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Questions and Answers
What is the primary purpose of pasteurization in microbial growth control?
What is the primary purpose of pasteurization in microbial growth control?
Which of the following statements about ionizing radiation is true?
Which of the following statements about ionizing radiation is true?
What type of filter is commonly used to remove microbes from liquids?
What type of filter is commonly used to remove microbes from liquids?
Which of the following factors does not influence the effectiveness of antimicrobial agents?
Which of the following factors does not influence the effectiveness of antimicrobial agents?
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What distinguishes targeted sequencing from whole genome sequencing?
What distinguishes targeted sequencing from whole genome sequencing?
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What is the primary goal of the human microbiome project?
What is the primary goal of the human microbiome project?
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Which layer of soil is primarily composed of organic material?
Which layer of soil is primarily composed of organic material?
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What is the role of leghemoglobin in nitrogen-fixing symbiosis?
What is the role of leghemoglobin in nitrogen-fixing symbiosis?
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During rhizodeposition, carbon from atmospheric CO2 is ultimately converted into what form around plant roots?
During rhizodeposition, carbon from atmospheric CO2 is ultimately converted into what form around plant roots?
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How does chemical communication facilitate symbiosis between nitrogen-fixing bacteria and legume plants?
How does chemical communication facilitate symbiosis between nitrogen-fixing bacteria and legume plants?
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What is a reason why bacteria are considered ideal models for studying fundamental processes of life?
What is a reason why bacteria are considered ideal models for studying fundamental processes of life?
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Which factor is NOT associated with the survival and growth of bacteria in a specific environment?
Which factor is NOT associated with the survival and growth of bacteria in a specific environment?
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Which of the following accurately describes how viral replication is influenced?
Which of the following accurately describes how viral replication is influenced?
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What can cause alterations in the cellular structures and processes of bacteria?
What can cause alterations in the cellular structures and processes of bacteria?
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Which statement best describes a characteristic of viruses?
Which statement best describes a characteristic of viruses?
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What is the purpose of the Claim-Evidence-Reasoning structure in scientific inquiry?
What is the purpose of the Claim-Evidence-Reasoning structure in scientific inquiry?
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How do pathogenic bacteria typically interact with their hosts to cause disease?
How do pathogenic bacteria typically interact with their hosts to cause disease?
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What skill is important for a career in science and medicine as indicated in the course objectives?
What skill is important for a career in science and medicine as indicated in the course objectives?
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What is the primary difference between an F plasmid integrated in the chromosome and a free F plasmid during transfer to a recipient cell?
What is the primary difference between an F plasmid integrated in the chromosome and a free F plasmid during transfer to a recipient cell?
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Which molecule is most commonly used for studies involving 'molecular clocks' to measure evolutionary time?
Which molecule is most commonly used for studies involving 'molecular clocks' to measure evolutionary time?
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Which element is NOT typically a part of the interpretation of phylogenetic trees?
Which element is NOT typically a part of the interpretation of phylogenetic trees?
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What defines a niche in an ecological context?
What defines a niche in an ecological context?
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How do culture-independent methods analyze microbial communities?
How do culture-independent methods analyze microbial communities?
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Which of these approaches distinguishes between community sampling and environmental genomics?
Which of these approaches distinguishes between community sampling and environmental genomics?
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What best explains a freshwater lake as an example of a microbial ecosystem?
What best explains a freshwater lake as an example of a microbial ecosystem?
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In the context of microbial ecology, what is the difference between species richness and species abundance?
In the context of microbial ecology, what is the difference between species richness and species abundance?
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What is a key feature that enables the detection of an open reading frame (ORF) in a sequence?
What is a key feature that enables the detection of an open reading frame (ORF) in a sequence?
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Which statement best explains why parasites tend to have smaller genomes compared to free-living microbes?
Which statement best explains why parasites tend to have smaller genomes compared to free-living microbes?
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How does comparative genomics contribute to our understanding of different organisms?
How does comparative genomics contribute to our understanding of different organisms?
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What distinguishes a core genome from a pan genome?
What distinguishes a core genome from a pan genome?
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In prokaryotes, what occurs during coupled transcription/translation?
In prokaryotes, what occurs during coupled transcription/translation?
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What role does the lac repressor play in catabolite repression of the lac operon?
What role does the lac repressor play in catabolite repression of the lac operon?
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What is the effect of a frameshift mutation on the resulting protein?
What is the effect of a frameshift mutation on the resulting protein?
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Which factor is crucial for the regulation of transcription initiation using negative control with a repressor protein?
Which factor is crucial for the regulation of transcription initiation using negative control with a repressor protein?
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Study Notes
Microbial Growth Control
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Pasteurization is a heat treatment that reduces the number of microbes in food and beverages. There are two main methods:
- High Temperature Short Time (HTST): Heating at 72°C for 15 seconds.
