Exam 1 Review
The BIOL 2041 Lecture Exam 1 Review covers topics from chapters 1, 3, 4, 5, and 6. The review consists of definitions, comparisons, and descriptions related to microbiology.
Chapter 1:
Define microbiome, normal biota and transient microbiota: The microbiome (microbiota) is a group of microbes that live stably on or in the human body. Normal microbiota refers to the collection of acquired microorganisms on or in a healthy human being. Transient microbiota colonizes the body fleetingly.
Binomial nomenclature: Each organism has two names: the genus and the specific epithet. Scientific names are italicized or underlined, with the genus capitalized and the specific epithet in lowercase.
Characteristics of Bacteria: Bacteria are prokaryotes with peptidoglycan cell walls that divide via binary fission and can derive nutrition from organic or inorganic chemicals or photosynthesis.
Characteristics of Fungi: Fungi are eukaryotes that have chitin cell walls and absorb organic chemicals for energy.
Characteristics of Algae: Algae are eukaryotes with cellulose cell walls that use photosynthesis for energy, producing oxygen and carbohydrates.
Characteristics of Protozoa: Protozoa are eukaryotes that absorb or ingest organic chemicals and may be motile via pseudopods, cilia, or flagella.
Characteristics of Virus: Viruses are acellular and consist of a DNA or RNA core surrounded by a protein coat, being replicated only when they are in a living host cell.
Biogenesis vs spontaneous generation: Spontaneous generation is the hypothesis that life arises from nonliving matter, while biogenesis is the hypothesis that living cells arise only from preexisting living cells.
Scientists and their contribution for postulates, immunization, magic bullet theory, antibiotic, antisepsis
Robert Koch discovered that a bacterium causes anthrax and provided the experimental steps (Koch’s postulates) to demonstrate that a specific microbe causes a specific disease.
Edward Jenner inoculated a person with cowpox virus, who was then immune to smallpox.
Paul Ehrlich speculated about a "magic bullet" that could destroy a pathogen without harming the host.
Alexander Fleming discovered the first antibiotic, penicillin, made by Penicillium fungus that killed S. aureus.
Joseph Lister used a chemical antiseptic (phenol) to prevent surgical wound infections.
Definitions:
Bacteriology is the study of bacteria.
Mycology is the study of fungi.
Parasitology is the study of protozoa and parasitic worms.
Virology is the study of viruses.
Microbial genetics is the study of how microbes inherit traits.
Genomics is the study of an organism’s genes.
Molecular biology is the study of how genetic information is carried in molecules of DNA.
Recombinant technology involves DNA made from two different sources.
Chapter 3:
mL, Liter, uL conversion: 1 μm = 10⁻⁶ m = 10⁻³ mm and 1 nm = 10⁻⁹ m = 10⁻⁶ mm
Total magnification calculation: Total magnification is calculated by multiplying the objective lens magnification by the ocular lens magnification.
Resolution definition: Resolution is the ability of the lenses to distinguish two points.
Why use immersion oil: Immersion oil is used to keep light from refracting.
Types of Light microscope: Types of light microscopy include compound light microscopy, darkfield microscopy, phase-contrast microscopy, differential interference contrast (DIC) microscopy, fluorescence microscopy, and confocal microscopy.
Transmission and Scanning electron microscope: Transmission electron microscopy (TEM) is used for viewing detailed structures, with high resolution and magnification, while scanning electron microscopy (SEM) is used to view the surface of a specimen.
How is electron microscope different from light microscope: Electron microscopy uses electrons instead of light, providing greater resolution due to the shorter wavelength of electrons.
Differentiate an acidic stain from basic stain: In a basic dye, the chromophore is a cation, while in an acidic dye, the chromophore is an anion.
Gram stain steps: Gram stain steps include crystal violet application, iodine application (mordant), alcohol wash (decolorization), and safranin application (counterstain). Gram-positive bacteria appear purple, and gram-negative bacteria appear pink after staining.
Different stains used in Acid fast and Special stains: Acid-fast stain uses carbolfuchsin, acid-alcohol, and methylene blue. Special stains include negative staining for capsules, endospore staining, and flagella staining.
Why air dry and heat fix during smear preparation: The source does not specify why to air dry and heat fix during smear preparation, however, it does describe preparing smears for staining.
Chapter 4:
Compare Prokaryotic vs eukaryotic cells: Prokaryotic cells lack a nucleus and membrane-enclosed organelles, while eukaryotic cells have a nucleus and membrane-bound organelles.
Shape and arrangement of bacterial cells: Bacterial cells can be coccus (spherical), bacillus (rod-shaped), or spiral. Arrangements include pairs (diplococci, diplobacilli), clusters (staphylococci), and chains (streptococci, streptobacilli).
Function of pili: Pili are involved in motility and DNA transfer.
