micro exam 3 - questions
What is the age of planet Earth and the earliest known microfossil?
The Earth is ~4.5 billion years old •First evidence for microbial life can be found in rocks ~3.86 billion years old
What caused the formation of banded iron formation?
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Describe the common characteristics of family Enterobacteriaceae . List main organisms in this family and what effects do they have on humans or other animals.
Large family of enteric genera •Biochemical tests used to distinguish genera in addition to morphology, motility, growth responses •Escherichia ( E.coli), Salmonella, Shigella, Proteus, Enterobacter, Klebsiella and Serratia •Commensal, opportunistic, or true pathogens -Pathology is due to endotoxin and (in some cases) exotoxins -Cause 3 billion diarrheal infections and 3 million deaths worldwide annually Salmonella-typhoid fever, gastroenteritis •Shigella- bacillary dysentery •Klebsiella -pneumonia •Yersinia -plague •Erwinia-blights, wilts, etc., of crop plants
Describe the hypothesis of origin of life on Earth
Life originated at hydrothermal springs on ocean floor -Conditions would have been more stable -Steady and abundant supply of energy (e.g., H2 and H2S) may have been available at these sites
What are extreme halophiles and their requirements? Describe the main characteristics of Haloarchaea. Which strategies do halophiles use to cope up with osmotic stress?
Extreme halophile: obligate aerobes Extreme halophiles (halobacteria) -require at least 1.5 M NaCl, cell wall disintegrates if [NaCl] <1.5 M -growth optima near 2-4 M NaCl •Grow in hypersaline environments -Most found in hot, dry areas of world Strategies to Cope with Osmotic Stress •Increase cytoplasmic osmolarity -use compatible solutes (small organics) •"Salt-in" approach -use antiporters/symporters to increase concentration of K + and Na+ to level of external environment -Cellular components exposed to external environment require high Na+ to for stability, whereas internal environment requires high K+
What is FAME analysis? What does it measure?
Fatty acid analysis (FAME: fatty acid methyl ester) •Relies on variation in type and proportion of fatty acids present in membrane lipids for specific prokaryotic groups •Requires rigid standardization because FAME profiles can vary as a function of temperature, growth phase, and growth medium
Describe fungi physiology, structure and symbiosis. What are Mycorrhizae?
Fungal Physiology, Structure, & Symbioses •Most fungi are multicellular, forming a network of hyphae •Hyphae that extend above the surface can produce asexual spores called conidia -Conidia are often pigmented and resistant to drying •Hyphae form compact tufts called mycelia •Most fungal cell walls are made of chitin •Mycorrhizae- symbiotic fungi, help plant roots obtain phosphorus
What are the key differences between fungi and bacteria?
Fungi are multicellular, eukaryotic organisms, while bacteria are single-celled prokaryotes. The cells of fungi have nuclei that contain the chromosomes and other organelles, such as mitochondria and ribosomes. Bacteria are much smaller than fungi, do not have nuclei or other organelles and cannot reproduce sexually.
What are rhodopsins? List their function and importance.
Halobacterium salinarium and some other haloarchaea can catalyze a light driven synthesis of ATP • Has unique type of photosynthesis -not chlorophyll based -uses modified cell membrane (contains Bacteriorhodopsin) -absorption of light by Bacteriorhodopsin drives proton transport, creating Proton Motive Force for ATP synthesis Bacteriorhodopsin -Supports slow growth in extreme environment - Light-stimulated proton pump: pumps Na+out of the cell by activity of Na+ -H+ antiport system -Assist uptake of amino acids & K+ needed for osmotic balance Halorhodopsin -light energy to transport chloride ions into the cell to increase intracellular salt concentrations -Light- driven pump that pumps Cl- into cell as an anion for K
What are helminths and list their characteristics?
Helminths- parasitic worms Characteristics of parasitic helminths: Reduced digestive system ▪absorb nutrients ▪Reduced nervous system ▪host environment constant ▪Reduced locomotion ▪no need to search ▪Complex reproduction ▪several intermediate hosts for larval stages ▪definitive host for adult parasite and reproduction
What does a phylogenetic tree depict?
