Compound microscopes are light illuminated. The images are 2D. It is the most common microscope. They cost between 150-10,000 dollars. The source of radiation for the image formation is visible light. The medium is air. The specimen are mounted on glass slides. The lenses are glass. The focusing are mechanical. The magnification is adjusted by changing objectives. The specimen contrast is provided by light absorption.

Dissection microscopes are light illuminated. The images are 3D. It is used to look at large specimen. They cost between 100-1500 dollars. The source of radiation for the image formation is visible light. The medium is air. The specimen are not mounted. The lenses are glass. The focusing are mechanical. There is only one objective. The specimen contrast is provided by light scattering or light reflection.

Confocal microscopes use laser light. They cost between 20,000-100,000 dollars. The source of radiation for the image formation is laser light. The medium is air. The specimen are mounted on glass slides with dyed samples. The lenses are glass with dichromatic mirrors. The focusing is a digital computer focusing mechanism. The magnification is adjusted digitally enhancing. The specimen contrast is provided by laser light with dichromatic mirror concentrated at pinhole.

Scanning Electron Microscope use electron illumination. The image is 3D. They cost more than 50,000 dollars. The source of radiation for the image formation is electrons. The medium is vacuum. The specimen are mounted on aluminum stubs and coated with gold. There is one electrostatic lens with a few electromagnetic lenses. The focusing are electrical. The magnification is adjusted electrically. The specimen contrast is provided by electron scattering.

Transmission Electron Microscope are electron illuminated. The image is 2D. They cost more than 50,000 dollars. The source of radiation for the image formation is electrons. The medium is vacuum. The specimen are mounted on films of collodion. There is one electrostatic lens with a few electromagnetic lenses. The focusing are electrical. The magnification is adjusted electrically. The specimen contrast is provided by electron scattering.

Gram negative bacteria cells, unlike gram positive cells, cell walls consist mostly of outer membrane, not peptidoglycan, which is responsible for the strength of the cell. It’s like a second lipid bilayer but composed of lipid and polysaccharide, instead of protein and phospholipid. It’ made of one layer of lipopolysaccharide layer or LPS and the other is peptidoglycan. The polysaccharide in the lipopolysaccharide is made from O- specific polysaccharide and core polysaccharide. A unique characteristic of the lipopolysaccharide is its toxicity to animals. The lipid portion of the LPS layer is made of Lipid A, which contains an endotoxin that is responsible for its toxicity to animals. Another unique characteristic of the LPS layer in gram negative bacteria would be that the LPS acts like an anchor and types peptidoglycan to itself, creating a bilayer distinct from the cytoplasmic membrane. Between the cytoplasmic membrane and the outer membrane, is the periplasm. This space is filled with fluid that has a gel- like consistency due to all the proteins located there. Its purpose it to make sure that proteins that have activities outside the membrane do not diffuse away. The outer membrane is semipermeable to small molecules due to the presence of porins. It will not let in large molecules and proteins. Microbiologists are able to differentiate between gram positive cells and gram negative cells due to gram staining. Due to the structure of gram negative bacteria cell walls, it does not retain the purple color of the crystal violet iodine complex that forms in the cell, due to it being able to be extracted by alcohol. Thus it has to be counterstained with safranin, and appears pink. The thin layer of peptidoglycan is responsible for this occurrence.

Precursor Metabolites (Intermediates)-

• Glycolysis
  • Glucose 6-Phosphate
    • Results from glucose being phosphorylated by ATP
  • Fructose 6-phophate
    • Results from Glucose 6- P being isomerized
  • Fructose 1,6- Phosphate
    • Results from Fructose 6- P being phosphorylated
  • Glyceraldehyde 3-phophate and dihydroxyacetone phosphate
    • Results from the enzyme aldose splitting fructose 1,6- bisphosphoglyceric acid
  • 1,3- Biphosphoglycerate
    • Results from the oxidation of glyceraldehyde 3- phosphate
  • 3-P-Glycerate
    • ATP synthesized when 1,3- Bisphosphoglyceric acid is converted to 3-phosphoglyceric acid
    • Glycine and Cysteine amino acids
  • Citric acid cycle intermediates
    • α- ketoglutarate and Oxaloacetate are precursors of amino acids
      • Proline, Glutamine, and Arginine
    • Oxaloacetate
      • also a precursor to phosphoenolpyruvate, precursor of glucose
      • Asparagine, Lysine, Methionine, Threonine, Isoleucine
    • Succinyl-CoA
      • Precursor of cytochromes and chlorophyll
    • Acetyl-CoA
      • Precursor of fatty acid biosynthesis
    • Glyoxylate cycle
      • Glyoxylate intermediate
    • Adenosine diphosphoglucose
      • Precursor for glucose biosynthesis
    • Uridine diphosphoglucose
      • Precursor of some glucose derivatives needed for biosynthesis of polysaccharides

