BIOL 220 General Microbiology Study Guide

**BIOL 220 General Microbiology** **Exam 1 Study Guide** This study guide contains a list of guiding questions to prepare for the exam. It is not an exhaustive list of topics. Focus on the information covered in the lectures and use the textbook to enhance your understanding. Topics listed below a...

**BIOL 220 General Microbiology** **Exam 1 Study Guide** This study guide contains a list of guiding questions to prepare for the exam. It is not an exhaustive list of topics. Focus on the information covered in the lectures and use the textbook to enhance your understanding. Topics listed below are based off the learning objectives posted at the beginning of each lecture, and I've added additional topics/specificity to match the exam questions. **The exam is worth 100 points:** 25 multiple choice questions (worth 3 points each) 10 fill-in-the-blank questions (worth 1 point each) 3 short answer questions (choose 3 of 5 to answer, worth 5 points each) **Lectures 1 & 2: Course Overview & the History of Microbiology** - Know the definition of microbe. - Organism needing a microscope to be seen. - Microscopic organism (bacteria, virus, fungi, or protozoa) that can exist as a single cell or in a colony. - Provide examples of microbes that profoundly affected human history. - COVID-19 - Smallpox - Tuberculosis - Black Plague - Understand how all life forms are categorized on the phylogenetic tree of life. - **Bacteria** -- Simple, single-celled microbes (e.g., E. coli). - **Archaea** -- Single-celled microbes that live in extreme environments. - **Eukarya** -- Organisms with complex cells, including **protists, fungi, plants, and animals** (e.g., humans, trees, mushrooms). - Relate the biological diversity present among prokaryotes to that of eukaryotes. - **Prokaryotes (Bacteria & Archaea)** are more diverse in how they get energy and survive in extreme places. - **Eukaryotes (Plants, Animals, Fungi, Protists)** are more complex, with specialized cells and organelles. - Prokaryotes have **more metabolic variety**, while eukaryotes have **more structural complexity**. - Understand how endosymbiosis of prokaryotes contributed to eukaryotic evolution. - Eukaryotic cells evolved when larger cells **engulfed** smaller bacteria, which later became **mitochondria** (for energy) and **chloroplasts** (for photosynthesis). This helped eukaryotes grow and become more complex. **Lecture 3: Observing the microbial cell** - Describe ways to detect and observe microbe organisms. - **Microscopy** -- **Light microscopes** for basic cell shapes, **electron microscopes** for detailed structures. - **Staining** -- **Gram staining** differentiates bacterium types; **fluorescent stains** highlight specific cell parts. - **Culture Methods** -- Growing microbes on **agar plates** or in liquid media to study colonies. - **Molecular Techniques** -- **PCR** detects microbial DNA; **sequencing** identifies species. - **Biochemical Tests** -- Identify microbes based on how they process nutrients or chemicals. - Compare and contrast cell envelopes of Gram positive and negative bacteria. - **Gram-positive** bacteria have a **thick** peptidoglycan layer and no outer membrane. - **Gram-negative** bacteria have a **thin** peptidoglycan layer and an **outer membrane** that provides extra protection - Describe the structure, function, and importance of microbial cell membranes. **Structure** - Composed of a **phospholipid bilayer** with embedded **proteins**. - **Bacteria & Eukarya** have membranes with **ester-linked phospholipids**, while **Archaea** have unique **ether-linked lipids** for stability in extreme conditions. **Function** - **Barrier** -- Controls what enters and exits the cell. - **Energy Production** -- In prokaryotes, the membrane is the site of **ATP generation** (electron transport chain). - **Transport** -- Uses proteins for **nutrient uptake** and **waste removal**. - **Communication** -- Detects signals from the environment via **receptors**. - **Structural Support** -- Maintains cell shape and interacts with the cell wall. **Importance** - Essential for **cell survival** and **adaptation** in different environments. - In bacteria, **antibiotics like polymyxins** target the membrane, disrupting its function. - In archaea, unique