Microbiology Quiz on Metabolism and Sterilization

Nutritional Types

• Phototrophs: obtain energy from light
• Chemotrophs: obtain energy from chemicals
• Autotrophs: obtain carbon from inorganic sources (ex: CO2)
• Heterotrophs: obtain carbon from organic sources (ex: sugars, proteins)

Transport Processes

• Passive Transport: movement of substances across a membrane without requiring energy
  • Simple Diffusion: movement from high to low concentration
  • Facilitated Diffusion: movement with the help of membrane proteins
  • Osmosis: movement of water across a semipermeable membrane
    • Hypertonic Solution: higher solute concentration outside the cell causing water to move out
    • Hypotonic Solution: lower solute concentration outside the cell causing water to move in
    • Isotonic Solution: equal solute concentration inside and outside the cell, no net movement of water
• Active Transport: movement of substances across a membrane requiring energy
  • Primary Active Transport: directly uses ATP to move substances
  • Secondary Active Transport: uses the energy of an electrochemical gradient to move substances
  • Group Translocation: chemically modifies the transported substance as it crosses the membrane
• Bulk Transport: movement of large particles or fluids across a membrane
  • Endocytosis: imports substances into the cell
  • Exocytosis: exports substances out of the cell

Environmental Factors

• Temperature:
  • Psychrotrophs: grow best at low temperatures (0-20°C)
  • Mesophiles: grow best at moderate temperatures (20-40°C)
• pH:
  • Acidophiles: thrive in acidic environments (pH 1-5.5)
  • Neutrophiles: prefer neutral environments (pH 5.5-8)
  • Alkaliphiles: grow best in alkaline environments (pH 8.5-11.5)
• Osmotic Pressure:
  • Halophiles: require high salt concentrations for growth
    • Obligate Halophiles: require high salt concentrations (ex: Halobacterium)
    • Facultative Halophiles: can tolerate high salt concentrations, but don't require them (ex: Staphylococcus)
• Oxygen:
  • Obligate Aerobes: require oxygen for growth
  • Obligate Anaerobes: cannot grow in the presence of oxygen
  • Microaerophiles: require low oxygen concentrations
  • Aerotolerant Anaerobes: can tolerate oxygen, but don't require it
  • Facultative Anaerobes: can grow with or without oxygen

Microbial Growth

• Binary Fission: a single cell divides to form two identical daughter cells
• Growth Curve Phases:
  • Lag Phase: cells are adapting to their environment
  • Exponential (Log) Phase: rapid cell division
  • Stationary Phase: growth rate slows as resources become limited
  • Death Phase: cells begin to die off
• Generation Time: the time required for a population to double in size

Metabolism

• Anabolism: building larger molecules from smaller ones (endergonic: requires energy)
  • Condensation/Dehydration Reactions: release water molecules
• Catabolism: breaking down larger molecules into smaller ones (exergonic: releases energy)
  • Hydrolytic/Degradation Reactions: use water to break bonds

Enzymes

• Biological catalysts that increase the rate of reactions
• Characteristics:
  • Lower activation energy
  • Specific to their substrates
  • Can be reused
• Simple Enzyme: consists only of protein
• Holoenzyme: consists of a protein (apoenzyme) and a non-protein component (cofactor)
  • Cofactors:
    • Metal Ions: ex: Mg2+, Fe2+
    • Coenzymes: organic molecules, often derived from vitamins, ex: NAD+, FAD
• Active Site: region on an enzyme where the substrate binds

Factors that Influence Enzyme Activity

• Temperature: optimal temperature where the enzyme works best
• pH: optimal pH range for enzyme function
• Substrate Concentration: increasing substrate concentration increases enzyme activity until saturation is reached
• Inhibitors and Activators:
  • Competitive Inhibitors: bind to the active site and block substrate access
  • Noncompetitive Inhibitors: bind to a different site on the enzyme, altering its shape and reducing activity
  • Allosteric Inhibitors/Activators: bind to a regulatory site and affect enzyme activity
• Feedback Inhibition: the end product of a metabolic pathway inhibits an enzyme early in the pathway, regulating the pathway's activity

Cell Energetics

• Endergonic Reactions: require energy input
• Exergonic Reactions: release energy
• ATP (Adenosine Triphosphate): the universal energy currency of cells

