Microbiology Study Guide

Introduction to Microbiology and Evolution of Microbes

Review Topics:

Characteristics of Life

All living organisms share the following characteristics:

• Organization: Cells are the basic units of life, forming the structure of all living organisms.

• Metabolism: The ability to obtain and use energy, which encompasses all the biochemical reactions occurring within cells.

• Homeostasis: The process of maintaining stable internal conditions despite changes in the external environment, such as temperature and pH.

• Growth and Development: The increase in size and maturity of an organism, following specific genetic instructions.

• Reproduction: The capability to produce offspring, either sexually or asexually, ensuring the continuation of the species.

• Response to Stimuli: The ability to react to environmental changes or stimuli, facilitating adaptation and survival.

• Evolution: Genetic changes that occur over generations, leading to the adaptation and diversification of species.

Cell Theory

The Cell Theory encompasses three fundamental principles:

1. All living organisms are composed of one or more cells, which serve as the building blocks of life.

2. The cell is the fundamental unit of life, responsible for carrying out all life processes.

3. All cells arise from pre-existing cells through the process of cell division, emphasizing the continuity of life.

Cell Structure

• Prokaryotic Cells (e.g., Bacteria, Archaea): Lack a nucleus, have a simpler structure, and typically contain a single circular chromosome, allowing for rapid reproduction.

• Eukaryotic Cells (e.g., Plants, Animals, Fungi, Protists): Encompass a nucleus and membrane-bound organelles, featuring a more complex structural organization and typically larger in size.

Macroevolution

Refers to large-scale evolutionary changes that occur over extended periods, leading to the formation of completely new species. This contrasts with microevolution, which involves small, incremental changes within a species.

Key Topics in Microbiology:

Development of Microbiology as a Science

• Spontaneous Generation: The now-disproved theory suggesting that living organisms could spontaneously appear from non-living matter, debunked through rigorous experimentation.

• Invention of the Microscope: Pioneered by Antonie van Leeuwenhoek, allowing the first observations of microorganisms and the subsequent expansion of microbiological study.

• Louis Pasteur's Experiments: Disproved spontaneous generation through the swan-neck flask experiments, demonstrating that microorganisms come from existing microbes.

• Koch’s Postulates: A series of criteria established by Robert Koch that links specific microbes to particular diseases, providing a foundation for microbial diagnostics.

• Germ Theory of Disease: The understanding that microorganisms are responsible for causing diseases, leading to advancements in public health and medicine.

Comparison of Bacteria, Archaea, and Eukarya:

• Bacteria: Prokaryotic organisms characterized by peptidoglycan cell walls and a wide diversity in metabolic processes.

• Archaea: Similar in shape to bacteria but without peptidoglycan, often adapted to extreme environments (extremophiles) with a unique RNA polymerase.

• Eukarya: Comprises eukaryotic organisms, which are more complex and include multicellular life forms such as plants, animals, fungi, and protists.

Biological Nomenclature Rules:

The system used for naming organisms is binomial, comprising two parts: the genus name (capitalized) and the species name (lowercase), both italicized or underlined. An example is Escherichia coli (E. coli).

Major Evolutionary Events:

1. Origin of Life: Estimated at around 3.8 billion years ago, marking the first emergence of living organisms.

2. First Prokaryotic Cells: Emerged approximately 3.5 billion years ago, representing the earliest forms of life.

3. Oxygen Revolution: Occurred around 2.5 billion years ago, leading to significant atmospheric changes due to the photosynthesis of cyanobacteria.

4. First Eukaryotic Cells: Appeared approximately 1.8 billion years ago, marking the rise of more complex cellular organisms.

5. Multicellular Life: Evolved around 600 million years ago, allowing for the diversification of life forms in various environments.

Eukaryote Formation Model:

• Endosymbiotic Theory: Proposes that mitochondria and chloroplasts originated from bacteria engulfed by early eukaryotic cells, leading to a symbiotic relationship that benefited both parties.

Terminology:

• Spontaneous Generation: The disproven idea that life originates from non-living material.

• Germ Theory: The concept that microorganisms can cause disease.

• Cell Theory: The principle stating that all living organisms are composed of cells.

• Endosymbiotic Theory: Explains the evolution of eukaryotic cells from prokaryotic ancestors through symbiosis.

• Prokaryote: Single-celled organisms without a nucleus.

• Eukaryote: Organisms with a defined, membrane-bound nucleus.

• Genus: The first part of the binomial nomenclature, always capitalized.