membranes allow survival in **extreme heat, acidity, and salinity**. - Understand how membrane components impact membrane fluidity. **Fatty Acids** - Unsaturated (bent tails) → More fluid. - Saturated (straight tails) → Less fluid. **Temperature** - High temp → More fluid. - Low temp → Less fluid. **Sterols & Hopanoids** - Cholesterol (eukaryotes) and hopanoids (bacteria) help stabilize fluidity. **Lipid Chain Length** - Short chains → More fluid. - Long chains → Less fluid. **Membrane Proteins** - Can adjust local fluidity. - Understand why Gram-positive bacteria are more susceptible to destruction by penicillin than Gram-negative bacteria. - **Gram-positive bacteria** are easily killed by **penicillin** because they have a **thick peptidoglycan wall** but **no outer membrane** to block the  - **Gram-negative bacteria** are more **resistant** because their **outer membrane** protects their thin peptidoglycan layer. **Lecture 4: Microbial cell structure and function** - Describe the steps in the process of microbial cell division. - **DNA Replication** -- The bacterial chromosome copies itself. - **Cell Elongation** -- The cell grows, and the two DNA copies move apart. - **Septum Formation** -- A **dividing wall (septum)** forms in the middle. - **Cell Separation** -- The septum splits, creating **two identical daughter cells**. - Understand the implications of coupled transcription and translation in prokaryotes. - In **prokaryotes**, **transcription and translation happen at the same time** because there is **no nucleus**. - Faster growth -- Proteins are made quickly. - Quick response -- Cells adapt fast to changes. - More mutation effects -- Mistakes affect proteins right away. - Antibiotic target -- Some drugs block this process to kill bacteria. - Describe the function and role of specialized structures like thylakoids, carboxysomes, storage granules, pili, and flagella. - T**hylakoids** -- Help **photosynthetic bacteria** capture light for energy. - **Carboxysomes** -- Store **enzymes** to help bacteria use CO₂ efficiently. - **Storage Granules** -- Save **nutrients** for survival in tough conditions. - **Pili** -- Help bacteria **stick to surfaces** or **share DNA**. - **Flagella** -- Help bacteria **move** toward food or away from danger. **Lecture 5: Nutrition, Growth, and Development** - Define the nutrients microbes need to grow. - **Macronutrients (large amounts)** - **Carbon, Nitrogen, Phosphorus, Sulfur, Oxygen, Hydrogen** → Build cells and make energy. - **Micronutrients (small amounts)** - **Iron, Magnesium, Zinc** → Help enzymes work. - **Growth Factors** - **Vitamins, Amino Acids** → Some microbes can't make these, so they must get them from the environment. - Know the basic mechanisms employed by microbes to obtain these nutrients. - **Passive Diffusion** -- Small molecules (O₂, CO₂) enter freely. - **Facilitated Diffusion** -- Transport proteins help move molecules **without energy**. - **Active Transport** -- Uses **energy** to pull in nutrients. - **Group Translocation** -- Modifies nutrients as they enter (e.g., glucose). - **Siderophores** -- Help microbes **grab iron** from the environment. - **Endocytosis (only in eukaryotes)** -- Engulfs large particles. - Define terms relating to trophic state, such as heterotrophs, autotrophs, photoautotrophs and chemoautotrophs. - **Heterotrophs** -- Eat **organic food** (e.g., animals, fungi). - **Autotrophs** -- Use **CO₂** to make food (e.g., plants, some bacteria). - **Photoautotrophs** -- Use **light + CO₂** (e.g., plants, cyanobacteria). - **Chemoautotrophs** -- Use **chemicals + CO₂** (e.g., deep-sea bacteria). - Know the basic techniques to culture microbes (including types of media). **How to Culture Microbes** - Keep it sterile -- Use aseptic techniques to prevent contamination. - Inoculate -- Transfer microbes onto a growth medium. - Incubate -- Keep microbes at the right temperature to grow. **Types of Growth Media** - Defined -- Exact ingredients are known. - Complex -- Contains unknown nutrient amounts (e.g., nutrient broth). - Selective -- Only certain microbes grow (e.g., MacConkey agar). - Differential -- Shows differences between microbes (e.g., blood agar). - Enriched -- Extra nutrients for picky microbes (e.g., chocolate agar). - Analyze a bacterial growth curve and