Microbiology Exam 3 PDF

Microbiology Exam 3 MICROBIAL METABOLISM (Lecture Topic 5) Metabolism: Refers to all chemical reactions in a cell, including those that build up (anabolism) and break down (catabolism) molecules to produce energy. Redox reactions: These involve the transfer of electrons. Oxidized means a subst...

Microbiology Exam 3 MICROBIAL METABOLISM (Lecture Topic 5) Metabolism: Refers to all chemical reactions in a cell, including those that build up (anabolism) and break down (catabolism) molecules to produce energy. Redox reactions: These involve the transfer of electrons. Oxidized means a substance loses electrons. Reduced means a substance gains electrons. Enzymes: Proteins that speed up biochemical reactions. Apoenzyme: The protein part of an enzyme, without any cofactors. Cofactor: A non-protein component required by some enzymes to function (e.g., metal ions). Holoenzyme: The complete enzyme, consisting of the apoenzyme and its cofactor. Enzymes are crucial because they lower activation energy for reactions and are named often by adding “-ase” to the substrate or the type of reaction they catalyze. Impact of pH and temperature on enzymes: Enzymes work best at optimal pH and temperature. Extremes in either can denature enzymes (alter their structure), making them ineffective. Enzyme inhibition: Competitive inhibition: A substance competes with the substrate for binding to the active site. Allosteric inhibition: A substance binds elsewhere on the enzyme, changing its shape and reducing activity. NAD and FAD: These are electron carriers. NAD is reduced to NADH and FAD is reduced to FADH2 during metabolic reactions. They carry electrons to the electron transport chain for ATP production. Stages of aerobic respiration: Glycolysis, Krebs cycle, and Electron Transport Chain (ETC). They occur in this order. ATP production: Glycolysis: 2 ATP Krebs cycle: 2 ATP ETC: About 34 ATP Total: ~38 ATP for prokaryotes, ~36 ATP for eukaryotes. Cellular respiration steps: Glycolysis starts with glucose, producing pyruvate. Krebs cycle starts with acetyl-CoA, producing CO2. ETC starts with NADH and FADH2, producing ATP and water. Location of respiration: Prokaryotes: Glycolysis in the cytoplasm, Krebs in the cytoplasm, and ETC in the cell membrane. Eukaryotes: Glycolysis in the cytoplasm, Krebs in the mitochondrial matrix, and ETC in the inner mitochondrial membrane. ATP synthase: This enzyme creates ATP from ADP and inorganic phosphate, driven by a flow of protons (H+) across a membrane during oxidative phosphorylation. Metabolic pathways: EMP (Embden-Meyerhof-Parnas): The most common glycolytic pathway, produces 2 pyruvate and 2 ATP and 2 NADH PPP (Pentose Phosphate Pathway): Produces NADPH and ribose-5-phosphate for nucleotide synthesis. ED (Entner-Doudoroff): Alternative glycolytic pathway, produces pyruvate, used by some bacteria. produces 1 ATP 1NADPH Fermentation: Occurs when oxygen is not available, allowing cells to regenerate NAD+ by converting pyruvate into products like lactic acid or ethanol. Lipid and protein catabolism: These molecules are broken down during the Krebs cycle. Types of organisms: Photoautotrophs: Use light energy and CO2 (e.g., plants, cyanobacteria). Chemoautotrophs: Use chemical energy and CO2 (e.g., some bacteria). Photoheterotrophs: Use light for energy but organic compounds for carbon (e.g., purple non-sulfur bacteria). Chemoheterotrophs: Use organic compounds for both energy and carbon (e.g., animals, fungi). MICROBIAL GROWTH (Lecture Topic 6) Temperature groups of bacteria: Bacteria are classified into five groups based on their optimum growth temperatures: ○ Psychrophiles: Thrive at cold temperatures (below 15°C, optimal around 10°C). ○ Psychrotrophs: Grow between 0–30°C, optimal around 20–30°C (spoil food in refrigerators). ○ Mesophiles: Optimal growth at moderate temperatures, around 25–40°C (most human pathogens). ○ Thermophiles: Thrive at warmer temperatures, 50–60°C. ○ Hyperthermophiles: Can grow at extremely\ high temperatures, above 80°C, often found in hot springs. Physical and chemical requirements for microbial growth: ○ Physical requirements: Temperature, pH (most bacteria grow best between pH 6.5 and 7.5), and osmotic pressure (salt concentration). ○ Chemical requirements: Carbon, nitrogen, sulfur, phosphorus, trace elements (e.g., iron, magnesium), and in some cases, oxygen. Oxygen requirements for microbes: ○ Obligate aerobes: Require oxygen. ○ Obligate anaerobes: Cannot tolerate oxygen. ○ Facultative anaerobes: Can grow with or without oxygen, but prefer oxygen. ○ Aerotolerant anaerobes: Do not use oxygen but can tolerate its presence.  ○ Microaerophiles: Require lower levels of oxygen than present in the atmosphere. Thioglycolate broth is often used to determine oxygen preferences, as it allows an oxygen gradient, where bacteria grow based on their oxygen needs. Chemically defined vs. complex culture media: ○ Chemically defined media: The exact chemical composition is known. Used when precise nutrient requirements of microbes are known (e.g., in research settings). ○ Complex media: Contains a variety of ingredients like meat extracts or yeast extract, and the exact composition is not known. Often used in routine lab culture work (e.g., nutrient broth, tryptic soy agar). Selective, enrichment, and differential media: ○ Selective media: Suppresses the growth of unwanted bacteria while encouraging the growth of the desired microbe (e.g., MacConkey agar for Gram-negative bacteria). ○ Enrichment media: Provides conditions that favor the growth of a particular microbe but doesn’t suppress others (e.g., blood agar for growing fastidious organisms). ○ Differential media: Allows differentiation between species based on observable changes (e.g., blood agar differentiates organisms based on hemolysis). Biosafety levels (BSLs): ○ BSL-1: Low-risk microbes (e.g., non-pathogenic strains of E. coli). ○ BSL-2: Moderate-risk pathogens (e.g., Staphylococcus aureus). ○ BSL-3: High-risk microbes that can cause serious or potentially lethal diseases (e.g., Mycobacterium tuberculosis). ○ BSL-4: High-risk microbes with no available treatments or vaccines (e.g., Ebola virus). Prokaryote and eukaryote reproduction: ○ Prokaryotes: Replicate via binary fission, a simple division process. ○ Eukaryotes: Replicate via mitosis (somatic cells) or meiosis (sex cells). ○ Yeast: Use mitosis with budding, where a new cell forms as a bulge.  ○ Molds: Reproduce via conidiospores, which are asexual spores formed at the tips of hyphae. DNA replication is semi-conservative: Each daughter DNA molecule consists of one original strand and one newly synthesized strand. Cell cycle stages: ○ Interphase: Includes G1 (cell growth), S (DNA replication), and G2 (preparation for mitosis). ○ Mitosis: Includes prophase, metaphase, anaphase, and telophase. ○ Cytokinesis: The division of the cytoplasm, producing two daughter cells. Non-mitotic eukaryotic cells: Some specialized cells, like neurons and muscle cells, do not undergo mitosis. Treatment of related disorders often involves stimulating these cells or using stem cells to replace them. Microbial growth phases: ○ Lag phase: Bacteria adapt to their environment, little to no growth. ○ Log phase (exponential phase): Rapid bacterial growth and division. ○ Stationary phase: Nutrient depletion slows growth, and death rate equals division rate. ○ Death phase: Cells die at an accelerated rate due to harsh conditions. Colony-forming units (CFUs): A measurement of viable bacterial cells, where one CFU represents one bacterial cell or a group of cells that give rise to a colony. Countable range: Typically between 30 and 300 colonies on an agar plate for reliable counts. Direct and indirect microbial measurement methods: ○ Direct methods: Counting colonies (plate counts), counting cells under a microscope, or using flow cytometry. ○ Indirect methods: Measuring turbidity (cloudiness) in liquid culture, measuring metabolic activity, or dry weight. Control of Microbial Growth (Lecture Topic 7) Terms related to microbial control:  Sterilization: Complete destruction of all forms of microbial life, including spores (e.g., autoclaving surgical instruments). Disinfection: Reducing the number of pathogenic microorganisms on inanimate objects (e.g., using bleach on surfaces). Sepsis: The presence of harmful microorganisms or their toxins in tissues (e.g., sepsis after surgery). Degerming: Mechanically