Central Metabolism–

• All organisms conserve energy from the oxidation of chemicals or light
• Catabolism- Energy-yielding reactions
• Anabolism-the synthesis of complex molecules from simpler ones during which energy is added as input
• Glycolysis to Pyruvate
  • Stage 1
    • Glucose is phosphorylated by ATP, yielding glucose 6-phosphate
    • Glucose 6-Phosphate is isomerized to fructose 6-phosphate
    • Second phosphorylation produces fructose 1,6-biphosphate
  • Stage 2
    • Glyceraldehyde 3-phosphate oxidized to 1,3- bisphosphoglyceric acid, first redox reaction(occurs twice)
    • Glyceraldehyde-3-phosphate dehydrogenase reduces its coenzyme NAD⁺ to NADH
    • Glyceraldehyde 3-phosphate is phosphorylated by adding inorganic phosphate
  • Stage 3
    • During formation of two 1,3- bisphosphoglyceric acid molecules, two NAD⁺ reduced to NADH
    • NADH must be oxidized back to NAD⁺ for another round of glycolysis to occur
    • Reduction of pyruvate by NADH, re-oxidizes NADH back to NAD⁺
  • Fermentations
    • Classified by substrate fermented or products formed
    • All generate ATP by substrate level phosphorylation
    • Fermentations allow for additional ATP to be produced in addition to the 2 ATP in glycolysis
      • Occurs when product is a fatty acid, formed from coenzyme-A precursor molecule
    • Fermentation products are waste to some organisms and beneficial to others
      • For humans, fermentation products provide the foundation for makings food
  • Proton Motive Force
    • Results from the release of protons outside the cell causing a pH gradient and electrochemical potential across the membrane
    • Complex I
      • NADH transfers electrons to FAD
      • FADH donates electrons to Quinone
    • Complex II
      • Bypasses Complex I
      • Transfers electrons directly from FADH directly to Quinone pool
    • Complex III
      • Transfers electrons from Quinone to cytochrome c
      • Cytochrome c shuttles electrons to cytochromes a and a₃
    • Complex IV
      • Reduces O₂ to H₂O
    • ATP Synthase converts proton motive force into ATP
      • F₁ multiprotein complex- Responsible ATP synthesis
      • F_o proton- Responsible for ion translocation
    • Citric Acid Cycle
      • Oxaloacetate can be made from C₃ compounds by the addition of CO₂
      • Acetyl-CoA condenses with oxaloacetate to produce citrate
      • Citrate is then converted back to oxaloacetate, which then allows for another cycle with addition of the next molecule of acetyl-CoA
      • No CO₂ is released from succinate to oxaloacetate
    • Glycolysis and Citric Acid Cycle combine to produce a total of 38 ATP in aerobic respiration

Importance of Redox Reactions-

• Redox Reactions are reactions that release sufficient energy to form ATP. They are the sole provider of energy on the planet.
• Must occur in pairs or reaction will not succeed.
  • Oxidation- removal of electrons from a substance
  • Reduction- addition of an electron to a substance
• Electron donor is the substance oxidized
  • Energy sources
  • Consists of organic and inorganic compounds
• Electron acceptor is the substance reduced
• Electron donor is the substance oxidized
• Reduction potential defined as E₀’, measured in volts
• In microbial cells reactions are mediated by small molecules
  • NAD⁺ /NADH is an electron plus proton carrier
    • Transports 2 electrons and 2 hydrogens at the same time
    • NADH is a good electron donor
    • NAD⁺ is a weak electron acceptor
    • Coenzymes such as these enhance diversity of redox reactions possible in a cell by allowing chemically dissimilar electron donors and acceptors to interact

