Microscopes & Abiogenesis

• Micro was started

Microscopes

• Definition: Microscopes enlarge images using ocular and objective lenses.
• Light Microscope: Uses ocular and objective lenses for enlargement.
• Bright Field Microscope: Requires fixing and staining, is most commonly used in 2D.
• Dissection Microscope: Provides a 3D view, is used in parasitology.
• Dark-Field Microscope: Enhances contrast.
• Confocal Microscope: Uses laser light.
• Phase Contrast: Provides high magnification.
• Fluorescence Microscope: Uses UV illumination.
• Scanning Electron Microscope (SEM): Generates a 3D image.
• Transmission Electron Microscope: Generates a 2D image, involves an electron beam passing through the specimen.

Abiogenesis

• Abiogenesis: The concept that life arises from nonliving matter.
• John Needman supported Abiogenesis, stating that movement is spontaneous generation​.
• Lazzaro Spallanzani: Opposed abiogenesis, with 4 flasks in experiment.
• Louis Pasteur: Ended the debate around abiogenesis with experiment using an S-shaped (swan neck) flask.

Cell Types

• Prokaryotes: Lack a membrane and nucleus, includes archaea and bacteria​.
• Eukaryotes: Have a membrane, includes algae, fungi, and protozoans​.

Applied Microbiology

• Applied microbiology: Involves using microorganisms for various applications.
• Food Production: Production of yogurt and bread.
• Beverage Production: Production of alcoholic beverages like wine and beer.
• Water Treatment: Uses organisms as indicators
• Pharmaceuticals: Production of penicillin​.
• Agriculture: Involves soil microbes and the nitrogen cycle.
• Bioremediation: Uses petroleum-digesting bacteria.
• Energy: Fuel cells utilizing ethanol and methane.
• Forensics: Involves medicine, criminal justice, epidemiology, and bioterrorism​.

Atoms and Ions

• Atom: The smallest particle of an element.
• Composition: Atoms are made of protons (positive charge), neutrons (no charge), and electrons (negative charge)​.
• Atomic Nucleus: Composed of protons and neutrons, determines atomic weight.
• Atomic Number: Equal to the number of protons.
• Valence Electrons: Located in the outermost shell. A filled outermost shell makes an atom stable or inert.
• Electron Configuration: The first shell holds 2 electrons, and the next holds 8​.
• Ion: Positive ions are cations (positive charge), negative ions are anions (negative charge).

Isotopes

• Isotopes: atoms with the same number of protons but different numbers of neutrons.
• Atomic number: remains the same, while atomic weight differs.

Chemical Bonds

• Molecules: Formed by chemical bonding between valence electrons of atoms.
• Chemical Compounds: Made from atoms of different elements.
• Covalent Bonds: Result from sharing electrons.
  • Nonpolar: Equal sharing of electrons.
  • Polar: Unequal sharing of electrons.
• Ionic Bonds: Transfer of electrons from one molecule to another.
• Hydrogen Bonds: Weak chemical bonds.
• Van der Waals Forces: Weakest chemical bonds.

Chemical Reactions

• Synthesis (Dehydration Synthesis): Forms larger molecules from smaller ones (anabolism), releasing water (H2O).
• Hydrolysis: Breaks down large molecules (catabolism), requires water (H2O).

Acids and Bases

• Substances dissociate in water to form acids, bases, or salts.
• Acids: Release hydrogen ions.
• Bases: Release hydroxyl ions.

Arterial Blood Gas (ABG) Values

• pH Normal Range: 7.35-7.45.
• PaCO2 Normal Range: 45-35 mmHg.
• HCO3- Normal Range: 22-26 mEq/L.
• PaO2 Normal Range: 75-100 mmHg.
• SaO2 Normal Range: 94-100%.
• Acute Respiratory Acidosis: Low pH, high PaCO2, HCO3 unchanged.
• Acute Respiratory Alkalosis: High pH, low PaCO2, HCO3 unchanged.
• Acute Metabolic Acidosis: Low pH, normal PaCO2, low HCO3.
• Acute Metabolic Alkalosis: High pH, normal PaCO2, high HCO3.