removing microbes from a limited area (e.g., hand washing or using alcohol before an injection). Antiseptic: Chemical agents used on living tissues to reduce microbial load (e.g., iodine on skin). Sanitization: Reducing microbial levels on inanimate objects to safe public health levels (e.g., cleaning utensils in restaurants). Biocide/Germicide: Agents that kill microorganisms (e.g., bleach, hydrogen peroxide). Asepsis: The absence of significant contamination (e.g., using sterile techniques during surgery). Bacteriostasis: Inhibiting bacterial growth without killing the microbes (e.g., refrigeration). Joseph Lister’s contribution: Lister significantly reduced nosocomial (hospital-acquired) infections by using carbolic acid (phenol) to sterilize surgical instruments and clean wounds, preventing contamination. Nosocomial infections: Infections acquired in healthcare settings, such as hospitals, often due to poor aseptic practices or weakened immune systems of patients. Commercial sterilization: A process that kills Clostridium botulinum spores (which cause botulism), but not necessarily all forms of life. It is limited because it targets specific organisms of public health concern, particularly in food canning, but does not achieve full sterilization like autoclaving. "Static" vs. "Cide" terms: "Static": Refers to inhibiting growth (e.g., bacteriostatic agents like refrigeration slow bacterial growth). "Cide": Refers to killing (e.g., bactericide kills bacteria). Actions of microbial control agents:  Damage to cell walls or membranes: Detergents and alcohols can disrupt membranes, leading to cell leakage. Damage to proteins: Heat and chemicals (e.g., formaldehyde) can denature proteins, rendering enzymes non-functional. Damage to nucleic acids: Radiation and chemicals (e.g., ethylene oxide) can damage DNA, preventing replication. Effectiveness factors: Temperature, pH, time of exposure, the number of microbes, and presence of organic matter (e.g., blood) can influence the effectiveness of control methods. Physical methods of microbial control: Heat: Includes moist heat (autoclaving), dry heat (incineration), pasteurization. Filtration: Physically removes microbes from liquids or air (e.g., HEPA filters). Radiation: UV light causes DNA damage; ionizing radiation (gamma rays) penetrates and sterilizes. Low temperatures: Inhibit microbial growth (e.g., refrigeration, freezing). Desiccation: Drying out materials to inhibit microbial growth (removal of water). Osmotic pressure: High salt or sugar concentrations create an environment where microbes can't grow due to plasmolysis. Different materials require different methods because heat-sensitive materials (like plastics) cannot be autoclaved and might need filtration or radiation instead. Thermal death point vs. thermal death time: Thermal death point (TDP): The lowest temperature at which all microbes in a liquid culture are killed in 10 minutes. Thermal death time (TDT): The minimum time required to kill all microbes at a given temperature. Autoclave standard cycle: Typically, autoclaving involves heating at 121°C for 15 minutes at 15 psi. Times may vary based on the material being sterilized, load size, or type of material (e.g., longer for bulky materials). Chemical methods of microbial control:  Alcohols: Denature proteins and dissolve lipids (e.g., ethanol). Halogens: Include iodine and chlorine, which are strong oxidizers and disinfectants. Phenolics: Disrupt cell membranes (e.g., Lysol). Heavy metals: Such as silver and copper can inhibit microbial growth by denaturing proteins. Surface-active agents (surfactants): Lower surface tension, making microbes easier to remove (e.g., soaps, quaternary ammonium compounds). Aldehydes: Highly effective disinfectants that crosslink proteins (e.g., formaldehyde). Most resistant microbes: Prions: Proteinaceous infectious particles, highly resistant to sterilization methods. Endospores: Bacterial spores (e.g., Bacillus and Clostridium species) are highly resistant. Mycobacteria: Have waxy cell walls that resist many disinfectants. Gram-negative bacteria: Their outer membrane makes them more resistant to some antimicrobial agents. Microbial Genetics (Chapter 8) Differences between genes, genomes, genotypes, and phenotypes: Genes: Segments of DNA that code for specific proteins or RNA molecules. Genomes: The entire set of genetic material (DNA) in an organism. Genotype: The genetic makeup of an organism (the specific set of genes). Phenotype: The observable characteristics or traits of an organism, influenced by the genotype and the environment. Flow of genetic information: Expression: The process by which genetic information is used to produce proteins (gene -> mRNA -> protein).  