocks are more reduced than the substrates that made them.

How are protists classified

- By if they are motile or nonmotile. - Means of locomotion: flagella, pseudopodia, cilia, and nonmotile/Apicomplexa 9

How are prokaryotes classified?

- By the 16s rRNA. - rs rRNA: Component of 30s subunit that binds to SD sequence.

What can transcriptome data tell us that genomics data cannot?

- Can tell us how much of the gene is being expressed. - Genomics tells us what is available (tool shed). - Transcriptomics tells us what tools are being used and how often. - Organisms have different transcriptome under different environmental conditions -> good way of measuring expression and gene activation.

Chytridiomycosis

- Caused by aquatic fungus -> chytrid fungus - Infects amphibians, - Spores infect outer skin layers. - Frogs use their skin for nutrient uptake, hydration, and sometimes respiration. - When infected, the fungi makes their skin thick, inhibiting these processes. - Infection leads to death, and decreased numbers of population.

Gram-positive cell wall

- Cell envelope made of thick layer of peptidoglycans. - Constantly losing murein outside the cell membrane. - Peptidoglycan is always needed to be produced. - Have techioic acids that are unique to gram-positive cell wall, acting as negative charge and adherence. -

When do cells know to start replication

- Cell will need sufficient ATP, sufficient components to make two identical copies of its chromosome. - DnaA accumulates and once there is enough, it binds to DnaA boxes and ATP. - SeqA protein: Sequesters DNA to the origin.

Function of capsules and slime layers

- Cells can synthesize these layers in response to environmental cues or due to their cellular makeup. - Retains water and nutrients, protects against dessiccation, limits diffusion of harsh chemicals into cell. - Helps adherence to surfaces and builds multicellular communities (biofilm).

Assembling cell structures

- Cells must have same structures as progenitor. - Must have complex envelope, nucleoid, cytoplasm with enzymatic machinery and polyribosomes. - Macromolecular synthesis of proteins require highest energy cost and highest reducing power cost.

Phagocytes

- Cells that protect the body by ingesting harmful foreign particles, bacteria, and dead or dying cells. - Neutrophils, macrophages, dendritic cells, and lymphocytes use phagocytosis. - Opsonins -> peptides that attract phagocytes to eat certain particles. - When the prey is inside the phagocyte, lysosomes digest the prey. - Majority of bacteria that invade humans are killed or removed by phagocytes.

Missense mutation

- Change in base pair leading to a codon that encodes a different amino acid. - Effect: Varies from little effect to complete loss of function, depending on what amino acid is coded.

Nonsense mutation

- Change in base pair which prematurely codes for a stop codon (UAG, UGA, UAA). - Effect: Usually loss of function.

Silent mutation

- Changes in the base pair that encodes for the same amino acid as original. - Effect: No effect

Sec B

- Chaperone protein used in sec system that coats the proteins being transferred to prevent them from being folded while they are passing.

Methanogens

- Characterized by ability to generate methane as a byproduct of their metabolism. - Using hydrogen to reduce carbon dioxide. - Thrive in carbon-rich, anaerobic environments. - Psychrophilic and hyperthermal environments. - Eg. Gas from cattle and other ruminants release methanogens.

No attractant sensed

- CheA autophosphorylates at steady rate. - CheA transfers its phosphase to CheY. - Phosphorylated CheY will change direction of the rotation to clockwise. - CheZ dephosphorylates CheY so that tumbling is not permanent. - Alternation of tumbles and runs.

Why is yeast a useful model organism

- Cheap and easy to grow. - Small genomes - Can participate in asexual and sexual reproduction. - Genetics to study mitotic and meiotic cells. - Diploid cells can harbor recessive mutations in essential processes (cell division, replication, transcription). - Helps scientists understand the relationship between dominant and recessive. - Diploid form of growth -> two copies of genes -> can still grow if there's a mutation because there is a copy of its true DNA. - Can accept large plasmids for substance production.

Siderophore

- Chelates to metal ions using 2+ coordinate bonds in a binding molecule (usually organic). - Transports iron across cell membranes. - Strongest soluble Fe3+ binding agents known.

DNA synthesis

- DNA is semiconservatively replicated: Each strand is a template for a new complementary strand. - ~1000 nucleotides are added per second because DNA is circular in bacteria and works bidirectionally.

What happens in high temps?

- Chemical reactions go more slowly and eventually stop. - Macromolecules will denature. - Growth rate declines. - Protein thermostability determined by hydrogen bonding, hydrophobic internal packing, salt bridges. - Heat resistance is genetically encoded. - Proteins have higher charged amino acids on surfaces which promotes salt bridges. - Salt bridges are good for heat. - Salt bridges: Oppositely charged residues that help achieve higher thermostability. - Heat shock proteins + chaperones: Protect proteins from heat denaturation/facilitates folding and refolding of DNA. - DNA will separate in high temperatures. - Thermoprotective DNA binding proteins prevent this. - Reverse gyrase: Introduces positive supercoils (increases thermostability).

Symbiotic relationships

- Classified by interaction between two organisms. - These types of relationships are essential to many organisms and ecosystems, providing a balance that can only be achieved by working together.

How can existing antibiotics be used more effectively?

- Combine antibiotics to target multiple pathways (Ex. Cell wall inhibitor + gyrase inhibitor) - Only one drug may delay growth but two may stop growth and kill cells. - Precision antibiotics: Antibiotics targeting more specific responses rather than a wide range against many strains.

Gas vesicles

- Common in cyanobacteria (photosynthetic). - Tune the buoyancy of the cell to stay near surface of environment to gather maximum light. - Made of protein cells permeable to gas. - Impermeable to water. - Gas diffuses to reach equilibrium.

T helper cells

- Communicators that stimulate both branches of the immune system. - Make cytokines that stimulate both B and T lymphocytes. - Stimulate cytokines that result in inflammation.

Complement system

- Complement pathways are activated in response to infection. - Proteins that work to induce an inflammatory response. - Converge on C3 protein. - The complement system is activated by MAMPs (alternative pathway). - The lectin pathway uses lectin bound to cell surface sugars as an activator. - The 'classical' pathway requires antibody-antigen binding. - Activation of complement system means cleaving of complement proteins and undergo proteolysis. - These release peptides that are used in inflammatory response. - Includes membrane attack complex, chemotaxons (attract white blood cells to site of inflammation).

Reactivation

- Concept of viral latency that involves latent viruses become virulent again and multiplying. - Different factors could trigger reactivation.

Gram positive bacteria envelope

- Contains murein. - Lacks outer membrane. - Thick peptidoglycan cell wall -> enriches for polar molecules such as phosphates, sugars, charged amino acids. - Has teichoic acid: Provides rigidity and promotes stickiness of bacteria to specific surfaces. - Lipoteichoic acid: A type of teichoic acid that anchors to peptidoglycan cell wall to cell membrane. - Chemical feature: Contains LYSINE amino acid instead of DAP to crosslink peptide chains with d-alanine residue (links the layers).

Gram negative bacteria envelope

- Contains murein. - Thin peptidoglycan cell wall. - Has outer membrane that is resistant to harmful chemicals. - Inner leaflet made of phospholipids. - Outer leaflet made of lipopolysaccharide. - Lipopolysaccharide makes up most of outer membrane, increases structural integrity, aids in bacterial survival. - Contains DAP

Prokaryotic cytoplasm

- Contains ribosomes - Lacks true organelles -

Chemostat

- Continuous culture device. - Used in labs to keep culture at desired temperature and gas atmosphere. - Volume kept constant by adding fresh medium while culture medium is removed at the same time. - Medium is equilibrated to ensure consistency. - To function properly, cell density must not exceed the density that allows balanced growth in a batch culture. - Rate of addition of fresh medium determines the growth rate in the culture vessel. - Density of cells is determined by concentration of limiting nutrient.

Leading strand

- Continuously synthesized strand - Synthesized 3' to 5'. - DNA polymerase 3.

Human microbiome and human health

- Controls digestion and benefits your immune system. - Bacteria help with digestion, producing certain vitamins, regulate immune system, and keep us healthy. - Suppress and outcompete potentially pathogenic microbes. - Can help break down complex energy sources and help synthesize metabolites that our body cannot break down on our own. - Deviations to normal microbiome interactions can lead to disease and allow pathogens into gut. - This can cause certain bacteria to stop performing degradation and synthesis jobs.

Ammonification

- Conversion of assimilated nitrogen or organic nitrogen compounds into ammonia.

Nitrogen fixation

- Conversion of atmospheric nitrogen (N₂) into ammonia.

Lysogeny or lysis

- Depends on number of infecting particles per cell, the environment, physiological state of the host.

When does a virus choose to become lysogenic?

- Depends on the environmental conditions. - If the environment is good and the cell can be active, the virus will choose to be lytic and replicate.

What strategies help combat antibiotic resistance?

- Designing new antibiotics. - Identifying new targets for new classes of drugs. - Modifying existing drugs to increase their strength (new generations). - Develop new vaccines (won't need antibiotics as much). - Prolong usefulness of existing drugs. - Alternating between classes of antibiotics. - Restrict some antibiotic use. - Completing course of antibiotics. - Only use when positive test for infection.

Lytic virus

- Destruction of an infected cell and its membrane. - Characteristic of virulent phages. - Viral DNA is free-floating within the bacterial cell and replicates separate from host DNA.

