Bacterial Growth and Fermentation
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Questions and Answers

What is the term for the total of all biochemical reactions occurring inside the cell for survival and reproduction?

  • Fermentation
  • Anabolism
  • Catabolism
  • Metabolism (correct)

    • What type of transport involves the use of energy to bring in nutrients?

  • Iron uptake
  • Active transport (correct)
  • Passive transport
  • Siderophores

    • What is the process by which bacteria take in nutrients using a gradient?

  • Active transport
  • Passive transport (correct)
  • Siderophores
  • Iron uptake

    • What is the term for the breakdown of nutrients to produce energy?

    <p>Catabolism</p> Signup and view all the answers

    What is the term for the synthesis of new molecules using energy?

    <p>Anabolism</p> Signup and view all the answers

    What is the term for the process of growing bacteria in the laboratory?

    <p>Culture</p> Signup and view all the answers

    What is the term for the process by which bacteria produce energy in the absence of oxygen?

    <p>Anaerobic respiration</p> Signup and view all the answers

    What is the term for the process by which bacteria convert glucose into lactic acid?

    <p>Fermentation</p> Signup and view all the answers

    What type of fermentation occurs in muscles?

    <p>Lactic acid fermentation</p> Signup and view all the answers

    What is the primary mechanism of bacterial growth and replication?

    <p>Binary fission</p> Signup and view all the answers

    What is the optimal temperature range for most bacteria?

    <p>37°C - 121°C</p> Signup and view all the answers

    What type of bacteria require oxygen for growth?

    <p>Strict aerobes</p> Signup and view all the answers

    What is the purpose of additives in culture media?

    <p>To enrich the growth of certain bacteria</p> Signup and view all the answers

    What is the characteristic of defined culture media?

    <p>Exact composition is known</p> Signup and view all the answers

    What is the primary source of energy for bacterial growth?

    <p>Cellular respiration</p> Signup and view all the answers

    What is the term for bacteria that grow optimally in the absence of oxygen?

    <p>Strict anaerobes</p> Signup and view all the answers

    What is the primary advantage of using solid media for growing bacteria in the lab?

    <p>Allows for the isolation of single colonies</p> Signup and view all the answers

    Which of the following methods is used to quantify bacteria in the lab?

    <p>Cell counting under a microscope</p> Signup and view all the answers

    What is the typical wavelength used to measure optical density in the lab?

    <p>600 nm</p> Signup and view all the answers

    Which of the following media types is suitable for microaerophilic bacteria?

    <p>Semi-solid</p> Signup and view all the answers

    What is the purpose of serial dilution and plating on agar in bacterial quantification?

    <p>To determine colony-forming units</p> Signup and view all the answers

    What type of quantification can be achieved using qPCR?

    <p>Both relative and absolute quantification</p> Signup and view all the answers

    Which part of the gut has few viable bacteria due to its high acidity?

    <p>Stomach</p> Signup and view all the answers

    What is one of the functions of the gut microbiota?

    <p>Preventing pathogens from colonizing</p> Signup and view all the answers

    What happens to the oral microbiota after tooth eruption?

    <p>It increases in anaerobes</p> Signup and view all the answers

    What is one of the effects of the oral microbiota on human physiology?

    <p>Alteration of taste perception</p> Signup and view all the answers

    Which of the following is a characteristic of the large intestine?

    <p>Huge diversity of bacteria</p> Signup and view all the answers

    What is the relationship between the gut microbiota and pathogens?

    <p>The gut microbiota prevents pathogens from colonizing</p> Signup and view all the answers

    What is the role of the gut microbiota in nutrient absorption?

    <p>It aids in the absorption of nutrients</p> Signup and view all the answers

    What is the relevance of the study by Vanhatalo et al. to the oral microbiota?

    <p>It showed the oral microbiota affects blood pressure</p> Signup and view all the answers

    What is one of the main functions of the microbiome?

    <p>To protect the host against pathogens</p> Signup and view all the answers

    What is a characteristic of the microbiome composition?

    <p>It has huge diversity in composition</p> Signup and view all the answers

    What is a challenge in studying the microbiome?

    <p>Some members are culturable, but most cannot be cultured</p> Signup and view all the answers

    What is the significance of the 16S ribosomal RNA?

    <p>It is a highly-conserved gene between bacteria and archaea</p> Signup and view all the answers

    What is shotgun metagenomics?

    <p>The sequencing of every nucleic acid within a given sample</p> Signup and view all the answers

    When is the microbiome typically acquired?

    <p>In the first year of life</p> Signup and view all the answers

    What is a term used to describe the healthy balance of microorganisms in the body?

    <p>Homeostasis</p> Signup and view all the answers

    What is an example of a condition caused by microbiome dysbiosis?

    <p>All of the above</p> Signup and view all the answers

    What was the finding in the study comparing germ-free and conventional mice?

    <p>Germ-free mice could eat more and gain less weight than conventional mice.</p> Signup and view all the answers

    What is the term used to describe the collective microorganisms that live within and on the human body?

    <p>Microbiome</p> Signup and view all the answers

    What is a characteristic of the human microbiome?

    <p>It is diverse across the human body.</p> Signup and view all the answers

    What is the term for the state of infection where both the host and microbe benefit?

    <p>Symbiosis</p> Signup and view all the answers

    What is the term used to describe an organism that consists of a host and its associated microorganisms?

