MMG 301 Unit 2 LO

Briefly explain why microbes that live as parasites have smaller genomes than microbes that are free-living.

Because they don't need the information that codes for many proteins that function in metabolic pathways because they feed off their host.

Explain why microbial fermentation products are found in the interior of soil aggregates.

Because the O2 from the air gets used up by the microbes closer to the surface and so the interior microbes will undergo fermentation.

Describe why regulation of transcription is beneficial to an organism.

To conserve energy and resources. So, the cell doesn't waste resources and attempt to create proteins that aren't needed.

Order the steps of a genome sequencing project from small fragment sequences to annotation.

1. Alignment: the computer will find shared sequences on different fragments and arrange them together to form larger fragments of sequence data called contigs. 2. Overlapping regions of contigs form scaffolds. 3. In the gap closure and finishing step regions of low sequence data or inefficient data are sequenced further to form "draft genome." 4. Annotation: In the final step called annotation gene prediction occurs where the location of the genes is predicted this is called an open reading frame. Functions are then assigned to genes based on sequence similarity to known genes.

Describe what molecules are most commonly used for phylogenetic studies, and how these can be used as a "molecular clock" to measure evolution.

16s rRNA is usually used for these studies as every prokaryote has them. The 16s rRNA are sequenced and then compared and identified for mutations. This is why sequences can be known as a molecular clock, because over time there are more mutations and so an organism with more mutations is more likely to have evolved later.

Explain the different ways that a frameshift mutation affects the resulting protein.

A frameshift mutation is an insertion or deletion of bases within a coding region. Proteins can change after insertion/deletion site.

Explain what a genome is.

A genome is all the genes in an organism. These genes are kept in chromosomes, plasmids and/or viruses (if virus has infected the cell and become part of its DNA in the chromosome which is then called a provirus).

Differentiate between genotype vs. phenotype, and spontaneous vs. induced mutations.

A genotype is all the genes in an organism that determine its characteristics and a phenotype are the observable characteristics of an organism.

Distinguish the lytic and lysogenic paths that an E. coli cell can take after it is infected with bacteriophage lambda.

A lytic virus results in the lysis of host cell at the end of an ordered replication cycle. A lysogenic virus will result in the viral DNA being part of the host cell chromosome by enzymes integrating the viral DNA into the host cell DNA and then that cell dividing with combined chromosome. Lambda is a temperate bacterial virus, able to carrylysogeny.

Differentiate between a niche and a microenvironment.

A microenvironment is smaller habitats where microorganisms can be found. Whereas a niche is not a location but the resources utilized by microorganisms which are biotic and abiotic factors (water availibility, nutrient/oxygen availibility and temperature) that contribute to the success of a microorganism in a microenvironment.

Distinguish a pan genome from a core genome.

A pan genome is the sum of all genes in organisms being compared whereas a core genome is all the genes in common in the organisms being compared.

Describe the life cycle of phage T4 and how viral components are made precisely at the time they are needed. Create a diagram the steps after induction of a prophage and ending in cell lysis.

A prophage is the viral section of DNA in the host chromosome. First the T4 nucleases, DNA polymerase and new sigma factors are produced in the host cell (E. Coli). Then the cell's DNA is replicated with phage T4 DNA, which then produces phage head proteins. The tail, collar, base plate and tail fiber proteins are assembled which all together produces a mature T4 virion. The lysosome enzyme (encoded by T4) is then produced which will lyse the host cell and release the virus.

Describe how the correct functioning of an autoclave can be tested.

After the autoclave break the glass tube, with the spores, in the plastic container containing the growth medium with pH indicator. Wait 24 hours and then look for growth, if the medium changes from purple to yellow then there is growth and therefore the autoclave did not work.

Describe how allosteric regulation of enzyme activity works and this typically is used in multi-step biochemical pathway.