Methylation

- Developed DNA is usually methylated at each strand. - Newly synthesized strands are not yet methylated. - SeqA binds to the newly synthesized strands and prevents DnaA from prematurely binding and initiating DNA synthesis.

Gram stain

- Developed by Christian Gram to determine structures of bacteria using stains that contrasted their features. - Can be distinguished by gram positive or gram negative bacteria.

Coammamox

- Direct conversion of ammonia to nitrate. - Several species of Nitrospira perform this. - Low levels of nitrite are accumulated transiently and eventually oxidized to nitrate by cells. - Pathways for both ammonia and nitrite oxidation are activated at the same time.

FTsZ

- Directs cell division by making a constricting ring (Z-ring) where cell will eventually partition and close as cell divides. - Located at the septum (where division occurs). - Polymerizes to make the Z-ring.

Lagging strand

- Discontinuously synthesized strand. - Synthesized 5' to 3'. - Produces Okazaki fragments that are separated by RNA primers. - DNA polymerase only works in 5' to 3' so there are only short fragments that are produced. - Since DNA polymerase has to move backwards away from the fork, it discontinues.

How do we know organelles used to be endosymbionts?

- Divide by binary fission. (Chloroplasts and some mitochondria use FtsZ ring for division) - Protein synthesis starts with formylated methionine (bacterial) and uses ribosomes resembling those of prokaryotes. - Circular chromosomes and no histones. - Transfer of many ancestral bacterial genes to host cell nucleus and loss of many others.

DNA initiation

- DnaA and ATP bind to origin of replication, melting the strands. - DnaC and ATP interact with DnaA to load DnaB onto DNA strand. - SSBs stabilize the open stands. - Strands are relaxed by DNA gyrase (induces negative supercoils). - Helicase unwinds the strands and replication forks open.

Why are archaea able to grow at very high temperatures?

- Do not have phospholipid bilayers. - Have isoprenoids that are linked to glycerols to highly stable ether bonds rather than ether bonds. - Ethers are more stable than esters and monolayers are more stable than bilayers. - Monolayers are more table in high temperature, pH, and salinity. - Monolayers are single, packed layers or atoms.

Replicating DNA viruses

- Double stranded (dsDNA) can blend into host cell's machinery. - Recognized and transcribe by the host cell. - Linear dsDNA can even circularize to be easily recognized. - Linear genome will start to replicate like rolling circle replication. - Single stranded DNA (ssDNA) acquire other strands of DNA and then replicate like dsDNA. - ssDNA must have right polarity before replication.

DNA polymerase 1

- During replication, RNA primer fills the lagging strand of the DNA. - Exonuclease activity (enzyme) of DNA pol 1 removes RNA primer and replaces it with newly synthesized DNA in 5' to 3' direction. - Fills in DNA gaps that arise during DNA replication, repair, and recombination. - Editing, proofreading in lagging strand.

Slime layer

- Easily removable slime that is unorganized and extracellular. - High molecular weight polysaccharide, produced when environment demands for it. - Allows for retention of water, prevents diffusion of harsh chemicals, adhesion, deters phagocytosis. - Made of exopolysaccharides, glycoproteins, and glycolipids.

Allosteric inhibitor

- Effector that binds to the allosteric site. - Decreases the protein's activity.

Allosteric activator

- Effector that binds to the allosteric site. - Enhances the protein's activity.

Natural transformation

- Eg. Griffith's rat test - Transformation in a natural environment, not artificially.

Transmembrane ion gradient

- Energy can be harvested from an ion gradient generated across the cell membrane. - Higher concentrations of ions on one side of the membrane compared to the other. - Ions must pass through specific channels. - Energy is generated as ions pass down the concentration gradient to equilibrium. - Generates the proton motive force.

ATP synthase

- Enzyme complex that phosphorylates ADP to make ATP. - Lower portion rotates in response to movement of protons down concentration gradient in membrane. - 3-4 protons pass through to make 1 molecule of ATP. - Can work in opposite direction.

Topoisomerase I

- Enzyme that changes the topology of DNA without ATP hydrolysis. - Counteracts gyrase by making single strand breaks and relaxes negative supercoils.

Apicoplasts

- Ex-microbes that are organelles of Plasmodium protist species. - Function: Photosynthesis, synthesis of fatty acids, repair, replication, and transcription of DNA. - Result of an ancient event in which a eukaryotic ancestor acquired a chloroplast but converted it to a major photosynthetic factory with other abilities.

Alpha proteobacteria

- Ex. Rhizobium - Interacts with plants and either cause disease or benefit the host.

Kinetoplast

- Example of an ex-microbe that is a highly specialized mitochondrion. - Organized as a mesh of interwoven DNA circles that are like chainmail. - Encode for ribosomal RNA and proteins for energy transduction. - Encode for an RNA called guide RNAs that edit maxicircle RNA transcripts so they can be translated.

Dinoflagellates

- Example of diatom protists that encase themselves in a polymeric cell wall. - Some produce red photosynthetic pigments -> form algal blooms known as red tides. - Bioluminescent - Some produce potent neurotoxins that can be transmitted through the food chain.

Cordyceps

- Example of parasitic agent. - Spores that infect target insects through their respiratory/GI tract and mycelia grow towards the brain. - Secretes compounds into the brain that disorients the host and causes the insects to climb upward towards higher ground. - As the fungus propagates, it eventually kills the host and forms fruiting bodies, ready to disperse spores across a wider area.

Toxoplasma gondii

- Example of parasitic interaction. - Parasitic protist that is acquired as a toxic plasma from environment and colonizes the gut in different forms (sexual or vegetative). - Cats are primary/"definitive" host -> parasite colonizes their gut and releases oocytes that spreads through feces. - Rodents and humans are secondary hosts → infected by the cats feces - Infected rats become attracted to cat urine, increasing their chances of being eaten and passing T. gondii back to the cat. - Rat induces strong immune response to kill off the parasite but more resistant oocytes persevere and remain in rat's tissue. - In humans → can lead to acute toxoplasmosis symptoms including flu-like symptoms, seizures, and eye issues.

How can parasites manipulate host behavior?

- Exploit their hosts in various ways. - Behavior of animals or plants may be altered significantly by their interaction with parasitic microbes.

Episome

- Extrachromosomal element that replicates alongside host cell, like a plasmid.

Extreme halophiles

- Extremely salty environments. - Depends on high salt concentrations to grow. - Thrive in salt-evaporation ponds, that turn bright red from produced pigments. - Concentrate KCl intracellularly when growing near-saturated brine. - Their proteins are resistant to high concentrations of salt that can denature proteins. - Dependent on supply of oxygen. - Eg. Halobacterium halobium - Bacteriorhodopsin: Proton pump that generates sufficient ATP when oxygen becomes limiting.

Feeder pathway for glycolysis

- Feeds glucose or another starting material into the pathway.

Movement of phospholipids from inner to outer leaflets

- Floppase: Inner to outer - Flippase: Outer to inner - Scramblase: Bidirectional

Decatenation

- Following DNA replication, the genomes are concatenated -> DNA is interlocked and must be separated from each other. - Topoisomerase 4 introduces double stranded breaks in molecules and another enzyme reseals them once they're detangled.

Frameshift mutation

- Gain or loss of several base pairs so that the frame of codons is shifted over. - Effect: Usually loss of function.

Transformation

- Genetic change that occurs in a cell after it has taken up soluble DNA from its environment and recombined at least part of it into its genome. - Proteins on the cell wall bind to free-floating DNA in its environment. - Cells are called "competent" if they can transform.

Characteristics of LUCA

- Genetic code/DNA, ATP utilization as primary energy source, ribosome mediated protein synthesis, and cell membrane. - These are all common to both bacteria and archaea. - DNA exists in all domains of life and assuming all life comes from a common ancestor, LUCA will need DNA. - All cells uses ATP as their primary energy source, the different being how they make ATP. - Ribosome mediated protein synthesis is the only known way of producing proteins.

Metagenomics

- Genomes of multiple organisms.

Plasmodium

- Genus of protists that are obligate parasites of vertebrates and insects. - Life cycle involves development in a blood-feeding insect hosts, which then injects parasites into a vertebrate host during a blood meal. - Malaria is spread through 4 species of plasmodium -> most virulent is P. falciparum. - Malaria can be controlled by sanitary measures -> insecticides, drainage of pools of water where mosquitoes develop, and mosquito netting.

Delta proteobacteria

- Gram-negative bacteria with unique respiratory abilities. - Ex. Myxobacteria -> soil bacteria that glide on surfaces and form myxospores.

Actinobacteria

- Gram-positive - High GC content in genomes - Ex. Streptomyces - Abundant in soil, accounting for most of the breakdown of organic matter. - Form spores that allow for colonies to stick together. - Major contribution: Produce antibiotics - Antibiotics are a product of secondary metabolism typical of streptomyces, fungi, and plants.x

Griffith natural transformation experiment

- Griffith studied natural transformation of R cells to S cells. S cells are capsule-bearing strains that killed mice. - R cells are capsule-free strains that did not kill the mice. - Conclusion: The capsule was the component that killed the mice. - Heat killed S-cells survived. - Heat killed S-cells with R cells died -> The dead S cells transformed the R cells, turning them smooth and killing the mice. - These were recombinants. - R cells acquired the S cells chromosomes and recombined it with theirs, transforming them. - Probability: This occurs likely because of the proximity of the cells.

