MMG 301 Exam 2

Describe the process of determining a bacterial genome or set of genomes, transcriptome and proteome

1.isolate nucleic acid from sample 2. perform sequencing by synthesis and obtain small sequencing reads 3. assembling small sequences into larger Contigs (align to existing genomes if possible) Alignments can be done for sequence reads from a single microorganism or an entire microbial community that contains hundreds of species. 4. Use PCR and site specific sequencing to fill in any gaps 5. Analysis (annotation, phylogenetics) The genome sequence is analyzed for genes and open reading frames (protein coding regions), and these are assigned function based on similarities to other known genes.

Be able to describe what a niche is

A niche are a set of conditions needed for certain microorganisms to grow. NOT A LOCATION. Conditions utilized by microorganism, an microorganisms requirements.

What is a virus "titer" and how is it determined; how is a plaque formed on an agar plate

A virus "titer" is the concentration of the virus, and it can be determined by using agar plates to quantify the viruses. Plaque formed on these agar plates come from a single infected cell, and the infected colonies can be counted as a way of measuring virus "titer".

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

An E. coli bacteriophage lambda can replicate and lyse the host cell through the lytic pathway, or it can incorporate its viral genome into the host cell for it to be replicated with host cell DNA through the lysogenic pathway.

Define mutant

An organism with a heritable change in genome sequence

Review the different ether lipids of Archaea; what are the major types of lipids

Archaea membranes are made up of ether lipids, which can be diethers, tetraethers,etc. The membranes can contain a bilayer of phytanyl lipids, or monolayer of biphytanyl lipids.

Describe unique features of habitats around deep ocean hydrothermal vents

Benthic organism live and grow on the surface Warmer habitats provide an environment for microbes to grow Entire living ecosystems is based on CHEMICAL ENERGY instead of solar energy (chemosynthesis vs. photosynthesis)

Explain how and when single nucleotide changes can alter phenotype and when they cannot alter phenotype

Can Alter: Missense, nonsense. these can result in the protein made to be non functional which can result in a different phenotype, or alterations in the protein which can alter the phenotype. Reversions can alter the phenotype back to the wild type if the previous mutation resulted in a change. Cannot alter: silent, no changes to the protein are made

Provide examples of how biofilms affect humans

Causing infections that are difficult to treat b/c they are protected inside a matrix. Contact lens case Inside water pipelines Biofilm on teeth and gums

List the types of genetic elements found in bacteria

Chromosomes Circular thread like structures made of DNA molecules that contain genes. Plasmids genetic element that can replicate separately from the chromosome Double stranded circular DNA (few are linear) few thousand to hundreds of thousand of base pairs have a region called the origin of replication (replication proceeds bidirectionally) replication requires RNA primer have genes such as those for antibiotic resistance genes for conjugation (pilus and enzymes)

Distinguish how DNA sequences are analyzed by the community sampling or the environmental genomics approaches; what information does each approach provide

Community sampling: "What is in the community". Start with a microbial community, extract total community DNA, use PCR to amplify single gene, Sequence and generate a phylogenetic tree. Environmental genomics: Takes more time and $. Want to know everything about the community members. Start with microbial community, restriction digest total DNA and then shotgun sequence OR sequence directly (w/o cloning) using a high-throughput DNA sequencer, assemble and annotate.

Explain how can comparative genomics reveal genes important for causing disease

Comparative genomics: branch of genomics that examines similarities and differences between genomes

Order the major evolutionary events since the cooling of the earth's crust

Cooling of Earth's crust and formation of water Conversion of prebiotic reactions into cellular life Cellular common ancestor diverges into Bacteria and Archaea branches of life Rise of photosynthetic bacteria in the anoxic earth The oxidation event Multicellular life

Distinguish a core genome and pan genome

Core Genome- all genes in common. Pan Genome- all genes in all organisms being compared.