Oxidation and Reduction

• OIL RIG: Oxidation Is Loss of electrons, Reduction Is Gain of electrons
• Electron Carriers: molecules that accept and donate electrons, ex:
  • NAD+/NADH: nicotinamide adenine dinucleotide
  • FAD/FADH2: flavin adenine dinucleotide

Pathways of Bioenergetics

• 1. Aerobic Respiration:*
• Glycolysis:
  • Breaks down glucose into pyruvate
  • Occurs in the cytoplasm
  • Produces 2 ATP and 2 NADH
  • Summary: Glucose → 2 Pyruvate + 2 ATP + 2 NADH
• Pyruvate Oxidation:
  • Converts pyruvate into acetyl-CoA
  • Occurs in the mitochondrial matrix (in eukaryotes) or cytoplasm (in prokaryotes)
  • Produces 2 NADH
  • Summary: 2 Pyruvate → 2 Acetyl-CoA + 2 NADH
• Krebs Cycle (Citric Acid Cycle):
  • Oxidizes acetyl-CoA to carbon dioxide
  • Occurs in the mitochondrial matrix (in eukaryotes) or cytoplasm (in prokaryotes)
  • Produces 2 ATP, 6 NADH, and 2 FADH2
  • Summary: 2 Acetyl-CoA → 2 ATP + 6 NADH + 2 FADH2
• Electron Transport Chain (ETC):
  • A series of electron carriers that transfer electrons
  • Occurs in the inner mitochondrial membrane (in eukaryotes) or the plasma membrane (in prokaryotes)
  • Protons (H+) are pumped across the membrane, creating a proton gradient
• ATP Synthase:
  • Uses the proton gradient to generate ATP
• Final Electron Acceptor: Oxygen
• ATP yield: 38 ATP per glucose
• Overall Summary: Glucose + 6 O2 + 38 ADP + 38 Pi → 6 CO2 + 6 H2O + 38 ATP
• 2. Anaerobic Respiration:*
• Similar to aerobic respiration, but uses a final electron acceptor other than oxygen (ex: sulfate, nitrate)
• ATP yield varies depending on the final electron acceptor
• 3. Fermentation:*
• Uses glycolysis to produce ATP
• Does not require oxygen
• Final electron acceptor is an organic molecule (ex: pyruvate, acetaldehyde)
• Produces various end products (ex: lactic acid, ethanol, gases, acids)
• ATP yield: 2 ATP per glucose

Genomes

• Prokaryotes: single, circular chromosome; located in the nucleoid region
• Eukaryotes: multiple, linear chromosomes contained within the nucleus
• Viruses: genome can be composed of DNA or RNA, single or double-stranded

DNA vs. RNA

• Nucleic Acids: complex organic molecules that store and transmit genetic information
• Differences:
  • Sugar: DNA - deoxyribose, RNA - ribose
  • Nitrogenous Bases:
    • DNA - adenine (A), guanine (G), cytosine (C), thymine (T)
    • RNA - adenine (A), guanine (G), cytosine (C), uracil (U)
  • Structure: DNA - double helix, RNA - single-stranded
• Nucleotide: consists of a sugar, phosphate group, and a nitrogenous base
• Nucleoside: consists of a sugar and a nitrogenous base

DNA Structure

• Characteristics:
  • Double helix
  • Antiparallel strands (5' to 3' and 3' to 5')
  • Bases paired by hydrogen bonds: A-T (2 bonds) and C-G (3 bonds)

The Flow of Genetic Information

• Central Dogma: DNA → RNA → Protein
  • Gene: a segment of DNA that codes for a specific protein
  • Transcription: DNA is copied into RNA
  • Messenger RNA (mRNA): carries the genetic code from DNA to the ribosomes
  • Translation: mRNA is translated into protein
• Ribosomes: site of protein synthesis

DNA Replication

• Characteristics:
  • Semiconservative Model: each new DNA molecule contains one original strand and one new strand
  • DNA Polymerase: enzyme that synthesizes new DNA strands
• Steps:
  • Initiation: DNA is unwound and primers are attached
  • Elongation: new DNA strands are synthesized
  • Termination: replication is completed