specific stages of growth and interpret comparative growth curves. **Bacterial Growth Curve & Stages** - Lag Phase -- Bacteria adjust but don't grow yet. - Log Phase -- Fastest growth, bacteria multiply quickly. - Stationary Phase -- Growth slows as food runs out and waste builds up. - Death Phase -- Bacteria die as conditions become toxic. **Comparing Growth Curves** - Fast log phase → Bacteria grow quickly. - Long lag phase → Bacteria take longer to adjust. - Long stationary phase → Some bacteria survive longer. - Rapid death phase → Harsh conditions kill bacteria quickly. - Relate doubling time and number of generations to calculate total numbers of bacteria. - Doubling Time -- Time for bacteria to double in number. - Number of Generations: n=Total time/Doubling time ​ - Final Bacteria Count: N=N0×2nN=N0​×2n - N0​ = Starting bacteria - n = Number of times they double - N = Final bacteria count **Lecture 6: Environmental factors and microbial growth** - Know the basic classifications used to describe microbes based on their growth under various laboratory-controlled conditions and how that relates to their environment. - Temperature: - Cold lovers (Psychrophiles) -- 0--20°C - Moderate lovers (Mesophiles) -- 20--45°C (human pathogens) - Heat lovers (Thermophiles) -- 45--80°C - Extreme heat lovers (Hyperthermophiles) -- 80°C+ - Oxygen: - Needs oxygen (Obligate Aerobes) - Dies in oxygen (Obligate Anaerobes) - Prefers oxygen but can grow without it (Facultative Anaerobes) - Ignores oxygen (Aerotolerant Anaerobes) - Needs low oxygen (Microaerophiles) - pH (Acidity): - Acid lovers (Acidophiles) -- pH \< 5 - Neutral lovers (Neutrophiles) -- pH \~7 (most human pathogens) - Base lovers (Alkaliphiles) -- pH \> 9 - Salt: - Needs salt (Halophiles) - Tolerates salt (Halotolerant) - Explain how microbes adapt to variations or extremes in temperature, pressure, pH, levels of oxygen and osmotic stress. **Temperature:** - Cold-loving microbes → Have flexible membranes and antifreeze proteins. - Heat-loving microbes → Have heat-stable enzymes and stronger membranes. **Pressure:** - Deep-sea microbes strengthen membranes and proteins to survive high pressure. **pH:** - Acid-lovers (low pH) → Pump out extra acid and use acid-resistant enzymes. - Base-lovers (high pH) → Use special ion pumps to keep pH balanced. Oxygen: - No-oxygen microbes → Use fermentation instead of respiration. - Oxygen-using microbes → Have enzymes to remove toxic oxygen byproducts. **Osmotic Stress (Salt & Water Balance):** - Salt-loving microbes store special solutes to prevent water loss. - Freshwater microbes control solutes to prevent too much water from entering. - Describe the different ways humans use stress to control or eliminate microbes. - **Heat** -- Boiling, autoclaving, or pasteurization **kills microbes**. - **Cold** -- Refrigeration and freezing **slow growth** but don't always kill. - **Chemicals** -- Bleach, alcohol, and antibiotics **destroy microbes**. - **Salt & Sugar** -- Dry out microbes, stopping their growth (e.g., pickling, curing meat). - **Acids & Bases** -- Vinegar, lemon juice, and alkaline cleaners **kill bacteria**. - **Oxygen** -- Some bacteria **die when exposed to air**. - **Radiation** -- UV light and X-rays **damage DNA**, killing microbes. **Lecture 7: Microbial diversity** - Understand that all living organisms organized into three domains of life and the scientific evidence that supports this organization. **Three Domains of Life** - Bacteria -- Simple, single-celled microbes without a nucleus (e.g., E. coli). - Archaea -- Single-celled microbes that live in extreme places (e.g., hot springs). - Eukarya -- Complex cells with a nucleus, including plants, animals, fungi, and protists. **Why Scientists Use This System** - DNA & RNA studies show bacteria, archaea, and eukaryotes are very different. - Cell structure -- Archaea have unique membranes not found in bacteria or eukaryotes. - Metabolism & genes -- Archaea are a mix of bacteria and eukaryotes in how they function. - Describe similarities and differences between bacteria, archaea, and eukaryotes. **Key Differences** - Bacteria & Archaea are both prokaryotes (no nucleus), but archaea have unique membranes and live in extreme environments. - Eukaryotes are larger, more complex, and have a nucleus. **Key Similarities** - Bacteria & Archaea both reproduce by binary fission and have circular DNA. - Archaea & Eukaryotes share similar gene processing (e.g., introns, RNA polymerase). - Understand that phylogenetic trees represent evolutionary histories of organisms and how such trees are interpreted. **What is a Phylogenetic Tree?