Final Exam: Topics 1 - 14 Flashcards

Question

Compare and contrast of transmission and scanning electron microscopy, and atomic force microscopy.

Answer 1

Electron microscopy: Light microscope are limited by the wavelengths of visible light (up 1500X) Electrons can act like waves with a very short wavelength, so get amazing resolution and can magnify 100000x. The specimen must be prepared so cannot be alive. Two main types: Transmission Electron Microscope Scanning Electron Microscope Transmission Electron Microscope: Uses a beam of electrons focused by magnets Beam passes through a sample and then runs into the detector the captures the image. Specimens are a very thin section (20-100nm thick) Good for internal structures Scanning Electron Microscopy: Creates an image by collecting electron that are knocked off off a specimen with a beam of electrons Specimens are dried and often coated with gold Good for looking at the surfaces of larger objects or smaller samples Atomic force microscopy: can be used in several ways, including using a laser focused on a cantilever to measure the bending of the tip of a probe passed above the specimen while the height needed to maintain a constant current is measure; useful to observe specimens at the the atomic level and can be more easily used with nonconducting samples.

Answer 2

Direct counting methods count the number of organisms present in a sample. 1. Direct microscopic counts using a Petroff-Hauser chamber. - Take a small known volume of a culture to a calibrated slide and count the number of cells under a light microscope. - One disadvantage of this method is that you are counting dead cells too, but you can use a secondary stain to fix this. 2. Coulter Counter - The Coulter Counter counts the changes in electrical resistance in a saline solution. - Each bacterium causes a change in resistance and is counted. 3. Serial dilution, followed by plate count - Serial dilution is a method for determining the number of living bacterial cells in a culture by making a series of dilutions and plating the diluted cultures on agar plates. - Plate Counts: spread a small amount of culture on a bacterial plate and wait for colonies to grow. -Counts viable cells > Problem: only plates with 30-300 colonies are countable > To do this: you would have to spread 0.0000001 mL (0.1 μl) on a plate… not possible… > SOLUTION? Serial Dilution > Systematically reduces the concentration of cells in a sample, so you can get plate a volume that will yield 30-300 colonies on a plate. 4. Most probable number - The Most Probable Number method is used when bacterial count is too low for other methods. - Evaluates detectable growth by observing changes in turbidity or color due to metabolic activity. - Serial dilution in MEDIA to see when culture is diluted out. - Use MPN table for final determination of titer Indirect counting measure the turbidity (how cloudy) the sample is and is used as as estimation or to compare cultures.

Answer 3

General dilution Equation: V1D1=V2D2 V1 = Volume of first sample (or stock) added V2 = Final volume in new tube (diluent + V1) D1 = Dilution of first sample (=1 if stock–undiluted) D2= Final dilution in new tube If D1=1 (stock solution that is not diluted), then this is simplified to the Dilution Factor equation on the next slide. Dilution factor: (Amount or volume original solution added)/ (total amount or volume made) Example: You add 10 µL of a stock to 990 µL of water. What is the dilution within Tube 1? D2 = (V1D1)/V = V1/V D2= 10.0 macroliters/ 1000.0 macroliters = 1/100 = 10^-2 Original cellular density equation: OCD = CFU/(v x D) CFU= # of colonies on the plate v= volume plated D= total dilution Example: After making a series of dilutions of a bacterial culture and plating 0.1mL each dilution the plates are incubated, and colonies are counted. One plate has 40 colonies on it. The total dilution for that plate is 1/1000 = 0.001. What is the OCD of the starting culture? OCD= CFU/ (v x D) CFU= # of colonies on the plate = 40 cfu v= volume plated = 0.1mL D= total dilution = 0.001 OCD = 40cfu/(0.1mL)(0.001) = 400,000 CFU/mL or 4 X 10^5 CFU/mL

Answer 4

The prokaryotic genome is different than the eukaryotic genome. Prokaryotic genomes are smaller (1/1000 of the human genome) and usually circular. They are haploid, meaning they only have one copy of every gene. Prokaryotes often have additional DNA called plasmids, small circular pieces of DNA with non-essential genes. They are found in the nucleoid and associate with nucleoid-associated proteins that package and organize the DNA. Eukaryotic cells keep their chromosomes in the nucleus Have multiple, linear chromosomes Can be haploid or diploid DNA is packaged with proteins called histones (also for Archaea).

Answer 5

Prokaryotes divide by binary fission and must replicate their DNA. Bacteria reproduce by BINARY FISSION The bacteria chromosome is duplicated (DNA replication) One copy goes to each daughter.

Answer 6

horizontal gene transfer: when bacterial genetic recombination occurs Vertical gene transfer is the transfer of genetic information, including any genetic mutations, from a parent to its offspring.

Answer 7

The cell envelope encloses the cytoplasm and internal structures. Comprised of up to three layers Cell membrane (inner most) Cell wall (middle) Glycocalyx (outer most) All cells have a plasma membrane which is semi-permeable. Composed primarily of a bilayer of amphipathic phospholipids, but also has proteins embedded Structure is described by using the fluid mosaic model.

Answer 8

Diffusion is the tendency of molecule to move from an area of high concentration to low. Osmosis is diffusion of water. Water will move from areas of higher water concentration to areas of lower water concentration. This inversely corresponds to the solute concentration. Water moves across the membrane to help ‘dilute’ the solute until there is an equivalent % of water to solute on each side. Facilitated Diffusion: protein helps large, polar and/or charge molecules move WITH their concentration gradient. Active Transport: protein helps large, polar and/or charge molecules travel AGAINST their concentration gradient. Requires energy (ATP or concentration gradient).

Answer 9

Hypertonic: Solution with the higher solute concentration Pulls water towards it (greater pulling power) Hypotonic: Solution with lower solute concentration Water is pulled from it (lower pulling power) Isotonic: Same pulling power for water on both sides of membrane Flow of water is equal in both directions, so the net flow is zero.

Answer 10

Gram positive (thick layer of peptidoglycan) Gram positive bind stain better because they have a thick layer of peptidoglycan. Stain Purple Gram-positive bacteria have a very thick cell wall that often contains teichoic acid. Gram negative (thin layer of peptidoglycan) Gram negative bacteria only have a little peptidoglycan, so don’t hold on to the stain. Stain Pink Gram-negative bacteria have a thin layer of peptidoglycan and an inner membrane (IM) and an outer membrane (OM) separated by the periplasmic space.

Answer 11

Inclusion bodies: - Inclusions allow prokaryotes to store excess nutrients or other materials. - Not membrane bound Usually store nutrients > Glycogen or starch for carbon stores > Polyphosphate granules for inorganic phosphate used in metabolism > Sulfur granules for metabolism in Thiobacilius - Sometimes can store other things like gas or magnetic iron. Ribosomes: - All cells have ribosomes, but the prokaryotic ribosome is a bit different. - Ribosomes are the protein synthesis machinery made of a mix of RNA and proteins. - Prokaryotic ribosomes are smaller (70s) than eukaryotic ones (80s). - Many antibiotics target the prokaryotic ribosome. Thylakoids: - The principal functions of thylakoids are the trapping of light energy and the transduction of this energy into the chemical energy forms, ATP and NADPH. During this process, water is oxidized and oxygen is released.

Answer 12

Bacterial cells are generally vegetative, undergoing cell division and metabolism, but some can form endospores. Dormant bodies that are resistant to heat, radiation, and chemicals, freezing, dehydration Metabolically active vegetative cells can undergo sporulation in response to external stimuli Found among the Gram positive Bacillales and Clostridiales. Most well-known genera are Bacillus and Clostridium Endospores are desiccated and extremely hard to kill. Consist of several layers and many of the same structures found in vegetative cells Contain very little water Can persist in the environment for long periods of time

Answer 13

Prokaryotic flagellum is a rigid spiral made of flagellin protein and spins 360 degrees. This is different from eukaryotic flagella that move only 180 degrees, like a whip, is flexible, and made of microtubules. Motility is movement towards or away from stimuli. Flagella allow bacteria to move in response to chemical signals (chemotaxis), light (phototaxis), or changes in temperature (thermotaxis)

Answer 14

Cells walls in Archaea and Eukarya are quite different than in Bacteria. Archaeal cell walls are not made of peptidoglycan Usually, pseudopeptidoglycan where NAM subunit is replaced with something else Could be made of another glycoprotein or polysaccharide Eukarya cell walls are either made of cellulose (plants) or chitin (fungi)

Answer 15

> Positive –taxis: Movement towards a stimulus > Negative –taxis: Movement away from a harmful stimulus

Answer 16

Fimbriae and pili – allow for specialized attachments Fimbriae and pili are structurally similar but have some key differences. Fimbriae - Shorter and more numerous, covering the entire surface of the cell - Used to adhere to surfaces or other cells. - Can be a pathogenetic determinant. Pili - Longer and less numerous - Involved in conjugation.

Answer 17

Anabolic reactions involve the building of larger, complex molecules from smaller, simpler ones, and require an input of energy. (requires energy, builds larger, complex molecules from smaller, simpler ones and forms chemical bonds between molecules) Catabolic reactions are the opposite of anabolic reactions, and break the chemical bonds in larger, more complex molecules. (releases energy, breaks down large, complex molecules into smaller, simpler ones and breaks chemical bonds within molecules)

Answer 18

Molecular energy stored in the bonds of complex molecules is released in catabolic pathways and harvested in such a way that it can be used to produce high-energy molecules, which are used to drive anabolic pathways. NAD+ is the oxidized form of the molecule; NADH is the reduced form of the molecule. The oxidized form of flavin adenine dinucleotide is FAD, and its reduced form is FADH2. A living cell must be able to handle the energy released during catabolism in a way that enables the cell to store energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell. This chemical energy is stored in the pyrophosphate bond, which lies between the last two phosphate groups of ATP.