    <p>Holobiont</p> Signup and view all the answers

    What is an example of a disease that has been linked to dysbiosis of the microbiome?

    <p>All of the above</p> Signup and view all the answers

    What is the term for the acquisition of micro-organisms by the host?

    <p>Infection/Colonization</p> Signup and view all the answers

    What is the composition of the human body in terms of microbial and human cells?

    <p>10^14 microbial cells and 10^13 human cells</p> Signup and view all the answers

    What is the role of the microbiome in regulating fat storage?

    <p>It regulates fat storage as an environmental factor.</p> Signup and view all the answers

    What is the term for the 'normal' microbes present on the skin and in the oral, respiratory, and gastrointestinal tracts?

    <p>Commensals</p> Signup and view all the answers

    Why do humans need their microbiome?

    <p>To protect against foreign substances and pathogens</p> Signup and view all the answers

    What is the term for the combination of the host and microbiome?

    <p>Holobiont</p> Signup and view all the answers

    Where are commensal microorganisms typically found in the human body?

    <p>Skin and oral, respiratory, and gastrointestinal tracts</p> Signup and view all the answers

    What is the result of commensalism on the host?

    <p>No damage to the host</p> Signup and view all the answers

    What can metagenomics be used for?

    <p>Insights into population dynamics</p> Signup and view all the answers

    What is a characteristic of the skin microbiota?

    <p>Slightly acidic, high salt, low water content and inhibitory substances</p> Signup and view all the answers

    What is a function of bacteria on superficial skin?

    <p>Partially degrading skin oil to volatile fatty acids</p> Signup and view all the answers

    What is the result of bacteria partially degrading skin oil on superficial skin?

    <p>Body odour</p> Signup and view all the answers

    What can metagenomics be used to characterise?

    <p>The community</p> Signup and view all the answers

    What can be identified using metagenomics?

    <p>Subtyping, AMR genes, and virulence genes</p> Signup and view all the answers

    What is the mechanism used by Streptococci to evade the host's immune system?

    <p>Coating with host protein called plasmin</p> Signup and view all the answers

    What characterizes an acute infection?

    <p>Sudden onset, rapid progression, and often severe systemic symptoms</p> Signup and view all the answers

    What is an example of a virulence factor?

    <p>All of the above</p> Signup and view all the answers

    What is the term for the magnitude of harm caused by a pathogen?

    <p>Virulence</p> Signup and view all the answers

    What type of toxin is typically produced by Gram-positive bacteria?

    <p>Exotoxin</p> Signup and view all the answers

    What is an example of a long-term 'co-existence and subversion' infection?

    <p>Tuberculosis</p> Signup and view all the answers

    What is the first step in the infective process?

    <p>Adherence</p> Signup and view all the answers

    What is the term for the entry of pathogens into the bloodstream?

    <p>Bacteremia</p> Signup and view all the answers

    What is the purpose of capsules in pathogen survival?

    <p>To hide from the host immune system</p> Signup and view all the answers

    What is the term for the process of inhibiting phagocytosis?

    <p>Evasion</p> Signup and view all the answers

    Which of the following is an example of camouflage or molecular 'mimicry'?

    <p>Coating with host macromolecules</p> Signup and view all the answers

    What is the purpose of adhesins in pathogen adherence?

    <p>To facilitate adherence to host cells</p> Signup and view all the answers

    What is the term for the infection disease in the blood?

    <p>Septicemia</p> Signup and view all the answers

    What is the mechanism used by pathogens to actively penetrate the mucous membrane or epithelium?

    <p>Enzyme production</p> Signup and view all the answers

    What is a characteristic of opportunistic pathogens?

    <p>They are typically members of the normal microbial flora</p> Signup and view all the answers

    What is the ID50?

    <p>The number of micro-organisms required to cause disease in 50% of inoculated hosts</p> Signup and view all the answers

    Which of the following is an example of an opportunistic infection?

    <p>Candida albicans</p> Signup and view all the answers

    What is the relationship between virulence and host defenses?

    <p>The relationship between virulence and host defenses is complex and influenced by multiple factors</p> Signup and view all the answers

    What is the term for the disease process in which the normal microbial flora causes disease?

    <p>Dysbiosis</p> Signup and view all the answers

    What is an example of a niche that can be exploited by opportunistic pathogens?

    <p>Damaged heart valves</p> Signup and view all the answers

    What is the term for the process by which pathogens evade the host's immune system?

    <p>Immune evasion</p> Signup and view all the answers

    Which of the following is a characteristic of strict pathogens?

    <p>They always cause disease in a healthy individual</p> Signup and view all the answers

    What is dental calculus formed from?

    <p>Calcified dental plaque</p> Signup and view all the answers

    What inhibits the formation of dental calculus?

    <p>Pyrophosphates, zinc salts, and polyphosphonates</p> Signup and view all the answers

    What is the characteristic of the microbiota found on the tongue?

    <p>Lower volume than on teeth</p> Signup and view all the answers

    What type of bacteria is commonly found in the buccal region?

    <p>P. gingivalis</p> Signup and view all the answers

    What factors can influence the formation of dental calculus?

    <p>All of the above</p> Signup and view all the answers

    What is unique about the epithelium in the mucosal microbiota?

    <p>It is desquamated</p> Signup and view all the answers

    During puberty, what happens to the oral microbiome?

    <p>It becomes more susceptible to periodontal disease pathogens</p> Signup and view all the answers

    What is a characteristic of the saliva microbiome in adolescents?

