Chapter 2

• Cell


  The basic unit of all living organisms, many of which are unicellular, whereas others are multicellular forms, enabling cell specialization
• Prokaryotic cells


  Archaeans and eubacteria
• Eukaryotic cells


  Cells of fungi, protozoa, algae and other plants, and animal
• Prokaryotic cells


  • Normally less than 5µm in diameter
  • Single chromosome (DNA), circular or linear, in the nucleoid
  • Have cell walls or cell envelopes located outside the cytoplasmic membrane, which usually contain some peptidoglycan
  • Capsules or slime coats and propelling flagellae that are less complex than those of eukaryotic cells
  • Cell division in prokaryotes is normally by simple binary fission
• Eukaryotic cells


  • Generally larger than those of prokaryotes
  • Contain a range of membrane-bound organelles
  • Several linear chromosomes (DNA) in histone proteins and is housed in a double membrane bound nucleus
  • Eukaryotic cells divide by a complex process of mitosis and usually have a sexual lifecycle, involving meiosis
• The genome of Methanococcus jannaschii has been sequenced and found to contain 1760 genes composed of 1700 kilobase pairs (kbp)
• Subgroups of Eubacteria


  • Gram Negative Eubacteria
  • Gram Positive Eubacteria
• Gram Negative Eubacteria


  • Proteobacteria is a major kingdom that includes purple photosynthetic bacteria and non-photosynthetic bacteria
  • Enterobacteriaceae (e.g. Escherichia coli), along with Hyphomicrobium, Nitrobacter, Pseudomonas, Thiobacillus and Vibrio
• Gram Positive Eubacteria


  • Low G + C group- includes Bacillus, Clostridium, Lactobacillus, Leuconostoc, Staphylococcus, Streptococcus and Mycoplasma
  • High G + C group, which contains the actinomycetes (filamentous bacteria, e.g. Streptomyces), Corynebacterium, Mycobacterium and Micrococcus
• Escherichia coli (E. coli)

  • A Gram-negative bacterium discovered in 1885 by Theodor Escherich
  • Found in the colon of humans and the lower gut of other warm-blooded animals
  • Gram-negative facultative anaerobe, belonging to the family Enterobacteriaceae
  • 0.3–1.0mm wide and 1.0–3.0mm long
  • Oxidase-negative (lacking cytochrome c oxidase)
• Outer Membrane of a Gram Negative Bacterium


  • 7–8nm thick
  • Composed of lipopolysaccharide and mucopeptide
  • More permeable than the cytoplasmic membrane
  • Contains porin proteins that form narrow channels of about 1–2nm diameter through which small molecules can pass
  • Lipopolysaccharide is effective in protecting the cell from detergents and other antimicrobial agents
  • Braun's lipoprotein is the most common and extends through the outer membrane and links to the underlying peptidoglycan
  • Capsule is composed of polysaccharides and is influenced by chemical and physical conditions, providing a barrier to certain molecules, desiccation, or aiding attachment
• Peptidoglycan and the Periplasmic space

  • Covalently attached to the outer membrane through lipoprotein, is a thin layer of peptidoglycan some 2–3nm thick
  • Comprises 5–10% of the cell envelope and is composed of one to three layers
  • Periplasmic space is 12–15nm wide and contains a range of proteins, binding proteins, chemoreceptors and various enzymes
  • Binding proteins initiate transport of specific substances into the cell by taking them to their membrane-bound carriers
  • Chemoreceptors are involved in chemotaxis, the movement of a cell towards attractant and away from repellant chemicals
  • Hydrolytic enzymes, nucleases and proteases, are secreted into the periplasm from the cytoplasm to break chemical bonds and divide large molecules into smaller molecules
• Peptidoglycan


  • Prevents the bursting of the bacterial cell
  • Serves as the backbone which provides strength and mechanical rigidity to the bacterial cell through cross-linking
  • Maintains the morphology and the form of the bacterial cell during its life cycle
  • Takes part in bacterial cell division by binary fission
• Cytoplasmic Membrane


  • Lies below the periplasmic space and encloses the cytoplasmic matrix
  • Highly selective, controlling the entry of nutrients and the secretion of ions and larger compounds
  • Lipid bilayer, primarily composed of phosphatidyl ethanolamine
  • Contains transport proteins and pores made up of porins that selectively control the entry of molecules and charged ions into cells
• Cytoplasmic Matrix and Cell Contents

  • Maintained at pH 7.6–7.8, with differences between the intracellular and extracellular pH being controlled by the primary proton pumps associated with electron transport and respiration
  • Contains machinery for protein synthesis, both transcription and translation
  • RNA polymerases for transcribing the genetic code of DNA into messenger RNA (mRNA) with 18000 ribosomes and tRNAs
  • 10% of cell's volume, 4600 kbp, 4000 genes
  • Plasmids are circular extrachromosomal DNA molecules
• Bacillus subtilis