Allosteric regulation occurs through binding an effector molecule. End product of a multi-step pathway will bind to an enzyme in the pathway (usually in the 1st step) and inhibit it. The effector molecule will bind to "allosteric site" which is different than the active site and it will cause the enzyme to undergo a conformational change so that the substrate can no longer bind to the active site.

Understand in a general way how microbial populations and diversity change as food moves through the intestinal tract.

As you move through the GI tract from upper to lower the pH increases becoming more basic, the O2 decreases as it has been used up, and the species diversity increases.

Describe how is a freshwater lake an example of a microbial ecosystem and explain what the energy inputs.

Because it contains many communities of microorganisms that live together There are aerobes and faculatative aerobes doing respiration and phototrophs doing photosynthesis all at the top of the lake in the water. In the sediment portion (sand/dirt) there is no oxygen beacuse it has been consumed above and so this community is anoxic. The energy inputs are sunlight, organic carbon inputs from photosynthesis or externally and reduced inorganic compounds.

Explain the effect of temperature on growth rates; how do the survival curves for thermophiles and mesophiles differ.

Cardinal temperatures: critical temperatures that define the range suitable for microbial growth. Minimum: below which there is no growth because the temperature is too low for enzymes to catalyze reactions. Optimal: where there is max growth, shortest generation times, enzymes work at max rates, membranes are functioning at optimum and transport across membrane is at its most rapid rate. Maximum: above which there is no growth because proteins and enzymes are denatured, membranes fail, and nucleic acids could also denature... this rate is usually close to optimum. Thermophiles (45-80C) do not require as high of an optimum temperature as mesophiles (15-45C).

Create a circuit diagram that shows catabolite repression and how cAMP, CRP, lac repressor, and lactose control transcription of the lac operon.

Catabolite repression is using glucose over other carbon sources, so if glucose is present then it will be used as the carbon source and all other pathways will be turned off. cAMP is an internal second messenger molecule that controls the "glucose switch." As glucose levels decrease, ATP gets converted into cAMP which binds to the cAMP receptor protein (CRP) and activates it to bind to lactose operon at the C activator binding site which is prior to the RNA polymerase binding site (the promoter). Then allolactose acts as the inducer to bind to the repressor so it will not be bound to operon and RNA polymerase will bind and transcribe.

Describe comparative genomics and how it is useful.

Comparing genomes of different organisms to identify where they differ. Can be helpful in comparing pathogenic vs non-pathogenic to reveal regions involved in virulence and further in what kind of disease/what the genes are doing. Can be compared linearly and spherically.

Explain what culture-independent methods are and the examples shown in the module; what are the two types of culture-independent analysis that can be done without using DNA sequencing.

Culture-independent methods are where there is no growth of the sample being studied; it is studied directly. Example with ocean water: take a sample of ocean water, isolate the microorganisms and directly from that extract the DNA or do some other studeis. While microscopic analysis and genetic analysis can be done on these culture-independent microbes, only microscopic can be done without sequencing. The two types of microscopic analysis are- viability stains and FISH.

Define a decimal reduction time and how it is affected by exposure to temperatures above the growth maximum.

Decimal reduction time is the time to reduce viable cells by 10-fold. This measurement is used when exposing microorganisms to temperatures above their maximum. The higher the temperature the shorter the decimal reduction time, if viable cells are exposed to a temperature above their growth maximum, they will be easier to kill. Decimal reduction time is measured by taking a sample of cells in a growth medium and heat it to the different temperatures and then do viable cell count by plating every two minutes or so until experiment is over. Decimal reduction times are longer for thermophiles and shorter for mesophiles because thermophiles are adapted to higher temperatures than mesophiles. Experiments for this area of decimal reduction time is done with a fixed time for the viable cell count by plating.

Explain the interpretation of branch length, nodes, clades, and evolutionary time in a phylogenetic tree.

Each species represents a letter and where those letter branches connect is called a node which is represents a common ancestor. The species' that share a common ancestor are collectively called a clade. The distance that each species is from one another represents the correlation in relationship between them.