Retroviruses

- Group of RNA viruses that insert a DNA copy of its genome into host cell to replicate. - Ex. HIV - When in the host, virus uses its own reverse transcriptase to produce DNA from RNA genome. - DNA is incorporated into host cell genome by integrase and host replicates DNA with the viral DNA. - Due to the undetectable nature, virus will be able to persist in host DNA

Swarming motility

- Groups of rod shaped bacteria moving on surfaces. - Theorized that this allows the bacteria to push others along. - Swarming requires a slime.

Glyoxylate cycle

- Growth of acetate -> glyoxylate cycle - Alternative to TCA cycle, bypasses two carboxylation reactions. - Carbon is conserved and used to synthesize macromolecules instead of being released as CO2. - Synthesizes: Carbohydrates

Decimal reduction time

- Heating time in minutes at a constant temperature will result in reducing microorganisms by a factor of 10. - Ex. (1000-100)/1000 = 900/1000 = 90%

Sliding clamp

- Helps hold DNA pol 3 in place while nucleotides are being added.

Carbon source

- Hetero = Organic compounds - Auto = Inorganic (CO2)

Enterosomes

- Heterotrophic bacterial version of carboxysomes. - No RuBisCo but allows for metabolization of other compounds with likely harmful intermediates.

Protists

- Highly diverse group of 50k mostly unicellular species with a eukaryotic body plan. - Carry out half of all photosynthesis on Earth, mainly in oceans. - Other protists live by eating smaller microbes. - Certain protists contribute to geology of our planet by making insoluble shells of silica or calcium carbonate. - Purify wastewater, source of food to aquatic animals, decompose plant matter, consume great amounts of bacteria. - Make industrial products.

How can multidrug resistance arise?

- Horizontal gene transfer - Certain genes encoding enzymes that are resistant from the effects of antibiotics can transfer via conjugation to a cell.

How can horizontal gene transfer promote antibiotic resistance?

- Horizontal gene transfer allows nonresistant strain of bacterial to acquire the genetic mutation/code that another cell has survived through evolution. - This means that as long one bacterial cell has acquired resistance, the surrounding cells can acquire resistance. - The surrounding cells can acquire through that cell rather than trying themselves. (R factors)

Mutation and pathway

- If enzyme is not able to function at any step in the pathway, any compound in the pathway can still be produced as long as there are precursor metabolites on either step of the defective enzyme. - Since the central pathways are connected, they could use a different pathway to reach the same product.

Negative feedback control loop

- If there is a high concentration of end product, the cell will no longer need to synthesize it. - Brings the system to homeostasis.

Innate immune response

- Immediately prevents the spread of foreign pathogens throughout the body.

Adaptive immune response

- Immunity that occurs after exposure to an antigen either from a pathogen or a vaccination. - Uses immunological memory to learn about the threat and enhance the immune response accordingly. - T and B cells

4 major mechanisms for acquiring antibiotic resistance

- Inactivation of drug by enzymes - Activation of efflux pump - Inhibition of drug uptake - Alteration of drug target

Gamma proteobacteria

- Include human pathogens, most that infect digestive system. - Ex. E.coli, pseudomonas

Assimilation

- Incorporation of nitrogen into the organism. - Using nitrogen to make cellular constituents such as proteins, nucleic acids, and phospholipids.

Monocytes/macrophages

- Long-lived cells that can differentiate further. - Arrive at sites of infection after neutrophils and clean up debris left by neutrophils. - Communicate with other arms of the immune system by releasing cytokines -> activate complement system, promote inflammation, or set off adaptive immunity.

Myxococcus xanthus

- Individual cells gather into swarms that move via gliding motility. - They kill and consume other microbial cells in their path and take up amino acids and other molecules. - They pool together their resources and reach sufficient concentration to secrete enzymes that break down molecules. - When prey is scarce: Cells switch from adventurous to social motility. - Cells packed in aggregation centers and start to pile, forming fruiting body. - Has a definite form and size. - Tips of fruiting bodies have sporangioles. - Half of cells lyse to become nutrients for survivors. - Survivors become resistant resting cells called myxospores.

Prions

- Infectious agents that can be genetic or sporadic. - They are misfolded proteins that cause disease. - Do not contain capsid and are proteins instead of DNA/RNA. - Made up of a single protein. - When DNA is misfolded into prions, they become highly resistant to chemicals, proteases, and high temperatures. - Prion diseases are slow developing. - Some common degenerative diseases involve misfolding of proteins. - Categorized under epigenetics -> Changes that do not result from altered genome sequences.

Lag phase

- Initial still period of bacterial culture growth that is characterized by cellular activity but not growth. - Placed in a nutrient rich medium that allows them to synthesize proteins and other molecules necessary for replication. - Increasing in size, but no cell division. - Adaptation to new conditions.

Lysogenic virus

- Integration bacteriophage nucleic acid into bacterium's genome. - Bacterium will live normally but prophage of bacteriophage will transmit into bacteria's daughter cells. - Later, other triggers will cause it to release new phages.

Competition

- Interaction between organisms where both organisms are harmed. - Limited supply of at least one resource used by both could be a factor.

Predation

- Interaction between organisms where one organism consumes the other.

Parasitism

- Interaction between two organisms where one lives on or in another organism, causing it some harm and is adapted structurally to this way of life.

Antagonism

- Interaction between two organisms where one organism benefits at the expense of another. - Any action of an organism that suppresses or interferes with normal growth and activity of the other organism.

Syntrophy

- Interaction of cross-feeding of nutrients often with mutual benefits. - One species lives off the products of the other species.

Commensalism

- Interaction of two organisms where one benefits but the other is unaffected.

Mutualism

- Interaction of two organisms where they both benefit.

What happens in low temps?

- Interactions of proteins weaken and may become misshapen. - This affects activity and speed of reactions. - Affects assembly of ribosomes.

Alarmone

- Intracellular signal m molecule that is produced due to harsh environmental factors.

Specialized transduction

- Involves packing of specific genes from a host. - Temperate phages: Incorporate their genome into the host genome at specific attachment sites (att) and remain dormant for some time. - Later on, attB site in E.coli is flanked by nearby DNA sequences. - Abnormal excision events can accidentally remove some of the genes along with the phage genome.

Bacterial nucleoid

- Irregularly shaped region within the cell that contains all or most of the genetic material. - Genome is generally circular double-stranded DNA. - DNA is supercoiled and helps compact the DNA into condensed shape.

Ammonia

- Is used to make glutamate and glutamine when assimilated.

Enrichment plating

- Isolating technique that involves streaking on a plate that has minimal media (so auxotrophs cannot grow) and add a bacterial agent that is only effective against dividing bacteria such as penicillin. - Kills/stops the growth of cells that do not have the mutation. - Ex. Culture with His+ and His- cells, the culture has no histidine. - His- cells cannot divide due to lack of histidine. - His+ cells die off (without mutation), His- cells remain in culture because it was not dividing. - The cells that are dividing and making a cell wall is killed off.

Hook

- Joint between filament and basal body. - Made of one protein. - Short, curved hook structure. - Attaches filament to cell envelope allowing rotation.

Lipopolysaccharide

- Large molecules consisting of lipid and polysaccharide. - Found in outer membrane of gram-negative bacteria. - Makes up most of outer membrane and increases structural integrity. - Aids in bacterial survival. - Structural support, recognized by immune systems, filters hydrophobic compounds, main reason for antigenic variety among gram negative bacteria.

Flagella

- Lash-like appendage that protrudes from the cell body of certain bacteria. - Polar structure: Located at end of cell. - Peritrichous structure: At random points around the periphery of the cell. - Parts: Basal body, hook, filament.

Phospholipids

- Lipid that contains a phosphate group in its molecule. - Has polar hydrophilic head and non-polar hydrophobic tail. - Used to form cell membrane. - Amphipathic: Having both hydrophilic and hydrophobic parts. - Formed self-organizing micelles, which formed bilayer that merged into a vesicle. - Trapped RNA and started growing until division could possible.

Gram-negative cell wall

- Lipoproteins non-covalently connect to peptidoglycan layer between outer membrane and plasma membrane. - Cell wall made of outer membrane, peptidoglycan layer, and a periplasm. - Lipopolysaccharide acts as virulence factor -> causes disease in animals.

Euryarchaeota

- Lived in salty, saturated environments. - Methanogens and extreme halophiles. - Larger group of Archaea

Fluctuation test

- Luria-Delbruck test to detect mutation induction in bacteria by chemicals, carried out in liquid medium. - Scored by counting the number out of ~50 tubes. - Found that mutations arise in the absence of selection. - High fluctuation: If mutations occur randomly, there will be wildly different numbers. - Reproducible/similar occurrence: If mutations are induced, then each culture should generate similar numbers of phage-resistant colonies. - From this test, we learn that mutations occur first, then selection occurs on random mutations.

Methyl accepting chemotaxis proteins

- MCPs - Scout for chemicals in the environment, detecting their concentration and transmit signals to control flagellar rotation. - Sensor: CheA - Each MCP detects a specific attractant/repellent.