• Species: The second part of the binomial nomenclature, not capitalized.

• Heterotroph: Organisms that consume organic matter for energy.

• Autotroph: Organisms that produce their own food through photosynthesis or chemosynthesis.

• Abiogenesis: The theory concerning the origin of life from non-living materials.

• Cellular: Composed of cells.

• Acellular: Not made of cells (e.g., viruses).

Critical Thinking Questions and Answers:

Placing a Microbe in Evolutionary History:

• If a microbe is anaerobic and lacks a nucleus, it likely evolved in the early stages of Earth's history, while a photosynthetic microbe may date back to the oxygen revolution.

Rules for What Is Studied in Microbiology:

• Microbiology focuses on studying bacteria, viruses, fungi, archaea, and protists, but does not encompass larger organisms such as insects.

Classifying Organisms into Domains:

• Organisms with peptidoglycan in their cell walls are categorized as Bacteria; those thriving in extreme conditions without peptidoglycan are classified as Archaea, and organisms possessing a nucleus fall under Eukarya.

Inferring Relatedness from Names:

• For example, Staphylococcus aureus and Staphylococcus epidermidis share the same genus, indicating a close genetic relationship.

Sorting Organisms into Taxonomic Groups:

• An example includes gram-positive cocci with a thick cell wall being classified into the Firmicutes phylum.

• Give an example using microbes

Microbial Growth

Mechanism of Microbial Reproduction:

• Binary Fission: This asexual reproduction method involves a single bacterial cell dividing into two identical progeny cells, allowing quick population growth under favorable conditions.

Estimating Doubling Time and Growth Rate:

• Generation Time: Refers to the time required for a population of organisms to double its size.

• Exponential Growth Equation: The formula used is Nt = N0 × 2^n where Nt is the population at a given time, N0 is the initial population, and n is the number of generations completed.

Natural vs. Lab Growth:

• In natural environments, microbial growth is more complex and influenced by various environmental factors, including nutrient availability and interactions with other microorganisms (biofilms). In contrast, lab growth occurs in controlled conditions, often utilizing nutrient-rich media for optimal growth.

Growth in a Closed System (Batch Culture):

1. Lag Phase: Cells adapt to their environment, and no substantial growth occurs.

2. Exponential Phase: Characterized by rapid cell division and an increase in population.

3. Stationary Phase: Growth slows due to nutrient depletion and increased waste products.

4. Death Phase: The number of viable cells decreases exponentially as environmental conditions become unfavorable.

Environmental & Nutritional Conditions:

Temperature Classes:

• Psychrophiles: Microorganisms that thrive in cold environments, with optimal growth between -5°C to 15°C.

• Mesophiles: Organisms that prefer moderate temperatures, generally between 25°C and 45°C; many human pathogens belong to this group.

• Thermophiles: Heat-loving organisms that grow best at temperatures between 45°C and 70°C.

Oxygen Requirements:

• Obligate Aerobes: Organisms that require oxygen for survival.

• Facultative Anaerobes: Can grow in both the presence and absence of oxygen, utilizing aerobic respiration when oxygen is available.

• Obligate Anaerobes: Cannot tolerate oxygen and rely on anaerobic processes for energy production.

Terminology:

• Binary Fission: Method of asexual reproduction in bacteria.

• Generation Time: Time required for a population to double its number.

• Exponential Growth: Rapid increase in the number of organisms in a population.

• Lag Phase: Initial phase of adaptation with no growth.

• Exponential Phase: Phase of rapid growth.

• Stationary Phase: Growth rate levels off as resources become limited.

• Death Phase: Phase where the number of dying cells exceeds the number of new cells formed.

• Psychrophile, Mesophile, Thermophile: Categories based on optimal temperature for growth.

• Obligate Aerobe, Facultative Anaerobe, Obligate Anaerobe: Classifications based on oxygen requirements.

Critical Thinking Questions & Answers:

Given an object, can you determine the appropriate protocol to make it “safe”?This involves assessing the material of the object, the types of microorganisms it may harbor, and selecting an effective sterilization or disinfection method, such as autoclaving, using chemical disinfectants, or UV radiation to eliminate potential pathogens.

Control of Microbial Growth

Review Topics

Microbial growth can be effectively controlled through a combination of physical and chemical methodologies. The effectiveness of sterilization and disinfection protocols can be quantitatively assessed.

Key Topics in Microbial Control:

Methods of Microbial Control:

• Physical Methods:

• Heat: Methods such as autoclaving, pasteurization, and dry heat denature microbial proteins, effectively killing most microbes.