** - A phylogenetic tree is a diagram that shows how organisms are related by evolution. **How to Read It:** - Root -- The earliest ancestor of all organisms in the tree. - Branches -- Show how species split and evolve. - Nodes -- Where branches meet, showing a common ancestor. - Leaves (Tips) -- The organisms being compared. **Key Ideas:** - Closer branches = More closely related. - Longer branches = More genetic changes over time. - Shared nodes = A common ancestor between species. - Give examples of major microbial phyla. **Bacteria** - Proteobacteria -- Includes E. coli (gut bacteria) and Salmonella (food poisoning). - Firmicutes -- Includes Bacillus (spore-forming) and Staphylococcus (skin bacteria). - Actinobacteria -- Includes Streptomyces (makes antibiotics) and Mycobacterium (causes TB). - Cyanobacteria -- Photosynthetic bacteria like Anabaena (makes oxygen). - Spirochaetes -- Spiral bacteria like Treponema (syphilis) and Borrelia (Lyme disease). **Archaea** - Euryarchaeota -- Includes methanogens (make methane) and halophiles (love salt). - Crenarchaeota -- Includes thermophiles (love heat, found in hot springs). **Eukarya (Microbial Protists & Fungi)** - Ascomycota (Fungi) -- Includes yeast (used for bread & beer). - Amoebozoa (Protists) -- Includes Amoeba (moves with \"fake feet\"). **Lecture 8: Origins and genome evolution** - Understand how microbes have helped to shape current environmental conditions on Earth. - **Made Oxygen** 🌱 -- **Cyanobacteria** created Earth's oxygen-rich air through photosynthesis. - **Helped Plants Grow** 🌾 -- **Nitrogen-fixing bacteria** give plants nutrients. - **Recycled Nutrients** ♻️ -- **Bacteria & fungi** break down dead matter, returning nutrients to the soil. - **Affect Climate** 🌡️ -- **Methanogens** produce methane, and microbes help store & release carbon. - **Support Soil Life** 🌍 -- Microbes improve **soil health** and help plant roots grow. - **Help Form Clouds** ☁️ -- Some microbes release particles that make rain clouds. - Describe the different lines of geological evidence for early life on Earth. - **Stromatolites 🪨** -- Layered rocks made by **ancient bacteria** (\~3.5 billion years old). - **Microfossils 🔬** -- Tiny **fossilized bacteria** found in old rocks (\~3.4 billion years old). - **Carbon Isotopes 🧪** -- Chemical signs in rocks (\~3.8 billion years old) show **microbial activity**. - **Banded Iron Formations ⛏️** -- Layers of iron in rocks prove early microbes **made oxygen**. - **Organic Molecules 🏔️** -- Old rocks contain ancient **biological molecules** from microbes - Understand how microbes undergo genetic divergence and the role of natural selection. - Mutations -- Random DNA changes create new traits. - Gene Swapping -- Microbes share DNA using plasmids or viruses. - DNA Rearrangement -- Genes get copied or shuffled, leading to new functions. - Helpful changes → Microbes survive and grow (e.g., antibiotic resistance). - Harmful changes → Microbes die out. - Neutral changes → No effect now but might help later. - Understand the application of and assumptions associated with the "molecular clock". **What is the Molecular Clock?** - A tool that estimates when species evolved by tracking DNA changes over time. - Based on the idea that mutations happen at a steady rate. **Key Assumptions** - Mutations occur at a constant rate -- DNA changes happen predictably over time. - More mutations = More time passed -- The more genetic differences, the older the split. - Different genes change at different speeds -- Some evolve fast, some slow, so scientists choose the right gene for each study. **Uses** - Find out when species evolved 🦠➡️🧬 - Track viruses & diseases (e.g., COVID-19 variants) 🦠 - Study common ancestors in evolution 🌍 - Differentiate between mechanisms of vertical and horizontal gene transfer. - **Vertical transfer** = **generation to generation** (like parents to children). - **Horizontal transfer** = **between unrelated microbes** (like bacteria swapping genes).