Describe the central dogma of molecular biology

DNA → RNA → Proteins The Central Dogma is the process by which the instructions in DNA are converted into a functional product (the protein) with the intermediary of the RNA. The central dogma of molecular biology explains the flow of genetic information, from DNA to RNA to Proteins DNA→ RNA = transcription They are the same "language" of nucleic acids RNA → Proteins = translated They are not the same language so it needs to be translated to this new language

Describe how early bacteriology classification comparisons were done; what was the manual that was used

Early methods of classification relied on staining/microscopy and biochemical tests. Use Bergey's manual of determinative bacteriology to follow a series of tests in a flowchart to identify microorganisms

What are the two types of associations of fungi with plant roots; how do plants and mycorrhizal fungi benefit from each other

Ectomycorrhizae: forms a sheath around the outside of root Endomycorrhizae: colonize the root interior Fungi can take up nutrients that these plants cannot . They convert these nutrients to a form that plants can more easily utilize. Exchange those nutrients INSIDE of the roots (busticles). In turn the plants provide carbon that the fungi uses as a nutrient to carry out this whole process.

Diagram an RNA molecule including sites needed for translation initiation and termination

In bacteria the small ribosomal subunit attaches directly to certain sequences in the mRNA. These Shine-Dalgarno sequences come just before start codons and "point them out" to the ribosome. In initiation, the ribosome assembles around the mRNA to be read and the first tRNA (carrying the amino acid methionine, which matches the start codon, AUG). This setup, called the initiation complex, is needed in order for translation to get started.

The function of sigma factors

In prokaryotes, a protein that binds to RNA polymerase, allowing the complex to bind to and stimulate the transcription of a specific class of genes (e.g., those involved in sporulation). initiates transcription of genes. It dissociates from the gene when RNA polymerase binds to the specific part of DNA and unwinds, creating single strand, then the core enzyme will convert the DNA info to RA and the single strand gets longer until it's mRNA

Explain how and why oxygen levels change in the microenvironments within soil aggregates; why are microbial fermentation pathway products found within soil aggregates

In the inside of soil, O2 concentration is lower than in the air. This is due to the fact that microbes cocnsume O2. When the O2 is all gone, they switch metabolism to fermentation. Leading to alot of fermentation end products in the interior.

Know the possible outcomes of infection by certain animal viruses and what "transformation" is

Infection by animal viruses can result in a latent infection, in which the virus is present but not replicating (like bacterial lysogen & can revert to lytic infection), or it can result in a persistent infection, in which there is a slow release of virus without causing cell death. Transformation is a process in which some animal viruses can convert a normal host cell into a tumor cell.

Explain how Pseudomonas aeruginosa is associated with cystic fibrosis, and how Dornase can help

It creates extra polysaccharides/ leading to an increase more biofilms in the lungs. This leads to pneumonia in CF patients. Dornase is an enzyme that breaks down DNA in the lungs, reducing viscosity.

Justify why molecular sequences are best for determining phylogenetic relationships; what sequence is most commonly used

It shows how similar/different the sequence is, can use that to order what is more closely related. Is faster and more precise than other methods Small subunit ribosomal RNA (16s rRNA) All organisms have this, so all organisms can be compared Not too long or too short

What major product is made by the fungus Penicillium notatum

Its major product is the antibiotic penicillin.

What are methanogens and understand what the methanogenesis pathway does

Methanogens are some archaea that derive energy from methanogenesis pathways that convert CO2 (or other methyl-containing substrates) into methane. They're anaerobes that contain enzymes/cofactors that are not found anywhere else in nature.

What are microbial mats and stromatolites

Microbial mats: Multi Layered sheets of microorganisms Stromatolites: fossilized microbial mats

List and show examples of single nucleotide mutations

Missense: changes codon, so amino acid is different Nonsense: Creates stop codon Silent: Makes a different codon but same amino acid Reversions: a second mutation event at the same site in restoration of a genotype. (usually happen after a frameshift).

Describe the three major energy production organelles of Eukaryotes; how does each create energy

Mitochondrion: rod/spherical, surrounded by 2 membranes with the internal one being folded (cristae), and uses oxygen for energy through respiration & oxidative phosphorylation Hydrogenosome: similar to mitochondria but lack TCA cycle enzymes & cristae; they're anaerobic so they create energy by fermentation-oxidation of pyruvate to H2, CO2, & acetate; substrate-level phosphorylation is also involved Chloroplast: chlorophyll-containing, found in phototrophic eukaryotes, they have flattened membrane discs called thylakoids & their lumen is called stroma; they create energy by photosynthesis.