Compare foregut fermenters to hindgut fermenters animals.

Foregut fermenters are organisms that use the bacteria from the plants to ferment. Some examples are ruminants like cows, sheep and goats. Hindgut fermenters are organisms rely on the bacteria in their intestines to ferment.

Differentiate between F+ cells and Hfr cells.

F+ cells contain the F plasmid and Hfr cells have the F plasmid incorporated into their chromosome.

Explain the advantages and disadvantages of the two most commonly used personal protective filtration devices.

Facemasks reduce person-to-person aerosol droplets but not as efficiently as N95 respirators which fit tighter on the face and do a better job but are usually more expensive.

Describe the sequence of events of ruminant digestion and know the major type of nutrients that pass through the rumen wall into the animal.

First food enters the rumen where the microbes begin anaerobic cellulose digestion. The mixture will then go to the omasum and is concentrated by water absorption. Then the mixture goes to the abomasum which is the true stomach, and the acid will kill and digest the food and microbes. Then the digested food and microbes go to the small intestine for further absorption of nutrients. The major type of nutrients that pass through the rumen wall into the bloodstream are volatile fatty acids.

In general terms, describe how phylogenetic trees are constructed starting with a set of similar sequences from different organisms.

First the 16s rRNA are aligned with the best fit for the sequences, this can contain gaps and mismatches. Then a computer calculates the difference matrix and builds the tree.

Describe the steps in formation of a root nodule, starting with bacteria in the soil and ending with nodule formation.

First the root excretes flavonoids through rhizodeposition which the bacteria will sense and take up. Bacteria then synthesize nod factors which the root hairs will sense and take up. Once this occurs the root hairs will curl which traps the bacterial cells. The bacteria will then start growing and dividing, forming an infection thread which lies in the now formed nodule.

Order the sequence of steps involved in homologous recombination, including the functions of the molecules involved: nicked DNA, RecA, SSB, donor DNA, recipient DNA, Holliday junction.

First there is a nick or break in one of the two strands of donor DNA. A single-strand binding protein (SSB) prevents broken DNA from base pairing. Then strand invasion occurs which is base pairing of identical sequences on recipient and donor which is facilitated by Rev A protein. The next step is crossed-strand exchange where other enzymes connect the ends of the DNA to make a Holiday junction. In the final step, called resolution, enzymes cut the holiday junction back into double-stranded DNA. This results in heteroduplex DNA (region of DNA where strands originated from different organisms, 1 strand from donor and 1 from the recipient).

Explain how the major groups can be distinguished on thioglycolate-resazurin agar, including the roles of thioglycolate and resazurin.

First, autoclave agar to 42C (liquid), add cells, add thioglycolate, which will react with O2 creating an O2 gradient in the tube. Also add resazurin (a dye), which turns red in the presence of O2 so we can see where in the tube the O2 is. Put in unsealed but capped tubes (so air can get in from outside) to cool. After time the O2 gradient will form due to the thioglycolate and the resazurin will distinguish where the oxygen is in the tube. The cells will aggregate in correlation to the amount of O2 their metabolic pathways favor.

Order the steps for the basic method of Fluorescence In Situ Hybridization and explain what the method is used for.

First, synthesize oligonucleotide (probe) which is a short DNA sequence that will base pair with specific organism. Then chemically attach a fluorescent molecule ("tag"). Then treat the sample to make cells permeable to probe (oligonucleotide). The carry out fluorescent microscopy. This is useful because if the species is not present in the population then the probe will not base pair and the cells will not light up with the fluorescent tag.

Provide examples of the types of information that can be determined by sequencing all of the genomes in a microbial community.

From the sequenced genes we can compare with similar known genes (this is called annotation) and then assign function to those genes and that is how we are able to get different metabolic pathways from genomes. This is information that could not be obtained through culturing in a lab.