  • A Gram-positive bacterium
  • Rod-shaped, chemoheterotrophic
  • 0.5–2.5mm wide and 1.2–10mm long
  • Some species are strictly aerobic, others are facultative anaerobes or microaerophilic
  • Can produce oval or cylindrical endospores resistant to adverse environmental conditions and provide a selective advantage for survival and dissemination
  • A common soil microorganism that is often recovered from water, air and decomposing plant residues
  • No disease traits, unlike B. anthracis
  • Produces extracellular enzymes that contribute to nutrient cycling
• Endospore


  A dormant, tough, and non-reproductive structure produced by certain bacteria from the Bacillota phylum
• Enzymes of Bacillus subtilis

  • Amylases and proteases
• Fungi


  • A diverse group of eukaryotic microorganisms that occupy a variety of habitats
  • Composed of filamentous hyphae and are often referred to as moulds, whereas the yeasts are unicellular fungi
  • Relatively few filamentous fungi are used for industrial purposes
  • Chemoheterotrophic absorptive nutrition- hydrolytic enzymes that degrade complex molecules into smaller units
  • Form symbiotic and mutualistic relationships with other organisms
  • Individual hyphae are 1–15mm in diameter depending upon the species
  • Originate from either fragments of hyphae or dispersed spores that germinate under suitable environmental conditions
  • Hyphae can grow rapidly in length, at rates of up to several micrometres per minute, but there is generally little increase in girth
• Yeast


  • Unicellular phase, such as baking or brewing yeasts
  • Member of the ascomycetes and are facultative anaerobes
  • Heterotrophic and are found in a wide range of natural habitats
  • C. albicans can become a serious opportunistic pathogen
• Microbial Nutrition - The biosynthesis of cellular components necessary for growth, reproduction and maintenance requires a supply of basic nutrients
• Fungi


  • Degrade complex molecules into smaller units
  • Form symbiotic and mutualistic relationships with other organisms
• Hyphae


  Individual hyphae are 1–15mm in diameter depending upon the species
• Hyphae originate


  From either fragments of hyphae or dispersed spores that germinate under suitable environmental conditions
• Hyphae


  • Can grow rapidly in length, at rates of up to several micrometres per minute
  • There is generally little increase in girth
• Yeast


  • Unicellular phase, such as baking or brewing yeasts
  • Member of the ascomycetes and are e facultative anaerobes
  • Heterotrophic and are found in a wide range of natural habitats
• C. albicans can become a serious opportunistic pathogen
• Microbial Nutrition


  The biosynthesis of cellular components necessary for growth, reproduction and maintenance requires a supply of basic nutrients and an energy source
• Nutritional classification based on specific sources of energy, electrons/hydrogen and carbon

  • Chemotrophs- oxidation of organic or inorganic compounds
  • Phototrophs use energy derived from light
• Composition of Microorganisms - Macronutrients

  • Carbon
  • Hydrogen
  • Oxygen
  • Nitrogen
  • Phosphorus
  • Sulphur
• Composition of Microorganisms - Minor elements

  • Calcium
  • Iron
  • Potassium
  • Magnesium
• Composition of Microorganisms - Trace elements

  • Cobalt
  • Copper
  • Manganese
  • Molybdenum
  • Nickel
  • Selenium
  • Zinc
• Autotrophic fermentations that utilize CO2 are rarely operated on an industrial scale: almost all involve heterotrophic growth
• Heterotrophic fermentations


  • Carbon sources (sugars) are required at relatively high media concentrations, often around 10–20g/L or greater
  • Hydrogen and oxygen can be obtained from water and organic compounds
  • Nitrogen source is normally supplied in growth media at concentrations of 1–2g/L
• Phosphorus


  Generally provided as inorganic phosphate ions, often as a pH buffer (not greater than 100mg/L)
• Sulphur


  Often supplied as an inorganic sulphate or sulphide salt at a concentration of 20–30mg/L
• Trace elements


  Usually required at concentrations of 0.1–1mg/L, or less, for a number of specific enzymes
• Microorganisms


  • Prototrophs – Minimal medium, merely containing carbon and energy sources, and basic mineral elements
  • Auxotrophs - unable to grow without additional organic substances, such as amino acids or vitamins
• Nutrient Uptake


  • Nutrients from the environment must be transported across the cell membrane into the cell
  • This is often the rate-limiting step in the conversion of raw materials to products and therefore is of major importance to industrial fermentation process
• Passive Diffusion


  • An inefficient mechanism, as the rate of uptake is dependent on the magnitude of the concentration gradient across the membrane
  • The process in which molecules move from a region of higher concentration to one of lower concentration because of random thermal agitation