DNA polymerase 3

- Main enzyme that adds nucleotides in 5' to 3' direction. - Helps with editing of mismatched nucleotides.

Main pathways targeted by existing antibiotics

- Main pathways: 1. DNA replication 2. Protein production 3. Cell wall synthesis - Other pathways 4. RNA transcription 5. Outer membrane 6. Antimetabolites (drugs that interfere with one or more enzymes or their reactions necessary for DNA synthesis)

Energy change

- Maintains energy change because pathways are interconnected and reversible. - Cells maintain an energy charge balance in order to function, they like to keep a lower energy charge due to increasing ATP to generate pathways and decrease biosynthetic pathways. - More [ADP] and [AMP] = lower energy change - Cells keep energy change of about 0.87-0.95 by balancing ATP, AMP, ADP. - [ATP] + ½ [ADP] / [ATP] + [ADP] + [AMP]

Proteobacteria

- Major phylum of gram-negative bacteria.

Classifying viruses

- Major virus groups share little structure, nucleic acids, or protein sequences. - No classes of molecules that define their relations. - Classified by their host, size and shape, presence or absence of an envelope, and nucleic acid. - Also group based on the shape of their genome (linear or circular, DNA or RNA first, single or double stranded).

Thylakoids

- Membrane folds that enhance light-gathering abilities. - Maximizes surface area of structure. - Enhances light- gathering abilities of photosynthetic bacteria by greatly increasing the membrane surface area. - Similar structures are made by chemolithoautotrophs. - Stacks of membrane sac that have a shared lumen.

Acid-fast envelope

- Membrane glyocolipids and long chain of fatty acids that are bound to peptidoglycan. - Contains large amounts of waxes called mycolic acids. - Do not have a full membrane. - Regular gram stains do not work because they cannot penetrate waxy layer. Pros: - Can protect against harsh chemicals, strong acids, antibiotics, and resist phagocytosis. Cons: - Porins located in surface to allow nutrients in, but takes much longer. - Cells are slow growing in binary fission due to tough outer shell.

Magnetosomes

- Membrane-bound iron-containing structures. - Several crystals chained together act as a compass needle. - Attached to cell membrane. - Fe3O4 or Fe3S4 - Can sense the Earth's magnetic poles. - Helps organisms orient themselves to oxygen-rich concentrations.

Pentose phosphate pathway

- Metabolic pathway parallel to glycolysis. - Generates NADPH and pentoses and 5 ribose-phosphate. - No energy is used in this pathway. - Purpose: To produce sugars that make up DNA and RNA. - Uses products of glycolysis.

Cell growth

- Metabolism is the sum of chemical processes in a living system needed for a cell to divide. - Growth exerts a demand for energy when a cell is in a favorable environment. - Fueling pathways are highly variable among prokaryotes.

Replica plating

- Method of screening to isolate mutant auxotrophs from wild-type bacteria. - Can make two identical copies of the colonies on a petri dish under different conditions.

Epsilon proteobacteria

- Microaerophilic species, chemolithoautotrophs, extremophiles - Ex. Helicobacter pylori -> cause of stomach ulcers.

Microbial predation

- Microbes are considered to mainly be prey, commonly in oceans. - Microbial populations are kept controlled through predation. - Predation can also be seen between bacteria. - Bacterial predator can either penetrate prey or graze upon prey. - Ex. Bdellovibrio: Encounters prey (a gram-negative bacterium), enters the periplasm, multiplies, then causes cell lysis. - Causes the host to have a leaky inner membrane and introduce hydrolytic enzymes into host's cytoplasm.

How are microbes involved in cycling elements on Earth?

- Microbes catalyze the processes necessary to propagate cycles. - Most of the processes are redox reactions. - Notable cycles are nitrogen, oxygen, and carbon.

Microbes and weather

- Microbes play role in turnover of main atmospheric gases. - Climate: Black sludge called cronconite, present in the holes full of meltwater, is progressively getting worse as they are able to absorb more light and create deeper holes. - These deeper holes lead to more bacterial cronconites to grow, leading to further ice melting. Weather: Plankton produce DMSP, which then gets turned into DMS by marine bacteria. - DMS reacts with oxygen to form SO2 which then produces CCN (Cloud condensation nuclei), which has great effects on the weather. - Basically microbes contribute to cloud formation.

Biofilm

- Microbial communities form on surfaces where nutrients can be taken up. - Attachment is reversible. - Exopolymeric substances (EPS matrix): Where communal reactions take place, absorbs water and nutrients, allow waste products to exit, provides protective armor. - Can build flat biofilms or 3d structures.

What factors make it difficult to classify microbes?

- Morphology is not sufficient to categorize microbes. - Some strains of same species have difference in DNA of up to 20% such as E.coli. - Bacteria have different morphologies depending on environmental conditions. - Some organisms are unculturable.

Major features of viruses

- Obligate intracellular parasites: relies on the host to do all of its replication. - They all pretty much carry their nucleic acid within a protein shell (capsid). - Optional: envelope, spikes - Can have DNA or RNA genome circular, linear, or multiple molecules (segmented). - Multiply using host machinery. - Do not contain ribosomes -> do not synthesize proteins.

Chemotaxis

- Movement of a motile cell or organism in a direction corresponding to a gradient of increasing or decreasing concentration of a particular substance. - Binding of chemoattractant or repellent to methyl-accepting chemotaxis proteins (MCPs) regulates frequency of runs and tumbles. - Each MCP can sense a different attractant or repellant. - CheA is the sensor. - Outcomes: Nothing sensed, sensed, no attractant. - Transmembrane ion gradient powers the bacterial flagellum. - Advantageous for survival, virulence, growth-promoting.

Horizontal gene transfer

- Movement of genetic material between unicellular and/or multicellular organisms that are not related (offspring). - Ex. Transformation, transduction, conjugation

Gliding motility

- Movement that occurs without the use of flagella on a solid surface. - Observed in cyanobacteria, myxobacteria, mycoplasmas. - Isolated cells -> adventurous motility - Groups of cells -> social motility

Multicellular eukaryotes and symbiosis

- Multicellular eukaryotes harbor bacteria that can produce essential nutrients or break down nutrients that are hard to break down and would otherwise be inaccessible to the eukaryote. - Example: Buchnera can produce essential amino acids that aphids use and need while aphids provide precursors needed to make these amino acids and provide a safe habitat for the Buchnera.

Basidiomycetes

- Mushrooms and other filaments - Basidium cells form from dikaryons. - Separates directly open to the air for dispersal.

Nitrogen assimilation

- NO₃ (nitrate) -> NO₂ (nitrite) -> NH₃ (ammonia) - Nitrogen extracted from environment as nitrate and nitrite, then converted to ammonia. - Energy intensive, enzymatic process. - Only prokaryotes are able to fixate atmospheric N₂ (16-24 mol of ATP needed to make one molecule of N₂ to ammonia). - Ammonia is assimilated to make glutamate using the reducing power of NADPH.

Antibodies

- Neutralize microbial toxins and render them ineffective. - Facilitate the removal of infectious agents by acting as opsonins, clumping bacteria into larger particles, and utilizing the body's filtering mechanisms. - Interact with complement system to lyse certain bacteria. - Very specific and various.

How does the cell segregate the chromosome

- Newly replicated regions are recondensed, which also pulls them apart from each other. - Muk proteins bind distend DNA sequences and use ATP to bring them together. - SeqA binds at origin and associates the new origin to a spot on the cell membrane.

mRNA

- Newly synthesized RNA transcript to be used in translation. - Translation may start while transcription occurs due to coupling.

Microbes and nitrogen

- Nitrogen is an essential element of all cells (13% of dry weight). - Global cycling starts with nitrogen fixation -> initially only done by prokaryotes until humans found a way to do it chemically. - All fixed nitrogen that organismal life uses is derived from atmospheric dinitrogen. - Half life of nitrogen is 20 million years and cycling of nitrogen is rapid. - If microbes were to cease fixing nitrogen, soil will be depleted of fixed nitrogen in 1 week.

Nitrogen-fixating bacteria and legumes

- Nitrogen-fixation (nitrogen gas to ammonia) conducted by bacteroids that are contained in root nodules on plant roots. - Plant excretes flavenoids that attract the bacteria and signals nodulation factors that cause nodule formation. - Bacteria binds to tip of root hairs and invades, causing root hair curling. - Bacteria develops in vesicles of root cortex and forms a nodule. - Bacteroids receive organic acids that provide energy and reducing power needed for nitrogen fixation. - Bacteroids provide plant with ammonia that can be used for biosynthesis.

What complex fixes nitrogen

- Nitrogenase enzyme complex. - Highly conserved and oxygen sensitive.

Lactose (+), glucose (+)

- No transcription - Very little to none because glucose is burned through first instead. - "Glucose effect" - cAMP is not made because glucose is present. - LacI repressor blocking RNAP from associating. - OPERON OFF: CAP not bound because glucose is present.

Lactose (-), glucose (+)

- No transcription of lac operon because lacI repressor bound to operator preventing transcription. - cAMP level is low -> not binding to CAP and CAP cannot bind to DNA. - OPERON OFF because lac repressor bound and CAP not bound.