    <p>It is more abundant in periodontal disease pathogens</p> Signup and view all the answers

    What is a mechanism by which puberty influences the oral microbiome?

    <p>Hormones provide a nutrient source for gram-positive anaerobes</p> Signup and view all the answers

    What is a factor that influences the composition of the saliva microbiome?

    <p>All of the above</p> Signup and view all the answers

    What is a consequence of the shift in the oral microbiome during puberty?

    <p>Increased risk of periodontal disease</p> Signup and view all the answers

    What is a study that has investigated the development of the saliva microbiome?

    <p>Holgerson et al.</p> Signup and view all the answers

    What is the primary factor contributing to the increase in oral microbiome diversity during childhood?

    <p>Tooth eruption and establishment of solid foods</p> Signup and view all the answers

    Which of the following bacteria is increasingly abundant during oral microbiome development in childhood?

    <p>Fusobacterium</p> Signup and view all the answers

    What is the result of the changes in oral microbiome during childhood?

    <p>An increase in oral microbiome diversity, making it more adult-like</p> Signup and view all the answers

    What is the potential consequence of an altered oral microbiome during childhood?

    <p>Increased risk of periodontal disease</p> Signup and view all the answers

    At what age is the oral microbiome typically established?

    <p>6 months</p> Signup and view all the answers

    What is the significance of the establishment of solid foods in oral microbiome development?

    <p>It provides a non-shedding tooth surface for biofilm maturation</p> Signup and view all the answers

    What is the primary function of neutrophils?

    <p>To kill bacteria and make pus</p> Signup and view all the answers

    What is the process by which microorganisms are coated before being engulfed by phagocytic cells?

    <p>Opsonisation</p> Signup and view all the answers

    Which of the following types of white blood cells is responsible for specific immunity against viruses?

    <p>Lymphocytes</p> Signup and view all the answers

    What is the term for the movement of cells towards a chemical stimulus, such as fMLP?

    <p>Chemotaxis</p> Signup and view all the answers

    Which of the following types of white blood cells becomes macrophages?

    <p>Monocytes</p> Signup and view all the answers

    What type of cells are relatively longer lived than granulocytes and include dendritic cells, macrophages, and B cells?

    <p>Antigen Presenting Cells (APCs)</p> Signup and view all the answers

    What is the term for the activation of the complement system by bacterial products such as peptidoglycan and lipopolysaccharide?

    <p>Opsonisation</p> Signup and view all the answers

    What is the result of activating TLRs?

    <p>Cytokine production, chemokine production, and activation of bacterial killing mechanisms</p> Signup and view all the answers

    Which of the following types of white blood cells is involved in immunity against parasitic infections, especially in the intestine?

    <p>Eosinophils</p> Signup and view all the answers

    What is the function of gingipain in the oral cavity?

    <p>It corrupts adhesion complexes, allowing access of microbial products to underlying tissue</p> Signup and view all the answers

    What is the role of Toll-like receptors in the immune system?

    <p>To recognise and respond to bacterial products</p> Signup and view all the answers

    Which of the following is an oxygen-independent pathway used by phagocytic cells?

    <p>Lysosomal enzymes</p> Signup and view all the answers

    What is the function of dendritic cells in the immune response?

    <p>To present antigens to T-cells</p> Signup and view all the answers

    Which of the following is an example of a Pathogen-Associated Molecular Pattern (PAMP)?

    <p>Lipopolysaccharide</p> Signup and view all the answers

    What is the primary function of opsonins in the immune response?

    <p>To increase the ability of phagocytes to adhere to microbes</p> Signup and view all the answers

    What is the consequence of defective neutrophil function?

    <p>Inflammation and microbial accumulation</p> Signup and view all the answers

    What is the primary function of myeloperoxidase?

    <p>To produce reactive oxygen species</p> Signup and view all the answers

    What is the term for the process of engulfing and digesting foreign particles?

    <p>Phagocytosis</p> Signup and view all the answers

    What is the consequence of neutropenia in the oral cavity?

    <p>Development of ulcer, gingivitis, and periodontitis</p> Signup and view all the answers

    What is the role of chemokines in the immune response?

    <p>To attract neutrophils and macrophages to infected tissues</p> Signup and view all the answers

    Which MHC class displays foreign antigens?

    <p>MHC class II</p> Signup and view all the answers

    What is the primary function of CD28 in T-cell activation?

    <p>Binding to CD80 or CD86 to promote proliferation</p> Signup and view all the answers

    What is the role of CTLA-4 in T-cell activation?

    <p>Limits T-cell expansion</p> Signup and view all the answers

    What is the primary function of IL-12 in T-cell differentiation?

    <p>Directs T-cells towards Th1 phenotype</p> Signup and view all the answers

    Which of the following is a characteristic of adaptive immunity?

    <p>Specificity to pathogen epitopes</p> Signup and view all the answers

    What is the primary function of MHC class I?

    <p>Displays self-antigens</p> Signup and view all the answers

    What is the role of CD4 and CD8 in T-cell activation?

    <p>Bind to MHC class II</p> Signup and view all the answers

    What is the primary function of IL-2 in T-cell activation?

    <p>Promotes T-cell proliferation</p> Signup and view all the answers

    What is the characteristic of antigen recognition by B cells?

    <p>Recognizes antigens in their native unprocessed forms</p> Signup and view all the answers

    What is the role of CD40 in T-dependent antigen recognition?

