RANDOM NOTES:- archaea have ether linkages; while bacteria and eukarya have ESTHER linkages.- The phosphotransferase system is a type of group translocation. (Group translocation involves phosphoenolpyruvate)- The periplasm is located between the cytoplasmic membrane and the outer membrane in gram-negative bacteria- Pseudomurein is found in some Archaeal cell walls.- LPS layer is only found in gram-negative cells- Endotoxin is produced in the LPS layer of gram-negative cells.- Peritrichous flagella are found all over the bacterial cell, while lophotrichous bacteria are found as “tufts” on the ends of bacterial cells.- The membrane of the gas vesicle is composed of protein.- The tetraETHER molecule within the membrane structure of the ARCHAEAyields the lipid monolayer.Chapter 1Understand the characteristics, evolution, and habitat of microbes.• Microbes are the oldest forms of life. Microbes are also the largest mass of living material on Planet earth. • Microbes carry out major processes for biogeochemical cycles• Can live in places that are unsuitable for other organisms• Other life forms require microbes to survive.• THE CELL: forms the fundamental unit of life; cells have cytoplasmic membranes and bacteria have cell walls.- Microbes exhibit metabolism, reproduction, differentiation, communication (via pili and chemical signals), movement, and evolution.- Microorganisms exist in nature in populations of interacting assemblages of microbes called MICROBIAL COMMUNITIES. The environment in which a microbial population lives is known as its HABITAT. An ECOSYSTEM refers to all of the living and nonliving chemical constituents of a microbe’senvironment.- Microbial ecology is the study of microbes in the natural environment.- ******The Diversity and abundance of microbes are controlled by resources(nutrients) and environmental conditions (e.g., temperature, pH, and Oxygen availability)- Microbes also interact with their physical and chemical environments  they change their environments through their activities; they might remove nutrients from the environment or excrete wastes or perform bioremediationLUCA: The last universal common ancestor from which all cells descended.- The earth is about 4.6 billion years old- MICROBIAL CELLS APPEARED 3.8-3.9 BILLION YEARS AGO!- The earth was Anoxic until about 2 billion years ago. (Metabolisms were completely anaerobic until the evolution of oxygen-producing phototrophs occurred)- Most microbes are found in oceanic and terrestrial subsurfaces.- Microbial biomass is an important reservoir of essential nutrients such as carbon, phosphorus, and nitrogen.Be able to identify contributions of microbes to human activities.- Microbes can be both beneficial and harmful to humans.- Microbes are mostly beneficial!- Many aspects of agriculture rely on microorganisms; microorganisms perform nitrogen fixation so that plants can obtain nitrogen, they degrade cellulose in the rumen of ruminant animals; and they regenerate nutrients in soil and water.- NEGATIVE: they can spoil food and cause animal and plant diseases.- However, we still rely on bacteria and other microorganisms such as yeasts and live active cultures to produce cheese, yogurt, sauerkraut, pickles, certain breads, and BEER- Microorganisms can produce BIOFUELS.  Many microbes can produce methane, ethanol, and hydrogen, which are all useful energy sources for humans.- We exploit microorganisms to produce mass quantities of antibiotics,enzymes, and various chemicals.- We can genetically engineer microbes to generate products that are valuable to humans, such as insulin (this is called biotechnology)- Applied microbiology  clinical medicine; research and development!Understand the contributions of Leeuwenhoek, Pasteur, and Koch to microbiology.Antoni van Leeuwenhoek: Leeuwenhoek was the first to describe bacteria; he invented his own small little microscope and was able to see microbes in his own stool sample when he was sick. We now believe that he was looking at his own giardia.Louis Pasteur: ***most importantly defeated the theory of spontaneous generation.- DISPROVED THE THEORY of spontaneous generation  which led to methods for aseptic technique.- Louis Pasteur also developed vaccines for anthrax, foul cholera, and rabies.- Sterilized a flask full of culture media with microbes by boiling it  showed that then no microbes grew  then he dipped the flask over so it touched the contaminated neck park  then he showed that microbes could grow in the media again  defeated spontaneous generation!!Robert Koch: Infectious Disease, and the Rise of Pure cultures- Demonstrated the link between microbes and infectious diseases by formulating his Four Postulates- *****Identified causative agents of anthrax, and tuberculosis.- Koch studied tuberculosis- Koch developed techniques (solid media) for obtaining PURE CULTURES.- Koch was the father of medical microbiology.- Koch developed pure cultures!! And was the first to use solid media!!! (his wife helped him decide to use agar)- Koch discovered that using solid media provided a simple way to obtain pureculturesKoch’s Four Postulates: helped determine that certain microbes caused infectious diseaseChapter 2Understand the basic features of microscopy.• With a microscope, there are TWO SETS OF LENSES that form the image: there is an ocular lens and an objective lens. There is also a condenser lens within the microscope that helps concentrate light on the object of interest.• BRIGHT FIELD SCOPE: images are visible due to a difference in contrast(density) between specimens and their backgrounds.• Resolution defines how much we can see with a given microscope. Resolution is the ability to distinguish two adjacent objects as separate and distinct.• Staining improves contrast. Dyes bind to specific cellular materials in specimens.• Improving Contrast in Light Microscopy: Differential stains such as the gramstain!!!!- Gram stains separate gram-negative bacteria from gram-positive bacteria.Phase-contrast and Dark-Field microscopy allow us to see live samples. Neither of these requires stains. Dark-field is excellent for observing motility.Fluorescence Microscopy: Utilizes fluorescent dyes, or is used to visualize specimens that fluoresce. Differential Interference Contrast Microscopy: (DIC) gives structures such as endospores, vacuoles, and granules a three-dimensional appearance.  gives a