Answer 19

Enzymes: major cellular catalysts typically proteins (some R N A s) highly specific as a result of structure substrate: in reaction, enzyme combines with reactant (substrate: chemical reactants of an enzymatic reaction), forming enzyme-substrate complex, releasing product and enzyme active site: region of enzyme that binds substrate an allosteric site, a location other than the active site, and still manages to block substrate binding to the active site by inducing a conformational change that reduces the affinity of the enzyme for its substrate. allosteric site: location within an enzyme, other than the active site, to which molecules can bind, regulating enzyme activity

Answer 20

Autotrophs convert inorganic CO2 to organic compounds. Heterotrophs get their carbon from complex organic compounds (often from autotrophs) Phototrophs get their energy from electron transfer from light. Chemotrophs get their energy from electrons by breaking chemical bonds

Answer 21

A T P generated through 1 of 3 mechanisms Substrate-level phosphorylation: energy-rich substrate bond hydrolyzed directly to drive A T P formation (e.g., hydrolysis of phosphoenolpyruvate) Oxidative phosphorylation: Movement of electrons generates proton motive force (electrochemical gradient) used to synthesize A T P Photophosphorylation: light used to form proton motive force

Answer 22

Respiration: Aerobic respiration: Terminal acceptor is oxygen Anaerobic respiration: Alternative terminal electron acceptors NO3-, SO4-2, CO2 Lower energy yields than O2 Fermentation (anaerobic): Organic substrate for NADH oxidation Low energy yield

Answer 23

Four Phases: Glycolysis: Energy is added to a glucose molecule by adding a phosphate group to each end. Carbon-carbon bond is broken, 2 NAD+ are reduced, and 2 inorganic phosphates are added. Phosphates are transferred from carbon to ADP to form ATP (staring material: glucose, products: 2 NADH, 2 ATP(net), and 2 pyruvate, this takes place in cytoplasm and no oxygen is required) Transition reaction: Starting materials: 2 pyruvate Products: 2 NADH 2 CO2 2 acetyl CoA Takes place in: Mitochondrial matrix Oxygen required? YES Krebs cycle (also known as Citric acid cycle or TCA cycle): Krebs Cycle Starting materials: 2 acetyl CoA Products: 4 CO2 6 NADH 2 FADH2 2 ATP Takes place in: mitochondria Oxygen required? YES Electron transport chain: Starting materials: NADH, FADH2, O2 Products: ATP: 3 from each NADH 2 from each FADH2 H2O Takes place in: mitochondria Oxygen required: yes

Answer 24

When certain organisms can’t do cellular respiration, they do glycolysis, followed by fermentation instead. Many cells are unable to carry out respiration because of one or more of the following circumstances: Lacking enough of any appropriate, inorganic, final electron acceptor to carry out cellular respiration. (TEMPORARY) Lacking genes to make appropriate complexes and electron carriers in the electron transport system. (PERMENANT) Lacking genes to make one or more enzymes in the Krebs cycle. (PERMENANT)

Answer 25

Light-dependent reactions: Energy from sunlight is captured by photopigments and stored as chemical energy. The light-dependent reactions produce ATP and either NADPH or NADH to temporarily store energy. These energy carriers are used in the light-independent reactions to drive the energetically unfavorable process of “fixing” inorganic CO2 in an organic form, sugar. Light-independent reactions: Chemical energy from the light-dependent reaction is used to build sugar molecules from CO2 The light-independent reactions (Calvin cycle) use the chemical energy from the light-independent reactions and uses it to build CO2 into sugar. CO2+H2O –> C6H12O6+O2

Answer 26

Oxygenic: Water is source of e- and H+ O2 is released Anoxygenic: Compounds other than water are the electron and proton donor Purple non-sulfur bacteria use dissolved organic material like succinate or malate or hydrogen gas (1. Sunlight/energy 2. Light-dependent reactions 3. Light-independent reactions)

Answer 27

Binary fission is the process of bacterial cell division. Each bacterial cell makes an exact copy of itself. The time required to perform a division is the generation time. Wide diversity in Generation time Ranges from 20 minutes in a well fed and aerated E. coli culture to weeks in a Mycobacterium sp culture to centuries in some oligotrophic environments Binary Fission Steps 1. DNA replication 2. Cell elongation 3. Formation of division septum 4. Cell separation

Answer 28

1. Lag: No division Cells are settling into their new environment Lots of metabolic activity as cells get ready to divide 2. Log: Once cells have enough energy and materials they start rapidly dividing Growth is logarithmic The relationship between time and number of cells is not linear but exponential. 3. Stationary: Growth slows and population size reaches equilibrium of cells made = # of cells dying Growth rate is 0 4. Death/decline: More cells die than are being made Cells are killed by built up waste products or lack of nutrients

Answer 29

Physical requirements for growth: temperature, pH, and osmotic pressure/salt concentration Chemical growth requirements: 6 most common elements in organisms? C,H,O,N,P,S Other common elements: K, Mg, Fe, Ca, Mn Trace Elements Zn, Co, Cu, Mo

Answer 30

Temperature preference; Psychrophiles: also known as psychrotolerant, prefer cooler environments, from a high temperature of 25 °C to refrigeration temperature about 4 °C. They are found in many natural environments in temperate climates. Mesopholes: adapted to moderate temperatures, with optimal growth temperatures ranging from room temperature (about 20 °C) to about 45 °C. As would be expected from the core temperature of the human body, 37 °C (98.6 °F), normal human microbiota and pathogens (e.g., E. coli, Salmonella spp., and Lactobacillus spp.) are mesophiles. Thermophiles: Organisms that grow at optimum temperatures of 50 °C to a maximum of 80 °C Hyperthermophiles: characterized by growth ranges from 80 °C to a maximum of 110 °C, with some extreme examples that survive temperatures above 121 °C, the average temperature of an autoclave. pH preference; acidophiles: Microorganisms that grow optimally at pH less than 5.55 neutrophiles: meaning they grow optimally at a pH within one or two pH units of the neutral pH of 7 alkaliphiles: microorganisms that grow best at pH between 8.0 and 10.5. Vibrio cholerae, the pathogenic agent of cholera, grows best at the slightly basic pH of 8.0; it can survive pH values of 11.0 but is inactivated by the acid of the stomach.

Answer 31

Growth is highest at the OPTIMAL GROWTH TEMPERATURE. The lowest temperature the bacteria can survive and reproduce is called its minimum growth temperature. The highest the bacteria can survive and reproduce is called its maximum growth temperature. Higher up on the extreme temperature scale we find the hyperthermophiles, which are characterized by growth ranges from 80 °C to a maximum of 110 °C, with some extreme examples that survive temperatures above 121 °C, the average temperature of an autoclave. Not much protection is available against high osmotic pressure. In this case, water, following its concentration gradient, flows out of the cell. This results in plasmolysis (the shrinking of the protoplasm away from the intact cell wall) and cell death. This fact explains why brines and layering meat and fish in salt are time-honored methods of preserving food. Microorganisms called halophiles (“salt loving”) actually require high salt concentrations for growth. These organisms are found in marine environments where salt concentrations hover at 3.5%.

Answer 32

Obligate aerobes: need abundant oxygen. Facultative anaerobes: thrive on O2 but can live for a while without it Obligate anaerobes: oxygen is toxic to them Aerotolerant anaerobes: do not use oxygen but can tolerate it Microaerophiles: require a small amount of oxygen We can test the oxygen preference of a species by growing bacteria in thioglycolate tubes.

Answer 33

Bacteria can be grown on solidified agar medium either in a test tube (slant) or in a petri dish. You can also grow your microbe in a watery nutrient broth. general, all-purpose and support many different organism specialized: Enriched media for fastidious bacteria, with complex nutritional needs chemically defined, meaning that every component is known and quantified. (Water, Glucose, NH4Cl, KH2PO4, K2HPO4, MgSO4, Na acetate, Alanine, Arginine, Asparagine, Aspartic acid, Cysteine, Glutamic acid, Glycine, Histidine, Isoleucine, Etc.) complex, made of extracts or digests from yeast, meat, or plants so the components are undetermined and variable (Water, Peptone, Beef extract, NaCl) Selective media inhibits the growth of unwanted microorganisms and supports the growth of the organism of interest by supplying nutrients and reducing competition Differential media: make it easy to distinguish colonies of different bacteria by a change in the color of the colonies or the color of the medium.

Answer 34

Obtaining a pure culture of bacteria is usually accomplished by spreading bacteria on the surface of a solid medium so that a single cell occupies an isolated portion of the agar surface. This single cell will go through repeated multiplication to produce a visible colony of similar cells, or clones.