• Filtration: Physical removal of microbes from liquids and air, commonly utilized in water purification and sterilization processes.

• Radiation: Utilizes UV light or gamma rays to disrupt nucleic acids, effectively killing cells by damaging their DNA.

• Chemical Methods:

• Disinfectants: Agents like bleach, alcohol, and phenolic compounds that are effective at killing microbes on non-living surfaces.

• Antiseptics: Chemicals such as hydrogen peroxide, iodine, and alcohol deemed safe for application on human skin, used to prevent infection during medical procedures.

Effectiveness of Sterilization & Disinfection:

• Microbial Death Curve: A graphical representation of the rate of bacterial death over time when exposed to antimicrobial agents.

• Decimal Reduction Time (D-value): Defined as the time required to reduce the microbial population by 90% at a set temperature, this measure helps in establishing the efficiency of sterilization methods.

Classification of Medical Equipment Based on Infection Risk:

• Critical Instruments: Items that must be sterile, such as surgical tools, as they come into contact with sterile tissues.

• Semi-Critical Instruments: Tools that come into contact with mucous membranes require high-level disinfection, exemplified by endoscopes.

• Non-Critical Instruments: Equipment that contacts intact skin necessitates intermediate or low-level disinfection, like stethoscopes.

Terminology:

• Sterilization: The complete elimination of all forms of microbial life, including spores.

• Disinfection: The reduction of microbial load on inanimate surfaces, aiming to kill most pathogenic microorganisms.

• Sanitization: The process of lowering microbial counts on surfaces to safe levels.

• Bactericidal: Agents that actively kill bacteria.

• Bacteriostatic: Substances that inhibit bacterial growth without necessarily killing them.

• Decimal Reduction Time (D-value): Time required to decrease a microbial population by 90% under specified conditions.

• Critical Instrument: Must be sterile, e.g., surgical scalpel.

• Semi-Critical Instrument: Requires high-level disinfection, e.g., endoscope.

• Non-Critical Instrument: Requires intermediate or low-level disinfection, e.g., blood pressure cuff.

Critical Thinking Questions & Answers:

Given an object, can you determine the appropriate protocol to make it safe?

• Example: A surgical scalpel must be sterilized as it penetrates bodily layers and interacts with sterile tissues.

• Example: A stethoscope requires low-level disinfection since it contacts the skin and is less likely to introduce pathogens into deeper tissues.

Microbial Cell Structure

Review Topics:

Key structural differences at the cellular level among the three domains of life play a crucial role in defining their characteristics and functions. These cellular features grant bacteria specific functionalities essential for their survival and ecological roles.

Key Topics in Microbial Cell Structure:

Bacterial Cell Shapes and Arrangements:

• Shapes:

• Cocci: Spherical-shaped bacteria.

• Bacilli: Rod-shaped bacteria.

• Spirillum: Spiral-shaped bacteria.

• Vibrio: Comma-shaped bacteria.

• Arrangements:

• Strepto-: Chain-like arrangements of bacterial cells.

• Staphylo-: Clustered arrangements resembling grapes.

Bacterial Cell Wall Composition:

• Gram-Positive Bacteria: Feature a thick peptidoglycan layer that retains the crystal violet stain during the Gram staining process, producing a purple color.

• Gram-Negative Bacteria: Possess a thinner peptidoglycan layer coupled with an outer membrane containing lipopolysaccharides (LPS), which stains pink due to the loss of the crystal violet.

Extracellular Features & Their Functions:

• Capsule: A protective layer that defends against the host immune response and facilitates adherence to surfaces.

• Flagella: Tail-like structures that enable motility and direct movement in response to chemical gradients (chemotaxis).

• Pili/Fimbriae: Hair-like structures used for adhesion to surfaces and gene transfer between bacterial cells.

Intracellular Structures:

• Genome: Typically consists of a single circular DNA molecule that contains all genetic information necessary for replication and function.

• Ribosomes: Cellular machinery responsible for protein synthesis using messenger RNA templates.

• Endospores: Specialized structures formed by some bacteria, providing resistance to extreme environmental conditions, ensuring survival.

Terminology:

• Bacteria: Prokaryotic microorganisms essential to many ecological processes.

• Archaea: Prokaryotic extremophiles that often inhabit extreme environments, distinguished from bacteria primarily by genetic and biochemical markers.

• Eukarya: Domain encompassing all eukaryotic life forms.