Review the nitrogen fixation pathway inside bacteroids; what is the overall reaction for nitrogen fixation; explain the source of energy, how much energy is expended for each N2, and the role of leghemoglobin

N2 + 8H + 16 ATP + 16H2O → 2 NH3 +H2 +16 ATP + 16 Pi Get energy from aerobic respiration (o2) Leghemoglobin supples that O2 to e- transport so that aerobic respiration can happen Carbon comes from organic acids from photosynthesis Nitrogenase N2 → NH3

How does Nanoarchaeum live; what does it derive from its host

Nanoarchaeum live as a parasite that can only exist on the surface of host cells Ignococcus hospitalis. They are dependent on their host cell for genes to encode synthesis of amino acids, nucleotides, and other crucial molecules.

Indicate how genomics technologies can assist in understanding bacterial evolution

New enzymes and proteins can evolve after gene duplication events. By comparing the genomes to each other, you can see how closely related they are to each other and tracing the relationships back through looking for similarities mutations rearrangements horizontal gene transfer

N cycle: know meaning of nitrification, denitrification, nitrogen fixation, ammonification, assimilation

Nitrification: this occurs when bacteria that live in the soil take up ammonia and change it into nitrate and nitrite Denitrification: this occurs when bacteria break down nitrates and produce N2 that is released into the atmosphere Nitrogen fixation: the process of converting the N2 in the atmosphere into the chemicals nitrate, nitrite, and ammonia Ammonification: decomposers break down the bodies of dead organisms, urine, and dung into ammonia. Returns N2 back into the atmosphere Assimilation: this occurs when plant cells use nitrate, nitrite and ammonia to produce the proteins and nucleic acids needed by the cells

Why is N2-fixing symbiosis important to certain plants and to agriculture

Nitrogen is an important nutrient needed for plant productivity and growth. For specific plants that perform N2-fixation w/specific symbiotic bacteria, that can affect this limitation.

Describe the four vertical horizons found in mature soils; what are soil aggregates

O horizon: layer w/undecomposed plant materials A horizon: surface soil, used for argriculture, growing plants, microbial activity is HIGH B horizon: subsoil (minerals, humus) C horizon: Soil base, bed rock, LOW microbial activity Soil aggregates are what make up the soil. Organic Plant Matter Sand, Silt, Clay

Explain how oxygen levels rose in the atmosphere; what is one type of geological evidence for this "great oxidation event"

Organisms evolved the ability to use H2O as an electron source, leading to a rise in O2 as a byproduct of photosynthesis Evidence Iron banding forming in rock formations

What the challenges to organisms living at high temperatures

Organisms living at high temperatures have to face the stability of small molecules, like ATP, being reduced, proteins/enzymes unfolding at higher temperatures, DNA/RNA can denature & degrade, and the ability of membrane lipids to function can be limited by high temperatures.

What are the key features of the global carbon cycle; review what processes happen in oxic vs. anoxic parts of the cycle; where is methane formed, and where carbon enters and exits living systems

Oxic pathway: CO2 is fixed into organic matter by oxygenic photosynthesis and chemolithotrophic organisms (chemolithotrophy- for energy). Organic matter is broken down to CO2 Anoxic pathway: Co2 fixation by acetogenesis that make acetate or by anoxygenic photosynthesis which powers the energy to bring CO2 into those organism. That makes organic matter that can be decomposed by the action of anaerobic respiration using terminal e- acceptor other than O2 and fermentation pathways.

What are phylochips and what are they used for; what is hybridization of DNA

Phylochips can measure different phylotypes in a microbial community. Used for phylogenetic classification rather than measuring messenger RNA.

Distinguish populations, guilds, communities, habitats, and ecosystem; how is a freshwater lake an example of a microbial ecosystem; what are the energy inputs

Populations: groups of related organisms where cells grow and divide Guilds: populations that do related metabolisms. Communities: a group of microorganisms that share a common living space Habitats: Large environments of guilds living in the same kind of environment Ecosystem: a system of all living organisms that live in a physical environment and function together as a unit. A freshwater lake is an example of a microbial ecosystem because the communities within the lake (photic zone, oxic zone & anoxic sediments) interact with each other. Energy inputs: Sunlight, Organic carbon: photosynthesis & allochthonous carbon (outside), and reduced inorganic compounds (source of anaerobic respiration).