Answer 35

biofilm: complex ecosystem of bacteria embedded in a matrix

Answer 36

Genetics: the study of how genes and how traits are passed down from one generation to the next. genome: entire genetic content of a cell chromosome: discrete DNA structure within a cell that controls cellular activities gene: a sequence of DNA that codes for a single protein = one gene one polypeptide genetic code: correspondence between mRNA nucleotide codons and the translated amino acids Genotype: precise sequence of nucleotides found in that individual organism For example: the sequence of the gene encoding the lactase enzyme Phenotype: observable characteristics that result from the organism’s genotype For example: ability to digest lactose

Answer 37

DNA replication is the process by which the genome’s DNA is copied in cells. DNA replication is semi-conservative. Semi-conservative means that each daughter strand has one parental strand and one newly synthesized strand. The old strand is used as a pattern to make the new strand using complementary binding. Step 1: Helicase breaks the hydrogen bonds holding the two strands together, so they separate Step 2: DNA polymerase adds nucleotides to the growing new strand, complementing the bases on the template strand

Answer 38

The Central Dogma of Biology describes the flow of information in the cell. central dogma states that DNA organized into genes specifies the sequences of messenger RNA (mRNA), which, in turn, specifies the amino acid sequence of proteins. a single protein = one gene one polypeptide

Answer 39

Both DNA and RNA are nucleic acids made of nucleotides involved in gene expression. What are the differences between DNA and RNA? bases (RNA: uracil, DNA: thymine) Sugar (RNA: ribose, DNA: deoxyribose) # of strands (RNA: 1, DNA: 2)

Answer 40

Translation is the decoding of the mRNA message into a polypeptide by the ribosome. The language is called the GENETIC CODE. Translation is the process of decoding the mRNA into a sequence of amino acids. What is required for translation? mRNA template Ribosome: made of a mix of rRNAs and protein tRNA Transcription begins when RNA polymerase binds to a promoter sequence near the beginning of a gene (directly or through helper proteins). RNA polymerase uses one of the DNA strands (the template strand) as a template to make a new, complementary RNA molecule. Transcription ends in a process called termination. Termination depends on sequences in the RNA, which signal that the transcript is finished. Eukaryotic transcription is carried out in the nucleus of the cell by one of three RNA polymerases, depending on the RNA being transcribed, and proceeds in three sequential stages: Initiation. Elongation. Termination. Prokaryotic transcription is the process in which messenger RNA transcripts of genetic material in prokaryotes are produced, to be translated for the production of proteins. Prokaryotic transcription occurs in the cytoplasm alongside translation. Prokaryotic transcription and translation can occur simultaneously.

Answer 41

Ribosome: Translation Machinery Found in the cytoplasm Made of BOTH protein and ribosomal RNAs (rRNAs) Made up of 2 parts: the small subunit and the large subunit Translation: using the information carried by the mRNA to make a protein mRNA enters the cytoplasm from the nucleus The first tRNA is released A tRNA with an anticodon which complements the next 3 bases on the mRNA then delivers its amino acid A ribosome and a tRNA with the UAC anticodon and the amino acid methionine, assemble on the mRNA There are no tRNAs that have an anticodon for this last codon; it is a STOP. The ribosome falls off the mRNA and the peptide is released The ribosome moves to the next codon A peptide bond forms between the 2 amino acids In prokaryotes, multiple RNA polymerases can transcribe a single bacterial gene while numerous ribosomes concurrently translate the mRNA transcripts into polypeptides. Is this possible in eukaryotes? This allows prokaryotes to respond to their environment faster.

Answer 42

Reminder: mutations are random and permanent changes in the DNA sequence. Mutations can be as small as an alteration of a single base Mutations occur randomly and generally do not interfere with the organism. However, if a mutation occurs in a gene it is usually deleterious, but it can also result an advantageous effect. If the DNA in a gene is altered, the mRNA transcribed from that gene will also be altered and the protein will be altered (might not fold correctly)

Answer 43

Spontaneous mutations come from DNA replication. DNA polymerase makes 1 uncorrected mistake in every 30 million base pairs. Induced mutations: come from exposure to mutagens, either chemical agents or radiation. Point mutation: substitution of a single base Silent mutation: has no effect on the protein sequence missense mutation: results in an amino acid substitution nonsense mutation: substitutes a stop codon for an amino acid frameshift mutation: insertion or deletion of one or more bases insertion or deletion mutation: results in a shift in the reading frame

Answer 44

mutagen: type of chemical agent or radiation that can induce mutations Spontaneous mutations come from DNA replication. DNA polymerase makes 1 uncorrected mistake in every 30 million base pairs. Induced mutations: come from exposure to mutagens, either chemical agents or radiation. Nucleoside analogues are nucleosides which contain a nucleic acid analogue and a sugar. Intercalating agents are hydrophobic heterocyclic ring molecules that resemble the ring structure of base pairs, and include ethidium bromide, acridine orange, and actinomycin D. Insertion of these agents distorts the DNA double helix, thereby interfering with DNA replication, transcription, and repair.

Answer 45

The Ames Test: Uses a genetically engineered bacteria which cannot grow without histidine being added to the media (auxotrophs: nutritional mutant with a loss-of-function mutation in a gene encoding the biosynthesis of a specific nutrient such as an amino acid) Treat the bacteria with the potential mutagen Add rat liver extract and Salmonella to top control tube; add rat liver extract, possible mutagen, and Salmonella to bottom experimental tube. Plate and incubate both samples using medium lacking histidine. Compare growth on plates to identify revertants, which suggest mutagen causes mutations.

Answer 46

- Radiation is an example of a physical mutagenic agent. There are also many chemical agents as well as biological agents (such as viruses) that cause mutations. One very important fact to remember is that radiation increases the spontaneous mutation rate, but does not produce any new mutations. - Proofreading by DNA polymerase - Mismatch repair soon after mistake. - Repairing thymine dimers > Photoactivated > Break bonds between dimerized bases - Dark repair > Endonuclease breaks defective strand > DNA polymerase synthesizes a replacement strand > Exonuclease removes damaged strand > Ligase seals gap

Answer 47

Gene Regulation: Repressor Proteins Usually Determine Whether Operon is ON or OFF Only a fraction of the genes in a cell are expressed at any one time. The variety of gene expression profiles characteristic of different cell types arise because these cells have distinct sets of transcription regulators. Some of these regulators work to increase transcription, whereas others prevent or suppress it.

Answer 48

operon: a group of genes with related functions often found clustered together within the prokaryotic chromosome and transcribed under the control of a single promoter and operator repression sequence

Answer 49

There are 2 types of operons: Repressible and Inducible Expression of genes regulated in two main ways: Repressible Operon: The genes are usually turned “on” or expressed unless there is a signal to turn them “off” Inducible Operon: The genes are usually turned “off” unless there is a signal to turn them “on”

Answer 50

Trp operon: genes that encode proteins used to synthesize (make) tryptophan, which is an amino acid. Repressible =Operon is always On, unless it is turned Off Analogy: Ford car assembly line is always on, unless there are too many cars that haven’t been sold, then it gets turned off In the absence of tryptophan, the trp repressor dissociates from the operator, and RNA synthesis proceeds. When tryptophan is present, the trp repressor binds the operator, and RNA synthesis is blocked.

Answer 51

Inducer Example: Lac Operon E. coli prefers to have glucose for energy, but if no glucose is available and lactose is present, E. coli turns on the lac operon to be able to use the lactose instead. Genes code for proteins used to breakdown LACTOSE Inducible= operon is OFF, unless a molecule is present to turn it on Analogy: Gas shortage so Ford turns on assembly line for electric cars (use available food source) Repressor (LacI) is constitutively expressed (always made). Without inducer, the repressor is ACTIVE (meaning it is the right shape to bind to the operator DNA sequence) and blocks RNA polymerase binding. Alloactose (inducer) binds to the repressor, changing its shape, so it can’t bind the operator. E. coli prefers glucose over lactose if both are present. There is another layer of control of expression of the Lac operon. Glucose utilizing genes are expressed constitutively. If both glucose and lactose are present in the medium, the bacterium will use the glucose first, so the Lac operon will be repressed even though lactose is available. When glucose is depleted, the Lac operon is de-repressed (turned back on). In the absence of lactose, the lac repressor binds the operator, and transcription is blocked. In the presence of lactose, the lac repressor is released from the operator, and transcription proceeds at a slow rate.

Answer 52

When high levels of glucose are present in a cell, the amount of a signal molecule, cAMP (cyclic adenosine monophosphate) is low. This inhibits the formation of a cAMP-CAP (catabolite gene activator protein) complex that promotes RNA polymerase-DNA binding. The operon is not efficiently transcribed. When glucose levels in the cell are low, cAMP levels rise, and the formation of the cAMP-CAP complex is more likely. The cAMP-CAP-DNA complex promotes RNA polymerase-DNA binding and increases transcription of the operon To get efficient lac operon transcription, glucose must be low AND allolactose must be present. In absence of cAMP, CAP does not bind the promoter. Transcription occurs at a low rate. cAMP-CAP complex stimulates RNA polymerase activity and increases RNA synthesis. In the presence of cAMP, CAP binds the promoter and increases RNA polymerase activity. However, even in the presence of cAMP-CAP complex, RNA synthesis is blocked when repressor is bound to the operator.

Answer 53

Biotechnology: The science of using living systems to benefit humankind. Biotechnology can be used for industrial, medical, and agricultural applications with synthetic biology (assembling D N A pieces into new genetic elements)

Answer 54

Recombinant DNA technology (also called DNA cloning): a piece of DNA is copied from one organism and pasted into a small piece of DNA called a plasmid. The insulin gene from humans was inserted into a plasmid. This recombinant DNA plasmid was then inserted into bacteria. As a result, these transgenic microbes are able to produce and secrete human insulin. Many prokaryotes are able to acquire foreign DNA and incorporate functional genes into their own genome through “mating” with other cells (conjugation), viral infection (transduction), and taking up DNA from the environment (transformation).

Answer 55

1. PCR makes multiple copies of GeneX THe polymerase chain reaction (PCR) is DNA replication invitro, multiplying segments of target DNA(a few kbp in length) up to the billionfold during amplification. PCR requires the following components which are mixed in a tube: Template DNA—contains the target DNA to be amplified Primers—short pieces of DNA that designate where the copying will begin and end DNA polymerase—enzyme that will replicate the DNA Buffer solution—provides the proper pH and salt concentration for the replication reaction to occur efficiently Steps in PCR: 2. Denaturation– separate strands of template D N A by heating at a high temperature 3. Annealing: lower temperature to allow primers to bind to target sequence 4. Extension: D N A polymerase extends primers using original D N A template 5. Restriction enzymes cut the PCR products and plasmid 6. Ligate the plasmid and PCR products together 7. Transform the cell

Answer 56

The P C R amplifies specific D N A sequences. (a) Target D N A is heated to separate the strands, and a large excess of two oligonucleotide primers, one complementary to each strand, is added along with D N A polymerase. (b) Following primer annealing, primer extension yields a copy of the original double-stranded D N A. (c) Two additional P C R cycles yield four and eight copies, respectively, of the original D N A sequence. (d) Effect of running 20 P C R cycles on a D N A preparation originally containing 1 copy of a target gene. Note that the plot is semilogarithmic.