Lactose (-), glucose (-)

- No transcription, leaky expression. - Only a few enzymes are made. - cAMP level is high due to lack of glucose, CAP is active, which helps RNAP bind to promoter. - LacI is not being stopped by allolactose because allolactose is not present when lactose is not present. - RNAP will continually be blocked and halted in the process. - Sometimes gets through. - OPERON OFF because lac repressor bound.

Type 6 secretion system

- Not Sec-dependent - Most likely evolved from bacteriophage injection mechanisms. - Targets both prokaryotic and eukaryotic cells. - Found in a quarter of bacterial species both gram-negative and gram-positive species. - Injects through bacteria directly.

Macromolecules

- Nucleic acids, proteins, carbohydrates, lipids. - Made from building blocks. - Proteins from amino acids - Nucleic acids from nucleotides - Lipids from fatty acids - Polysaccharides from simple sugars.

Factors that limit growth in bacterial culture

- Nutrient availability - Build-up of metabolites

DNA elongation

- Occurs at max rate of 1000 nucleotides per seconds. - DnaG (primase) adds RNA primer to start synthesis. - Prompts polymerase 3 to start adding nucleotides. - Both leading and lagging strands work together. - RNase H chews up primer in lagging strands, Pol 1 fills in gaps. - DNA ligase ligates the exposed ends. - Replication can induce supercoils and catenanes.

RNA elongation

- Once clearing the promoter, RNAP releases sigma factor and adds ribonucleotides at 3' end of RNA. - Synthesizes in 3' to 5' direction. - Proteins help with elongation. - Ex. NusA helps move RNAP when there are hairpin loops.

Inhibition of drug uptake

- One of the major mechanisms for acquiring antibiotic resistance. - Bacteria can acquire altered proteins so drugs can never enter and antibiotic never reaches target.

Inactivation of drug by enzymes

- One of the major mechanisms for acquiring antibiotic resistance. - Drug enters, hangs around, but gets cleaved by enzyme so it does not bind to the target anymore.

Activation of efflux pump

- One of the major mechanisms for acquiring antibiotic resistance. - Drug enters, reaches target but is pumped out so quick it that the cell never reaches proper concentration to cause damage to growth.

Alteration of drug target

- One of the major mechanisms for acquiring antibiotic resistance. - Target site is modified, "puzzle piece doesn't fit anymore".

Firmicutes

- Only bacterial phylum that produces spores. - Gram-positive - Ex. Staphylococcus aureus - Human pathogens, can even be made yogurt and cheese. - First colonizers of the intestine of newborns.

Helicase

- Opens the DNA helix by breaking hydrogen bonds between the nitrogenous bases. - Easier to open at origin of replication because they are AT-rich and have weaker hydrogen bonding interactions than GC.

Mitosomes

- Organelles surrounded by double membrane that do not make ATP. - Found in parasitic protists that live in anaerobic or microaerophilic conditions. - These organelles were found to be mitochondrial remnants.

Endosymbiont theory

- Organelles were once bacteria that found their way inside another cell and evolved together.

Phototrophs

- Organisms that can grow in simple media and synthesize their own building blocks (eg. vitamins, amino acids) - Lifestyle/habitat: Lives anywhere as long as necessary inorganic, trace, and carbon/energy source ingredients needed for growth are present. - Can synthesize all organic growth factors required. - Can function in media that is missing a required compound.

Auxotrophs

- Organisms that cannot grow on minimal media and cannot synthesize at least one or more essential building block. - Relies on an organic growth factor. - Can grow on a defined media.

Reducing power

- Organo = Organic compounds (NADH, NADPH) - Litho = Inorganic compounds (sulfur, phosphorus, nitrogen)

Nitrification

- Oxidation of ammonia to nitrate via a nitrite intermediate. - Done by ammonia-oxidizing bacteria or archaea that reduce oxygen to form ammonia to nitrite. - Nitrite is then converted to nitrate by reducing oxygen again. - These steps are done by different specialized microbes. - They live in close proximity to carry these steps out.

Cyanobacteria

- Oxygenic photosynthesizers of the prokaryotic world and ancestors of the modern chloroplasts. - Emerged 2.8 to 2.5 billion years ago and diversified. - By devoting resources to photosynthetic membranes, they increased their energy budget, gained more genes, and increased in complexity. - Eg. Prohlorococcus marinus -> member of marine phytoplankton and most abundant photosynthetic organism on Earth. - Original producers of atmospheric oxygen, still contribute half of all oxygen released to atmosphere.

Condensation of chromosomes

- Packed tightly inside. - Cations bind to DNA and DNA-binding proteins fold DNA into loops, organizing them into a core. - Supercoils are formed.

Facilitated diffusion

- Passive movement of molecules along their concentration gradient. - Guided by the presence of another molecule (usually a pore or a channel).

Beta protobacteria

- Pathogens - Ex. Bordetella pertussis -> whooping cough - Ex. Neisseria gonorrhoeae -> gonorrhea

Beta lactam antibiotics

- Penicillin - Binds and inhibits the activity of transpeptidase, basically inhibiting cell wall synthesis. - Peptidoglycan layer is important for cell wall integrity. - When bacteria replicates, it has cell wall that is broken down and remade during replication. - DD-transpeptidase: Helps fix the cross-links that are opened up during replication. - Peptidoglycans are used to fill in the spaces. - Antibiotics inhibits DD-transpeptidase. - No cross-linking occurs, the cell becomes unstable and could be destroyed.

Transpeptidase

- Penicillin binding proteins. - Add crosslinks when forming cell wall. - Can be inhibited by beta-lactam antibiotics and penicillin.

Generalized transduction

- Phages randomly pack and exchange any of the host's genes. - Uses rolling-circle mechanism: Strand of DNA is cut and separated to allow replication. - Does not have to deal with simultaneously replicating two strands. - 10 phage genomes are joined end to end after several rounds of replication.

Group translocation

- Phosphotransferase system (PTS) transports a solute while phosphorylating it (usually a sugar). - Transports it in cell and traps it inside.

Energy source

- Photo = light - Chemo = chemical (H2, NH3, NO2, H2S)

Archaea

- Phylogenically diverse - Not restricted to extreme environments - Methanogenesis likely appeared once and early in evolution with Euryarchaeota -> methanogens evolved once in the past. - Archaeal ancestor must have been small and had simple physiology based on anaerobic cycling of carbon and hydrogen.

Cytotoxic T lymphocytes

- T cells - Infected cells display some foreign component on surface (antigens). - Most cells posses surface glycoproteins called MHC that bind and hold foreign antigens in a recognizable orientation. - T lymphocytes can be triggered to produce clones that recognize and kill other cells with same agent.

Conjugation

- Plasmids transfer DNA from one cell to another through direct contact. - F-plasmid most well studied. - F-factor is a DNA sequence that codes for proteins that make up the sex pilus. - Sex pilus is used eto pull donor and recipient together. - Type 6 secretion occurs, transferring plasmid DNA. - Plasmid is nicked at oriT and brought to transfer plasmid DNA. - Rolling circle replication is performed and single strand of DNA is pulled back into the cell.

Pure culture

- Population of cells or multicellular organisms growing in the absence of other species or types. - May originate from one single cell or organism, which means the cells are genetic clones of one another. - Genome can be sequenced and its metabolism and physiology investigated under controlled conditions. - This can allow for identification of microbes in a particular environment. - Single species taken from a mixed culture, used to initiate growth in a new/sterile medium. - Benefit: Provides clues to what similar but not-yet-cultivated microbes are doing in the environment, predict the environment. - Drawbacks: Could cause unintentional bias, could change its mode of growth or domesticate strains, causing them to lose certain abilities. - Only a fraction of environmental microbes can be recovered in a pure culture.

Acidophile

- Prefers environments that are very acidic. - pH 1.0

Akalophile

- Prefers environments that are very basic. - pH 11.5

Halophile

- Prefers environments with high concentrations of salt

Thermophile

- Prefers environments with high optimal temperature - 60-80ºC

Psychrophile

- Prefers environments with low optimal temperature - -20-10ºC

Mesophile

- Prefers environments with moderate optimal temperature - 20-45ºC

Enzyme catalysis

- Process of cells using enzymes to accelerate slow reactions and support rapid cell growth. - Helps run reactions forward or backward and lowers activation energy. - Makes reactions more favorable. - Reaction coupling: Links energetically favorable to unfavorable reactions to drive processes.

Rolling circle replication

- Process of unidirectional nucleic acid replication that can rapidly synthesize multiple copies of circular molecules of DNA or RNA, such as plasmids and genomes of bacteriophages. - Nicks one of the double stranded DNA at double strand origin. - 3' end elongated and displaced DNA is used to create copy of 5' strand. - Replication occurs around the circular DNA and produce single stranded linear copies.

Proton motive force

- Process used for ATP synthase to make ATP. -

What is aerobic respiration?

- Produce the most ATP possible.

What happens in high pH levels?

- Prokaryotes can grow over a wider range of pH than their proteins can tolerate by pumping protons in and out of their cells to maintain constant pH. - Proton motive force responsible for ATP production. - If H+ ions are neutralized by -OH, concentration gradient will collapse, energy production ceases. - pH disrupts hydrogen bonding in proteins. - An unadapted culture can die in a new pH level.