• Peptidoglycan: A structural component of bacterial cell walls that provides rigidity and protection.

• Cocci, Bacilli, Spirillum, Vibrio: Different bacterial shapes that classify microbes based on morphology.

• Strepto-, Staphylo-: Descriptors for specific arrangements of bacterial cells.

• Endospore: A dormant form of bacteria that offers protection in harsh conditions.

• Flagella: Structures that facilitate movement in bacteria.

• Capsule: A protective and adhesive outer layer found in some bacteria.

• Biofilm: A community of bacteria encased in a matrix of polysaccharides, often formed on surfaces.

• LPS (Lipopolysaccharide): A significant component of the outer membrane in Gram-negative bacteria, playing a role in eliciting immune responses.

• Chemotaxis: Directed movement toward or away from chemical stimuli, crucial for bacterial survival.

Critical Thinking Questions & Answers:

Why is the bacterial cell wall important medically?

• The composition of the bacterial cell wall is crucial for determining antibiotic effectiveness; for instance, penicillin targets the peptidoglycan layer, significantly affecting Gram-positive bacteria, while Gram-negative bacteria resist certain antibiotics due to the protective LPS barrier.

Microbial Metabolism

Review Topics:

Microbes possess distinct metabolic capabilities, dictated by the enzymes they harbor, allowing them to transform energy through redox reactions. They utilize various energy sources, electron carriers, and carbon sources for growth and reproduction.

Key Topics in Microbial Metabolism:

Energy Storage and Transfer:

• ATP (Adenosine Triphosphate): The primary energy currency of all cells, used in numerous biochemical processes.

• Electron Carriers: Molecules such as NADH and FADH₂ transport electrons throughout various metabolic pathways, facilitating energy transfer.

Types of Metabolic Pathways:

• Aerobic Respiration: Utilizes oxygen as the final electron acceptor, yielding a high amount of ATP compared to anaerobic processes.

• Anaerobic Respiration: Involves alternative electron acceptors (like nitrate or sulfate), resulting in lower ATP yield than aerobic respiration.

• Fermentation: An anaerobic process that there is no electron transport chain, yielding products like lactic acid or ethanol while regenerating NAD+ necessary for glycolysis.

Catabolism of Carbon:

• Glycolysis: The initial phase of glucose metabolism, breaking glucose down into pyruvate and generating ATP and NADH.

• Krebs Cycle: A key metabolic pathway generating electron carriers (NADH and FADH₂) while releasing CO₂.

• Electron Transport Chain: The final step in aerobic respiration, where the majority of ATP is generated via oxidative phosphorylation.

Fermentation Pathways:

• Lactic Acid Fermentation: Carried out by some bacteria and muscle cells, producing lactic acid as a byproduct.

• Alcoholic Fermentation: Conducted by yeast, converting sugars to ethanol and CO₂.

Macromolecule Synthesis in Bacteria:

• Anabolism: The biosynthetic pathways where organisms build macromolecules, like proteins and nucleic acids, from simpler precursors, requiring ATP and reducing power.

Terminology:

• Exergonic/Endergonic: Classifications of reactions; exergonic reactions release energy, while endergonic reactions require energy input.

• Catabolism/Anabolism: Catabolism refers to the breakdown of molecules for energy release, whereas anabolism is the synthesis of complex molecules from smaller units.

• Metabolism: The overarching term for the cumulative biochemical processes occurring within a cell.

• Aerobic/Anaerobic Respiration: Refers to oxygen-dependent versus oxygen-independent forms of energy production.

• Fermentation: An anaerobic metabolic process generating ATP without necessitating an electron transport chain.

• ATP: The critical cellular energy molecule that powers various biological processes.

• Electron Transport Chain: The biochemical pathway where electron carriers facilitate ATP production through oxidative phosphorylation.

• Oxidation-Reduction (Redox) Reactions: Reactions that involve the transfer of electrons between molecules, fundamental to energy metabolism in microbes.

Critical Thinking Questions & Answers:

Why are enzymes important?

• Enzymes are critical as they lower the activation energy necessary for biochemical reactions, enabling those processes to occur more efficiently and at a faster rate under physiological conditions.

How does metabolism relate to energy requirements?

• Metabolism involves a delicate balance between energy input and output, as cells rely heavily on ATP for various processes; thus, maintaining this balance is essential for survival and function.

Metabolism encompasses all chemical reactions that sustain life, including catabolic pathways that break down molecules to release energy and anabolic pathways that utilize energy to construct cellular components.