Answer 57

Restriction endonucleases (restriction enzymes) are used to cut the DNA at specific sequences called restriction sites. Why might bacteria have these naturally? Protect the bacteria from invading bacteriophages (viruses) - DNA fragments separated by gel electrophoresis

Answer 58

Any DNA molecules cut with same restriction enzyme can be joined together by another enzyme called ligase because of sticky ends.

Answer 59

Agarose gel acts like a maze of small holes Small DNA fragments move quickly through the small pores Larger fragments take more time to “wiggle” though. DNA (negatively charged) moves through gel toward the positive end by adding an electrical current

Answer 60

Plasmid vector: Carries the inserted piece of DNA into the bacterium where it gets replicated/expressed Plasmid vectors usually contain: 1. Ori (origin of replication) 2. Antibiotic resistance markers, usually at least two 3. Known restriction sites often in the form of several grouped together called a multiple-cloning site or polylinker.

Answer 61

There are 3 different methods: 1. Transformation: competent cells take up DNA directly from their environment 2. Transduction: DNA transferred by bacteriophage (virus that infects bacteria) 3. Conjugation: One live bacterium transfers the plasmid to another live bacterium via a pilus.

Answer 62

Transformation is when competent cells take up DNA from the environment. Cells are either naturally competent or artificially competent - Natural: Competence factors: surface proteins that allow bacteria - Artificial: treatments can increase membrane permeability (CaCl2, electroporation ) Large (7,00-10,000 bp) DNA fragments can be accepted. 1. Donor DNA associates with DNA binding protein on the cell surface 2. One strand of the DNA is transported into the cell while the other strand is hydrolyzed by a nuclease. 3. At least part of the donor DNA can move into the cell’s chromosome by homologous recombination

Answer 63

Transduction: using a virus that infects bacteria to pass genes from one bacteria to another. Viruses can infect using to different approaches - Virulent viruses infect using the lytic cycle - Temperate viruses infect using the lysogenic cycle 1. A bacteriophage injects its DNA into a bacterium - During the lytic cycle of virulent phage, the bacteriophage takes over the cell, reproduces new phages, and destroys the cell 2. Phage DNA is replicated, and the bacterium’s chromosome is broken down. Viral proteins are synthesized 3. When new phage particles are assembled, some phage heads may get stuffed with bacterial rather than viral DNA 4. If that phage infects another bacterium, it can transfer genes from the lysed bacterium into a new cell. Temperate phage can incorporate into the cell’s chromosome (lysogenic) but can be induced into a lytic cycle in which many infective phage particles are produced. Transduction occurs when a bacteriophage transfers bacterial DNA from one bacterium to another during sequential infections. There are two main types: 1. Generalized transduction: when the virus picks up a random piece of bacterial chromosome by mistake during the lytic cycle. 2. Specialized transduction: occurs at the end of the lysogenic cycle, when the prophage is excised, and the bacteriophage enters the lytic cycle.

Answer 64

Conjugation: when DNA is transferred between 2 liver bacteria. - DNA is transferred between cells - Requires physical contact between cells - F plasmids; code for pilus

Answer 65

We use antibiotic resistance and a reporter gene. Each plasmid has an antibiotic resistance gene, so if we grow the bacteria on media containing that antibiotic, only bacteria that took up the plasmid will live.

Answer 66

A reporter gene is another gene sequence artificially engineered into the plasmid that encodes a protein that allows for visualization of DNA insertion. Blue/white screening - Insertional inactivation of gene within lacZ (encodes the β-galactosidase enzyme) used to detect cloned D N A - Transformants are plated on media containing ampicillin and X-gal which turns blue when broken down by β-galactosidase. - Cells containing vector with insert are white because no β-galactosidase formed.

Answer 67

Genome editing: Use of C R I S P R/Cas9 system from Streptococcus pyogenes to alter eukaryotic genomes in living cells Sequence Targeting by the Cas9 Protein - Cas proteins of C R I S P R systems function as endonucleases when guided to nucleic acids by binding of C R I S P R R N A s (c r R N A s) - Synthetic R N A (synthetic guide R N A [s g R N A]) can be designed to recruit Streptococcus Cas9 and bind to target D N A, enabling cutting in genome of almost any cell - At cut site, D N A can be ligated or used to insert new D N A Sequence Targeting by the Cas9 Protein . Also requires protospacer adjacent motif (P A M) on target D N A for complete endonuclease activity - Various methods of C R I P S R system delivery by injection . Plasmid . s g R N A and mR N A can be made in vitro - Homologous recombination can be used to incorporate new D N A (insertion) - Nonhomologous double-stranded D N A break repair pathway can ligate after deletion

Answer 68

C R I S P R Editing in Practice: - Edit genomes of crops and farm animals - Edit the human genome to treat genetic diseases - Treat other diseases (for example, viral diseases) - Diagnostic tool to detect pathogens Ethical questions about use in humans: https://www.npr.org/sections/health-shots/2023/03/06/1158705095/genome-summit-gene-editing-ethics-crspr

Answer 69

acellular: not made of cells Obligate intracellular parasites: - Lack genes needed for successful reproduction - Require a host cell to reproduce obligate intracellular pathogen microorganism that cannot synthesize its own ATP and, therefore, must rely on a host cell for energy; behaves like a parasite when inside a host cell, but is metabolically inactive outside of a host cell 1. Infectious, acellular pathogens 2. Obligate intracellular parasites - Lack genes needed for successful reproduction - Require a host cell to reproduce 3. DNA or RNA genome 4. Genetic material is surrounded by a capsid (protein coat)

Answer 70

virion: inert particle that is the reproductive form of a virus

Answer 71

All viruses have genetic material and a capsid. - Capsid(protective coat): made of capsomeres protein subunits - Nucleic acid (DNA or RNA) Some viruses have an envelope (enveloped) and others do not (naked or non-enveloped). - Envelope (phospholipid membrane) - Spike proteins (glycoproteins that help cell entry)

Answer 72

Most viruses can only infect one kind of cells or a few species = HOST RANGE - Having a wide host range is rare. - Viruses that infect bacteria are called bacteriophages. Why is host range so limited? - Cells must have specific receptor sites that the virus can attach to - Cell must contain the enzymes the virus needs to uncoat - Cell must have the rest of the synthetic machinery

Answer 73

Transmission: how a virus is passed from host to host. Viruses can be passed by 1. Direct contact 2. Indirect contact through an object 3. Vector: which is an animal that passes the virus from one host to another - Mechanical vector: virus travels outside vector - Biological vector: virus travels inside

Answer 74

Viruses can vary in the shape of their capsids The shape of the capsid is determined by their capsomeres. Helical: rod-shaped Polyhedral: many sided Complex: have features of both

Answer 75

Viruses are not classified under the three domains of life, but still need classification. However, they can mutate so quickly that it’s difficult to label them with a genus and species. There are two main systems of classification: - International Committee on Taxonomy of Viruses (ICTV) classifies viruses into families and genera based on viral genetics, chemistry, morphology, and mechanism of multiplication. - The Baltimore System classifies viruses according to their genomes.

Answer 76

[Genome, family, example virus, clinical features] dsDNA; enveloped: (Poxviridae, Orthopoxvirus, skin papules, pustules, and lesions), (Poxviridae, Parapoxvirus, skin lesions), and (Herpesviridae, Simplexvirus, Cold sores, genital herpes, sexually transmitted disease) dsDNA, naked: (Adenoviridae, Atadenovirus, Respiratory infection (common cold)), (Papillomaviridae, Papillomavirus, Genital warts, cervical, vulvar, or vaginal cancer), and (Reoviridae, Reovirus, Gastroenteritis severe diarrhea (stomach flu)) ssDNA, naked: (Parvoviridae, Adeno-associated,dependoparvovirus A, Respiratory tract infection), (Parvoviridae, Adeno-associated dependoparvovirus B, Respiratory tract infection) dsRNA, naked: (Reoviridae, Rotavirus, Gastroenteritis) +ssRNA, naked: (Picornaviridae, Enterovirus C, Poliomyelitis), (Picornaviridae, Rhinovirus, Upper respiratory tract infection (common cold)), and (Picornaviridae, Hepatovirus, Hepatitis) +ssRNA, enveloped: (Togaviridae, Alphavirus, Encephalitis, hemorrhagic fever), (Togaviridae, Rubivirus, Rubella), and (Retroviridae, Lentivirus, Acquired immune deficiency syndrome (AIDS)) −ssRNA, enveloped: (Filoviridae, Zaire Ebolavirus, Hemorrhagic fever), (Orthomyxoviridae, Influenzavirus A, B, C, Flu), and (Rhabdoviridae, Lyssavirus, Rabies)

Answer 77

Viral Replication in prokaryotic hosts occurs via the lysogenic or lytic cycle. - The lytic cycle results in the death of the bacteria. - The lysogenic cycle results in the viral genome combining with the host until induction into the lytic cycle. 1. The phage infects a cell 2. The phage DNA becomes incorporated into the host genome 3. The cell divides, and prophage DNA is passed on to daughter cells 4. Under stressful conditions, the prophage DNA is excised from the bacterial chromosome and enters the lytic cycle 5. Phage DNA replicates and phage proteins are made 6. New phage particles are assembled 7. The cell lyses, releasing the newly made phages

Answer 78

1. Attachment 2. Penetration 3. Uncoating 4. Viral genome replication: mechanism depends on genome type 5. Maturation 6. Release

Answer 79

Genomes of ssRNA viruses for positive(+) vs negative (-): - If the genome sequence is the mRNA sequence it’s a positive (+) strand virus. (sense: 5’UGACCAUGGGA3’) - If the genome sequence is complementary to the mRNA sequence it’s a negative (-) strand virus. (antisense: 3’ACUGGUACCCU5’) +ssRNA virus: 1. Virions enter the cell by endocytosis and are uncoated to release the +ssRNA genome. 2. +ssRNA genome is translated by host cell’s ribosomes to produce viral proteins including RNA dependent RNA polymerase (RdRp). 3. RdRp synthesizes -ssRNA complementary copies of the +ssRNA genome. 4. RdRp synthesizes +ssRNA complementary genomic copies of this –ssRNA. 5. The newly synthesized copies of the genome and the viral proteins are assembled. 6. The virions exit the cell. -ssRNA virus: 1. Virions enter the cell by endocytosis and are uncoated to release the -ssRNA genome and RNA dependent RNA polymerase (RdRp). 2. RdRp synthesizes +ssRNA complementary copies of the -ssRNA genome. 3. The +ssRNA complementary copies are translated by the host cell’s ribosomes to produce viral proteins including more RdRp. 4. RdRp synthesizes the -ssRNA genome using additional copies of the +ssRNA as the template. 5. The newly synthesized copies of the genome and the viral proteins are assembled. 6. The virions exit the cell.

