Exam 2 study guide

1. Macromolecules

• Proteins

o Definition: __________________________________________________________

o Structure: _________________________________________________________

▪ Levels: Primary, Secondary, Tertiary, Quaternary

o Function: ___________________________________________________________

▪ Enzymatic catalysis, structure, transport, and regulation.

Drawing: Draw the general structure of an amino acid.
![Protein Structure Drawing]

• Carbohydrates

o Definition: __________________________________________________________

o Types: Monosaccharides, Disaccharides, Polysaccharides

o Function: __________________________________________________________

▪ Energy storage (e.g., starch, glycogen) and structure (e.g., cellulose).

Drawing: Draw a glucose molecule (monosaccharide).
![Glucose Drawing]

• Lipids

o Definition: __________________________________________________________

o Types: Fats, Oils, Phospholipids, Steroids

o Function: __________________________________________________________

▪ Membrane structure, energy storage, signaling.

Drawing: Draw a phospholipid structure with hydrophilic and hydrophobic regions.
![Phospholipid Drawing]

• Nucleic Acids

o Definition: __________________________________________________________

o Types: DNA, RNA

o Function: __________________________________________________________

▪ Store and transfer genetic information.

Drawing: Draw the structure of a nucleotide.
![Nucleotide Drawing]

2. Enzymes

• Definition: __________________________________________________________

o Enzymes are proteins that catalyze chemical reactions.

• Enzyme Function: _____________________________________________________

o Lower activation energy of reactions, speeding up the process.

• Factors Affecting Enzyme Activity:

o Temperature: _______________________________________________________

o pH: ______________________________________________________________

o Substrate concentration: __________________________________________

o Inhibitors: _________________________________________________________

▪ Competitive: _____________________________________________________

▪ Non-competitive: ________________________________________________

Drawing: Sketch a basic enzyme-substrate complex.
![Enzyme Drawing]

3. Metabolic Pathways

• Catabolism: ______________________________________________________

o Breakdown of complex molecules to release energy.

• Anabolism: ______________________________________________________

o Synthesis of complex molecules from simpler ones, using energy.

4. ATP (Adenosine Triphosphate)

• Role in Cells: _____________________________________________________

o Energy currency of the cell, used for various cellular processes.

• ATP Hydrolysis: __________________________________________________

o ATP → ADP + Pi (energy release).

Drawing: Draw ATP molecule and show hydrolysis.
![ATP Hydrolysis Drawing]

5. Redox Reactions

• Oxidation: ______________________________________________________

o Loss of electrons.

• Reduction: ______________________________________________________

o Gain of electrons.

• Electron Carriers:

o NAD+ / NADH: __________________________________________________

o FAD / FADH2: ___________________________________________________

o Coenzyme A: ___________________________________________________

Drawing: Draw an electron transport chain with NADH and FADH2 involvement.
![ETC Drawing

Chapter 8: Microbial Metabolism

Key Concepts

1. Overview of Metabolism

• Metabolism: ______________________________________________________

o All chemical reactions in a cell.

• Catabolic Pathways: ____________________________________________

o Breakdown of complex molecules.

• Anabolic Pathways: ____________________________________________

o Building up complex molecules from simpler ones, consuming energy.

2. Glycolysis

• Definition: ______________________________________________________

o The breakdown of glucose into pyruvate.

• Location: ________________________________________________________

o Cytoplasm.

• Key Steps:

o Energy Investment Phase: ___________________________________________________________

o Energy Payoff Phase: ___________________________________________________________

• Products: ______________________________________________________

o 2 ATP (net), 2 NADH, 2 Pyruvate.

Drawing: Draw the glycolysis pathway.
![Glycolysis Pathway Drawing]

3. Fermentation

• Definition: ______________________________________________________

o Anaerobic breakdown of glucose to produce ATP.

• Types of Fermentation:

o Lactic Acid: ___________________________________________________

o Alcohol: _______________________________________________________

• ATP Yield: _____________________________________________________

o 2 ATP per glucose molecule.

Drawing: Draw the fermentation process (e.g., lactic acid or alcohol fermentation).
![Fermentation Drawing]

4. Aerobic Respiration

• Definition: ______________________________________________________

o Breakdown of glucose in the presence of oxygen to produce ATP.