Distinguish between primary endosymbiosis and secondary endosymbiosis

Primary endosymbiosis ends at the acquirement of mitochondria/chloroplasts from aerobic/photosynthetic bacteria, while secondary endosymbiosis continues towards a process in which red or green algae are engulfed and their chloroplasts are retained by the host cell.

Describe the basic processes whereby complex polymers are converted to methane and CO2

Primary fermenters: converts monomers and makes H2, CO2, organic acids, and alcohols, Secondary fermenters: use H2, Co2, acetate to make CH4 (methane) for energy

Indicate functions and steps of two component systems

Regulation of genes and operons in response to external molecules is usually controlled by two component systems Sensor kinase protein type of signal transduction system are proteins spanning the cytoplasmic membrane that respond to specific environmental signals is phosphorylated from ATP when a signal binds Response regulator protein type of signal transduction system dephosphorylates the sensor kinase that is bound to an environmental signal > DNA control protein binds to operator/activator and can act as a repressor, activator, etc Steps 1. environmental signal binds to kinase, kinase is phosphorylated from ATP 2. response regulator takes the P from the kinase 3. regulator becomes a DNA binding protein

Describe how thermal stratification results in anoxic conditions in the hypolimnion; Why are hydrogen sulfide concentrations higher in the hypolimnion

Results in anoxic conditions in hypolimnion b/c at that depth, all of the O2 is used up. For organisms to get energy that have to do anoxic/ anaerobic respiration. SO4 to H2S (increases Hydrogen Sulfide)

Describe how are T4 viral components made precisely at the time they are needed

Right after the time of infection in the host cell (approx. 5 minutes), T4 nucleases, DNA polymerase, and sigma factors are made available. Then the replication process of phage DNA begins, and translation of phage DNA into T4 phage proteins begins as well. The phage head protein, tail, collar, base plate, and tail fiber proteins that are made are then self-assembled into mature T4 viruses. These viruses are made just in time to produce the lysozymes needed to cut peptidoglycan for lysis.

How have metagenomic methods been applied in analyzing microbial communities in the Sargasso Sea and the human microbiome

Seawater samples were filtered to separate out microbial life. DNA was extracted and sequenced (environmental genomics approach)

Identify second site suppressor mutations and their mechanism of action

Second site suppressors: Mutations that occur in tRNA recognition can read mutant mRNA sequence, but insert the correct amino acid Suppressor tRNA: inserts a correct amino acid, and normal protein is made

Describe the basic structure of an operon

Single transcription unit. (multiple genes being transcribed together) Promoter (starts) Coding genes ORF (g1g2 etc) Terminator (stops)

How do some Archaea generate ATP energy from light; what are bacteriorhodopsin and retinal

Some halophilic archaea can use light to produce ATP, and can do so using bacteriorhodopsin and retinal. Bacteriorhodopsin is a protein that allows archaea to get energy directly from light without chlorophyll or photosynthesis. Retinal is attached to bacteriorhodopsin, and allows certain microorganisms to convert light energy into metabolic energy (ATP).

Explain the difference between species richness and species abundance

Species richness (diversity): the number of different species present in any sample. A high total # of species=high richness. Fox 16S rRNA sequencing, richness is expressed by the diversity of PHYLOTYPES. Species abundance: the proportion of each species within a community. Alot of species = high abundance

Diagram translation termination

Termination is the stage in which the finished polypeptide chain is released. It begins when a stop codon (UAG, UAA, or UGA) enters the ribosome, triggering a series of events that separate the chain from its tRNA and allow it to drift out of the ribosome. After termination, the polypeptide may still need to fold into the right 3D shape, undergo processing (such as the removal of amino acids), get shipped to the right place in the cell, or combine with other polypeptides before it can do its job as a functional protein.

How some members of the Archaea important for the global nitrogen cycle; what adaptation is important for its survival

Thaumarchaeota archaea are an important part of the global nitrogen cycle since they derive energy from the chemolithotrophic oxidation of ammonia to nitrite, which is the first step of nitrification. Nitrification is an important part of the global nitrogen geochemical cycle. They are able to adapt to very low nutrient levels for survival in open/deep ocean habitats.

Be able to briefly describe the Human Microbiome Project

The Human Microbiome Project was used to identify the role of microbes in human health. Determine what microbes are found in the healthy human body and how the microbial community can change as a result of nutrition, disease and medical treatment.