Answer 80

The flow of events during the life cycle: 1. Entry and uncoating of the retrovirus. 2. Reverse transcriptase activity, two steps. 3. Viral DNA enters nucleus and integrates into the host genome. 4. Transcription by host RNA polymerase forms viral mRNA and genome copies. 5. Translation of mRNA forms viral proteins; new nucleocapsids assembled and released through the host cytoplasmic membrane by budding.

Answer 81

- Latent: viruses that hide or stay dormant in the cell after an acute infection but can reemerge. (example: varicella-zoster virus [chicken pox/ shingles]) - Chronic: virus that cause persistent symptoms over time; if body can’t eliminate virus, the virus can persist in tissues for years before symptoms. (example: HIV)

Answer 82

Plant viruses are more like animal viruses than they are like bacteriophage. - May be envelope or non-enveloped - May have a DNA or RNA genome - May have a broad or narrow host range - How do you think they are transmitted? > Mechanical vectors (insects) > Through wounds from pruning or damage

Answer 83

Viral growth curve: described by viral titer: number of virions per unit volume. 1. Inoculation: inoculum of virus binds to cells 2. Eclipse: virions penetrate the cells 3. Burst: host cells release many viral particles 4. Burst size: number of virions released per bacterium

Answer 84

Picornaviridae: large family containing 47 genera and 110 species; virion: non-enveloped, 30-32 nm (small), icosahedral; genome: +ssRNA; host range: vertebrates; examples: enterovirus: polio and rhinovirus: common cold Retreoiridae: large family of viruses that reverse transcribe their RNA to DNA = RETROVIRUSES; virion: enveloped, 80-100 nm (medium), spherical capsid; genome: dimer(2) +ssRNA; host range: human and animal vertebrates; examples: Human Immunodeficiency Virus (HIV), which is the virus that causes AIDS Paramyxoviridae: Many members of this family cause human diseases such as measles, mumps, and some parainfluenzas; virion: enveloped, 300-500 nm (large), mostly spherical; genome: -ssRNA; Host range: mammals, birds, fish, and reptiles; spread by physical contact or airborne transmission Coronaviridae: Virion: enveloped, 120-160 nm (medium-large) helical capsid; genome: -ssRNA with 7-8 segments; host range: mammals, birds, and fish; examples: influenza (Hemagglutinin and Neuraminidase in envelope) and Coronavirus

Answer 85

Viriods: composed of a short strand of circular RNA that can self replicate Virusoids: ssRNA that’s not self-replicating and needs a “helper virus” to cause disease Prions: infectious protein particles, no DNA or RNA required

Answer 86

Fomites: various items that humans interact that might harbor microbes; examples: doorknobs, toys, cell phones, etc. To decide how to clean a surface, you need to ask 2 questions: 1. What’s the application for which that item is used? If the item is inserted in the body, then it must be much cleaner. 2. How resistant are the potential pathogens to antimicrobial treatment? Because C.botulinum can produce endospores that can survive harsh conditions, it must be killed by extreme temperature, etc.

Answer 87

BSL-1: microbes are not known to cause disease in healthy hosts and pose minimal risk to workers and the environment. (nonpathogenic strains of E.coli) BSL-2: Microbes are typically indigenous and are associated with disease of varying severity. They pose moderate risk to workers and the environment. (S.aureus) BSL-3: Microbes are indigenous or exotic and cause serious of potentially lethal disease through respiratory transmission. (M.tuberculosis) BSL-4: Microbes are dangerous and exotic, posing a high risk of aerosol-transmitted infections, which are frequently fatal without treatment or vaccines. Few labs are at this level. (Ebola and Marburg viruses)

Answer 88

1. Sterilization: complete removal or killing of all vegetative cells, endospores, and viruses. - Most extreme measure - Used in laboratories, medical, and food industry - Can be done through physical means, chemical means, or by filtering -Chemicals that achieve sterilization are called sterilants. 2. Disinfection: inactivates most of the microbes on a fomite by chemicals or heat. - Surface isn’t sterile after disinfection because endospores remain. - Should be fast acting, cheap, and easy to used. - Examples: vinegar, bleach 3. Sanitization: the cleansing of fomites to a level deemed safe for public health. - Done by application of heat or chemicals - Example: commercial dishwashing or cleaning public restrooms

Answer 89

Aseptic technique: prevents contamination of sterile surfaces. - Collection of protocols that maintain sterility (asepsis) - If not done correctly in a clinical setting, can cause sepsis in the patient, which is a systemic inflammatory response that can lead to death. - Medical procedures with risk of infection must be done in a sterile field, a designated area to remain free of all metabolically active microbes, endospores, and viruses Antiseptics: antimicrobial chemicals safe for use on living skin or tissues. - Disinfection on surfaces is done using this. - They must kill bacteria, but not damage tissue. (examples: hydrogen peroxide and isopropyl alcohol) Degerming: reducing microbial number by gentle scrubbing and using a mild chemical. (examples: hand washing, alcohol swabs)

Answer 90

Microbial Death Curve: describes the effectiveness of a certain protocol. - The percentage of microbes killed is the most useful information. - The amount of time it takes for the population to decrease 10-fold is the decimal reduction time (DRT) or D value

Answer 91

1. Length of time of exposure 2. Susceptibility of the organism to that disinfectant or protocol 3. The concentration of the disinfectant or intensity of exposure

Answer 92

Physical methods for controlling microbe growth include heat, cold, pressure, desiccation(drying), and radiation. How do they damage microbe? - Disrupting membranes - Changing membrane permeability - Damaging proteins or nucleic acids - Degradation - Chemical modification

Answer 93

Heat: Thermal death point (TDP) is the temperature at which a microbe is killed after a 10-minute exposure. Thermal death time is the length of time needed to kill a microbe at a certain temperature. Boiling: oldest form and quite effective on bacteria, but not on endospores (can withstand 20 hours of boiling). - Dry-heat: is direct application of high temperatures like a Bunsen burner. > Oxidizing molecules > Often involves open flame - Moist-heat: uses steam and is generally more effective because it penetrates cells better. - Denatures proteins and nucleic acids. Moist-heat: > Autoclaves: use high temperature, steam, and pressure - 121oC for 20 min - Slow exhaust - Materials must be loosely wrapped and have indicator tape. > Pasteurization: used when boiling or autoclaving would ruin the food (like milk) but does not sterilize. - Reduces microbe number to prolong time before spoilage - high-temperature short-time (HTST) pasteurization, exposes milk to a temperature of 72 °C for 15 seconds - ultra-high-temperature (UHT) pasteurization, in which the milk is exposed to a temperature of 138 °C for 2 or more seconds. Doesn’t need refrigeration, but changes taste. Cold: - Refrigeration and freezing is also effective at controlling microbe growth. > Refrigeration (0-7 degree C) slows growth. > Freezing (-2) may kill microbes or halt growth, but when thawed growth can continue. > Long term storage is best at -70 degrees C or in liquid nitrogen. Pressure and Desiccation (drying): > Pressure: exposure to high pressure often kills many microbes (but not endospores). - Often used in the food industry to maintain food quality and extend shelf life. - Pressure between 100 and 800 Mpa > Hyperbaric oxygen therapy: can be used to treat infections in clinical settings - Patient breaths pure oxygen at higher-than-normal pressure - Increases oxygen saturation in tissues that have become hypoxic due to infection - Increased oxygen saturation also increases efficiency of immune system cells and antibiotics - Disadvantages: rarely causes oxygen toxicity or can damage delicate tissue due to increased air pressure Desiccation (drying): has been used to preserve food for a long time. - Cells need water to survive, so drying controls their growth. - Can be dried by the sun or freeze-dried (lyophilization) - The water activity (the water content) can also be decreased by addition of high concentrations of salt or sugar Most bacteria can’t grow in high osmotic pressure Radiation: Radiation is the use of high energy radiation or sunlight is used to kill microbes or slow growth. - Ionizing radiation: permeates the cell, damages DNA and forms peroxides which are strongly oxidizing Penetrates packaging to sterile lab supplies that cannot be autoclaved - Non-ionizing radiation: not powerful enough to permeate packaging UV rays can even be used at home - Microwaves Not effective against spores since they contain little water