    <p>It is a costimulatory molecule involved in T cell activation</p> Signup and view all the answers

    What is the result of mass apoptosis of lymphocytes in the absence of antigen presentation?

    <p>Self-limitation is promoted</p> Signup and view all the answers

    What is the characteristic of B1 cells?

    <p>They produce 'natural antibody' - IgM only</p> Signup and view all the answers

    What is the result of affinity maturation in B cells?

    <p>Decrease in the dissociation constant (Kd)</p> Signup and view all the answers

    What is the characteristic of T-independent antigens?

    <p>They do not require T cell help for activation</p> Signup and view all the answers

    What is the primary function of immune memory in acquired immunity?

    <p>To enhance the immune response upon subsequent exposure to the same antigen</p> Signup and view all the answers

    Which of the following is a characteristic of Class II MHC molecules?

    <p>Expressed on professional antigen-presenting cells</p> Signup and view all the answers

    What is the role of antigen-presenting cells in the immune response?

    <p>To present antigens to T cells and activate an immune response</p> Signup and view all the answers

    Which of the following is a characteristic of T cell activation?

    <p>Requires the presence of antigen-presenting cells</p> Signup and view all the answers

    What is the role of co-stimulation in T cell activation?

    <p>To provide a secondary signal for T cell activation</p> Signup and view all the answers

    Which of the following is a characteristic of B cell activation?

    <p>Results in the production of antibodies</p> Signup and view all the answers

    What is the role of antigen presentation in the immune response?

    <p>To present antigens to T cells and activate an immune response</p> Signup and view all the answers

    What is the relationship between antigen presentation and T cell activation?

    <p>Antigen presentation is required for T cell activation</p> Signup and view all the answers

    What type of transport requires energy and moves against the concentration gradient?

    <p>Active transport</p> Signup and view all the answers

    What type of proteins help in the movement of substances that cannot cross the lipid bilayer due to size, charge, or polarity?

    <p>Carrier proteins</p> Signup and view all the answers

    What type of proteins allow passive movement of water through the membrane down its concentration gradient?

    <p>Aquaporins</p> Signup and view all the answers

    What is the process by which cells transport substances out of the cell?

    <p>Exocytosis</p> Signup and view all the answers

    What is the process by which cells take in substances from outside the cell?

    <p>Endocytosis</p> Signup and view all the answers

    What is the term for the movement of water through a semi-permeable membrane to equalize the concentration of solutes on both sides?

    <p>Osmosis</p> Signup and view all the answers

    What is the term for the pressure that opposes osmosis?

    <p>Hydrostatic pressure</p> Signup and view all the answers

    What type of proteins form channels in the membrane to allow passive movement of solutes?

    <p>Channel proteins</p> Signup and view all the answers

    What is the primary function of biological membranes?

    <p>To control the movement of substances into and out of cells</p> Signup and view all the answers

    What is the characteristic of the phospholipid bilayer in the plasma membrane?

    <p>It has a hydrophilic head and a hydrophobic tail</p> Signup and view all the answers

    What is the purpose of selective permeability in the plasma membrane?

    <p>To allow certain molecules to enter the cell while keeping others out</p> Signup and view all the answers

    What is the role of cell adhesion in biological membranes?

    <p>To recognize and adhere to other cells</p> Signup and view all the answers

    What is the function of aquaporins in biological membranes?

    <p>To facilitate the transport of water molecules</p> Signup and view all the answers

    What is the process by which cells release molecules into the extracellular environment?

    <p>Exocytosis</p> Signup and view all the answers

    What is the process by which cells take in molecules from the extracellular environment?

    <p>Endocytosis</p> Signup and view all the answers

    What is the term for the balance of fluid within the body?

    <p>Fluid balance</p> Signup and view all the answers

    What is the primary function of Aquaporins in cells?

    <p>To form pores that allow the passage of water by osmosis</p> Signup and view all the answers

    What type of transport involves the use of energy to move molecules against their concentration gradient?

    <p>Active transport</p> Signup and view all the answers

    What is the term for the process by which cells release molecules into the extracellular space?

    <p>Exocytosis</p> Signup and view all the answers

    What is the term for the process by which cells take in molecules from the extracellular space?

    <p>Endocytosis</p> Signup and view all the answers

    What is the primary function of carriers or transporters in facilitated diffusion?

    <p>To bind specific molecules and transfer them across the cell membrane</p> Signup and view all the answers

    What type of transport protein is responsible for the movement of ions across the cell membrane?

    <p>Pump</p> Signup and view all the answers

    What is the term for the state of a cell in which the concentration of solutes is the same inside and outside the cell?

    <p>Isotonic</p> Signup and view all the answers

    What is the result of a cell being placed in a hypertonic solution?

    <p>Water moves out of the cell</p> Signup and view all the answers

    What is the purpose of intravenous fluid therapy?

    <p>To maintain body fluid and electrolyte balance</p> Signup and view all the answers

    What is the term for the accumulation of excess water in the tissues?

    <p>Oedema</p> Signup and view all the answers

    Which of the following is a neurotransmitter?

    <p>Glycine</p> Signup and view all the answers

    What is the role of β-cyanoalanine synthase (β-CAS) pathway in cyanogenic plants?

    <p>Removal of cyanide from nature</p> Signup and view all the answers

    Which of the following is a derivative of tyrosine?

    <p>Dopamine</p> Signup and view all the answers

    What is the function of β-cyanoalanine?