Transcription

• Gene: a segment of DNA that codes for a specific protein
• Characteristics:
  • RNA Polymerase: enzyme that synthesizes RNA
  • Steps:
    • Initiation: RNA polymerase binds to the promoter region of the gene
    • Elongation: RNA is synthesized
    • Termination: RNA polymerase reaches a termination signal

Translation

• Codons: three-nucleotide sequences in mRNA that code for specific amino acids
  • Sense Codons: code for amino acids
  • Nonsense Codons (Stop Codons): signal the end of translation
• Involves:
  • mRNA: carries the genetic code from DNA to the ribosomes
  • tRNA: brings specific amino acids to the ribosomes
  • rRNA: component of ribosomes
• Genetic Code: the set of rules that dictates which codons correspond to which amino acids

Operons

• Inducible Operons: genes are expressed only when needed
  • Lac Operon: involved in the metabolism of lactose
    • Promoter: region where RNA polymerase binds
    • Operator: region where the repressor protein binds
    • Structural Genes: code for proteins involved in lactose metabolism
    • Inducer: (ex: allolactose) binds to the repressor, preventing it from binding to the operator, allowing transcription
• Repressible Operons: genes are normally expressed unless repressed
  • Trp Operon: involved in the synthesis of tryptophan
    • Corepressor: (ex: tryptophan) binds to the repressor, activating it, preventing the repressor from binding to the operator, preventing transcription

Mutations

• Changes in the DNA sequence
• Types:
  • Substitution (Point Mutation): one base is replaced with another
    • Silent Mutation: no change in amino acid sequence
    • Missense Mutation: change in amino acid sequence
    • Nonsense Mutation: results in a stop codon, leading to a truncated protein
  • Frameshift Mutation: insertion or deletion of one or more bases, shifting the reading frame of the gene
    • Insertion: addition of a base
    • Deletion: removal of a base

Horizontal Gene Transfer

• Transfer of genetic material between existing cells
• Types:
  • Conjugation: transfer of genetic material through direct contact between cells
    • Sex Pilus: structure that connects donor and recipient cells
    • F+ Cell: contains the F factor (fertility factor)
    • F- Cell: lacks the F factor
    • Hfr Cell: F factor is integrated into the bacterial chromosome
  • Transformation: uptake of naked DNA from the environment
    • Griffith's Experiment: experiment that demonstrated bacterial transformation
    • S Strain: virulent (smooth)
    • R Strain: non-virulent (rough)
  • Transduction: transfer of genetic material through bacteriophages (viruses that infect bacteria)

Decontamination

• Removal or reduction of microbes
• Inanimate Objects (Fomites):
  • Sanitization: reduces microbial populations to safe levels
  • Disinfection: eliminates most pathogens
  • Sterilization: eliminates all microbes
• Living Tissue:
  • Degermation: reduces microbes on living tissue
  • Asepsis: techniques that prevent contamination of a sterile field

Relative Susceptibilities of Microbes to Antimicrobial Agents

• Prions: Most resistant
• Endospores: Highly resistant
• Naked Viruses: Less resistant
• Hardy Vegetative Bacteria: Resistant
• Enveloped Viruses: Less resistant
• Vegetative Bacteria: More susceptible

Factors that Influence the Killing Rate by Antimicrobial Agents

• Length of Exposure: longer exposure = greater effectiveness
• Number of Microbes/Microbial Load: higher load = more difficult to eliminate
• Nature of Microbes: some microbes are more resistant than others
• Mode of Action:
  • Microbicidal: kills microbes
  • Microbistatic: inhibits microbial growth
• Concentration of Agent: higher concentration = greater effectiveness
• Temperature of Environment: higher temperature = greater effectiveness
• Presence of Interfering Material: substances like blood, mucus, and feces can interfere with the effectiveness of antimicrobial agents

Heat

• Moist Heat: more effective than dry heat
  • Pasteurization: heating at 72°C for 15 seconds to kill pathogens in milk
  • Boiling Water: heating at 100°C for 10 minutes to kill most vegetative cells
  • Autoclave: heating at 121°C under pressure to sterilize
• Dry Heat: requires longer exposure times
  • Dry Oven: heating at 160-170°C for 2 hours to sterilize
  • Incineration: burning to ash to sterilize