Answer 94

Chemicals can be used to control microbial growth by denaturing proteins or disrupting the membrane. > How can we choose the proper disinfectant or antiseptic?; Consider: - What kind of microbe are we trying to control? - How clean does the item need to be? - Is the chemical toxic to people, animals, or plants? - How costly is it? - How easy is it to use? Phenolics inhibit microbes by denaturing proteins and disrupting membranes. Heavy Metals kill microbe by acting an inhibitors of enzymes. - Effective in very low concentrations. - Disadvantage: toxicity not limited to microbes (can accumulate in human cells and be toxic) - Examples: > Mercury: has been used for many years to treat syphilis but is not banned in US for toxicity > Silver: lined water jugs with silver in ancient times - Sometimes combined with antibiotics to make them more effective > Copper, Nickel, and Zinc - Copper used in swimming pools as an algicide, becoming more popular - Zinc chloride is very safe, found in mouthwashes Halogens (iodine, chlorine, and fluorine) Oxidize cellular components, destabilizing them > Betadine: an iodine containing liquid that’s used to prep skin before surgery > Chlorine gas: used to clean drinking water but, exposure to people working at treatment plants must be minimized. - Also used in swimming pools - Doesn’t kill everything, sometimes boiling’s required. > Fluoride: added to drinking water for dental health. Alcohols quickly denature proteins and disrupt membranes. > Effective concentration: 70-100%[hand sanitizer] > Mostly bactericidal and fungicidal, but only kill viruses that are enveloped Surfactants are amphipathic and wash away microbes > Not considered antiseptics or disinfectants, but may effectively reduce microbes on surfaces by degerming Peroxygens: Hydrogen peroxide oxidized cellular components Superchemical Gases: Carbon dioxide lowers intracellular pH Natural and Chemical Food Preservatives: decrease pH and inhibit enzymes Triclosan is another bisphenol compound that has seen widespread application in antibacterial products over the last several decades. At high concentrations, triclosan works by interfering with the outer membrane that protects bacteria, making it permeable so that triclosan can penetrate it and kill the microorganism. At lower concentrations, triclosan attacks several targets.

Answer 95

Good antimicrobial agents exhibit selective toxicity. > Selectively kills microbial targets while sparing host. > Most antimicrobials are antibiotics because prokaryotes have more unique targets than fungi or viruses. > Common targets: - Cell Wall - Plasma Membrane - Ribosomes - Metabolic Pathways - DNA synthesis

Answer 96

Effect on target > Bacteriostatic: agent causes a reversible inhibition of growth > Bactericidal: agent kills target. Spectrum of Activity > Broad spectrum kills many different types (overuse may lead to resistant infections) > Narrow spectrum kills only a few types

Answer 97

Antibiotic resistance happens when germs like bacteria and fungi develop the ability to defeat the drugs designed to kill them; the germs that are not killed, will keep growing. 1. Lots of germs. A few are drug resistant 2. Antibiotics kill bacteria causing the illnesses, as well as good bacteria protecting the body from infection 3. The drug-resistant bacteria is now allowed to grow and take over 4. Some bacteria give their drug-resistance other than bacteria, causing more problems

Answer 98

Antiviral: a substance that fights against viruses and inhibits their growth. - Purine and pyrimidine analogs > Ribavirin (Virazole) and Acyclovir (Zovirax) are guanine analogs > AZT interferes with reverse transcriptase - Protease inhibitors; interferes with protein processing - Interferon - Immunoenhancers

Answer 99

Primary pathogens can cause disease regardless of the host’s microbiota or immune system. Opportunistic pathogens can only cause disease in a host with compromised defenses. Pathogenicity is the ability of an organism to produce an infectious disease in another organism. Infection: successful colonization of a host by a microorganism, which can lead to disease An infectious disease is caused by a primary pathogen that can be a bacterium, fungus, virus, etc. communicable, which means they can be spread from person to person either directly or indirectly though an object contagious, meaning that can be spread directly from person to person Iatrogenic disease: Diseases that are a result of a medical procedure Nosocomial disease: Disease contracted in a hospital Zoonotic disease can be passed from animals to humans. Noncommunicable disease cannot be passed from human to human. Noninfectious disease is not caused by a pathogen like cancer or a genetic disorder. Resistance: the capacity of bacteria to withstand the effects of a harmful chemical agent. Virulence refers to the degree that a pathogen causes illness or “how sick you get.”

Answer 100

Human Microbiota is the types of microbes present in an environmental habitat such as those on the human skin or in the gastrointestinal tract. Roles of the Human Microbiota: - Aid in food digestion. > Produce enzymes to breakdown proteins, carbohydrates, and lipids - Make molecules that we need but cannot produce. > Bacillus, Pseudomonas, and Lactobacillus make vitamin B12 > Bifidobacterium make folate and biotin - Development of the immune system > The immune system does not properly develop in the absence of microbial stimulation - Occupy space to prevent pathogen colonization

Answer 101

Signs: objective and measurable indicators of disease i.e., changes in body temperature, changes in breathing rate or blood pressure Symptoms: subjective indicators reported by the patient. Can’t be measured. i.e., Nausea, loss of appetite, pain Subject to memory bias, sometimes can be reported on a scale Syndrome: a specific set of signs and symptoms. Different causes can lead to the same symptoms or signs

Answer 102

Acute disease has a rapid onset and goes away over days or a week. Example: Flu Chronic disease can change over weeks, months or years. Example: Stomach ulcers from H. pylori Latent disease is where the pathogen goes dormant in the body without replicating for long periods of time Example: the virus that causes chicken pox and then shingles

Answer 103

For a pathogen to be “successful,” it must accomplish the following steps: 1. Gain entry to the host and adhere. 2. Travel to the location where it can cause infection (invasion) 3. Evade the host’s immune system for a time. 4. Cause damage to the host by multiplication, production of virulence factors and toxins

Answer 104

1. Alimentary: vomiting, diarrhea, saliva. 2. Genitourinary: sexual contact. 3. Respiratory: secretions from coughing, sneezing, or talking. 4. Skin: open wounds.

Answer 105

Pathogens enter a host through a portal of entry. > Encounter with a potential pathogen is called exposure or contact. > Major portals of entry include the skin, mucous membranes (respiratory tract, gut), or parenteral routes (breach in skin or mucosal membrane). > Most pathogens are suited to a certain portal of entry

Answer 106

Virulence is how severe the disease is that the pathogen causes. We can quantify the virulence of a pathogen by using an LD50 curve. The LD50 is the dose of pathogen that leads to death in 50% of the animals.

Answer 107

- Endotoxins: Part of the Gram-negative cell wall - Exotoxins: proteins released from the pathogen cell as it grows Comparison of Exotoxins and Endotoxins: - Exotoxins: High potency, inactive at 60-80 degrees Celsius, and protein composition - Endotoxins: Low potency, stable(resists at 120 degrees Celsius), and Lipopolysaccharide composition

Answer 108

- Epidemiology: the study of the occurrence, distribution, and determinants of health and disease in a population - Public health: the health of the population as a whole > Identifying the nature of a disease and its transmission is a major goal of epidemiology > In developed countries, infectious diseases cause fewer deaths than noninfectious diseases. However, in developing countries, infectious diseases account for nearly half of all deaths.

Answer 109

Epidemiology looks at the prevalence of a pathogen in a population. - How is a population defined? > Can be geographically or if only some people are susceptible, may be more complicated. > Is there a condition, behavior, or membership that makes an individual more susceptible? Once the population is defined, then we can analyze the disease with empirical measurements.

Answer 110

Morbidity: the state of being diseased > Morbidity rate: - Number of affected individuals during a set period compared to the total population (cases per 100,000) Mortality rate: - Number of deaths due to the disease of a period compared to total population (deaths per 100,000) Incidence: number of new cases in a population Prevalence: total number infected with a disease (almost always higher than incidence since prevalence is cumulative) Common source epidemics: contact with a contaminated material(eg: contaminated egg salad at a picnic) - Many cases in a short time period Propagated epidemic: spread person to person - Slower spread, more difficult to track and eliminate

Answer 111

When studying an epidemic, scientists must first find the etiological (causative) agent; - It’s not enough to observe an association - Need to determine direct causation…how do we do that? - Remember: GERM THEORY OF DISEASE by Robert Koch 1. The suspected causative agent must be absent from all healthy organisms but present in all diseased organisms 2. The causative agent must be isolated from the diseased organism and grown in pure culture 3. The cultured agent must cause the same disease when inoculated into a healthy, susceptible organism 4. The same causative agent must then be reisolated from the inoculated, diseased organism

Answer 112

- John Snow (1813-1858) is the Father of Epidemiology. > Was able to tie an outbreak of cholera to a contaminated water pump in the Soho neighborhood of London - Florence Nightingale (1820-1910): > Part of a group of nurses dispatched during Crimean war to take care of wounded soldiers > Took meticulous notes and presented a monthly report of cause of death, which turned out mostly be infectious disease

Answer 113

There are two main types of epidemiological studies: observational and experimental. 1. Observational: > Data are gathered from participants through measurements or answers to interview questions. > No manipulation by scientists > Explores associations but doesn’t determine cause Observational studies explore correlation, not causation. There are different observational methods: - Descriptive: gathers info to see how disease spread over time > Who gets sick, how many get sick, where do they get sick - Analytical: goal is to generate hypothesis for cause > Compares affected and unaffected individuals - Retrospective: gather data from past to present cases - Prospective: follow patients and monitor their disease state throughout study 2. Experimental: - Scientists manipulate the subjects to explore the causative agent associated with a disease or assess treatment options or prevention - Much less common because of ethical reasons - Can use animals or human subjects > Koch’s Germ Theory of Disease - Example: Drug efficacy > Most often double-blinded to avoid the placebo effect

Answer 114

Reservoirs are places where pathogens normally reside. - Reservoirs can be living or non-living > some pathogens can reside in soil or water, either naturally or as a result of contamination - Humans: Communicable disease > Carriers: 1. Passive carrier: not sick but, passes the pathogen to next host 2. Active carrier: those who harbor (and shed) and infective agent > Might be during incubation period or convalescence > Asymptomatic: do not show signs or symptoms: Typhoid Mary (Salmonella typhi)