    <p>All of the above</p> Signup and view all the answers

    What is the role of histamine in the body?

    <p>Local mediator of allergic reactions</p> Signup and view all the answers

    Which of the following is an intermediate in urea biosynthesis?

    <p>Ornithine</p> Signup and view all the answers

    What is the use of azaserine?

    <p>Treating acute childhood leukemia</p> Signup and view all the answers

    Which of the following is a glutamate decarboxylation product?

    <p>GABA</p> Signup and view all the answers

    What is the primary function of antibodies in the immune system?

    <p>To defend the body from antigens</p> Signup and view all the answers

    What is the role of carriers and transport proteins in the body?

    <p>To shuttle substances such as oxygen, nutrients, and waste products through the blood</p> Signup and view all the answers

    What is the function of enzymes in the body?

    <p>To speed up reactions in the body</p> Signup and view all the answers

    What is the role of structural and mechanical support proteins in the body?

    <p>To provide strength and flexibility to body tissues</p> Signup and view all the answers

    What is the function of hormones in the body?

    <p>To direct specific activities, such as regulating blood glucose levels</p> Signup and view all the answers

    What is the role of acid-base balance proteins in the body?

    <p>To act as buffers to maintain the pH of body fluids</p> Signup and view all the answers

    What is the primary function of HSPs in cells?

    <p>To protect the cell from damage and stress</p> Signup and view all the answers

    What is the role of fluid balance proteins in the body?

    <p>To ensure that body fluids are evenly dispersed</p> Signup and view all the answers

    What is the start codon in mRNA translation?

    <p>AUG</p> Signup and view all the answers

    What is the role of the small subunit in ribosomes?

    <p>Binds to the mRNA and links codon with anti-codon in tRNA</p> Signup and view all the answers

    What is the result of peptide bonds formation in protein synthesis?

    <p>Amino acids are linked together</p> Signup and view all the answers

    What is the role of tRNA in protein synthesis?

    <p>Act as adapter molecules</p> Signup and view all the answers

    What is the consequence of reaching a stop codon in mRNA translation?

    <p>Protein synthesis is terminated</p> Signup and view all the answers

    What is the term for the process of adding amino acids to a growing protein chain?

    <p>Elongation</p> Signup and view all the answers

    What is the function of the large subunit of ribosomes?

    <p>Catalyses peptide bond formation</p> Signup and view all the answers

    What is the result of post-translational modification?

    <p>Protein is modified</p> Signup and view all the answers

    What is the term for the sequence of amino acids that make up a protein?

    <p>Peptide</p> Signup and view all the answers

    How many different amino acids are known in animals, plants, fungi, and prokaryotes combined?

    <p>700</p> Signup and view all the answers

    Study Notes

    Bacterial Growth

    • Bacterial growth occurs primarily by binary fission, where one bacterium splits into two, requiring energy.

    Conditions Affecting Bacterial Growth

    • Temperature: Most bacteria grow optimally at 37°C, but can vary from 0 to 121°C.
    • pH: Most bacteria grow optimally between pH 7-8, but can vary from pH 0 to 11.
    • Oxygen:
      • Strict aerobes require oxygen for growth.
      • Facultative aerobes prefer oxygen for growth.
      • Facultative anaerobes prefer no oxygen for growth.
      • Strict anaerobes cannot tolerate oxygen.

    Growing Bacteria in the Lab

    • Culture media is a substance that supports bacterial growth in the laboratory.
    • Media can be:
      • Defined (exact composition known)
      • Complex (extracts from plants or animals; exact composition unknown)
    • Additives can be incorporated to enrich or inhibit certain bacteria.

    Bacterial Metabolism

    • Metabolism is the total of all biochemical reactions occurring inside the cell for survival and reproduction.
    • Defined as "from food to energy".
    • Bacteria uptake nutrients through:
      • Passive transport (involves nutrient gradient)
      • Active transport (utilizes energy to bring in nutrients)
    • Iron uptake is facilitated by siderophores.

    Quantifying Bacterial Growth

    • Methods for quantifying bacterial growth:
      • Cell counting under a microscope
      • Serial dilution and plating on agar (colony forming units)
      • qPCR (relative or absolute quantification)
    • Optical density measurement at 600 nm wavelength is used to interrogate growth dynamics in the lab.

    Gut Microbiota

    • The stomach has few viable bacteria due to its highly acidic environment
    • The small intestine has few viable bacteria due to the presence of acid and bile juices
    • The large intestine has a huge diversity of microbiota, with 10^12 cells per gram of stool
    • Symbiotic relationships in the gut microbiota:
      • Produce biotin and vitamin K
      • Prevent pathogens from colonizing
      • Aid in the absorption of nutrients

    Oral Microbiota

    • The mouth is colonized soon after birth
    • After tooth eruption, there is an increase in anaerobes such as Porphymonas, Prevotella, and Fusobacterium
    • Symbiotic relationship between oral microbiota and the host:
      • Alters taste perception
      • Differs between "super-tasters" and non-tasters
      • Varied tongue microbiota

    Changes to the Oral Microbiota

    • Nitrate-responsive oral microbiome modulates nitric oxide homeostasis and blood pressure in humans

    Homeostasis and Dysbiosis

    • Example of dysbiosis: Obesity
    • Germ-free mice vs. conventional mice:
      • Same diet, but germ-free mice could eat more and gain less weight
      • Microbiota affected caloric absorption
    • Dental conditions caused by microbiome dysbiosis:
      • Dental caries
      • Periodontal disease
      • Oral cancer