A phylogeny, or evolutionary tree, represents the evolutionary relationships among a set of organisms or groups of organisms, called taxa (singular: taxon). The tips of the tree represent groups of descendent taxa (often species) and the nodes on the tree represent the common ancestors of those descendants.
What features are unique to Archaea?
Unique to Archaea rRNA sequences, methanogenesis
How do fungal spores differ from bacterial spores?
1. reproductive spores (detaches from parent and germinates into new mold) 2. can survive for extended times in dry/hot do not exhibit extreme longevity of endospores
List key steps in building a phylogenetic tree.
1; The first step in making a tree is to align sequences 2; A distance matrix is calculated from the number of sequence differences 3: The tree is constructed by adding nodes to join lineages that have the fewest differences
Why the evolution of cyanobacteria is considered a critical step in evolution?
2.7 billion years ago, cyanobacteria developed a photosystem that could use H2O instead of H2S, generating O2 •By 2.4 billion years ago, O2 concentrations raised to 1 part per million; initiation of the Great Oxidation Event •O2 could not accumulate until it reacted with abundant reduced materials in the oceans (e.g., FeS, FeS2) Banded iron formations: laminated sedimentary rocks; prominent feature in geological record Development of oxic atmosphere led to evolution of new metabolic pathways that yielded more energy than anaerobic metabolism
Define what is methanogenesis? Which organisms produce methane? Under which conditions does methanogenesis takes place? List the ecological and practical importance of methanogenesis?
All methanogenic microbes are Archaea -called methanogens: produce methane •Methanogenesis -last step in the degradation of organic compounds -occurs in anaerobic environments •e.g., animal rumens •e.g., anaerobic sludge digesters •e.g., within anaerobic protozoa Anaerobic methanogens -Degradation organic compounds to produce methane gas •Important in wastewater treatment •Methane can be used as clean burning fuel and energy source •Is a greenhouse gas and may contribute to global warming -Can oxidize iron (corrosion of pipes) - Can form symbiotic relationships with certain bacteria, assisting carbon/sulfur cycling
Describe how conjugation, transformation, and transduction are similar. How are they different?
All the three methods are similar as it consists of transfer of genetic material by bacteria by means of recombination Bacteria undergoes recombination by taking an extra DNA from other sources. Bacteria undergoes recombination in all the three methods of conjugation , transformation and transduction. Conjugation consists of acquisition of DNA directly from another bacteria, in Transformation the bacteria picks up DNA from the environment while in transduction a bacteria acquires DNA from a bacteriophage intermediate.
Distinguish F+, Hfr, F-and F' cells from each other. Explain how Hfr and F' cells arise.
An F+ cell will contain a circular plasmid seperate from the chromosome. the Hfr cell has the f factor integrated into its chromosome. in F' strains the f factor exists as a seperate circular plasmid but the plasmid carries bacterial genes that were originally part of the bacterial chromosome. The F- strain does not contain the f factor and can recieve DNA from cells that contain the F factor. (F+, Hfr, and F' ) Hfrx F- mating F plasmid in Hfr strain has functional tra operon •DNA transfer- Starts at oriT -Initially F plasmid is transferred, followed by donor's chromosome -Connection breaks before the entire chromosome is transferred •The recipient cell remains F-cell
How does genetic transfer take place in Archaea?
Archaea contain single circular chromosome •Genetic manipulation of Archaea lags behind Bacteria -Archaea need to be grown in extreme conditions -Most antibiotics do not affect Archaea -No single species is a model organism for Archaea •Examples of transformation, transduction, and conjugation exist •Transformation works reasonably well in Archaea
What major physiological (morphological) properties do Archaea share with Eukarya or with Bacteria?
Bacteria- Unicellular prokaryotes Majority have cell wall made of peptidoglycan Archaea- Genetically distinct rRNA sequences from Bacteria - Lack peptidoglycan in cell walls; have unique membrane lipids - Some have unusual metabolic characteristics Eukarya : Microorganisms in this domain include protists (algae, protozoa, and slime molds) and fungi (yeast, molds)
Describe the process of transduction? Compare and contrast generalized vs. specialized transduction.