Describe general concepts of biogeochemical cycles and the role of microbes in nutrient cycling.

The biogeochemical cycle is responsible for microbial growth and transformation of elements. It involves BIOLOGICAL and CHEMICAL processes that result in the cyclic interconversions of key elements needed to sustain productive life processes in the biosphere.

If given a diagram of the individual components of viruses; including nucleic acid, capsomeres and capsids and envelope, assemble these into a complete virus; where does the envelope originate from

The envelope is a membrane phospholipid bilayer that originates from proteins from the infected host cell.

Describe how a ribosome initiates translation

The initiator tRNA interacts with the start codon AUG of the mRNA and carries a formylated methionine (fMet). fMet is inserted at the beginning (N terminus) of every polypeptide chain synthesized by E. coli. In E. coli mRNA, a leader sequence upstream of the first AUG codon, called the Shine-Dalgarno sequence (also known as the ribosomal binding site AGGAGG), interacts through complementary base pairing with the rRNA molecules that compose the ribosome. This interaction anchors the 30S ribosomal subunit at the correct location on the mRNA template. At this point, the 50S ribosomal subunit then binds to the initiation complex, forming an intact ribosome.

Arrange in order the following DNA features and how they correspond to mRNA and protein.

The promoter (35 and 10) +1 of transcription Shine Dalgarno sequence (RBS) Start Codon Operators coding sequence stop codon transcriptional terminator

What replication enzyme is a distinguishing feature of retroviruses; what are the three major gene regions in retroviruses; what are oncogenes

The replication enzyme reverse transcriptase is unique to retroviruses (converts RNA to DNA). The three major gene regions in retroviruses are gag (the core/capsid proteins), pol (reverse transcriptase, integrase, & protease), and env (envelope proteins). Oncogenes are genes which can transform a cell into a tumor (cancer) cell, and are common in retroviruses.

What is the role of dechlorination in bioremediation; what is an example of a bioremediation pathway that involves several dechlorination steps

The role of dechlorination in bioremediation is to remove a halide, in this case Chlorine and replace it with a hydrogen ion,

What habitats is Sulfolobus found in; be able to state in general terms how it gets its energy

They are found in hot, acidic terrestrial sulfur springs called solfataras. They get their energy from respiration: the coupling of the oxidation of sulfur/iron/H2S to reduction of oxygen to water.

How do viruses efficiently use of their limited genome size

They have overlapping genes, that is they commonly have one piece of DNA that will encode for multiple proteins. This allows maximum use of the limited DNA.

Be able to describe the three types of mycoses

Three types of fungal diseases are superficial (on the skin-thrush), subcutaneous/invasive (under the skin-in tissues), and systemic (in the bloodstream-can affect many organs).

Distinguish between specialized and generalized transduction, including host DNA that is moved

Tranduction: viral transfer of DNA Generalized: random bacterial DNA is packaged inside a phage and transferred to a recipient cell Specialized transduction: Only genome DNA transferred to a recipient cell, only happens in lysogenic cells

Review the characteristics of O2, bacteria (+ organic carbon and BOD), algae, as they change downstream of a pollution entry point in a river; why is BOD proportional to the amount of dissolved organic pollution in a water sample

When pollution goes up→ bacteria grows → O2 decreases b/c bacteria is consuming O2 → BOD reading will shows an increase in O2 consumption when pollution is high. When food/pollutions runs out, bacteria decreases, the flow of water causes an increase in dissolved O2, more algae created O2 too.

Allosteric Regulation

a way to regulate enzyme activity found in enzymes catalyzing in the first step of a multi-step biochemical pathway common strategy is that the end product of a multi-step pathway inhibits the activity of the first enzyme: feedback inhibition 1. effector molecule (end product, allosteric effector) binds to enzyme and alters the conformation 2. substrate molecule can no longer bind and react in the active site

Describe how a polypeptide chain is formed

Elongation is the stage where the amino acid chain gets longer. In elongation, the mRNA is read one codon at a time, and the amino acid matching each codon is added to a growing protein chain. Each time a new codon is exposed: A matching tRNA binds to the codon The existing amino acid chain (polypeptide) is linked onto the amino acid of the tRNA via a chemical reaction The mRNA is shifted one codon over in the ribosome, exposing a new codon for reading During elongation, tRNAs move through the A, P, and E sites of the ribosome, as shown above. This process repeats many times as new codons are read and new amino acids are added to the chain.