    Microbe-Host Interaction

    • Humans are holobionts, comprising the host and microbiome
    • Microbes can either be beneficial or cause harm
    • The microbiome across the human body is diverse
    • The microbiome can be in flux

    Host-Microbe Interactions

    • Definitions:
      • Infection/colonization: acquisition of micro-organisms by the host
      • Commensalism: a state of infection that results in no damage to the host
      • Symbiosis/mutualism: a state of infection where both the host and microbe benefit

    Humans as Holobionts

    • A holobiont consists of the host and microbiome
    • The human microbiome includes all microbes that share our body space
    • Humans carry 10^14 microbial cells and 10^13 human cells
    • Humans need their microbiome for:
      • Beneficial tasks
      • Protection from foreign substances and pathogens

    Microbiome - Commensals

    • 'Normal' microbes present on the skin and in the oral, respiratory, and gastrointestinal tracts, but not in internal tissues
    • Protect the host against pathogens
    • Provide nutrients for the host
    • Acquired in the first year of life

    Microbiome Composition

    • Huge diversity in composition, including:
      • Bacteria
      • Fungi
      • Viruses
    • Some members are culturable, but most cannot be cultured
    • Culture-independent methods are used to study the microbiome

    16S Ribosomal RNA Sequencing

    • 16S rRNA is a subunit of the ribosome
    • Slow rate of evolution
    • Highly conserved between bacteria and archaea
    • Hypervariable regions for studying diversity

    Shotgun Metagenomics

    • Sequencing of every nucleic acid within a given sample, including:
      • DNA and/or RNA
      • Bacteria
      • Viruses
      • Fungi
      • Even host
    • Allows for extended characterization of the "community", including:
      • Subtyping
      • AMR genes
      • Virulence genes

    Metagenomics Insight into Population Dynamics

    • Metagenomics can be used to study population dynamics

    Host Microbiome Varies with Body Site

    • Skin microbiota:
      • Environment: slightly acidic, high salt, low water content, and inhibitory substances
      • Bacteria on superficial skin (dead cells) and sweat glands
      • Bacteria partially degrade skin oil to volatile fatty acids, producing body odor
    • Respiratory microbiota

    Infection Process

    • Adherence and invasion are the first steps in the infective process
    • Entry sites for pathogens include skin, oral, gut, respiratory tract, and eyes
    • Adherence can be non-specific or specific, with specific adhesins being pili, fimbriae, and capsules

    Invasion Strategies

    • Pathogens can actively or passively penetrate mucous membranes or epithelium
    • Active invasion and spread involve enzyme production and microbial toxins
    • Inhibition of phagocytosis is a key strategy for pathogens
    • Bacteremia occurs when pathogens enter the blood, while septicemia is an infection disease in the blood

    Surviving Host Defenses

    • Pathogens must overcome innate and adaptive immune systems
    • Protection strategies include hiding (within capsules, biofilms, or phagocytes), camouflage (coating with host macromolecules), and immune evasion (antigenic variation)
    • Examples of hiding include Streptococcus pneumoniae capsules and intracellular pathogens like Mycobacterium tuberculosis
    • Camouflage strategies include Streptococci producing streptokinase to coat bacteria with plasmin

    Acute and Chronic Infections

    • Acute infections are characterized by sudden onset, rapid progression, and severe systemic symptoms
    • Chronic infections involve the continued presence of infectious agents following primary infection and may include chronic or recurrent disease

    Virulence Factors

    • Virulence is the magnitude of harm caused by a pathogen
    • Virulence factors increase the pathogen's virulence, including rapid replication, integration of pathogen genome into host, and use of toxins
    • Toxins include exotoxins (Gram +ve, heat sensitive) and endotoxins (LPS on Gram -ve, heat stable, causing fever and shock)

    Pathogenicity

    • Pathogens can cause disease through simple 'hit-and-run' infections or long-term 'co-existence and subversion'
    • Strict pathogens always cause disease when present, while opportunistic pathogens only cause disease under certain conditions
    • Examples of strict pathogens include Mycobacterium tuberculosis, while opportunistic pathogens include Candida albicans

    Opportunistic Infections

    • Opportunistic infections occur when the immune system is weakened, such as through frequent antibiotic usage
    • Examples of opportunistic infections include oral thrush (Candida albicans) and bacterial endocarditis (Streptococcus viridans)
    • Opportunistic infections can occur when a pathogen enters a new niche, such as when Streptococcus viridans infects damaged heart valves

    Rate of Infection

    • The rate of infection is influenced by virulence and host defenses
    • ID50 is the number of micro-organisms required to cause disease in 50% of inoculated hosts

    Dental Plaque/Biofilm Formation

    • Mature plaque is calcified dental plaque with calcium phosphate mineral salts forming between and within viable microbes
    • People with elevated salivary calcium levels form calculus quicker
    • A biofilm layer covers the calculus
    • Inhibition of calculus formation can be achieved using pyrophosphates, zinc salts, and polyphosphonates

    Dental Calculus

    • Calcified dental plaque
    • Calcium phosphate mineral salts form between and within viable microbes
    • People with elevated salivary calcium levels form calculus quicker
    • Biofilm layer covers the calculus