Coupled transcription and translation

- Prokaryotes have chromosomes in nucleoid that has no membrane, which allows it to be easily exposed to ribosomes. - Circular chromosomes mean there is no need for ends to processed or synthesized before translation. - Prokaryotes react to environmental signals or changes and adapt faster by initiating/stopping protein synthesis. - Prokaryotes have no true nuclear membrane, therefore DNA is easily accessible to ribosomes in cytoplasm and can translate and transcribe at the same time.

RNA initiation

- Promoters are regions of DNA that signal initiation of transcription. - Promoter lies upstream at 5' end. - RNA polymerase binds at promoter at 35- and 10- sequences. - RNAP makes short transcripts at first (transcription is aborted prematurely and restarted multiple times). - Once it makes a transcript that is long enough, it escapes the promoter and drops sigma factor.

DNA termination

- Protein Tus binds to termination sites to halt replisome process. - Complexes converge halfway around the chromosome (180 degrees from OriC) at terC sequence. - The two sites work to ensure complete and non-overlapping replication. - Decatenation by topoisomerases II are required to fix the twisted DNA. - Double stranded break -> uncut helix to pass through -> resealed - Until this is resolved, the DNA strands are susceptible to homologous recombination.

DnaA

- Protein that activates initiation of DNA replication. - Is a initiation factor that promotes the unwinding of DNA at oriC. - The onset of initiation is determined by the concentration of DnaA.

Sec A

- Protein that recognizes N-terminal signal sequence, binds to it, and leads it to a cell membrane channel consisting of sec Y, sec E, and sec G.

Inserting proteins into the plasma membrane

- Proteins are transported with sequences that have signals of where to go. - These sequences are cleaved during transport. - Membrane proteins in cell membrane are hydrophobic! Have an affinity to be in the membrane. - Signal recognition particles (SRPs) bind to the signal sequences when proteins that can't easily come in. - Eg. Ffh, ffs - Carries it to secretion machinery and allow it to enter the cell.

Enveloped virus

- Proteins in lipid envelope bind to cell surface receptors. - Binding induces fusion with cell membrane. - Viral capsid enters into cell and releases nucleic acid once inside. - Contacts the plasma membrane first; needs the initial attachment step → tightens at the surface. - Enters the cell via vesicles and fuses w/ endocytic membrane → enveloped virus first taken in by endocytosis. - Viral envelope fuses with endocytic membrane. - Viral capsid is released. - They get out of cells by either budding or lysis - Non-enveloped viruses escape through lysis, enveloped viruses escape through budding.

Min protein

- Proteins that prevent uneven cell division by guiding FTsZ to polymerize in the middle. - "Minicells" - Lack chromosomes. - MinD = polymerizes at one pole, binds to MinC - MinE prevents MinCD from polymerizing in the middle region of cell. - Mutations of Min or FtsZ genes will cause cell to divide unevenly. - May cut through nucleoid and kill the cell. - Protein NO regulates this.

Integrating into host genome

- Provirus -> animal viruses - Prophage -> bacterial viruses

RNA virus

- RNA-dependent RNA polymerase encoded by virus RNA Replicase - dsRNA virus → has a strand (looks like mRNA) to make protein, template, and non-template strand - ssRNA virus → can sometimes strand DNA code directly to the protein or make complementary strand before it's turned into proteins - + mRNA: directly makes protein - - mRNA: needs to make a complementary strand to make protein.

Rho-independent termination

- RNAP will approach sequences of GC rich nucleotides and transcribe. - The RNA transcribed will fold back on itself, forming a hairpin and RNAP stalls. - Stalled polymerase and weak interaction with DNA will cause the enzyme to fall off.

Protein termination

- Reaches a stop codon (UAG, UAA, UGA) in A site, stalling the ribosome. - Release factors enter the A site and hydrolyze peptidyl-tRNA and releases the peptide. - Ribosome dissociates into two subunits. - IF1 and IF3 bind to small subunit in order to prevent immediate reassociation.

Toll-like receptor

- Receptors that are dedicated to microbial recognition. - Binding of microbial constituents to TLRs set off signaling cascade that leads to activation of key host cell transcription factor called nuclear factor. - This induces expression of cytokine genes and gene survival. - Also trigger macrophages.

DnaB

- Recruits the final replisome proteins. - Brought to DNA strand by DnaC and ATP.

Storage granules

- Refractile inclusion bodies - Stores food sources and essential elements. - Ex. Sulfur, calcium, phosphate, organic polymers. - Storage of useful materials when in abundance for later use.

Allosteric regulation

- Regulated by a ligand that binds to the end site (not active site).

Sensing a repellent

- Repellent binds to chemoreceptor -> causes conformation change. - Autophosphorylation of CheA is stimulated rather than inhibited. - This makes more CheY and increases tumbles. - Sensitivity of chemoreceptors is maintained because other proteins are activated to counteract methylation. - This is important because if the repellent is densensitized, then chemoreceptor will only detect higher concentrations of the repellent.

Auxotrophic mutation

- Requires an exogenous building block or growth factor (eg. amino acid, vitamin). - Challenge the cell to live on minimal media and can identify what the mutated cell cannot survive without. - Classified as mutation if previously could grow in a medium and now could not. - Depends on what is in the media.

Accommodation

- Resetting the sensitivity of CheA sensor so it can only be activated at higher concentrations of the chemoattractant. - Only a higher concentration will prolong the bacterium's run. - Part of molecular memory that helps cells to sense a change in attractant concentration and progress towards it.

Denitrification

- Returning fixed nitrogen to gaseous form. - Nitrate to N₂ gas. - Usually anaerobic process - NO3 -> NO₂ -> NO + N₂O -> N₂ - Exclusively biological. - Performed b y both autotrophs and heterotrophs. - Denitrifiers are common in treating wastewater.

Rho-dependent termination

- Rho-dependent termination: RNA has a binding site for Rho factor, which binds and climbs up the sequence towards RNAP. - Catches up to RNAP at the transcription bubble, pulling the RNA transcript and DNA template apart, releasing the RNA and ending transcription. - NOTE: Ribosomes will block Rho's access to recognition sequence on mRNA.

Basal body

- Rod and system of rings embedded in cell envelope. - M, S, P, L - Embedded in cell wall. - Uses ATP to function. - Equipped with rotor to turn.

Single stranded binding proteins

- SSBs - Binds to single stranded DNA to prevent hydrogen bonding between DNA strands.

DNA ligase

- Seals the gaps between Okazaki fragments on the lagging strand to create one continuous DNA strand. - Catalyzes formation of covalent phosphodiester linkage between 3-OH' end of one DNA fragment and 5' phosphate end of other fragment.

Type 3 secretion system

- Secretion system that most likely evolved from flagellar machinery. - Common on transferable plasmids, which are picked up by cells. - Not sec-dependent. - Secretion system that deposits toxins into other cells by poking holes with needle-like structure into target cell membranes to get them to release their nutrients. - Common with gram negative bacteria such as Salmonella and E.coli. - Requires hydrolysis of ATP to ADP.

Enrichment cultures

- Selectively favors growth of the desires microbes by adjusting the conditions of culture. - Drawbacks: Biases -> Microbes that are easier to culture a particular microbe, microbes can act differently in nature than in culture.

Heat shock response

- Sensor is mRNA encoding a sigma factor. - Heat stress causes hairpin to melt, opening mRNA Shrine-Delgarno sequence for translation. - Specific biomolecules sense the temperature fluctuations (thermosensors). - Sigma factor is the thermosensor. - Binds to RNAP to bind to promoters with gene transcribing heat shock regulon. - Signal: DnaK -> protein chaperone. - Facilitates proper folding of proteins, target sigma factors for degradation. - When DnaK is unnecessary, cellular proteins accumulate and divert it from sigma factor. - Mechanisms are induced to control transcription of genes coding for heat shock proteins.

Transcriptomics

- Sequencing of RNAs present in an environmental sample. - Alternative splicing stability. - Extra RNA during cultivation.

Fungal reproduction

- Sexually and asexually. - Spores can grow asexually forming filaments that fuse, then form a dikaryon (cell with two nuclei). - 2 nuclei will eventually merge and form true diploid cell.

Activity of Spo0A

- Sigma factors are synthesized to cause various spore genes to be expressed at specific times. - Sporulation depends on genes being expressed at proper times and places.

Lep B

- Signal peptide used in sec system to cleave signal peptide during transport.

Central metabolic pathways being reversible

- Significance of central pathways being able to operate in either direction permits microbes to grow under a wide array of circumstances and environmental conditions. - To avoid making excess reducing power. Examples: - TCA cycle under aerobic conditions can run in reverse to solely produce precursor metabolites and produce no energy. - TCA cycle under anaerobic conditions can run in both directions like separate moving parts. - One side produces precursor metabolites and the other produces energy. - Addition of malate to TCA cycle aerobically runs the main central pathways in reverse.

Zeta proteobacteria

- Single species -> iron oxidizer - Ex. Mariprofundus ferrooxydans

Capsule

- Slime is in one piece and remains attached to cells. - Polysaccharide layer that lies outside the cell envelope -> deemed to be part of the outer envelope. - Not easily washed off, can be the cause of various diseases. - Prevents desiccation, exposure to chemicals, no biofilm.

Fungal mating type

- Some fungi have more than two genders. - Differentiate gametes when cells of opposite mating type is present. - Pheromones indicate differentiate and become competent to mate. - Haploid nuclei fuse and form diploid nucleus -> zygote. - Can proliferate in diploid stage for prolonged period. - Then can differentiate into haploid spores. - Form spores based on whether they are ascomyces or basidium.