- Ultra High Temperature (UHT): Heating at 135-140°C for 2-5 seconds.
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Decimal Reduction Time (D-value): The time required to reduce the population of a microbe by 90% at a specific temperature. This is used to interpret survival curves for microbes under heat treatment.
Control of Growth by UV/Ionizing Radiation
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Ionizing radiation (e.g., gamma rays, X-rays) can damage DNA and proteins in microbes, leading to cell death. It is commonly used for food sterilization and medical supplies.
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UV light (e.g., 254 nm wavelength) is effective at killing microorganisms but only penetrates materials superficially. It is used for surface sterilization (e.g., in hospitals, water treatment plants).
Sterilization of Gasses and Liquids by Filtration
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Filter sterilization is the process of removing microorganisms from gasses or liquids using physical barriers (pore sizes).
- Membrane filters are commonly used for liquids, with pore sizes ranging from 0.2 µm to 0.1 µm.
- HEPA filters (High Efficiency Particulate Air filters) are used to remove microbes and other particles from air.
Non-therapeutic Chemical Antimicrobial Agents
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Static agents inhibit microbial growth without killing the cells.
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Cidal agents kill microbial cells.
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Lytic agents cause lysis (breakage) of microbial cells.
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Sterilizers kill all microbes, including spores and viruses.
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Disinfectants kill microbes on surfaces, but may not kill spores.
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Antiseptics are disinfectants safe for use on skin and tissues.
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Sanitizers reduce the number of microbes to a safe level.
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Factors Influencing Effectiveness of Antimicrobial Agents:
- Concentration
- Exposure time
- Temperature
- pH
- Organic matter
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Microbial Resistance:
- Highly resistant: Spores of bacteria like Bacillus and Clostridium
- Moderately resistant: Mycobacteria, enveloped viruses
- Least resistant: Vegetative bacteria, fungi, unenveloped viruses
Microbial Genomics
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Genome: The complete set of genetic information in an organism.
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Information Flow:
- Storage: DNA (deoxyribonucleic acid)
- Retrieval: Transcription (DNA to RNA)
- Execution: Translation (RNA to protein)
DNA Sequencing of Genomes
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Targeted Sequencing: Sequencing specific genes or regions of the genome.
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Whole Genome Sequencing: Sequencing the entire genome.
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Genome Sequencing Project:
- DNA extraction and fragmentation
- Sequencing of fragments
- Assembly of fragments into a contiguous sequence
- Annotation (identifying genes, regulatory elements, etc.)
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Open Reading Frame (ORF): A sequence of DNA that codes for a protein.
Genome Evolution
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Parasites: Microbes that live in or on other organisms often have smaller genomes than free-living microbes. This is because they rely on their host for certain functions.
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Genomes of uncultured organisms: Genome sequences can provide information about the metabolism, evolution, and potential functions of organisms that cannot be grown in the lab.
Comparative Genomics
- Comparative genomics: Comparing the genomes of different organisms to identify similarities and differences.
- Pan Genome: The complete set of genes found in all strains of a species.
- Core Genome: The set of genes common to all strains of a species.
Regulation of Metabolic Pathways
- Central Dogma of Biology: DNA -> RNA -> Protein
- Coupled Transcription/Translation: In prokaryotes, transcription and translation occur simultaneously.
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Transcription Termination:
- Rho-dependent: Requires the Rho protein.
- Rho-independent: Occurs through a hairpin structure in the RNA transcript.
Regulation of Transcription Initiation
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Negative control: Repressor proteins block transcription.
- Arg operon: Repressor protein binds to the operator region when arginine levels are high, preventing transcription of the genes for arginine biosynthesis.
- Lac operon: Repressor protein binds to the operator region when lactose is absent, preventing transcription of the genes for lactose metabolism.
Catabolite Repression
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Catabolite Repression: Glucose preferentially represses the expression of genes involved in the utilization of other sugars (e.g., lactose).
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cAMP: Cyclic adenosine monophosphate, accumulates in the cell when glucose levels are low.
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CRP: cAMP Receptor Protein, binds to cAMP and activates transcription of the lac operon.
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Diauxic Growth: When E. coli is grown with glucose and lactose, it first utilizes glucose, followed by an exponential growth phase on lactose.
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Small RNAs (sRNAs): Short RNA molecules that can regulate gene expression.
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Riboswitches: Regions in mRNA that can bind to small molecules and affect translation.
Bacterial Genetics 1: Mutations and Repair
- Genotype: The genetic makeup of an organism.
- Phenotype: The observable characteristics of an organism.
- Spontaneous mutations: Occur randomly due to errors in DNA replication.
- Induced mutations: Caused by exposure to mutagens (e.g., radiation, chemicals).