Answer 115

3 main types of transmission: 1. contact: direct or indirect through fomites - direct contract: when the pathogen is spread by physical contact of 2 people. > Vertical direct contact: from mother to child during pregnancy, birth, breastfeeding > Horizontal direct contact: other forms of contact > Droplet transmission: when an individual coughs or sneezes, small droplets of mucus that may contain pathogens are ejected (Spread of <1m (if over 1m: airborne transmission)) 2. Indirect contact: involves fomites that have become contaminated - example: droplets on a doorknob - A new host must touch the contaminated fomite and touch a susceptible portal of entry 2. vehicle: through water, food, or air - Contamination water leads to 500,000 deaths worldwide according to the WHO - Dust, aerosols, and long-distance droplet transmission are considered airborne vehicle transmission - Food borne illness: often spread by the oral-fecal route 3. vector: an animal that carries the pathogen from one host to another - Mechanical vectors: carry the pathogen from one host to the next without infecting themselves - Biological vectors: animals that become infected themselves and pass the pathogen

Answer 116

The Centers for Disease Control (CDC) is the main national public health agency in the US. - It protects the public from disease and injury - Certain diseases called notifiable or reportable diseases must reported by a physician if he/she diagnoses a patient with one. 58 on the list - Helps keep records on morbidity. - The CDC publishes the Morbidity and Mortality Weekly Report (MMWR). - Helps healthcare professionals keep on top of the latest epidemiological data The World Health Organization is an agency of the United Nations that looks a disease data globally. - Analyzes data about diseases. - Implements strategies to prevent their spread > Isolation of those with the disease > Quarantine; includes healthy individuals who were exposed > Immunization > Vector control The CDC and WHO prepare for emerging or reemerging diseases. - Diseases that are either new to the human population or have become more prevalent in the last 20 years.

Answer 117

Innate immunity: Everyone is born with innate (or natural) immunity, a type of general protection.

Answer 118

Anatomical/ Physical Barriers: 1. Skin - Comprised of tightly packed epithelial cells - Top layers dead > Comprised of keratin (protective waterproofing) - Top layer is continuously shed to help remove microbes - Dryness of skin helps inhibit growth - It’s impossible for microorganisms to penetrate intact skin - When skin is broken due to an injury (cut, burn, etc.) a subcutaneous infection develops > If you have a cut, this line of defense is breached > Using a band aid or disinfectant on the wound will prevent unwanted bacteria from coming inside the body - Sebaceous glands on skin (chemical barrier): > produces sebum (oil) which lowers the pH of skin and secretes antimicrobial fatty acids > Some bacteria can metabolize sebum and cause the inflammatory response associated with acne 2. Mucous membranes - Line gastrointestinal, respiratory and genitourinary tracts - Less protective than skin. - Outer epithelial cells secrete mucus (viscous glycoprotein) to trap microbes - Mucus removed from body by cilia Skin and mucosal membranes are made of tightly packed epithelial cells. These structures between cells limit pathogens from gaining access to the bloodstream. 3. Tears/Saliva and Sweat Glands - Tears : > Protect eyes by constantly washing and preventing microorganisms from “settling down” - Saliva: > Produced by salivary glands > Contains lactoperoxidase enzyme which can oxidize components of bacteria and viruses. . Our sweat, tears, saliva, nasal secretions, and urine also contain an enzyme called lysozyme that breaks down peptidoglycans in cell walls of bacteria. - Sweat Glands: > Produce perspiration, which helps maintain body temperature at a constant level and remove microorganisms from the surface of the skin > High lactic acid content and electrolytes inhibit microbial growth. > Also has antimicrobial peptides 4. Stomach acid and Secretions - Stomach Acid: > Contains hydrochloric acid, enzymes, and mucus > pH ~1.2-3 -> destroys most pathogens and toxins > Food particles shield some bacteria. - Secretions: > Defecation, urination, vaginal, vomiting all expel microorganisms . Helicobacter pylori can survive in acid conditions (neutralizes stomach acid). If it gets into the stomach, it causes ulcers because it triggers immune response. 5. Normal Micrbiota Function in Innate Immunity; If something is already living in a space, there is no room for new bacteria to grow - Normal microbiota: > Colonize the host without causing disease (“good niches”) > Prevent the overgrowth of pathogenic microorganisms > Maintains or alters pH levels, nutrient availability, oxygen levels > May inhibit growth of pathogen growth through competition Examples: - Vaginal secretions via Lactobacillus acidophilus produce lactic acid and keep pH too low for microbial growth by Candida albicans (causative agent of vaginitis). - In the large intestine, E.coli produce chemicals that inhibit the growth of Salmonella and Shigella. When the human microbiota is disrupted, pathogens can take advantage - taking broad spectrum antibiotics can affect the human microbiota - when the normal strains are wiped out in the gut, pathogens such as Clostridium difficile can colonize and cause severe diarrhea and even death - Fecal implants have been used to recolonize the normal flora to treat C.difficile infections.

Answer 119

What’s in our blood? - Blood composed of plasma (liquid) and formed elements (cells and cell fragments) - Erythrocytes (red blood cells) platelets - Leukocytes (White Blood Cells) Thymus: - Site of T cell development - Produce T cell receptors (TCRs) as they develop. - TCRs bind antigens on a pathogen to stimulate an immune response Lymph nodes: - Connected by lymphatic vessels which absorb fluid (lymph) that leaks out of blood vessels - Lymph circulates through lymph nodes and back to the blood. - Any pathogens that are in the lymph can be targeted by immune cells in the lymph nodes.

Answer 120

Adaptive Immune Defense: Third Line of Defense Against specific pathogens Includes humoral (antibody-mediated immunity) and cell-mediated immunity. Acquired immunity is also called specific immunity because it tailors its attack to a specific antigen previously encountered.

Answer 121

- Patrolling immune cells read the chemical “flags” on the outside of cells to determine whether they are foreign or not… - Pathogen-associated molecular patterns (PAMPs) are components of pathogens that can be recognized by immune cells. Some examples of PAMPs are LPS, peptidoglycan, and flagellin. - When the defense cell finds a cell without a “self flag”, the pattern recognition receptors (PRRs) on its surface such as Toll-like receptors bind to PAMPs on the outside of the microbe. - This interaction leads to immune system response.

Answer 122

Phagocytosis: Non-specific mechanism - When pathogens penetrate the skin and mucous membranes, they are attacked by phagocytes - Phagocytosis- engulfment of microbes by phagocytic cells (neutrophils, dendritic cells, eosinophils, and macrophages). - When an infection occurs, immune cells move to the infected area. > Monocytes mature and become active phagocytic macrophages and dendritic cells. - At the beginning of infection, neutrophils dominate the infected area, however as infection progresses macrophages concentration increases. > The pattern of white blood cell activity during infection can be seen in the differentiated white blood cell count. Stages of Phagocytosis: 1. Chemotaxis: - Chemical signals attract phagocyte. 2. Adherence: - Phagocyte plasma membrane interacts with microbe. - Microbial capsules interfere with adherence. 3. Ingestion: - Microorganism brought into the phagocyte in a membrane bound vesicle called phagosome. 4. Killing/Elimination: - The phagosome fuses with a lysosome and the microbe is killed and digested. -Digested material is removed from cell (exocytosis) Interferons protect cells from viral infection - Interferons: small proteins produced by certain WBCs and tissue cells with anti-viral activity > Infected cell produces interferons in response to infection by a virus. > When cell dies it releases both new viruses and interferons. > Interferon binds to cell surfaces of nearby cell to induce expression of anti-viral proteins by healthy cells. Natural Killer Cells - NK cells activate to destroy the target, which is likely a virally infected or cancerous host cell: > Granzyme: an enzyme that induces programmed cell death (apoptosis) > Perforin: pokes holes in (perforates) the target membrane The four classic signs are redness, fever, swelling, and heat. - An injury creates an opening in the skin, allowing pathogens to enter body tissues. - Mast cells release histamines and macrophages release cytokines - These chemicals attract more immune cells, such as neutrophils and dendritic cells, to help fight the infection. - Histamines make blood vessels “leaky,” which allows immune cells and fluid to leak out of blood vessels into the tissues where the infection is occurring. 1. Fever - Certain cytokines, particularly I L-1, will cause the host’s body temperature to rise, causing a fever - Fever-causing cytokines are called pyrogens because they generate (gen) heat (pyro) - A fever is beneficial because it increases circulation rate, which allows leukocytes to get to the site of infection - It is also beneficial because some pathogens cannot tolerate the increased temperature 2. Systemic inflammation and septic shock - Widespread (systemic) inflammation can lead to shock as the increased vascular permeability decreases a host’s blood pressure, which can cause damage to multiple organs at the same time - Gram-negative bacteria are particularly dangerous because they contain L P S, which triggers a proinflammatory cytokine response > Examples: Salmonella species or Escherichia coli, which can be introduced into the peritoneal cavity or the bloodstream by a ruptured or leaking bowel GOAL: to remove the injurious agent and its by-products or at least isolate it and to repair damaged tissue.

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- Antigens are substances that causes your immune system to produce antibodies > Capsules, cell walls, flagella, fimbriae, toxins of bacteria, coats of viruses, proteins on surface of foreign blood or cancerous cells > The certain part of the antigen that is recognized is the epitope

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- Antibodies are produced to match each specific foreign antigen’s marker > Antibodies are produced by activated B cells - Antibodies aid in the removal of antigens or prevent the ability of pathogens to cause widespread infection.