Function of flagella: Flagella propel bacteria.
Function of cilia: Cilia are used for locomotion or moving substances along the cell surface.
Function of fimbriae: Fimbriae allow for attachment and are involved in biofilm formation.
Parts of Flagella: The parts of flagella are the filament, hook, and basal body.
Capsule: Capsules prevent phagocytosis.
Glycocalyx: Glycocalyx contributes to virulence.
Parts of gram-positive cell wall: Gram-positive cell walls have a thick peptidoglycan layer and contain teichoic acids.
Parts of gram-negative cell wall: Gram-negative cell walls have a thin peptidoglycan layer, a periplasmic space, and an outer membrane made of lipopolysaccharide (LPS).
Full name of NAM and NAG: NAM is N-acetylmuramic acid, and NAG is N-acetylglucosamine.
Gram stain steps: Gram stain steps include crystal violet, iodine, alcohol, and safranin.
Structure of the cell wall: The cell wall is made of peptidoglycan in bacteria.
Function and chemistry of plasma/cell membrane: The plasma membrane is a phospholipid bilayer with peripheral and integral proteins, selectively permeable, and contains enzymes for ATP production.
Simple diffusion: Simple diffusion is the movement of a solute from an area of high concentration to an area of low concentration.
Facilitated diffusion: Facilitated diffusion involves integral membrane proteins that facilitate the movement of ions or larger molecules across the membrane with the concentration gradient.
Active diffusion processes: Active transport requires a transporter protein and ATP to move substances against the concentration gradient.
Osmosis: Osmosis is the net movement of water across a selectively permeable membrane from an area of higher water concentration to an area of lower water concentration.
Plasmolysis: Plasmolysis is the shrinkage of the cell's cytoplasm due to water moving out of the cell in a hypertonic environment.
Osmotic lysis: This occurs in a hypotonic solution where water moves into the cell, causing it to swell and potentially burst.
Isotonic: An isotonic solution has equal solute concentrations inside and outside the cell, resulting in no net water movement.
Hypertonic: A hypertonic solution has a higher solute concentration outside the cell, causing water to move out.
Hypotonic cells: A hypotonic solution has a lower solute concentration outside the cell, causing water to move in.
Define organelles: The review does not explicitly define organelles.
Structure and function of nucleus: The nucleus has a double membrane structure (nuclear envelope) that encloses the cell’s DNA.
Structure and function of mitochondria: Mitochondria have a double membrane, inner folds (cristae), and are involved in cellular respiration (ATP production).
Structure and function of chloroplast: Chloroplasts are the location of photosynthesis and contain flattened membranes (thylakoids) that contain chlorophyll.
Structure and function of Rough ER: Rough ER is studded with ribosomes and is the site of protein synthesis.
Structure and function of Smooth ER: Smooth ER synthesizes cell membranes, fats, and hormones.
Structure and function of Golgi apparatus: The Golgi apparatus modifies proteins from the ER and transports them via secretory vesicles to the plasma membrane.
Structure and function of ribosome: Ribosomes are the sites of protein synthesis.
Structure and function of peroxisome: Peroxisomes oxidize fatty acids and destroy H2O2.
Structure and function of lysosome: Lysosomes contain digestive enzymes.
Structure and function of centrosome: Centrosomes are the organizing center for the mitotic spindle and play a critical role in cell division.
Structure of plasma membrane in eukaryotes vs prokaryotes: Eukaryotic plasma membranes contain sterols, while prokaryotic membranes do not.
Which organelles and organisms have 70S ribosome: Chloroplasts and mitochondria.
Which type of cells have 80S ribosome: Eukaryotic cells.
Endospore: Endospores are resting cells resistant to desiccation, heat, chemicals, and radiation.
How they are formed: Endospores are produced inside certain bacterial cells when nutrients are depleted.
Which genera are involved: Bacillus and Clostridium.
Endosymbiotic theory of evolution: Larger bacterial cells engulfed smaller bacterial cells, developing the first eukaryotes.
Chapter 5:
What is Anabolism: Anabolism uses energy and building blocks to build complex molecules.
What is Catabolism: Catabolism breaks down complex molecules, providing energy and building blocks for anabolism.
Identify components of enzyme: Enzymes have an apoenzyme (protein portion) and a cofactor (nonprotein component).
Mechanism of enzyme action: Enzymes act on a specific substrate to form an enzyme-substrate complex, transforming the substrate into products.
How enzyme function: Enzymes speed up chemical reactions by lowering the activation energy.
Factors affecting the enzyme activity: Factors affecting enzyme activity include pH, temperature, substrate concentration, and inhibitors.
Oxidation process: Oxidation is the removal of electrons.
Reduction process: Reduction is the gain of electrons.
Number of ATP production in glycolysis: Glycolysis produces a net gain of 2 ATP molecules.