Explain the endosymbiosis theory and what evidence supports it

Endosymbiosis theory states that mitochondria evolved from aerobic intracellular symbiotic bacteria, and chloroplasts evolved from symbiotic oxygenic photosynthetic cyanbacteria. It is supported by the fact that mitochondria, hydrogenosomes, & chloroplasts contain their own circular genomes, and are replicated from pre-existing organelles. Eukaryotic chromosomes also contain genes derived from bacteria, and ribsomes encoded by these certain organelles' DNA are of the bacterial type rather than eukaryotic. In addition, these organelles are sensitive to antibiotics that are effective against bacterial ribosomes.

Diagram transfer of the F+ plasmid as either an episome or integrated into the chromosome

Episome: not part of the chromosome

What are the bacterial and eukaryotic primary producers in open ocean waters; explain why small cell size is an advantage to microbes living in the open ocean

Eukaryotic: Unicellular algae Bacterial: Cyanobacteria Small cell size is an advantage= high surface to volume ratio A large surface for feeding a small volume makes more efficient use of available low nutrients that are in open ocean

Define fitness; provide an example of evolution and fitness that has been observed in recent years

Fitness: the ability of an organism, with a given genotype or phenotype, to grow and reproduce, and to contribute its genetic information to future generations. (AKA ability to make babies) Example: Antibiotic resistant bacteria are more fit than other bacteria because they are more likely to survive antibiotics and be able to reproduce.

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

Fluorescence in situ hybridization (FISH) is used to detect specific organisms within populations. Synthesize oligonucleotide (the probe) specific for the organism you are looking for. Chemically attach a fluorescent dye molecule to the oligonucleotide Treat the sample containing the cells to make membrane permeable to the oligonucleotide + dye molecule. (Done to make sure it can go inside the cell to be bond. If not the exact base pair, it will not be bound) Examine the sample using fluorescence microscopy; only the cells in which the oligonucleotide has completely base-paired (hybridized) will be fluorescent.

Describe how microbes can be used for petroleum bioremediation

For cleaning up contaminated sites, from petroleum we can add microbes nutrients that may be lacking. By applying microbes, we can help speed up the process of bioremediation, Microbes can metabolize human-created chemical compounds and convert them into less harmful compounds or metabolize resources such as petroleum.

Describe a frameshift mutation and its effect on proteins/phenotype

Frameshift: caused by an insertion or deletion of an amino acid, shifting everything and resulting in different codons. Can make the resulting protein nonfunctional or change its function.

Know the key features of fungi; their roles in nature; major impacts to humans

Fungi contain cell walls of chitin, are commonly filamentous, and they are achlorophyllous chemoorganotrophs, meaning they get all their energy from the decomposition of organic matter. They are major contributors to the decomposition and mineralization of organic carbon in nature. Many are also pathogens of plants & animals (& humans), are a major cause of food spoilage, can be a food source (mushrooms, yeast), can be beneficial symbionts of plant roots, and have been useful metabolites in biotechnology

What is genetic drift and how has it been studied in E. coli populations

Genetic Drift: When a fraction of members of a population changes as a result of random sampling. (members of a population get seperated and over time this leads to genetic differences between the populations)

Order the steps, including the proteins involved in recombination

Homologous recombination: Exchange of genetic information between homologous DNA molecules.

Be able to diagram the step of retroviral (and other enveloped viruses) release from host cell by budding

I can not get the picture to load...

Create a graph showing liquid culture turbidity vs time for a lytic virus infection; also do this for virus count vs time

I can not get the picture to load...

Order the steps of the retrovirus life cycle, what type of genome, dsDNA intermediate, why are protease, reverse transcriptase, and fusion inhibitors helpful in treatment of HIV

I can not get the picture to load... Reverse transcriptase converts single stranded RNA and dsDNA intermediate to double stranded DNA. Inhibition of protease, reverse transcriptase and fusion into host genome would be helpful in the treatment of HIV because it would result in the prevention of retrovirus replication (HIV-1 is retrovirus).

Describe how a change in a nucleotide propagates through the various steps of information transfer, especially for frame shifts and changes in key features.