• Key Steps:

1. Glycolysis: _________________________________________________

2. Pyruvate Decarboxylation: ____________________________________

3. Citric Acid Cycle (Krebs Cycle): ___________________________

4. Electron Transport Chain (ETC): ____________________________

5. Oxygen as Final Electron Acceptor: ________________________

• ATP Yield: _____________________________________________________

o 38 ATP per glucose molecule.

Drawing: Draw the entire aerobic respiration pathway (include all 5 steps).
![Aerobic Respiration Pathway]

5. Anaerobic Respiration

• Definition: ______________________________________________________

o Similar to aerobic respiration, but uses an alternative electron acceptor (not oxygen).

• Alternative Electron Acceptors:

o Nitrate (NO₃⁻): ____________________________________________

o Sulfate (SO₄²⁻): ____________________________________________

o Carbonate (CO₃²⁻): _________________________________________

• ATP Yield: _____________________________________________________

o Less than aerobic respiration, but still produces ATP.

7. Chemotrophs vs. Phototrophs

• Chemotrophs: ____________________________________________________

o Organisms that obtain energy by oxidizing chemicals.

• Phototrophs: ___________________________________________________

o Organisms that obtain energy from sunlight.

8. Alternative Pathways

• Pentose Phosphate Pathway:

o Alternative to glycolysis.

• Entner-Doudoroff Pathway:

o Alternative to glycolysis in some bacteria.

Trophic Strategies

Microorganisms can be classified based on how they obtain energy and carbon. These classifications are important for understanding their metabolism and ecological roles.

a. Phototrophs

• Energy Source: Light.

• Carbon Source: Can be either autotrophic (fixing carbon from CO₂) or heterotrophic (using organic carbon).

Examples:

o Examples: Cyanobacteria, Algae, Plants.

• Anoxygenic Phototrophs: These organisms do not produce oxygen; they use compounds like hydrogen sulfide (H₂S) or organic molecules as electron donors.

o Examples: Purple sulfur bacteria (e.g., Chromatium), Green sulfur bacteria (e.g., Chlorobium), Heliobacteria.

b. Chemotrophs

• Energy Source: Chemicals.

• Carbon Source: Can be autotrophic (fixing CO₂) or heterotrophic (using organic carbon).

Types of Chemotrophs:

• Chemoautotrophs: These organisms use inorganic chemicals (such as hydrogen gas, hydrogen sulfide, or ammonia) to obtain energy and fix CO₂ to make organic molecules.

o Examples: Nitrosomonas (nitrifying bacteria), Sulfolobus (sulfur oxidizers), Thiobacillus (oxidize sulfur compounds), Methanogens (produce methane, found in anoxic environments).

• Chemoheterotrophs: These organisms obtain both energy and carbon from organic compounds.

o Examples: Most bacteria, fungi, and animals (e.g., Escherichia coli, Streptococcus species, humans).

Chapter 9: Microbial Growth

Key Concepts

1. Microbial Growth

• Definition:
Microbial growth refers to an increase in the number of cells, not the size of individual cells. Growth occurs through cell division, typically by binary fission in prokaryotes.

Drawing: Draw a diagram showing binary fission in a bacterial cell.
![Binary Fission Drawing]

2. The Growth Curve

• Phases of the Growth Curve:

1. Lag Phase: Cells are adjusting to the environment; no cell division occurs.

2. Log (Exponential) Phase: Rapid cell division and growth, where cells are most sensitive to antibiotics.

3. Stationary Phase: Nutrients become limited, and waste products accumulate, leading to a balance between cell division and death.

4. Death (Decline) Phase: Cells die due to depletion of nutrients and accumulation of toxic wastes.

Drawing: Draw the growth curve with labeled phases (Lag, Log, Stationary, Death).
![Growth Curve Drawing]

3. Factors Affecting Microbial Growth

• Physical Factors:

1. Temperature:

▪ Psychrophiles: Cold-loving organisms.

▪ Mesophiles: Moderate-temperature-loving organisms (human pathogens are often mesophiles).

▪ Thermophiles: Heat-loving organisms.

▪ Hyperthermophiles: Thrive in extremely hot environments (e.g., hydrothermal vents).

▪ Optimal Growth Temperature: The temperature at which the organism grows best.

Drawing: Create a graph showing growth rates of microorganisms at different temperatures.
![Temperature Growth Graph]

2. pH:

▪ Microorganisms grow best at different pH levels.