Radiation

• Ionizing Radiation: sterilizes by damaging DNA
  • X-rays and Gamma Rays: highly penetrating
• Non-ionizing Radiation: disinfects by damaging DNA
  • Ultraviolet (UV) Rays: poorly penetrating, mainly for surface disinfection

Chemicals

• Antimicrobial Agents: chemicals that kill or inhibit microbial growth
• Targets:
  • Cell Wall: interfere with cell wall synthesis (ex: penicillins)
  • Plasma Membrane: disrupt the membrane (ex: polymyxins)
  • Nucleic Acid Synthesis: interfere with DNA or RNA synthesis (ex: fluoroquinolones)
  • Protein Synthesis: interfere with protein synthesis (ex: aminoglycosides, tetracyclines)
  • Protein Function: denature proteins (ex: heavy metals)

Chemotherapy

• Use of chemicals to treat disease
• Antimicrobial Drug: a chemical that kills or inhibits microbial growth
  • Antibiotic: an antimicrobial drug produced by a microbe (ex: penicillin)
    • Natural: produced by microbes
    • Synthetic: made in the laboratory
    • Semisynthetic: modified natural antibiotics
• Narrow Spectrum: effective against a limited range of microbes
• Broad Spectrum: effective against a wide range of microbes

Major Drug Targets

• Cell Wall: ex: penicillins, cephalosporins
• Plasma Membrane: ex: polymyxins
• Nucleic Acids: ex: fluoroquinolones, rifamycins
• Ribosomes: ex: aminoglycosides, tetracyclines, macrolides
• Metabolic Pathways: ex: sulfonamides, trimethoprim

Major Antibacterial Drugs

• Cell Wall Synthesis Inhibitors:
  • Penicillins: block transpeptidation, the final step in peptidoglycan synthesis
  • Miscellaneous: vancomycin, bacitracin
• Plasma Membrane Disruptors:
  • Polypeptides: disrupt membrane integrity (ex: polymyxins)
• Nucleic Acid Synthesis Inhibitors:
  • Fluoroquinolones: interfere with DNA gyrase, an enzyme involved in DNA supercoiling
  • Rifamycins: inhibit RNA polymerase, blocking transcription
• Protein Synthesis Inhibitors:
  • Aminoglycosides: bind to the 30S ribosomal subunit, causing misreading of mRNA
  • Tetracyclines: bind to the 30S ribosomal subunit, blocking tRNA binding
  • Macrolides: bind to the 50S ribosomal subunit, blocking peptide bond formation
• Folic Acid Synthesis Inhibitors:
  • Sulfamethoxazole: inhibits dihydropteroate synthase, an enzyme involved in folic acid synthesis
  • Trimethoprim: inhibits dihydrofolate reductase, an enzyme involved in folic acid synthesis

Acquisition of Drug Resistance

• Mechanism:
  • Gene Transfer:
    • Conjugation: transfer of resistance genes through plasmids
    • Transformation: uptake of resistance genes from the environment
    • Transduction: transfer of resistance genes by bacteriophages
  • Gene Mutations: mutations in genes involved in drug binding or metabolism
• Consequences:
  • Drug Inactivation: enzymes break down the drug
  • Decreased Permeability: the drug cannot enter the cell
  • Activation of Drug Pumps: the drug is pumped out of the cell
  • Change in Drug Binding Site: the drug cannot bind to its target
  • Use of Alternative Metabolic Pathway: the cell bypasses the pathway blocked by the drug

Interactions Between Drug and Host

• Organ Toxicity: some drugs can damage organs (ex: liver, kidneys)
• Allergic Responses: the immune system can react to the drug
• Alteration of Microbiota: drugs can kill beneficial bacteria, leading to opportunistic infections

The Process of Selecting an Antimicrobial Drug

• 1. Identifying the Microbe: cultures are obtained and identified
• 2. Testing for Drug Susceptibility:
  • Kirby-Bauer Test: a disk diffusion test
  • Minimum Inhibitory Concentration (MIC): the lowest concentration of a drug that inhibits growth
• 3. Patient Factors: age, health status, allergies, and other medications are considered.