Describe where Helicobacter is found, why it is able to grow there, and what disease it causes.

H. pylori is found in the stomach and is associated with over 80% of stomach ulcers which lead to gastric cancer. 50% of adults in developing countries have H. pylori but are asymptomatic. H. pylori are not acidophiles but can live in the acidic conditions of the stomach because it uses urease enzyme. Ureases does this by converting urea to CO2 and NH3 which are great buffers against acid.

Distinguish the types of filters that are most commonly used to remove microbes from gasses and liquids.

HEPA (high efficiency particulate air): filters out 0.3 micron particles with 99.9% efficiency. Membrane filters: have uniform sized holes and are generally used in research labs. Holes are typically about 0.2 microns so no cells can pass through. PPE (personal protection equipment): filter out aerosol droplets that contain many pathogens. Used to reduce person-to-person aerosol transmission.

Explain the decimal reduction time and be able to interpret a survival semi-log graph.

Higher temperatures result in a shorter decimal reduction time.

Explain why you would use a targeted versus a whole genome sequencing approach.

If you wanted to compare 1 gene that is in many organisms or look for mutations within a gene in a population of an organism. Deep sequencing (sequencing genomes over 500x) to look for mutations.

Describe the difference between generalized and specialized transduction, including what DNA is transferred from donor to recipient.

In generalized transduction the virus infects the donor cell becoming a prophage. Then induction occurs incorrectly resulting in a random piece of chromosomal DNA incorporated into the virus this is called a transducing particle. So, then only donor DNA is transferred into the recipient cell and then incorporated into its chromosome through homologous recombination. Specialized transduction only occurs in temperate phages. In specialized transduction the virus infects the donor cell becoming a prophage. Then induction occurs incorrectly resulting in genome DNA adjacent to the prophage being transferred into the recipient cell. This occurs when lysogenic phage incorrectly excises and carries a piece of donor genome DNA in each phage. So the donor gene that has been transferred will become part of every recipient genome.

What parts of information flow are performed by storage, retrieval, and execution functions.

Information is stored in of genes as a G A T or C in the form of triplets which encode for a specific amino acid. This information can be changed by HGT or mutations. Information is retrieved when it needs to be transcribed. This retrieved information goes through execution in translation which will result in a protein from the given information.

Discuss the human microbiome project, including its goals and the major method used.

It is a National Institued of Health Initiative to identify the role of microbes in human health. They are looking at what microbes are found where in healthy humans and how the microbial community changes to do various factors. They use the 16s rRNA sequencing and the construction of phylogenetic trees.

Explain the steps of horizontal gene transfer by transduction.

It is a virus-mediated gene transfer. First the temperate virus infects the donor cell becoming a prophage. It then replicates and then releases new virus sometimes containing some of the donor DNA which is then transferred into recipient through homologous recombination.

Describe the features of a sequence that are used to detect an ORF​.

It is identified using a computer which looks at the ribosomal binding site, the start codon, the coding sequence (multiple of 3) and the stop codon.

Explain why homologous recombination is important in order for a horizontal gene transfer event to be successful.

It is the way of recipient and donor DNA joining together and is necessary so that the recipient can replicate with donor DNA. It is called homologous recombination because when the donor and recipient bases pair they are nearly identical, if they were really different that step would not happen.

Know what anti-microbial enzymes are in saliva and how they protect against some bacteria.

Lactoperoxidase is a salivary anti-microbial enzyme that produces a reactive species called hypothiocyanite (OSCN) as a product and kills bacteria. Lysozyme is a salivary anti-microbial enzyme that cleaves peptidoglycan.

Know what characteristics of the skin make a good habitat for microbes. Know the environmental stresses faced by microbes when colonizing the skin.

Many microbes have adapted to the skin environment and are able to use the nutrients like water, fatty acids, salts, and amino acids, that are secreted by the glands. However, the sebum secreted by the sebaceous glands is an anti-microbial.