Redox tower–

• Enables us to see electron transfer reactions in a convenient way
• Range of reduction potentials possible for redox couples in nature
  • Most negative E₀’ at top
    • Reduced
    • Greatest tendency to donate electrons
  • Most positive E₀’ at bottom
    • Oxidized substances
    • Greatest tendency to accept electrons
    • O₂ is the strongest electron acceptor
  • Difference in reduction potentials between donor and acceptor is quantified as Delta E₀’
    • Greater the difference the more energy released
  • _{Delta E0}’ is proportional to Delta G’
  • Electrons can be caught by acceptors at any intermediate level as long as the donor couple is more negative than the acceptor couple
  •                                                              

Bacterial pathogenesis is, on a fundamental level, the growth of bacteria that causes disease. Infections depend on several virulence factors that help the bacteria invade the host, evade host immune responses, and cause disease. Some significant virulence factors include adherence factors, invasion factors, capsules, endotoxins, and exotoxins.

Antibiotics are drugs used in treating and preventing bacterial infections. Although the mechanisms of action of antibiotics are varied, many antibacterial treatment regimens include the use of combinations of these antibiotics for maximum effect. Of note, most antibiotics are highly specific to bacteria and cannot be used against viruses. Additionally, the evolution and mutation of bacterial strains to resist antibiotics is a rising concern in modern medicine. Due to the rapid generational growth rate and evolution of bacteria as well as the development of modern medicine, epidemiology of infections are constantly changing. It is important to note that epidemiology of a particular species is relative to its environmental preferences and needs.

1) Loker, E. S., & Hofkin, B. V. (2015). Parasitology: a conceptual approach. New York: Garland Science.

2) Madigan, M. T., & Brock, T. D. (2012). Brock biology of microorganisms. Boston: Benjamin Cummings.

Immunology – Figure 1.
http://www.biology.arizona.edu/immunology/tutorials/immunology/page3.html

Biosynthesis-

• Glucogenesis
  • Synthesis of glucose from phosphoenolpyruvate
    • Phosphenolpyruvate can be synthesized from oxaloacetate
  • Pentose Phosphate Pathway
  • Amino acid biosynthesis
    • Carbon skeletons from glycolysis/citric acid cycle
    • Ammonia is incorporated by glutamine dehydrogenase
    • Ammonia group transferred by transaminase and synthase
  • Purine and Pyrimidine biosynthesis
    • PRPP( 5-Phosphoribosyl-1-Pyrophosphate)
      • Important precursor in synthesis of purines, pyrimidines, and amino acids
      • Made from ribose-5-phophate
      • Provides phosphoribose subunit for purines/pyrimidines
    • Purines
      • PRPP precursor for Inosine-5’-monophosphate (IMP)
        • IMP precursor for nucleotides adenosine and guanosine
      • IMP
        • Produces
          • GMP,GDP,GTP
          • AMP, ADP, ATP
        • Pyrimidines
          • Carbonyl Phosphate produced from glutamate, bicarbonate, and ATP
          • L-Aspartate and carbonyl phosphate join to produce N- Carbonyl- L- Aspartate
          • Dihydroorotate reacts with PRPP to form UMP
            • PRPP adds phosphoribose unit
          • Fatty acid Biosynthesis
            • Synthesize two carbons at a time by acyl carrier protein (ACP)
            • C₂ subunit originates from 3-carbon compound malonate which is attached to form malonyl-ACP
            • Unsaturated fatty acids
              • One or more double bonds in hydrophobic portion of molecule
              • Number of double bonds species/group specific
            • Branched Fatty acids
              • Synthesized using branched –chain initiating molecule
              • Odd carbon number fatty acids
            • Lipid biosynthesis
              • Fatty acids added to glycerol first
              • Simple triglycerides
                • All glycerol carbons are esterified with fatty acids
              • Complex lipids
                • One carbon atom paired with polar substance
              • In archaea lipids constructed from isoprene
                • Forms phytanyl or biphytanyl
              • Glycerol backbone of archaea contains also contains a polar group
            • Nitrogen Fixation
              • The ability to fix nitrogen frees an organism form dependence on fixed nitrogen in its environment and confers significant ecological advantage when fixed nitrogen is limiting.
              • Certain species of Baceria and Archaea can fix bacteria
                • Bacteria can be “free-living”, e.g. cyanobacteria, and dinitrogenase reductase are nitrogen fixing
              • Iron-molybdenum cofactor
                • Composed of iron and molybdenum in dinitrogenase
                • Reduction on nitrogen occurs at this site
              • Nitrogen is inhibited by O₂ because dinitrogenase reductase is irreversibly inactivated by O₂.
              • Obligate aerobes
                • Nitrogenase is protected from oxygen inactivation by a combination of the rapid removal of O₂ by respiration and the production of O₂-retarding slime layers
              • Heterocyst Cyanobacteria
                • Nitrogenase is protected from oxygen by its localization in a differentiated cell because the conditions are anoxic
              • Electron Flow
                • Elecctron donordinitrogenase reductase dinitrogenase N₂
                • 6 electrons are needed to reduce N₂ to NH₃
                  • 8 electrons are actually consumed in the process
                    • 2 electrons are lost as H₂ for each mole of N₂ reduced
                  • Reducing N₂
                    • Pyruvate donates electrons to Flavodoxin
                    • Flavodoxin reduces dinitrogenase reductase
                    • Electrons transferred to dinitrogenase one at a time. 2 ATP are consumed per electron