    Mucosal Microbiota

    • Epithelium includes gingival, buccal, and palatal regions
    • Desquamation occurs in mucosal microbiota
    • Lower volume of microbiota present on mucosa compared to teeth
    • Buccal region has P. gingivalis
    • Tongue contains papillae, providing protected sites for bacterial colonization
    • Tongue has S. mitis, S. salivarius, and medically compromised Candida albicans

    Oral Microbiome Development

    • At 6 months, tooth emergence and establishment of solid foods provide a non-shedding tooth surface for biofilm maturation and increased diversity of nutrients for the microbial community
    • This leads to an increase in the diversity of the oral microbiome, causing it to become more adult-like
    • Some of the increasingly abundant bacterial taxa emerging during this period include Fusobacterium, Lactobacillus, Neissera, Gemella, and Haemophillus

    Puberty and the Oral Microbiome

    • The later childhood oral microbiome is characterized by the further enrichment and increased abundance of bacterial taxa, including periodontal disease pathogens like Porphyromonas gingivalis
    • Hormones during puberty provide a nutrient source for gram-negative anaerobes like P. gingivalis

    Phagocytosis

    • Phagocytosis is the capture and digestion of foreign particles
    • Chemokines attract macrophages and neutrophils to infected tissues
    • Opsonins attach to microbes to increase phagocyte adhesion (opsonization)

    Oxygen Independent and Dependent Pathways

    • Oxygen-independent pathway involves lysosomal enzymes (e.g. collagenase, gelatinase, phospholipases or serine proteases)
    • Oxygen-dependent pathway involves oxidative burst, producing reactive oxygen and nitrogen species (RONS)

    White Blood Cells (WBCs)

    • Neutrophilic PMN (most common WBC): kills bacteria, makes pus
    • Monocytic PMN (second most common WBC): kills bacteria, eats debris, attacks intracellular pathogens, becomes macrophages
    • Lymphocytes (many types: T, B, NK): specific immunity, immunity against viruses, tumor protection
    • Eosinophils (rarest variety of WBC): becomes mast cells, contributes to allergy

    Chemotaxis and Opsonisation

    • Chemotaxis: directional movement of neutrophils towards bacterial products (e.g. fMLP, peptidoglycan) detected by surface receptors
    • Opsonisation: microorganisms must be coated before being bound and engulfed by phagocytic cells, using complement system or other coating agents

    Innate Responses

    • Cells involved: antigen-presenting cells (APCs), phagocytic cells (e.g. neutrophils, macrophages)
    • Pattern recognition receptors (PRRs) recognize pathogen-associated molecular patterns (PAMPs)
    • Effects of activating TLRs: cytokine production, chemokine production, activation of bacterial killing mechanisms, and activation of dendritic cells

    MHC and Antigen Recognition

    • MHC class I displays self-antigens, while MHC class II displays foreign antigens
    • All nucleated cells display MHC class I, while immune cells display both MHC class I and II
    • Each MHC displays one antigen at a time
    • High expression levels of peptide-MHC complexes increase the propensity to activate T-cells

    Characteristics of MHC

    • MHC class I: 6-16 amino acids
    • MHC class II: up to 30 amino acid residues

    T-Cell Activation

    • MHC-TCR engagement requires co-stimulation: T-cell coreceptors CD28 and CD80/B7.1 and CD86/B7.2 on the APC
    • IL-2 is immediately released by T cells and promotes proliferation
    • 3 signals for T-cell activation: TCR engages antigen on MHC, CD4 or CD8 binds MHC, and CD28 binds CD80 or CD86
    • Further engagement with ICOS, 4-1BB, and OX40 strengthens activation
    • 'Brakes' are applied through CD152, which limits expansion

    Cytokines and T-Cell Identity

    • Exposure to IL-12 from APC → Th1
    • Exposure to IL-4 from APC → Th2
    • Exposure to IL-6, IL-23 from APC → Th17

    Adaptive (Specific) Immunity

    • Specificity: every clone of T and B lymphocytes recognizes a different antigen
    • Acquired immunity: has a memory, provides improved protection on next exposure, and is the basis for immunity against re-infection and immunization

    Characteristics of Antigen-Presenting Cells

    • Dendritic cells, macrophages, B cells, and Langerhans cells are professional APCs
    • APCs express MHC class II and are highly effective at presenting antigens

    Immune Responses

    • Innate immune response: reduces pathogen load, immediate, and part of homeostasis
    • Adaptive immune response: has a memory, provides improved protection on next exposure, and is the basis for immunity against re-infection and immunization

    Antigen Presentation to T-Cells

    • Antigen presentation on MHC is a fundamental link between innate and adaptive immunity
    • Memory: accelerated and larger response, with fewer 'checkpoints' required for reactivation

    Antigen Recognition and B-Cell Activation

    • T-dependent antigens: require T-cell 'help', use costimulatory molecule CD40, and need cytokines
    • T-independent antigens: do not require T-cell help
    • BCRs recognize antigens in their native unprocessed forms (does not require peptide bound to MHC molecules)
    • Each B-cell is decorated with IgM with a unique specificity, with 10 billion combinations
    • Affinity maturation: decrease in the dissociation constant (Kd) following repeated stimulation, involving class switching from IgM to IgG

    Fluid Balance and Osmosis

    • Body fluid balance and distribution are crucial, and the movement of water in the body needs to be controlled to prevent swelling or dehydration.
    • Biological membranes act as a barrier for water movement, controlling the movement of substances into and out of cells, and regulating the composition within individual cells.