Bacteriophages facilitate gene transfer from one cell to another •Bacterial genes are transferred by virus particle • These genes are packaged in the virus particle due to errors made during the virus's life cycle •Virion containing these genes can transfer them to recipient cells •Lytic phages destroy host cells; Lysogenic (temperate) phages integrate into host cell genome as latent prophage Generalized transduction: DNA derived from virtually any portion of the host genome is packaged inside the mature virion Specialized transduction: DNA from a specific region of the host chromosome is integrated directly in the virus genome
What are CRISPR and its role in a prokaryotic cell?
CRISPR: Clustered Regulatory Interspaced Short Palindromic Repeats Type of prokaryotic "immune system" •Region of bacterial chromosome containing DNA sequences similar to foreign DNA (spacers) alternating with identical repeated sequences •CRISPR -associated proteins (Cas proteins) -Obtain and store segments of foreign DNA as spacers -Recognize and destroy foreign DNA
What kinds of evidence support the three-domain concept of life?
Carl Woese Pioneered the use of rRNA for phylogenetic studies in the 1970s •Established the presence of three domains of life: -Bacteria, Archaea, and Eukarya •Provided a unified phylogenetic framework for Bacteria The most widely used rRNAs are small subunit ribosomal RNA (SSU rRNA) genes •Found in all domains of life - 16S rRNA in prokaryotes and 18S rRNA in eukaryotes •Functionally constant •Sufficiently conserved (change slowly) •Sufficient length
Describe the features of the F factor (plasmid) and its role in conjugation
Conjugation is based on the presence of the conjugative plasmid •F plasmid (fertility factor) -best studied -F+ cells contain the plasmid : Donor cell -F- cells do not : Recipient cell -F factor is an episome: exist outside or be integrated into the bacterial chromosome
Describe strategies and structures that protozoa use to move?
Historically classified by motility: pseudopod, flagella, cilia, vectors (nonmotile apicomplexans) flagella; a slender threadlike structure, especially a microscopic whiplike appendage that enables many protozoa, bacteria, spermatozoa, etc., to swim. Pseudopods are temporary cytoplasmic projections of the cell membrane in certain unicellular protists such as amoeba Cillia: minute hairlike organelles, identical in structure to flagella, that line the surfaces of certain cells and beat in rhythmic waves, providing locomotion to ciliate protozoans The Apicomplexa (also called Apicomplexia) are a large phylum of parasitic protists. Most of them possess a unique form of organelle that comprises a type of plastid called an apicoplast, and an apical complex structure. The organelle is an adaptation that the apicomplexan applies in penetration of a host cell.Motile structures such as flagella or pseudopods are present only in certain gamete stages.
Define horizontal gene transfer and how does it differ from vertical gene transfer.
Horizontal gene transfer (HGT) is the movement of genetic material between unicellular and/or multicellular organisms other than via vertical transmission (the transmission of DNA from parent to offspring.) By contrast, vertical transfer occurs when an organism receives genetic material from its ancestor, e.g. its parent or a species from which it evolved.
List key characteristics of fungi? How do they differ from protist?
Include Yeasts, Molds, Mushrooms (fleshy fungi) Eukaryotic, spore-bearing, saprophytic; lack chlorophyll Important ecologically as decomposers •Many commercial uses -foods, drugs, organic acids The main difference between protista and fungi is that fungi need aerobic respiration to survive, whereas protists are able to live in an anaerobic environment without oxygen. Another difference between the two is that protists are always single-celled, but fungi can occasionally be multi-celled
What is the IJSTEM and what taxonomic function does it fulfil?
International Journal of Systematic and Evolutionary Microbiology (IJSEM) Formal recognition of a new prokaryotic species requires: -A descriptive genus names and species epithets following the binomial system of nomenclature used throughout biology -Deposition of a sample of the organism in two culture collections -Official publication of the new species name and description in the International Journal of Systematic and Evolutionary Microbiology (IJSEM)
List and describe the mechanisms of genetic exchange in bacteria
Mechanism of Genetic exchange: -Conjugation: cell-to- cell contact -Transduction: by bacteriophages -Transformation: from the environment •Collectively referred to as Horizontal gene transfer (HGT) •Genes transferred from one independent, mature organism to another mature organism
How do mushroom vegetative cells grow, colony terminology? How do yeast grow?