Know the meaning of loose association, adhesion, and colonization. Where are epithelial cells found and what are mucous membranes.

Mechanism of colonization in mucous membranes which are the outer layer of epithelial cells that are on the surface of many tissues. Colonization is the growth of microbes found at any anatomical site.

Describe what can a genome sequences reveal about uncultured organisms.

Metabolic pathways, energy production, nutrient requirements, and phylogenetic relationships.

Understand what parts of the human digestive tract contain microbes and how they benefit the human host.

Microbes are contained in the skin, mouth, upper respiratory, throat, stomach, intestines and urogenital tract and are good microbes. Microbes can also be contained in the blood, heart, lower respiratory, brain/nervous system, liver, spleen, kidney and bladder which will cause an inflammatory response which leads to tissue damage. They benefit the human host through vitamin synthesis, glycosidase activity, steroid metabolism, development/stimulation of immune system and antagonism of pathogens.

Correlate each of the 3 types of base pair substitutions with their effect on the resulting protein.

Missense is a change the amino acid encoded. Nonsense is a change that creates a stop codon and therefore an incomplete protein. Silent is a change in codon sequence but no change in amino acid.

Explain what mutagens are and describe the three main types of chemical mutagens.

Mutagens are anything that causes mutations at rates above normal levels. The three main types of chemical mutagens are nucleotide base analogs which are chemicals that are structurally similar to DNA bases. The next type of chemical mutagen is modifications of DNA bases which are alkylations, nitrosations and hydroxylations. The last type of chemical mutagen is intercalating agents which bind between bases.

Be able to briefly describe each of the biotic factors that define a niche.

Nutrient exchange (syntropy), antagonism which is where one cell has a negative effect on the other. Competition for food source, predation which is where one cell destroys the other. And parasitism which is where one cell is a virus and infects and destroys the other

Describe the major groups microorganisms based on their oxygen requirements.

Obligate (strict) aerobes must have oxygen to grow. Microaerophiles only grow in low O2 conditions. Facultative aerobes prefer O2 but can use other pathways if there is none. Obligate anaerobes must have no O2 to grow. Aerotolerant anaerobes grow in the presence of O2 but don't use it.

Describe how PCR of single genes can be used for analysis of microbial community diversity. Distinguish how DNA sequences are analyzed by the community sampling or the environmental genomics approaches and explain what information each approach provides.

PCR of single genes can be used through looking at ways the sequence can result in different restriction enzyme fragments or do sequencing of the gene and this will tell us what phylotypes exist in that community. This approach is called "community sampling" which is sampling a gene from all of the community members in order to do phylogenetic analysis and see what phylotypes are in the community. For the genomic approach, we want to know all sequences of all of the genes; try to get as many entire genomes as possible. First, we isolate the DNA and do whole sequencing on everything that we get from that and then have computers assemble the genomes.

Describe Pasteurization and explain the two methods it is applied.

Pasteurization is short-term heating to reduce the number of microbes. Used on heat-sensitive microbes like those in foods and more specifically in milk to increase shelf-life. An autoclave is not used because it would destroy the properties of the food. One method is continuous flow where the heat flows through a chamber being heated with hot water and then continues to flow through the chamber being cooled with cold water. The other method is batch method where the whole batch is heated to 63C for 30 minutes, being stirred constantly.

List some common legume plants. Explain the advantage of these plants having symbiotic nitrogen-fixing bacteria.

Peas, beans and clover.

List the important general characteristics of plasmids.

Plasmids are extrachromosomal DNA elements that replicate independently of the chromosome. Some important characteristics are... Separate genetic elements Many types and many types/cell. Mostly found in bacteria but sometimes in some archaea and eukaryotes. Have their own origin of replication for vertical transfer. Can have 1-100+ copies/cell. Named with first letter as "p." Used in biotechnology for gene cloning. 2-1000 base pairs as opposed to 4.6 million base pairs in bacterial chromosome.