Bacterial Genetics 1: Mutations and Repair, Continued
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Base Pair Substitutions:
- Missense: Changes the amino acid sequence of the protein.
- Nonsense: Creates a premature stop codon, resulting in a truncated protein.
- Silent: Does not change the amino acid sequence.
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Frameshift Mutations: Insertions or deletions of nucleotides that shift the reading frame of the gene, altering the entire amino acid sequence after the point of mutation.
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F plasmid: A circular DNA molecule that can transfer genetic material between bacteria.
- Integrated F plasmid: The F plasmid is integrated into the bacterial chromosome.
- Free F plasmid: The F plasmid is separate from the bacterial chromosome.
Evolution and Phylogeny of Prokaryotes
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Molecular phylogeny: Using molecular sequences (e.g., rRNA, DNA) to determine evolutionary relationships between organisms.
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Molecular Clock: The rate of evolution of a particular gene or protein can be used to estimate the time since two organisms diverged.
Phylogenetic Trees
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Domains of Life: Bacteria, Archaea, Eukarya. These were determined by analysis of rRNA sequences.
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Phylogenetic Tree Construction:
- Align similar sequences from different organisms.
- Calculate the number of differences (mutations) between sequences.
- Construct a tree based on the relatedness of sequences.
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Interpretation of Phylogenetic Trees:
- Branch length: Represents evolutionary distance.
- Nodes: Points of divergence.
- Clades: Groups of organisms that share a common ancestor.
- Evolutionary time: Position of the organisms on the tree relative to each other.
Microbial Ecology: Ecology Concepts and Methods
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Niche: The functional role of an organism within a community.
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Microenvironment: A very specific environment within a larger habitat.
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Biotic Factors that Define a Niche:
- Competition
- Predation
- Parasitism
- Mutualism
- Commensalism
General Concepts of Microbial Ecology
- Population: A group of individuals of the same species living in a particular area.
- Guild: A group of species that use the same resource (e.g., decomposers).
- Community: All of the different populations that live in an area.
- Habitat: A place where a particular organism lives.
- Ecosystem: All of the living organisms and their physical environment within a defined area.
Culture-Independent Methods of Community Analysis
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Culture-independent methods: Techniques that do not require growing microorganisms in the lab to study microbial communities.
- Microscopy: Direct observation of microorganisms in their natural environment.
- FISH: Fluorescence In Situ Hybridization, a technique that uses fluorescent probes to detect specific DNA sequences in microorganisms.
- Community sampling: PCR amplification of specific genes (e.g., 16S rRNA gene) in a microbial community to identify different species.
- Environmental genomics: Sequencing all of the DNA in a microbial community to identify species, genes, and functions.
- Metagenomics: Study of the complete genetic material of a microbial community.
- Metatranscriptomics: Study of the gene expression in a microbial community.
- Metabolomics: Study of the metabolism in a microbial community.
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Human Microbiome Project: A large-scale research project that aims to identify and characterize all of the microorganisms that live in and on the human body.
Beneficial Host Microbe Interactions: Plant
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Soil Microbiology:
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Soil Horizons:
- O horizon: Organic matter, decayed plant and animal material.
- A horizon: Topsoil, rich in organic matter and nutrients.
- B horizon: Subsoil, typically enriched in clay.
- C horizon: Parent material, bedrock or weathered rock.
- Soil Aggregates: Clumps of soil particles, creating microenvironments with different physical and chemical properties.
- Rhizodeposition: The release of organic compounds by plant roots, providing energy and nutrients for soil microbes.
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Soil Horizons:
Beneficial Host Microbe Interactions: Plant, Continued
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Legume Plant-Microbe N2-Fixing Symbiosis:
- Legumes: Plants that can form symbiotic relationships with nitrogen-fixing bacteria. Examples include beans, peas, lentils, alfalfa, clover.
- Nitrogen fixation: The conversion of atmospheric nitrogen gas (N2) into ammonia (NH3), which can be used by plants.
- Root Nodules: Specialized structures on legume roots, which house nitrogen-fixing bacteria (e.g., Rhizobium).
Beneficial Host Microbe Interactions: Animal
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Gut Microbiota: The community of microorganisms that live in the gut of animals, including humans.
- Mutualistic relationship: Provide benefits to both host and bacteria, including:
- Digestion of complex carbohydrates
- Production of vitamins
- Protection against pathogens.
- Gut Dysbiosis: Imbalances in the gut microbiota can be associated with health problems (e.g., inflammatory bowel disease).
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Ruminant animals: Herbivorous animals (e.g., cattle, sheep, goats) that have a specialized digestive system called a rumen.
- Rumen: A large fermentation chamber that houses a diverse microbial community that digests plant matter.
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