    Biological Membranes

    • Functions of biological membranes:
      • Control the movement of substances into and out of cells
      • Regulate the composition within individual cells
      • Control the flow of information between cells (recognizing or sending signals)
      • Capture and release energy (e.g., mitochondria)
      • Cell adhesion
      • Synthesize steroids, etc.
    • Structure and function of plasma membrane:
      • Bi-layer of phospholipids (phosphate group and 2 chains of fatty acids)
      • Amphipathic (head is hydrophilic, tail is hydrophobic)
      • Selective permeability (some molecules are allowed in, while others are kept out)
      • Permeable to lipid-soluble substances (e.g., O2)
      • Impermeable to charged molecules (e.g., ions)

    Body Fluid Compartments

    • Intracellular fluid: ~25 L
    • Interstitial fluid: ~12 L
    • Plasma: ~3 L
    • Extracellular fluid (ECF): plasma + interstitial fluid

    Osmosis and Water Movement

    • Osmosis: water moves through a semi-permeable membrane to equalize the concentration of a solution
    • Osmotic pressure (OP): created by a concentration difference of dissolved substances between two sides of a bio-membrane
    • Hydrostatic pressure: movement of water stops
    • Equilibrium is reached once sufficient water has moved to equalize the solute concentration on both sides

    Membrane Transport

    • Passive movement: follows the concentration gradient, does not require energy
      • Driving forces: concentration gradient, electrical potential
    • Active transport: against the concentration gradient, requires energy
      • Examples: endocytosis, exocytosis
    • Diffusion: passive movement across membranes, forming equilibrium
    • Facilitated diffusion: diffusion for substances that cannot cross lipid bi-layer due to size/charge/polarity, uses carrier proteins

    Membrane Proteins

    • Transport proteins: channels, pumps, and carriers
    • Enzymes
    • Intercellular junctions
    • Cell-cell recognition
    • Receptors
    • Adhesion to extracellular matrix

    Membrane Transport Proteins

    • Channels: allow passive movement of solutes through the membrane down their concentration gradient
      • Examples: ion channels, aquaporins
      • Gated: open or closed in response to local changes (e.g., ligand-gated, voltage-gated)
    • Pumps: active transport, against the concentration gradient, catalyze the hydrolysis of ATP to ADP
      • Examples: Na+/K+-ATPase, important for controlling movement of water and electrolyte balances
    • Carriers/Transporters: facilitate diffusion or active transport, bind specific molecules and transfer them across the membrane
      • Examples: uniporter, symporter, antiporter

    Cellular Transport

    • Exocytosis: vesicles containing material for export, waste removal, secrete hormones
    • Endocytosis: take in material, the reverse of exocytosis, white blood cell engulfing bacteria/viruses

    Water Imbalance and Treatment

    • Oedema: accumulation of excess water in the tissues, water leakage from capillaries
    • Intravenous fluid therapy: maintain body fluid and electrolytes balance, various types of fluid for different purposes

    Osmosis

    • Isotonicity: concentration of dissolved substances is the same in the solution as in the cell, same OP for both sides
      • Isotonic solution of animal cells: 0.9% w/v NaCl solution (saline)
    • Hypotonicity: outside solution has lower OP (less solute) than cell interior, water moves into cell
      • Example: 0.45% saline
    • Hypertonicity: outside solution has higher OP (more solute) than cell interior, water moves out of cell
      • Example: 3% saline

    Function of Proteins

    • Enzymes speed up reactions in the body
    • Hormones direct specific activities, such as regulating blood glucose levels (insulin)
    • Antibodies and complement system are involved in the immune system to defend the body from antigens (foreign invaders)
    • Structural and mechanical support proteins provide strength and flexibility to body tissues
    • Carrier proteins shuttle substances such as oxygen, nutrients (e.g., iron), and waste products through the blood and into and out of cells
    • Proteins help maintain fluid balance and acid-base balance in the body
    • Proteins provide energy when necessary

    Specialized Roles of Amino Acids

    • Glycine, GABA, and dopamine are chemical messengers (neurotransmitters)
    • Histamine is a potent local mediator of allergic reactions
    • Thyroxine is a thyroid hormone
    • Citrulline, ornithine, and homocysteine are intermediates in various metabolic processes

    Specialized Roles of Non-Standard Amino Acids

    • Azaserine is an antimicrobial, antifungal, antineoplastic, and immunosuppressive agent
    • β-Cyanoalanine is involved in the removal of cyanide from nature and is used in treating acute childhood leukemia

    Central Dogma - Flow of Genetic Information

    • The sequence of mRNA is translated into a sequence of amino acids
    • mRNA reads the sequence of codons (AUG, AAG, CCG, etc.)
    • tRNA reads the sequence of anti-codons and brings amino acids to the ribosome
    • Ribosomes are composed of rRNA and ribosomal proteins and have two subunits (large and small)

    Components of Translation

    • mRNA carries the genetic information
    • Amino acids are the building blocks of proteins
    • tRNA is the adapter molecule that brings amino acids to the ribosome
    • Ribosomes are the action stations where protein synthesis occurs
    • Enzymes and energy are necessary for translation

    Synthesis of Proteins from RNA

    • Initiation: starts with the start codon AUG (methionine)
    • Elongation: addition of amino acids by peptide bonds
    • Termination: ends with the stop codon (UAA, UAG, or UGA)

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    This quiz covers the processes of bacterial growth, replication, and fermentation. It includes topics such as binary fission and laboratory assessment.

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