If you change a single nucleotide in the DNA, you change the RNA and then you change the protein made. If this change causes the codon to change, the whole protein could be wrong, not work, or not be functional

Describe basic mechanism of quorum sensing and why a cell would use QS

an example of population dependent control of regulons by signal chemicals that are excreted by cells it is often necessary for cells to sense how many of their own kind are in the immediate environment way for cells to sample microbe excreted chemicals (autoinducers) in the environment to measure population density many cells > more chemical signals (linear, direct relationship) used during antibiotic production to switch on the genes needed for antibiotic production if enough cells are in the area to make a difference USe autoinducers chemicals secreted by cells and used for quorum sensing In general, each bacterial species produces its own unique autoinducer.

Summarize the process of gene annotation

comparing protein sequences with regions of known proteins to assign function; taking a gene and finding its function involves computational methods to detect genes, or open reading frames The genome sequences of individual species, or members of complex microbial communities can be determined. The sequences provide information about metabolism, virulence, physiology, phylogeny, and structure of microorganisms that cannot be isolated or cultured in a laboratory.

Create a simple experiment for selecting mutant

put on a selective medium

Summarize how advancements in sequencing have led to changes in microbiology

the advancements in sequencing have led to the costs being way less per sequence and have led to there being more sequences done per year on average and there is a database we can use to compare sequences.

Order the steps in isolating 16S rRNA genes by PCR and building a phylogenetic tree

DNA is isolated from pure cultures of microbes, or microbial communities 16s rRNA genes are amplified by PCR, use specific primers PCR products are checked by gel electrophoresis Sequences of 16 rRNA gene are compiled into a computer alignment program Sequences in data set are aligned and compared Differences are calculated to make a distance matrix A tree is constructed Distances of branches and nodes show evolutionary distance

Illustrate the molecular processes of - Repression - Induction - Activation

- Repression transcription goes on unless corepressor binds to repressor protein and stops polymerase - Induction repressor protein always attached unless inducer attaches to repressor protein and releases, which allows polymerase to go - Activation involves a DNA binding protein that is required for RNA polymerase to bind

Describe the sequence of steps in establishment of plant-rhizobia symbiosis; what chemicals are used for plant↔microbe communication

Bi-directional chemical communication between bacteria and plants roots. Plants excrete flavenoid (chemical) thats going to go from the root to soil Flavenoid is going to be sensed by bacteria which will cause bacteria to turn on gene to make nod factors (chemical) Once nod factors (a communication chemical) are ccreated, they are sensed by the plant. Nod factors cause root hair to grow in a non-symmetric manner so that it curls. Root hair curling takes place. It traps cells that are attached into the rod hair. An infection thread forms where bacteria starts growing in an internal tube. The thread extends while the bacteria is growing & goes to the interior of the root. Establishes a symbiotic relationship called a Nodule. Bacteria converts to a bacteroid state before N2 fixation.

Describe the methods used to determine microbial community composition; what staining methods are used for microscopic analysis; what is a live/dead stain

Cultural-independent methods: Doesn't need to be grown in a laboratory. Take a sample from the environment & find out whats is there. Microscopic analysis: uses staining and nucleic acid probes. -Staining methods: use microscopy and fluorescent dyes that stain DNA or discriminate dead cells from live cells. - Viability stains: Live/dead stains. Non-fluorescent dye goes into a cell, an enzyme reacts creating a fluorescence. If the cell is dead, that enzyme is not going to work. Genetic analysis: uses PCR and/or sequencing and microarray methods (uses the specificity of DNA binding to nucleic acis of complementary sequences)

Compare the information determined by genomics, metagenomics, transcriptomics and proteomics

Genomics the genes of the sample Comparative genomics looks at differences between two similar microorganisms to see what genes are different or unique. can compare two strains of the same bacteria, one is a pathogen one is a nonpathogen pathogenic strains contain clusters of genes that the nonpathogen does not have Metagenomics the study of the complete complement of small chemicals present in a cell at any given time aka environmental genomics complex communities containing uncultured organisms can be analyzed by genome and/or RNA sequencing what organisms are there? can either use PCR to amplify rRNA genes > construct phylogenetic trees OR can isolate cells, extract DNA, and perform shotgun sequencing > construct genomes EX: human intestinal microbial community changes during growth (identify phyla) Transcriptomics study of what mRNAs are produced from the genome, study of the transcriptome; genes needed for growth are transcribed and mRNA is increased, genes not needed aren't transcribed and there is decreased mRNA. sum total of the of the mRNA molecules expressed from the genes of an organism Proteomics the study and comparison of all the proteins that result from an organism's genome

Relate changes in genotype to changes in phenotype

Genotype: nucleotide sequence Phenotype: observable properties of an organism When you change the genotype it's possible to change the phenotype. A change in a flowers color genotype might result in a new phenotype, a new flower color.