Remaining latent

- Some latent viruses make proteins that inhibit or divert immune system that will catch the virus. - Can inhibit apoptosis. - Must keep expression of reproduction in control. - Keeps on genes that help with prolonged maintenance.

Mutations in genes that promote antibiotic resistance

- Some spontaneous mutations or some genes acquired through horizontal gene transfer may make the bacterium resistant to antibiotics. - If we treat the bacterial population with that specific antibiotic, only the resistant bacteria will be able to multiply since the antibiotics select for them. - These bacteria can now increase in numbers and the end result is a colony or population of mainly resistant bacteria.

Peptidoglycan

- Specific to prokaryotes. - Polymer of disaccharides cross-linked by short chains of identical amino acids.

Gram positive stain

- Stain with primary stain (crystal violet). - Add iodide which binds to crystal violet and traps it in cell. - Rapidly wash with ethanol or acetone to decolorize, the violet will wash out. - Counterstain with secondary stain, which will not retain. - Stains purple because thick peptidoglycan wall that retains the crystal violet.

Gram negative stain

- Stain with primary stain (crystal violet). - Add iodide which binds to crystal violet and traps it in cell. - Rapidly wash with ethanol or acetone to decolorize, the violet will wash out. - Counterstain with secondary stain. - Stains red because it does not retain crystal violet and retains the secondary stain.

Clinical latency

- State or period of virus living or developing in the host without producing clinical symptoms.

Stringent response

- Stress response of bacteria to amino acid starvation and other stress conditions. - Signaled by alarmone (p)ppGpp. - Divert the cell to divert resources away from growth and division and towards amino acid synthesis. - RelA protein senses stalled ribosomes and convert GTP into ppGpp. - ppGpp is the global signal to shift cell into starvation mode. - Cellular processes will begin to divert resources.

Lac operon

- Structural genes: LacZYA - Promoter: P - Operator: O - Regulatory gene: lacI (made by default, binds to operator sequence to prevent creation of proteins, blocks transcription from occurring since it is an inhibitor) - Inducer -> allolactase -> binds to lacI to release it from operator when there is lactose present

Viral envelope

- Surrounds the capsid. - Made of lipid-carbohydrate-proteins which use lipids and carbohydrates from host cells. - Envelope can have attachment structures (ex. spikes).

Primase

- Synthesizes RNA primers needed to start replication.

Non-enveloped viruses

- T4 phage - Tail fibers and base plate responsible for recognition of a potential host. - Tail holds inner tube and releases it on contact. - Tip proteins degrade peptidoglycan and allow injection of DNA into host.

Cultivation-independent identification

- Take an environmental sample → extract DNA → amplify the pieces with PCR → amplify it (make copies of it) with the help of 16rRNA. - Polymerase chain reaction (PCR): take the pieces of DNA and purify it. - Do a sequencing reaction to find out the bps → tells the nucleotide sequence in order from the primer. - Once we have sequences → data analysis → OTU classification → draw trees & plots.

Terminal vs reversible

- Terminal: Once a certain stage is reached, there is no reverting to the original form. - Reversible: Has the possibility to return to its original form once environmental conditions prove to be unfavorable.

Neutrophils

- Terminally differentiated cells that live for only a few days. - They seek out foreign particles, ingest them, and try to kill them. - First responders of immune system. - Sense chemotactic gradients well and act rapidly. - Require opsonins. - Contain cytoplasmic granules that act as lysosomic bombs. - Defensins are back up responses to kill the ingested prey that may lyse out. - Hydrolases and oxidative enzymes are used to kill invaders.

RNA termination

- Termination sequence forms a hairpin in the RNA (usually a rich GC sequence). - RNAP stalls at hairpin and transcript breaks free. - Bonding is weak between template and transcript RNA. - Rho-dependent termination - Rho-independent termination

Antisense strand

- The DNA strand that acts as template for RNA strand.

Sense strand

- The RNA strand that is complementary to the antisense strand.

Polycistronic operon

- The benefit to a polycistronic mRNA is that it is shorter, faster. - Bacteria can quickly utilize multiple different metabolic resources, and all of the proteins for a single enzymatic pathway will be available.

Diffusion

- The natural movement of a substance going from a high concentration to a low concentration.

RNA synthesis

- The production of an RNA molecule from the nucleotides adenine, guanine, cytosine, and uracil. - The nucleotides are joined together by RNA polymerase. - Difference from DNA synthesis: Does not require a primer.

Transcription bubble

- The unwound region of DNA that prompts initiation of RNA transcription.

Entering the host cell

- The viral membrane must fuse to host cell membrane. - Some are taken up by endosymbiosis -> fuses to the membrane of endocytic vesicle, then virus escapes into cell.

Infecting the host cell

- The virus must release its nucleic acids from its capsid. - Uncoating process must occur -> either while entering or after entering. - Enveloped viruses: Uncoat after entering - Phages can uncoat while entering.

Crenarchaeota

- Thermoacidophiles - Grow at high temperatures and highly acidic environments. - Metabolize elemental sulfur. - Found in open ocean, most likely play an unknown role in marine environment.

Fungi

- They are eukaryotes. - Clustered by morphology. - Grow sexually and asexually. - Ergosterol -> cholesterol counterpart found in cell walls of all fungi - Major activity is recycling vegetable matter on Earth. - Can play role as partners with plants, produce antibiotics, cause disease, plant pathogens.

How do other protists such as entamoeba and Giardia grow within the host and survive outside the host?

- They are free-living and obligate stages. - Both produce cysts that are dormant when outside the host. - They reproduce within the host. - Anaerobes. - Giardia have mitosomes. - Entamoeba has both invasive and noninvasive infection type.

How can transcription and translation occur simultaneously?

- They both occur in 5' to 3' direction. - There are no membrane components separating transcription and translation. - In bacteria, RNA do not need to go through processing.

Auxotrophic mutants

- They need a nutrient source that is external to survive. - Screening isolates different cells, depending on whether they are auxotrophic or not. - Informs us about the metabolic pathways because they show that cells need specific nutrients for growth by comparing the mutants with wild-type normal cell.

Biosynthetic pathways being reversible

- To make substances out of precursor metabolites.

Artificial transformation

- Treatments are applied to affect the permeability of a cell's membrane. - Treatments could be high concentrations of calcium ions on ice, followed by heat shock, and electroporation (makes transient holes in cytoplasmic membrane) - Firing DNA coated onto a metal into the cell. - Typically using plasmid DNA.

Neutralism

- Two organisms interact without having any costs or benefits received.

Protist body structure

- Typical eukaryotic organization: Nuclei, mitochondria, and plastids. - Can even have those that contain two nuclei. - Some function without a mitochondria. - Some are large, some are very tiny. - Can even possess structures that resemble a mouth, stomach, bladder, anus, etc. - Have different metabolisms and lifestyles. - Protists are categorized into "supergroups". - Unicellular eukaryotes emerged 2 billion years ago.

Exporting lipids and proteins into outer membrane

- Typical of gram negative bacteria because they have outer layer. - Sec system used. - Chaperone protein Skp holds onto peptide once it is in periplasm. - Skp brings it to Bam complex + SurA transports peptide into the outer membrane, folding it through the beta-barrel assembly complex. - Misfolded proteins are degraded by DegP.

Conditional lethal mutation

- Unable to grow in a particular environment (eg. high temp) in any medium. - Survives in only one specific environment. - Depends on how and where the cells are growing.

Diatoms

- Unicellular algae - Abundant in plankton and sediments of marine and freshwater ecosystems. - Cell walls of silicon dioxide -> GLASS!!! - Allows for intricate geometric patterns that is resistant to mechanical breakage. - It can speed up photosynthesis and act as a pH buffer. - Accounts for ~20% or more of carbon fixation on Earth. - Some diatoms have mismatched structures that allow for the diatom to undergo meiosis when the shell gets too small and make gametes. - Diatoms are nearly indestructable and have made deposits that have gone back to Cretaceous period. - Diatoms live in a variety of climates and their structures give information on past environments. - Ex. Dinoflagellates

Sec system

- Used for exporting proteins beyond inner membrane. - Fueled by ATP or proton motive force. - Sec A, sec B, and Lep B - Periplasm is in between inner and outer membrane. - Contains proteins that help bind to nutrients to transport them in a cell and proteins that carry out enzymatic reactions. - Proteins translated in cytoplasm, sec B binds to the protein and keeps it unfolded. - Sec B brings it to sec A, then it goes through sec YGB. - Sec A acts as plunger, using ATP to shove protein in the channel LOL. - ATP hydrolysis causes sec A to release the protein. - Sec A binds to ATP and pushes more ATP through. - Protein sequence will have signal sequence cleaved off. - Protein is then delivered to periplasm.

Carboxysomes

- Used in bacteria that fix CO2 (autotrophs). - Carbon fixation: Converting inorganic carbon into organic carbon molecules. - Protein shells - Enhance the function of RuBisCo (energetically unfavorable enzyme used in carbon fixation).