Number of ATP production in Krebs cycle: The Krebs cycle generates 2 ATP.
Number of ATP production in aerobic respiration: The review does not explicitly state the total ATP production in aerobic respiration, but it involves glycolysis, the Krebs cycle, and the electron transport chain.
Number of ATP production in fermentation: Fermentation produces only small amounts of ATP.
Chemiosmosis: Chemiosmosis is the process wherein ATP is generated from ADP using the energy derived from the electron transport chain.
Oxidative phosphorylation: Oxidative phosphorylation involves electrons transferred along an electron transport chain, releasing energy to generate ATP.
Photophosphorylation: Photophosphorylation occurs in photosynthetic cells, where light energy is converted to chemical energy in the form of ATP.
Substrate level phosphorylation: ATP is generated when a high-energy phosphate is directly transferred from a phosphorylated compound to ADP.
Electron transport chain: Electrons pass down the electron transport chain while protons are pumped across the membrane, establishing a proton gradient.
Products of glycolysis: The products of glycolysis are ATP, NADH, and pyruvic acid.
Products of Krebs cycle: The products of the Krebs cycle are ATP, NADH, and carbon dioxide.
How many ATP are formed from 1 NADH: The review does not specify the exact number of ATP formed from 1 NADH.
How many ATP are formed from 1 FADH2: The review does not specify the exact number of ATP formed from 1 FADH2.
Starting molecule of glycolysis: Glucose.
Starting molecule of Krebs cycle: Pyruvic acid.
Starting molecule of electron transport chain: NADH.
Final electron acceptor in aerobic respiration: Oxygen.
Final electron acceptor in anaerobic respiration: A molecule other than oxygen.
Final electron acceptor in fermentation: An organic molecule (pyruvate or a derivative).
Light vs dark reaction of photosynthesis: Light reactions convert light energy into chemical energy (ATP and NADPH), while dark reactions use ATP and NADPH to convert carbon dioxide into glucose.
Metabolic diversity among organisms:
Photoautotrophs use light as an energy source and CO2 as a carbon source.
Photoheterotrophs use light as an energy source and organic compounds as a carbon source.
Chemoautotrophs use inorganic chemicals as an energy source and CO2 as a carbon source.
Chemoheterotrophs use chemical energy and organic compounds as a carbon source.
Chapter 6:
Types of organisms based on pH: Neutrophiles grow best between pH 6.5 and 7.5, acidophiles grow in acidic environments, and alkalophiles grow in basic environments.
Types of organisms based on temperature: Psychrophiles are cold-loving, mesophiles are moderate-temperature-loving, and thermophiles are heat-loving.
Types of organisms based on osmotic pressure (salt): Extreme or obligate halophiles require high salt concentrations, while facultative halophiles tolerate high salt concentrations.
Types of organisms based on oxygen requirements: Obligate aerobes require oxygen, facultative anaerobes can grow with or without oxygen, anaerobes are unable to use oxygen, aerotolerant anaerobes tolerate but cannot use oxygen, and microaerophiles require oxygen concentration lower than air.
Physical and Chemical requirements for bacterial growth: Physical requirements include temperature, pH, and osmotic pressure, while chemical requirements include carbon, nitrogen, sulfur, phosphorus, trace elements, oxygen, and organic growth factors.
Effect of Oxygen on the growth of various types of Bacteria: Obligate aerobes require oxygen, facultative anaerobes can grow with or without oxygen, anaerobes are unable to use oxygen and most are harmed by it. Aerotolerant anaerobes tolerate but cannot use oxygen and microaerophiles require oxygen concentration lower than air.
Biosafety level organisms:
BSL-1: no special precautions.
BSL-2: lab coat, gloves, eye protection.
BSL-3: biosafety cabinets, negatively pressurized, equipped with air filters.
BSL-4: sealed, negative pressure, exhaust air is filtered twice through HEPA filters, workers wear "space suits" with an air supply.
Different types of culture media: Chemically defined media, enrichment and complex media.
Define bacterial growth: Bacterial growth is represented by an increase in the number of cells, not cell size.
Binary fission: Binary fission is a cell division process used by most bacteria.
Bacterial division phases of growth: Lag phase, log phase, stationary phase, and death phase.
Calculation for cell number after certain generation: Total number of cells = 2number of generations.
Direct count of bacteria from plate: Plate count involves counting colonies on plates that have 30 to 300 colonies (CFUs).
Direct count of bacteria from spread plate: Counts are performed on bacteria spread on the surface of a plate (spread plate method).
Microscopic count: Direct microscopic count involves placing a volume of bacterial suspension on a slide and calculating the average number of bacteria per viewing field.
Filtration: Filtration involves passing a solution through a filter that collects bacteria, which is then transferred to a Petri dish.
Indirect method of measuring cell growth: Turbidity, metabolic activity, and dry weight.