▪ Acidophiles: Prefer acidic environments (pH < 5.5).

▪ Neutrophiles: Prefer neutral pH (pH 6-8).

▪ Alkaliphiles: Prefer basic environments (pH > 8.5).

Drawing: Show the range of pH tolerance for different groups of microbes.
![pH Tolerance Chart]

3. Oxygen:

▪ Microorganisms have varying needs for oxygen.

▪ Obligate Aerobes: Require oxygen for growth.

▪ Obligate Anaerobes: Cannot grow in the presence of oxygen.

▪ Facultative Anaerobes: Can grow with or without oxygen.

▪ Aerotolerant Anaerobes: Tolerate oxygen but do not use it.

▪ Microaerophiles: Require oxygen but at lower concentrations than in the atmosphere.

Drawing: Draw a chart showing different oxygen requirements (e.g., Obligate Aerobes, Facultative Anaerobes, etc.).
![Oxygen Requirements Chart]

4. Water Availability:

▪ Microorganisms require water to grow, but some are adapted to dry conditions.

▪ Halophiles: Salt-loving organisms that thrive in high salt concentrations.

▪ Xerophiles: Organisms that grow in dry environments.

4. Measuring Microbial Growth

• Methods of Measuring Growth:

1. Direct Methods:

▪ Plate Counts: Counting colonies on agar plates.

▪ Filtration: Used for low numbers of organisms in liquid samples.

▪ Microscopic Counts: Counting cells under a microscope (using a hemocytometer or other counting chambers).

Drawing: Draw a petri dish with colonies to illustrate plate count.
![Plate Count Drawing]

2. Indirect Methods:

▪ Turbidity: Measuring the cloudiness of a culture with a spectrophotometer. The more cells present, the more light is scattered.

▪ Metabolic Activity: Measuring the byproducts of microbial metabolism (e.g., CO₂ production).

▪ Dry Weight: Weighing the microbial biomass after drying.

5. The Role of Nutrients in Growth

• Essential Nutrients:

1. Macronutrients: Required in large quantities for microbial growth.

▪ Examples: Carbon, Nitrogen, Phosphorus, Sulfur, Potassium, Magnesium, Calcium, Iron.

2. Micronutrients: Required in trace amounts, often as cofactors for enzymes.

▪ Examples: Zinc, Copper, Manganese, Molybdenum, Cobalt.

• Nutrient Media:

o Complex Media: Contain complex materials like beef extract or yeast extract (e.g., nutrient broth).

o Defined Media: Have a precise chemical composition.

o Selective Media: Encourage the growth of specific microorganisms and inhibit others.

o Differential Media: Allow distinguishing between different microorganisms based on appearance (e.g., color changes).

Drawing: Draw a petri dish with differential media showing microbial growth with varying color changes.
![Differential Media Drawing]

6. Biofilms and Microbial Communities

• Definition:
Biofilms are complex communities of microorganisms that adhere to surfaces and are surrounded by a self-produced matrix of extracellular polymeric substances (EPS). Biofilms can form on living tissues, medical devices, and industrial systems.

Key Features of Biofilms:

o Microbial cells in biofilms are more resistant to antibiotics and environmental stresses.

o Biofilms are involved in many infections and are difficult to treat due to their resistance.

Drawing: Draw a diagram of a biofilm with layers of microbes embedded in the extracellular matrix.
![Biofilm Diagram]

7. Control of Microbial Growth

• Physical Methods:

o Heat:

▪ Autoclaving: High pressure and temperature used to sterilize materials.

▪ Pasteurization: Mild heat treatment to reduce microbial load without altering the product.

▪ Dry Heat: Used for sterilizing materials that can tolerate high temperatures.

o Filtration: Removal of microorganisms from liquids or gases using filters with small pores.

o Radiation: UV light and ionizing radiation (e.g., X-rays, gamma rays) to kill or sterilize microorganisms.

Drawing: Draw the process of autoclaving or pasteurization.
![Autoclave Drawing]

• Chemical Methods:

o Disinfectants: Used on surfaces to kill or inhibit microbial growth.

o Antiseptics: Used on living tissues to reduce microbial growth.

o Sterilants: Chemical agents that kill all forms of life, including spores.

Drawing: Draw examples of disinfectants (e.g., bleach, alcohol) or antiseptics (e.g., iodine)