Distinguish populations, guilds, communities, habitats, and ecosystem.

Populations are individual cells reproducing which grow into populations. Guilds are populations that do related metabolism. Communities are populations/guilds that live together. Habitats are the environments that provide favorable nutrients/conditions.

Explain regulation of transcription by negative control with a repressor protein using the arg operon, and lac operon as examples, including all required proteins and DNA regulatory regions.

Regulation by negative control results in the repression of transcription. In the arg operon, when arginine is present it acts as a corepressor to bind to the repressor protein activating it to bind to the operator to block RNA polymerase from transcribing. In the lac operon, it is the opposite. The genes in the lac operon are for utilizing transcription as a carbon source. So, when lactose is present it acts as an inducer (in its isomer "allolactose") to bind to the repressor protein activating it to unbind from the operator and allow RNA polymerase to carry out transcription. So, in the lactose operon, it will be repressed when there is no allolactose present.

Explain what reversions are and how a second site insertion/deletion mutation can correct a frame shift mutation.

Reversions are mutations that restore a genotype or phenotype. Either through a second mutation at the same site that restores genotype or a second frameshift occurs which restores normal reading frame (reading frame=order of triplets). A deletion will restore an insertion and vice versa.

Distinguish small RNAs and riboswitches: how does each control translation of mRNA?

Small RNA molecules (sRNA) are transcribed from a location away from the genes that they regulate. They have a base pair sequence with a specific base pair sequence on mRNA. When the sRNA binds with mRNA the hfq protein targets mRNA for destruction. In riboswitches the 5' end of mRNA will bind to small molecules which will change stem loop so that it contains the Shine-Dalgarno sequence (ribosomal binding site) and therefore translation is blocked.

Explain the features of a conjugative plasmid, including the structure and function of a pilus.

Some plasmids encode genes for conjugation. In E. Coli the conjugative plasmid is the F (fertility) plasmid which contains all the genes needed to transfer a copy of F plasmid which includes the genes for a pilus and genes for moving DNA. A pilus is a long, protein tube that extends off a bacterium to adhere to another to perform mating.

Explain the difference between species richness and species abundance.

Species richness is the number of species present, it is the diversity. Species abundance is the fraction or proportion of each species within a community.

Using semi-log graphs of viable cell number, total cell number vs time, plot the effects of the three types of chemical antimicrobial agents (static, cidal, lytic) based on their effect on microbial growth.

Static: stops growth, often reversible, may not kill organism so total and viable cell counts stay the same. Cidal: kills organism so total cell count stays the same because of turbidity but viable cell count goes down. Lytic: kills by lysis of the cell wall and therefore the cells are destroyed so total and viable cell counts decrease because lysed cells cannot scatter light.

Briefly state the purpose and uses of sterilizers, disinfectants, antiseptics, and sanitizers.

Sterilizers kill all microbes and spores, they are very toxic to animals and are used in hospital labs on equipment, instruments and medical devices. Disinfectants are used on non-living surfaces, some kill spores, they are used in homes and hospitals, they are less toxic and therefore safer for people to use. Antiseptics are non-toxic for living tissues, they can be used directly on the body like on skin, wounds, and surgical sites. Sanitizers reduce the number of microbes but may not kill all, they are low toxicity to animals. Used in food preparation.

Trace the carbon involved in rhizodeposition, starting with atmospheric CO2 and ending with nutrients in soil around roots.

The CO2 is used in photosynthesis of the plant and the products of photosynthesis go out of the roots into the soil for nutrient enrichment for the microbes, this is called rhizodeposition. Up to 25% of the carbon from photosynthesis goes out of the roots.

Describe the O, A, B, and C horizons in a mature vertical soil profile. Describe the types of conditions found in the various microenvironments within soil aggregates.