Molds/Mushroom ▪The fungal thallus consists of hyphae; a mass of hyphae is a mycelium (visible to unaided eye) ▪Identified by colony and spore characteristics ▪Reproduce through spore formation ▪Unicellular fungi ▪Fission yeasts: divide symmetrically ▪Budding yeasts divide asymmetrically ▪Identified by biochemical tests
How do fungi reproduce? Describe the role of spores in reproduction
Most fungi reproduce by asexual means (three forms) -Growth and spread of hyphal filaments -Asexual production of spores -Simple cell division (budding yeasts) •Some fungi produce spores as a result of sexual reproduction -Sexual spores can originate from the fusion of two haploid cells to form a diploid cell (ascospores, basidiospores, zygospores) -Spores are resistant to drying, heating, freezing, and chemicals
Define: Mycology, Mycologist, Mycoses and Mycotoxicology
Mycology: study of fungi Mycologists -scientists who study fungi Mycoses -diseases caused by fungi Mycotoxicology- study of fungal toxins and their effects
Give examples of key helminths and how they cause infection in humans.
Nematodes: Roundworms Include pinworms, whipworms, hookworms, heartworms Human infection divided into 2 categories: ●Egg infective ○roundworms, whipworms, pinworms ●Larva infective ○roundworms, heartworm, hookworms Tapeworms absorb nutrition through cuticle
What major phenotypic and genotypic properties are used to classify organisms in bacterial taxonomy?
Phenotypic analysis examines the morphological, metabolic, physiological, and chemical characters of the cell - Genotypic anaylsis: Multilocus sequence typing (MLST) -Method in which several different "housekeeping genes" from an organism are sequenced -Has sufficient resolving power to distinguish between very closely related strains Ribotyping •Method of identifying microbes from analyzing DNA fragments generated from restriction enzyme digestion of genes encoding SSU rRNA •Highly specific and rapid •Used in bacterial identification in clinical diagnostics and microbial analyses of food, water, and beverages
Which technique is used to amplify SSU rRNA gene sequence?
Polymerase chain reaction (PCR) is a technique used in molecular biology to amplify a single copy or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence
Describe the nutritional strategies used by protists? Define saprophytes, osmotrophy, holozoic, and mixotrophic nutritional strategies.
Protozoa are chemoheterotrophic protists -saprophytes -nutrients obtained from dead organic matter through enzymatic degradation -osmotrophy - absorb soluble products -holozoic nutrition - solid nutrients acquired by phagocytosis •Photoautotrophic protists - strict aerobes, use photosystems I and II for oxygenic photosynthesis •Mixotrophic protists -use organic and inorganic carbon compounds simultaneously
What strategies are employed by microorganisms to resist high temperature in their environment.
Stability of monomers -Protective effect of high concentration of cytoplasmic solutes -Use of more heat-stable proteins •Protein folding and thermostability -Increased hydrogen bonding contribute to the stability of proteins •Chaperonins -Class of proteins that refold partially denatured proteins •DNA stability -High intracellular levels of polyamines stabilize DNA and RNA -DNA-binding proteins (histones) compact DNA into nucleosome -like structures •Lipid stability -Possess dibiphytanyl tetraether type lipids; form a lipid monolayer membrane structure •SSU rRNA stability -Higher GC content
What are taxonomy, phylogeny and systematics?
Taxonomy is the field of biology that classifies living and extinct organisms according to a set of rules Phylogeny- the development or evolution of a particular group of organisms. ... the evolutionary history of a group of organisms, especially as depicted in a family tree Systematics- the study of the diversification of living forms, both past and present, and the relationships among living things through time.
What is the endosymbiotic hypothesis (SET) for the origin of mitochondria and chloroplasts? What evidence supports this hypothesis?
Two hypotheses exist to explain the formation of the eukaryotic cell: 1. Eukaryotes began as nucleus-bearing lineage that later acquired mitochondria and chloroplasts by endosymbiosis 2. Eukaryotic cell arose from intracellular association between O2 -consuming bacterium (the symbiont), which gave rise to mitochondria, and an archaeal host The first piece of evidence that needed to be found to support the endosymbiotic hypothesis was whether or not mitochondria and chloroplasts have their own DNA and if this DNA is similar to bacterial DNA. This was later proven to be true for DNA, RNA, ribosomes, chlorophyll (for chloroplasts), and protein synthesis