Fluorescent stains

- Used with light microscopy. - Fluorescence is emitted from chemicals known as fluorochromes when exposed to incident light of a shorter wavelength. - Can visualize specific types of molecules. - Specific to particular bacteria. - Reacts or attaches to a molecule or receptor that reacts with desired cell target. - The tags light up when excited by wavelength given off by fluorescent microscope. - Proteins can be tagged and tracked to see their localization. - Green fluorescent protein (GFP): First fluorescent protein derived from a jellyfish.

When is 16s rRNA sequencing useful? When might it not be helpful?

- Useful to find which prokaryotes are most related. - Not as helpful when trying to find the mutation frequency of a sample because it is too conserved/stable, won't change much over time. - Not helpful for short-term studies because mutation in the 16s rRNA occurs very slowly.

Active transport

- Uses ATP or reducing power as a source of energy. - Ion-coupled transport - ATP binding cassette

Gyrase

- Uses energy from ATP hydrolysis. - Cuts double helix and introduces negative (right-handed) supercoils. - If it does not stop, gyrase can cause strand to become all negatively supercoiled and break DNA.

Light microscopy

- Uses visible light to examine microscopic-sized objects that cannot be seen by the naked eye. - Allows finer detail than the naked eye.

Dissimilation

- Using nitrogen as a source of energy. - Coupled to ATP production. - Oxidation of ammonia to nitrate. - Reduction of oxidized nitrogen compounds (as terminal electron acceptor) in anaerobic respiration.

Virome

- Viral genome - Not well defined. - Progress has been made toward directly sequencing the genome.

Virions

- Viral particles released by lysed bacteria.

Viriods

- Viroids are like viruses but without the capsid. - They are a circle of single stranded RNA and usually infect plants. - Do not encode a single protein. - Thought to cause disease through RNA silencing. - Viroid RNAs target host mRNA or DNA to alter gene expression. - Copied by rolling circle mechanism.

DNA virus

- Virus uses host cell machinery to make DNA, RNA and proteins. - Encodes proteins for capsids and other virus specific proteins. - There's an additional step for ssDNA virus where it needs to go through a dsDNA intermediate to make copies → needs to make complemented strand to make a template and make more viral genome. - Uses mRNA to make proteins or make capsomere proteins for enveloped.

Attachment of virus

- Viruses bump into host cells at random. - Absorption: Does not require energy, but requires specific ionic conditions and pH level. - Ligands on surface of virus will bind to receptors on host cell. - Viruses penetrate their host cell envelope uniquely.

Electron microscopy

- Visualize objects much smaller than those resolved optically. - Use accelerated electrons instead of light photons. - Samples are fixed with chemicals to cross-link molecules to preserve their structure.

What is fermentation?

- Way to make ATP without oxygen and keep the aerobic respiration chain. - NADH is unable to drop off electrons and become NAD. - Extra reactions allow NAD to regenerate by having final e- acceptor as pyruvate. - Oxidation of NADH.

Antibiotic resistance

- When bacteria change in response to use of antibiotics. -

Tumbles

- When flagella is rotated clockwise, dissociating the bundles. - The flagella alternate between clockwise and counterclockwise, resulting in undefined direction.

Runs

- When flagella is rotated counterclockwise. - Forces all the flagella to entwine in stiff bundles and results in productive directed motion.

Antimicrobial resistance

- When microorganisms stops an antimicrobial from affecting it. - Target is more broad: Affects bacteria, fungi, protists, etc.

When does lysogenic cell turn lytic

- When phage repressor is inactivated, prophage is induced and initiates a lytic cycle. - It turns lytic when environmental conditions are favorable. - If there is a high amount of glucose in the cell then cAMP levels decrease and Hfl levels increase. - Hfl degrades CL. - CL: Repressor protein that represses expression of the virus so when it is degraded, the virus is expressed and turns lytic. - Rec A (for the Lambda Prophage); when UV light damages the host cell's DNA the process that begins to repair it, the cell accumulates short stretches of single stranded DNA. - These pieces of single stranded DNA are bound by the recognition protein, RecA. - RecA forms a complex with ssDNA which degrades a host repressor called LexA. - This keeps the cells SOS response off. - RecA can also degrade the lambda repressor since LexA and the lambda repressor are structurally similar - When the lambda repressor is gone, the phage genes are expressed---> lytic genes are expressed.

Quorum sensing

- Widespread form of cellular communication that empowers cells to exhibit certain behaviors only when the population exceeds a certain threshold value. - Population density is signaled by the secretion of an autoinducer called pheromone.

Ascospores

- Yeasts and molds - Ascus: Sac holding 8 spores

Yeast reproduction

- Yeasts can alternate between haploid and diploid life cycles for long periods of time. - Asymmetrical growth - Budding: Starts as a protrusion from "mother cell" and gradually enlarges until it is nearly the size of the mother cell. - Cell separates and a bud scar forms at the separation, no other bud forms at scar.

How does exposure to an infectious agent grant you increased ability to combat it upon re-exposure?

- Your B cells create antibodies that can target the specific pathogen. The B cells serve as the memory of the pathogen so when you get reinfected, the B cells can act faster to get rid of it since they are already around.

Why do bacteria degrade their mRNA and proteins, given how much they cost to energetically synthesize?

- mRNA is short-lived, unstable RNA. - Lasts 1 min in 37ºC - By erasing its instructions for making proteins, the bacterial cell, the bacterial cell is poised to respond to both its physiological status and its environment. - More economical than making unnecessary proteins.

Polycistronic mRNA

- mRNA that encodes several proteins, characteristic of many bacterial and chloroplast mRNAs. - Can be cleaved into individual messages each that can translate into a single protein or a large polypeptide chain. - Advantageous because it increases efficiency and speed of protein synthesis.

Replicating RNA viruses

- ssRNA are either positive or negative polarity. - Some use the RNA genomes as templates to make dsDNA replicas. - Some bypass that and code positive sense RNA that can be translated into proteins. - RNA is able to be genome of virus and its own mRNA. - RNA replicase: Special RNAP that makes RNA from RNA. - Retroviruses (HIV): Genome has ssRNA of positive polarity and follow dsDNA intermediate steps. - ssRNA genome is copied into ssDNA copy of opposite polarity and then synthesizes dsDNA. - DNA is encoded into integrase, RNAP makes RNA transcripts from the DNA.

Stages of endospore formation

1. Axial filament - Triggered by starvation, lack of resources in the cell, DNA condenses. 2. Septum forms - Asymmetric, DNA divides. 3. Mother cell engulfs forespore - Spore gets eaten by mother, forming another membrane layer. 4. Cortex formation - Mostly murein and may have protein spore coat; internal change: Small acid-soluble proteins -> protect DNA in harsh conditions. 5,6. Further refinement - Metabolic compounds are protected (coat formation) 7. Release - Complete endospore, contains no detectable metabolism, no enzymes are active, they are not synthesizing.

Metabolism

1. Energy and carbon sources 2. Fueling products are created (ATP and reducing power NADPH) 3. Building blocks synthesized (from 13 precursor metabolites) 4. Macromolecules synthesized (nucleic acids, proteins, carbohydrates, lipids) 5. Assembling cell structures 6. Cell divides

Three central pathways

1. Glycolysis -> glucose oxidation to obtain 2. Citric acid cycle (Krebs' cycle) -> acetyl-coA oxidation in order to obtain GTP and intermediates. 3. Oxidative phosphorylation -> disposal of the electrons released by glycolysis and citric acid cycle. - All interconnected and make products that are reactants of others.

NAD+ regeneration

1. Regeneration in fermentation with the oxidation of NADH. - NADH electron dropped off to pyruvate to regenerate NAD+ 2. Regeneration via respiration through TCA cycle backwards. - NADH gives electrons to ETC 3. Regeneration of NAD+ drives glycolysis forward.

Plasmodium in humans

1. The sporozoites formed in moquito are injected into human blood stream from mosquito's saliva. 2. Travel bloodstream and enter the liver. 3. Once in liver, they mature into cells called tissue schizonts. 4. Released into bloodstream as merozoites where they invade red blood cells. 5. Some of the parasites remain dormant in the liver. 6. In the red blood cells, parasites mature into ring shaped forms and other asexual stages known as trophozites and schizonts. 7. Fully mature parasites lyse the red blood cells and are released to infect other ones. 8. Sexual forms of gametocytes differentiate and are read to be picked up by mosquitoes.

Plasmodium in mosquito

1. When taken up by the mosquito, the gametes further differentiate. 2. The gametes mate to form a zygote. 3. Zygote penetrates mosquito's gut. 4. Develops into an oocyte that develops into cells. 5. The cells migrate to salivary glands.

What characteristics of viruses can be used for antiviral drugs?

In the case of HIV, there are certain characteristics that antiviral drugs can target: - Integrase enzyme that incorporates the viral DNA into the genome (integrase inhibitors). - Membrane glycoprotein that mediates entry (fusion/entry inhibitors). - Protease that cleaves a long protein made from the virus RNA (protease inhibitors). - Reverse transcriptase that makes HIV DNA from RNA (reverse transcriptase inhibitors). - Viral strains have high rates of mutation, which means high rates of resistance to antiviral drugs.

Final concentration of the culture

N = final # of cells n = how many times cell divides (# of generations) N0 = starting # of cells N = 2ⁿ × N₀ n = (log N - log N₀)/0.301 (# of generations) g = t/n t = time g = generation time