The O horizon is just under ground and stands for organic where there are undecomposed plant materials. The A horizon is just under the O and stands for surface soil where decomposing organic matter and a lot of microbes are. The B horizon is just under the A and stands for subsoil where there is less organic matter, fewer microbes and humus. The C horizon is just under B and stands for substratum or soil base where there are even fewer microbes.

Distinguish rho-dependent and rho-independent termination of transcription.

The Rho protein binds to the region of mRNA that is after the amino acid coding region to cause the unwinding of DNA and RNA base-pairing. This causes RNA polymerase to pause and fall off. This is Rho-dependent termination of transcription. In Rho-independent termination of transcription mRNA will base-pair with itself to form a stem loop which tells RNA polymerase to terminate transcription.

Describe the step leading to formation of plaque and tartar.

The bacteria begin as a layer of glycoprotein on a clean tooth that attaches and colonizes to form a biofilm. Growth of the biofilm results in plaque. Calcification of the plaque results in tartar.

Explain the source of energy for nitrogen fixation, and the role of leghemoglobin in this process.

The energy for nitrogen fixation comes from the ATP generated through the electron transport chain in aerobic respiration of the bacterium. Leghemoglobin (Lb) carries O2 in legume to the bacterial membrane/electron transport chain to act as the terminal electron acceptor.

Describe the factors that influence effectiveness of antimicrobial agents, and what types of microbes are most and least resistant.

The factors that influence are the concentration of the agent, the exposure time (longer=more killing), the addition of other chemicals, the level of resistance of the microbe and the population size of the microbe. From most to least resistant is spores, mycobacteria, non-envelope or small viruses, fungi, vegetative bacteria and then enveloped viruses.

Illustrate the steps in formation of a Hfr cell from a F+ cell and how homologous recombination is involved. Create a diagram that explains the two mechanisms of F plasmid transfer in E. coli - either when a separate plasmid (F+) or integrated into a host chromosome

The first mechanism is the transfer from F+ to F-. First the donor extends its pilus to the recipient. Once the pilus attaches it draws the recipient to the donor. Enzymes then copy the F+ plasmid and transfer the copy into the recipient cell. The second mechanism is transfer from F+ to F- but instead of being separate the F plasmid is incorporated into the chromosome. The plasmid and the chromosome will contain insertion sequences which are short sequences of nearly identical DNA. Because they are nearly identical homologous recombination can occur, incorporating the plasmid into the chromosome. This is called an Hfr cell and when it goes on to be the donor of F plasmid, it will transfer some of its chromosomal DNA with it because of the incorporation.

Know how pH and oxygen affect microbial populations and how the stomach acts as a barrier to pathogen entry.

The higher the pH the lower the O2 and the more diversity in species. The stomach has a low pH and therefore kills many microbes and so there is a low abundance and diversity in the stomach.

Explain what the human microbiome is.

The human microbiome is all of the microorganisms that are on or in the human body.

Explain how chemical communication is used to establish symbiosis between nitrogen-fixing bacteria and plants.

The root of the legume excretes a chemical that the microbe will take up and then the microbe will excrete a chemical that causes the root hair to curl and trap bacteria and in turn they will perform nitrogen fixation.

Create a temperature vs time graph for a typical autoclave sterilization cycle and explain each stage of the process.

The temperature of the organism being sterilized initially lags behind the temperature of the chamber because the heat has to get through the container it is in.

Explain the domains of the phylogenetic tree of life and how they were determined.

The three domains of life are eukarya, archaea, and bacteria.

Describe the locations of the upper and lower respiratory tract and where microbes can be found.

The upper respiratory contains many microbes but the lower respiratory is sterile.

Know the bacterium that colonizes the vagina and what role it has in protecting against pathogens.

The vagina has lactobacillus acidophiles (produced by glycogen) which ferment glycogen and produce acids which lowers the pH to about 5 so most pathogens an bacteria are inhibited.

Know why herbivores are dependent on microbes.

To breakdown/ferment plant fibers like cellulose.