Dominant vs. recessive genes: Dominant genes express their traits even if only one copy is present (heterozygous). Recessive genes require two copies to express the trait (homozygous). mRNA and tRNA functions: mRNA (messenger RNA): Carries the genetic code from DNA to ribosomes, where proteins are synthesized. tRNA (transfer RNA): Brings amino acids to the ribosome during protein synthesis, matching them to the codons on mRNA. Transcription and translation: Transcription: The process of copying DNA into RNA. Occurs in the nucleus (eukaryotes) or cytoplasm (prokaryotes). ○ Enzymes involved: RNA polymerase. ○ Product: mRNA. Translation: The process of converting mRNA into a protein. Occurs in the ribosome (in both prokaryotes and eukaryotes). ○ Biomolecules involved: mRNA, tRNA, ribosomal RNA (rRNA), amino acids. DNA to RNA conversion and codons: DNA to RNA: A process known as transcription. In RNA, thymine (T) is replaced by uracil (U). ○ Example: DNA sequence ATGCGT would transcribe to RNA as UACGCA. Codons: A sequence of three nucleotides on mRNA that codes for a specific amino acid. The start codon is AUG, which codes for methionine. Process of translation: As mRNA moves through the ribosome, each codon is read and matched with the appropriate tRNA carrying its corresponding amino acid. The amino acids are linked together to form a polypeptide chain (protein). Mutations and mutation rates:  Mutations: Changes in the DNA sequence, which can occur spontaneously or be induced by external factors like radiation. Typical mutation rate: Varies, but is generally around 1 in 10^9 (one error per billion nucleotides). Types of mutations: ○ Point mutation: A single nucleotide change. ○ Frameshift mutation: Insertion or deletion of nucleotides, altering the reading frame of the gene. ○ Silent mutation: A mutation that does not affect the protein sequence. ○ Missense mutation: A change in one nucleotide that results in a different amino acid. ○ Nonsense mutation: A mutation that results in a stop codon, truncating the protein. Radiation and mutation repair: Radiation (e.g., UV light): Can cause thymine dimers (two adjacent thymine bases bonding to each other), disrupting DNA replication. DNA repair mechanisms: Cells use enzymes like photolyases (light repair) and excision repair systems to correct damage caused by radiation. Ames test: A test used to identify potential mutagens (substances that cause mutations). It uses Salmonella bacteria that cannot synthesize histidine and measures whether exposure to a chemical increases mutation rates, allowing the bacteria to regain the ability to produce histidine. Gene transfer in bacteria: Transformation: The uptake of naked DNA from the environment. Conjugation: Direct transfer of DNA between two bacterial cells through a pilus. Transduction: Transfer of DNA from one bacterium to another via a virus (bacteriophage). Genetic transformation and Streptococcus pneumoniae:  Genetic transformation was discovered through experiments with Streptococcus pneumoniae by Frederick Griffith. He showed that dead virulent bacteria could "transform" non-virulent bacteria into virulent ones by transferring DNA. Plasmids: Small, circular DNA molecules found in bacteria that are separate from chromosomal DNA. Plasmids often carry genes for antibiotic resistance and can be transferred between bacteria, which is why microbiologists are concerned—they contribute to the spread of antibiotic resistance. Pros and cons of mutations: Pros: Mutations can lead to new traits or abilities, such as antibiotic resistance, which may benefit the organism in certain environments. Cons: Mutations can be harmful, leading to non-functional proteins, diseases, or cell death.