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Mediated by two types of cells: B cells and T cells > They undergo maturation, learning how to recognize an antigen as a foreign molecule and how to recognize self-antigens as the body’s own molecules, in different tissues = B cells mature in the bone marrow and are important for antibody production in humoral immunity. (B-cells build an army of antibodies and let them do the fighting) = T cells mature in the thymus and play a role in cell-mediated immunity. (T-cells fight with bacteria in hand-to-hand combat) Steps in adaptive immune response: - Antigen presentation by phagocytes and other infected cells > Presented on MHC surface proteins - T-cell activation > Helper T-cells activate B-cells (also T-cell independent activation) > Cytotoxic T-cells destroy infected cells - B-cell expansion > Antibody production > Memory T-independent antigens activate B cells without the help of T helper cells. - Different antigens: usually lipopolysaccharides and polysaccharides - Bacterial capsules can contain repeated T-independent antigens and produce weaker immune response without generating any memory cells. - Infants usually do not have T-independent immune response until the age of 2. Cell-mediated Immunity: T cells - T-cells cellular-mediated immunity - T-cells are SPECIFIC for a particular antigen: > Through the T cell receptor (TCR) present on the surface of a T-cell - T cells act directly against antigens and foreign cells when the antigen is presented by macrophages Types of T cells - Helper T cells > Stimulate B and T cells > B cells must be activated by helper T cells before they can produce antibodies > AIDS: loss of helper T cells-no antibodies produced = Cytotoxic T cells > Responsible for cell mediated immunity > Specific for a certain antigen > Directly attack cells physically and chemically by releasing perforins (which makes holes in the plasma membrane of the target cell) and granzymes which induce cell death. = Regulatory T cells (used to be called Suppressor T cells > Inhibit B and T cell activity > Modulate (turn off) the immune response; Help prevent autoimmune disorders

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Naturally acquired: 1. Active immunity: antigens enter the body naturally; body induces antibodies and specialized lymphocytes (ex: immunity to chicken pox after you have it) 2. Passive immunity: antibodies pass from mother to fetus via placenta or to infant via the mother’s milk Artificially acquired: 1. Active immunity: antigens are introduced in vaccines; body produces antibodies and specialized lymphocytes (ex: immunity to chicken pox after getting the vaccinated) 2. Passive immunity: preformed antibodies in immune serum are introduced by injection (ex: anti-venom)

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Vaccine: - Inject a tiny amount of weakened non-infectious virus or bacteria - The body’s immune system will generate an immune response (antibodies). - If the person becomes affected with the virus again in the future: > Body already knows how to kill it and will kill it fast - The person will not develop severe symptoms of the infection

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1. Immunodeficiencies: these are cases when the immune system is compromised, so that it doesn’t work as well > Example: AIDS (acquired immune deficiency syndrome) is a virus that destroys helper T cells, thus reducing the effectiveness of cell-mediated immunity to fight infection or cancer. 2. Autoimmune diseases: The immune system incorrectly labels certain cell of its own body as foreign and eliminates them. > Example: Multiple sclerosis or systematic lupus erythematosus 3. Hypersensitivities: when the immune system starts to fight a perceived threat such as pollen or a food protein that is indeed harmless. > May be mediated by antibodies and give almost immediate response or may activate T cells and cause a delayed response. What’s an allergy? - Known as an immediate hypersensitivity - Body has detected that matter as “foreign” and made antibodies and memory cells against it - All further exposures to the agent will be classified as an attack on the body - A full immune response will be mounted

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1. Carbon 2. Hydrogen 3. nitrogen 4. oxygen 5. phosphorous 6. sulfur

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Biogeochemical cycle: the cycling of inorganic material from organisms to their non-living environment

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The Carbon Cycle - Living things on earth require carbon to build biological molecules. - Photoautotrophs and chemoautotrophs can use external energy sources to reduce inorganic carbon (CO2) to organic carbon (glucose, etc). - Heterotrophs require organic carbon they can break down for energy. - Autotrophs take CO2 and convert it to organic carbon. - Both autotrophs and heterotrophs take organic carbon and oxidize it to CO2. - Phototrophic organisms produce organic or fixed carbon and reduce the level of carbon dioxide in the atmosphere > Oxygenic phototrophic organisms can be divided into two groups: plants and microorganisms = Plants dominate terrestrial environments = Microorganisms dominate aquatic environments - Carbon is cycled through all of Earth’s major carbon reservoirs > Includes atmosphere, land, oceans, freshwater, sediments, rocks, and biomass > All nutrient cycles are linked to the carbon cycle, but the nitrogen (N) cycle links particularly strongly because, other than water (H2O), C, and N make up the bulk of living organisms - Reservoir size and turnover time are important parameters in understanding the cycling of elements - C exists in different forms in different reservoirs: > Inorganic carbon in rock (limestone): largest reservoir > Organic carbon > Gaseous carbon (CO2, methane, CO) - Exchange between reservoirs can be very slow or very fast > Fastest for atmospheric CO2 Carbon turnover - CO2 is returned to the atmostphere by respiration and decomposition as well as by human-related (anthropogenic) activities > Microbial decomposition is the largest source of CO2 released to the atmosphere > Since the Industrial Revolution, human (anthropogenic) activities have increased atmospheric carbon by 40%

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- Methanotrophs: microorganisms that use methane for their energy source - Methanogens: microorganisms that produce methane as a byproduct of metabolism

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Methanogens and methanotrophs: considerations for climate change - Methane is about 30x more potent as a greenhouse gas than CO2. - Responsible for about 30% of global warming. - About 70% of total methane emissions are from biological sources. - Produced biologically by methanogens as the final step in the degradation of organic matter.

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Nitrogen Cycle: Nitrogen - key constituent of cells - exists in several oxidation states - four major nitrogen transformations: 1. nitrification - Nitrification: oxidizing ammonia compounds (NH3, NH2) to nitrate (NO3) or nitrite (NO2) - Nitrifying bacteria are aerobic chemoautotrophs that use this oxidation to produce energy. - Once nitrification is complete, the nitrogen can then be assimilated into organic molecules by organisms. - In marine systems, nitrates can contribute to eutrophication (accumulation of nutrients) in the aquatic environments, which causes algal blooms then death of aquatic organisms. 2. denitrification - Nitrate and other nitrogen oxides are converted to N2 NO3–>NO-2–>NO–>N2O–>N2 - Process is strictly anaerobic, but most denitrifiers are facultative aerobes and prefer to use oxygen as their terminal electron acceptor - This activity reduces soil nitrogen content and therefore its fertility - But is important in waste treatment to remove nitrogen from effluent 3. anammox 4. nitrogen fixation - Symbiotic bacteria incorporate atmospheric nitrogen into organic molecules: Nitrogen fixation - Atmosphere is almost 80% nitrogen, but it is in the form N2 or N≡N - Eukaryotes cannot break this triple bond - Some bacteria can reduce N2 to NH3 Many biological molecules including proteins and nucleic acids include nitrogen - Getting nitrogen into organisms is difficult because much of the earth’s nitrogen is environmental N2, which is triple-bonded and unusable by plants. - Prokaryotes play an important role by doing nitrogen fixation.

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Sulfur is essential for the synthesis of certain macromolecules - It is part of certain amino acids and in certain vitamins. - Several microorganisms are responsible for carrying out the sulfur cycle in complex processes. - Anoxygenic photosynthetic bacteria and chemoautotrophic archaea and bacteria use hydrogen sulfide as an electron donor. - H2S is oxidized it first to elemental sulfur (S0), then to sulfate. - Decomposing bacteria remove sulfate groups and make hydrogen sulfide and release it back into the air.

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Bioremediation uses microbial metabolism to remove xenobiotics and other pollutants. - Xenobiotics are substances made by humans and released into the environment. - Examples of such contaminants: adhesives, dyes, lubricants, oil and petroleum products, pesticides, etc. - Two very concerning xenobiotics: > polycyclic aromatic hydrocarbon (PAH, carcinogen from crude oil) > trichloroethylene (TCE) which is a ground water contaminant Bioremediation can happen at the site (in situ) or transported to another location (ex situ). - In situ is when the remediation happens at the original contamination site. Bioremediation can happen at the site or transported to another location. - Can use native species or introduce foreign species who can degrade certain contaminants. - Scientist might alter conditions to encourage degradation. > For example, Rhodococcus and Pseudomonas are known for their ability to degrade many environmental contaminants, like those found in oil. Environmental Consequences of Large Oil Spills and the Effect of Bioremediation - Prokaryotes have been used in bioremediation of several major crude oil spills - The rectangular plot (arrow) was treated with inorganic nutrients to stimulate bioremediation of spilled oil by microorganisms, whereas areas above and to the left were untreated. Bioremediation and Microbial Degradation of Major Chemical Pollutants: Chlorinated Organics and Plastics - Plastics of various types are xenobiotics that are not readily degraded by microorganisms - The recalcitrance of plastics has fueled research efforts into a biodegradable alternative (biopolymers or microbial plastics) Wastewater Treatment 1. Wastewater - Domestic sewage or liquid industrial waste - “Gray water” is the water resulting from washing, bathing, and cooking - Sewage is water contaminated with human and animal fecal material 2. Wastewater treatment - Relies on industrial-scale use of microbes for bioconversion - Following treatment, the discharged treated wastewater (effluent water) is suitable for > release into surface waters > release to drinking water purification facilities

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The food industry also uses bacteria to make certain foods 1. Fermentation - Bread - Beer and wine - Cheese, yogurt - Pickles, sauerkraut, kimchi, olives > Acids produced during fermentation lower the pH enough to suppress the growth of spoilage organisms - Soy sauce, tofu, miso - Lactic acid bacteria such as Lactobacillus, Lactococcus and Streptococcus are used in the manufacture of dairy products 2. Food preservation - Preventing the incorporation of microorganisms into food > Sanitation - Preventing the multiplication of microorganisms in food > Chemical preservatives > Processing at high temperatures > Refrigeration > Pasteurization > Radiation > Desiccation > Bacteriophage (FDA, 2006, ready –to eat meat products)

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