Explain how Geobacter can metabolize uranium for respiration; how are pili involved

Geobacteria can use uranium as a substrate for respiration Soluble U6+ is reduced to insoluble U4+ The bacteria will take those electrons and reduce that Uranium into an insoluble form. We can then process that, filter it, to remove that Uranium from that water. The rxn takes place on electron conducting pili.

Explain how halophilic Archaea maintain water balance while living in high salt conditions

Halophilic archaea have physiological adaptations for survival in high salt conditions. They maintain water balance by synthesizing/accumulating internal solutes (compatible solutes) that equalize the water activity between the inside and outside of the cell.

Draw DNA and its RNA transcript and illustrate important sequences for recognition of RNAP and ribosomes Describe how genes may be regulated at various points within gene expression, including non transcriptionally

Promoters are the important part for the recognition of RNAP RNA polymerases are enzymes that transcribe DNA into RNA. Using a DNA template, RNA polymerase builds a new RNA molecule through base pairing. RNA polymerase always builds a new RNA strand in the 5' to 3' direction. That is, it can only add RNA nucleotides (A, U, C, or G) to the 3' end of the strand. Each gene (or, in bacteria, each group of genes transcribed together) has its own promoter. A promoter contains DNA sequences that let RNA polymerase or its helper proteins attach to the DNA.

List some of the benefits of living in biofilms; what happens in each stage of biofilm development

Protection from antibiotics Protections from the immune system Protection from chemical (antimicrobial) agents-disinfectants Protections from drying Allow for binding to matix nutrients STAGES OF BIOFILM DEVELOPMENT 1. Attachment: one cell/few cells attach to a solid surface by polysaccharides, fimbriae, flagella, pili 2. Colonization: Growth + polysaccharide formation 3. Development: More growth & chambers: ways for fluid to get in and out -exchange of nutrients 4. Dispersal: cells move to another surface & triggered by cell availability

Describe the adaptations of proteins and DNA so they can function in high temperature habitats

Proteins and enzymes can have increased stability in high temperature environments by having the protein secondary structure stabilized by a hydrophobic core, salt bridges creating strong contacts within polypeptide chain, and stable folding confirmation facilitated by chaperonins. DNA can have increased stability in high temperatures by having internal ions to stabilize/protect the DNA, by having a tighter conformation through reverse DNA gyrase to prevent separation, and by having DNA binding proteins to keep DNA from flying apart during processes such as transcription.

Explain non-transcriptional mechanisms of gene regulation

Translation of mRNA can be controlled: two common mechanisms are small RNAs (short RNA that base-pairs with, and blocks transcription, of mRNA) and riboswitches (metabolite-induced folding of mRNA into a conformation that inhibits translation. non-coding RNA molecules can control translation of operons small RNA molecules (sRNA): transcribed elsewhere on the chromosome; specifically base pair with a region of a mRNA (facilitated by Hfq protein); binding to the ribosomal binding site or 3' end of mRNA can either prevent or stimulate translation riboswitches: mRNAs that can bind small regulatory molecules in a region upstream of the ribosomal binding site; takes advantage of the fact that RNA can bind small molecules; base pairing of the mRNA changes so now the ribosomal binding site cannot function

Distinguish between vertical and horizontal gene transfer

Vertical: Mother to daughter cells. Splitting replicated genes for division Horizontal: Donor to recipient (transduction, transformation, conjugation)

Determine the state of each regulator of the lac operon given environmental conditions

•The Lac operon (utilization if lactose as carbon source) of E. coli is transcribed when 1) glucose is absent (controlled by catabolite repression), and 2) lactose is present (controlled by the lac repressor). one switch is lactose: no lactose, transcription is off; with lactose, switch is on other switch controlled by glucose: no glucose switch is one, with glucose switch is off WANTS TO USE GLUCOSE