When some bacteria organisms sense that nutrients in its environment are low, they start to make structures called endospores through a process called the sporulation cycle. A single bacterial cell will make one endospore inside itself when nutrient sources are low, or if the cell is starving, and release it when the cell undergoes autolysis. Endospores are highly differentiated cells that are resistant to heat, chemicals, and radiation. They can survive in a dormant state until optimal growth conditions occur. This survival is due to its unique cellular structure. This unique structure is what differentiates endospores from vegetative cells. First, endospores have a core, also known as a protoplast. The core contains the spore chromosomal DNA, calcium dipicolinate, ribosomes, and other enzymes but it is not metabolically active. The calcium dipicolinate is thought to protects DNA and help make the call heat resistant. It also makes up 20% of the cell’s dry weight. Small Acid Soluble Proteins (SASPs) are also partly responsible for resistance in endospores. It protects from UV radiation chemicals that damage DNA. Next is the spore wall. It is the innermost layer surrounding to the spore and contains peptidoglycan. During vegetation it becomes the cell wall of the bacteria. After the spore wall comes the cortex. This also contains peptidoglycan and is the thickest layer of the endospore. Lastly is the coat. It is this layer that is the cause for impermeability of the endospore. When the endospore is ready to become an active bacterial cell it undergoes a process called germination. To become a vegetative cell, it must first undergo activation. During this step of germination, metabolic processes start and the spore coat is ruptured or absorbed. Next is the initiation of germination, which only happens if environmental conditions are favorable. The cortex of peptidoglycan will undergo autolysis and water will be taken up. The last step in germination is outgrowth. During this phase the cell will be able to start multiplying again.

What is microbiology and why is it important? First we need to know that microbiology is the study of microorganisms and how they work. Microbiology is about how microorganisms impact the environment, agriculture, medicine, where they live and how they arose and why. There are two main themes that microbiology center around. They are understanding microorganism’s nature and how they work and applying that understanding to benefit mankind and Earth.
Studying microorganisms showed us that cells have a lot in common and helped microbiologists understand the fundamental processes of life. This explains microbiology as a basic biological science. Microbiology as an applied biological science is integral to many aspects of human life. Microorganisms are active in agriculture, human and veterinary medicine, biofuels, and so many more. Microorganisms are the most diverse and abundant form of life on the planet, even though they are the smallest, and predate humans by billions of years. Without microbial activity human and plant life would not be possible. It was cyanobacteria, a microorganism, that started producing oxygen as waste and made earth habitable for more complex organisms. Microorganisms are also responsible for recycling and degrading material needed for human survival.
So, what is microbiology and why is it important? Microbiology is the study of microorganisms and how they effect humans and the environment It also studies how they work, where they live, and how they function. It’s important because it effects humans and the earth in so many ways. Microorganisms are integral in veterinary and human medicine, agriculture, the status of the environment, and human and animal life as we know it. Without microorganisms there would be no animal or plant life, so be grateful for the little guys!