Provide examples of how molecular sequences are used to determine phylogenetic relationships of organisms.

They are used to compare between organisms to see what genes are similar and this can be used to determine relation.

Understand the essential role of microbes in the human gastrointestinal tract.

They are used to ferment plant fibers like cellulose ingested by hosts. They also function in synthesizing vitamins, glycosidase activity, steroid metabolism, development/stimulation of immune system and antagonism of pathogens.

Understand where and how microbes grow in the mouth and what diseases they cause. Compare dental caries and gingivitis and the role microbes play in development of these diseases.

They form a biofilm in the mouth by first beginning as a layer of glycoprotein on surface of clean tooth. The bacteria then attach and colonize and grow into a biofilm. Continued growth forms a plaque and continued plaque growth and calcification forms tartar. Biofilm is facilitated by dietary sugars. The diseases are dental caries which occurs when anaerobic microbes in an oral biofilm ferment dietary sugars and produce lactic acid which demineralizes tooth enamel. And gingivitis which is an infection of the gingival crevice which leads to tissue inflammation.

Know why intestinal microbes are beneficial.

They synthesize vitamins, assist in the digestion of food that cannot normally be metabolized (glycosidase activity), they turn bile into other bio-active steroids, the stimulate the immune system and they block pathogenic colonization (microbial interference).

Provide details about how diauxic growth is observed when E. coli are grown with lactose and glucose.

They will first use up all of the glucose for the carbon source and then switch to use lactose which will have a slower growth rate.

Understand that dietary changes can lead to microbial community changes.

This is called dysbiosis.

Describe coupled transcription/translation in prokaryotes.

Transcription and translation occur simultaneously in prokaryotes because they have no membrane bound organelles. So, technically while transcription happens in the nucleoid region and translation happens at the ribosomal unit, they both occur in the cytoplasm.

Create a diagram that summarizes the three horizontal gene transfer mechanisms.

Transformation is when a cell dies and its DNA fragments are released and taken up by recipient cell and put into chromosome by homologous recombination. Transduction is a virus-mediated gene transfer where the virus infects the donor cell, the virus replicates and releases new virus which sometimes contains some of the donor DNA which is then transferred into recipient through homologous recombination. Conjugation is mating where a copy of the donor DNA moves into recipient via a pilus and then becomes part of the chromosome through homologous recombination.

Describe the main ways that UV and ionizing radiation damage DNA (see table on slide 10).

UV damage the DNA and RNA. Ionizing radiation (gamma rays) damage DNA, RNA and proteins.

Provide examples of biological damage caused by ionizing radiation and UV light.

UV light causes DNA and RNA damage, Gamma rays (ionizing radiation) causes DNA, RNA and protein damage. The amount of killing by radiation is dependent on the size of the genome, nucleoid and organism. The larger the more radiation hits needed.

Provide examples of the most appropriate use of UV or ionizing radiation.

UV light is used for disinfecting surfaces, air and water. Ionizing radiation is used for sterilizing medical devices, foods, and pharmaceuticals.

Describe the roles of the activator protein and DNA regulatory regions involved in transcriptional regulation of the maltose operon.

Used for utilizing maltose as a carbon source. If maltose (inducer) is present it will bind to the activator protein which activates it to bind to the activator-binding site. Once the activator protein is bound then RNA polymerase will bind to the promotor region to transcribe. Because prokaryotes have compact, circular DNA, the activator-binding site and promotor don't have to be next to each other.

Explain what viability staining is and how it can be useful for studying microbial communities.

Viability stains uses a type of chemical to distinguish between live and dead cells in an environmental sample. They do this by shooting non-fluorescent chemicals into a cell and if the cell is alive the light will come out fluorescent due to enzymatic activity. This can be helpful in determining the efficientcy of certain anti-microbials.

Describe conditions that impact the digestive microbial community composition.

pH, oxygen, antibiotics, obesity.