Water Solutions

• Hypotonic: Solute concentration is higher inside the cell than outside.
• Hypertonic: Solute concentration is lower inside the cell than outside.
• Isotonic: Solute concentration is equal inside and outside the cell.

Organic Molecules

• Organic molecules: Have carbon and hydrogen components.
• Carbohydrates (Sugars): Include monomers, disaccharides, and polysaccharides.
  • Monomers: Monosaccharides like glucose, fructose, galactose, ribose, deoxyribose.
  • Disaccharides: Two monosaccharides joined covalently. Examples: sucrose (glucose + fructose), lactose (glucose + galactose), maltose (glucose + glucose).
  • Polysaccharides: Many monosaccharides linked together. Examples: starch (glucose storage in plants), glycogen (glucose storage in animals), cellulose (component of plant cell walls, fungi, and algae).

Proteins

• Monomers: Amino acids.
  • 20 naturally occurring amino acids.
  • Dipeptide: Two amino acids joined by a peptide bond.
  • Polypeptide: 10 or more amino acids.

Phospholipids

• Phospholipids: Glycerol, two fatty acid chains, phosphate group on one end.
  • Polar heads (charged) and non-polar tails (non-charged).
  • Found in the cellular membrane.

DNA

• DNA: Deoxyribonucleic acid, stores genetic information.

Membrane Proteins

• Membrane Proteins: Integral (embedded in phospholipid bilayer) and peripheral (inside or outside of membrane).
• Functions: Structural support, molecule transport, regulate enzyme activity, hormone receptors, and surface antigens.

Peptidoglycan

• Present: In the thick layer of the cell wall of gram-positive bacteria, also in the thin layer of gram-negative bacteria​.

Steps of Gram Staining

• Gram Stain Steps:
  • Apply crystal violet.
  • Apply iodine.
  • Alcohol wash.
  • Apply safranin.

Organelles

• Nucleus: Present only in eukaryotes, contains DNA, nuclear pores, nuclear envelope, chromatin (euchromatin is expressed DNA, heterochromatin is not expressed DNA)​.
• Endoplasmic Reticulum (ER):
  • Rough ER: Protein synthesis.
  • Smooth ER: No ribosomes, lipid and carbohydrate synthesis.
• Golgi Apparatus: Modifies, sorts, and packages proteins to other parts of the cell; produces lysosomes and secretory vesicles.
• Lysosomes: Break down invading microbes.
• Peroxisomes: Remove toxic substances.
• Mitochondria: Produce ATP.
• Chloroplasts: Only found in plants and algae, function in photosynthesis.
• Ribosomes: Make proteins.
• Vacuoles: Storage.

Cellular Processes

• Phagocytosis: Cell eating.
• Pinocytosis: Cell drinking.
• Osmosis: Diffusion of water through a selectively permeable membrane.
• Diffusion: Movement of molecules from high to low concentration areas.

Glycolysis

• Glycolysis: Can be anaerobic or aerobic cellular respiration.
  • The first pathway: Occurs in the cytoplasm and converts glucose into two molecules of pyruvic acid.

Enzymes

• Enzymes: Biological catalysts that speed up chemical reactions without being changed.
  • Most are proteins.
  • Active site and allosteric site.
  • Substrate specific (lock and key model).
  • Enzyme + Substrate = Product.
• Enzyme Inhibition:
  • Competitive inhibition: Molecules compete for the active site.
  • Non-competitive inhibition: Substances bind to the allosteric site, changing the enzyme's configuration.

Electron Transport Chain (ETC)

• Electron Transport Chain: A linked series of proteins in the mitochondria.
  • Each protein: Accepts electrons and is reduced.
  • Passes electrons: To the next protein (oxidized), releasing energy (exergonic reaction = ATP).
  • Produces: 26 ATP in ETC​.

Anaerobic Cellular Respiration

• Anaerobic Cellular Respiration: Follows the lactic acid pathway.
  • Requires: No O2, and involves glycolysis and fermatation.

Aerobic Cellular Respiration

• Aerobic Cellular Respiration: requires O2, glycolysis, Krebs cycle, ETC.
• The final electron acceptor: An inorganic molecule instead of oxygen.
• Fermentation: Starts with glycolysis, with end products like lactic acid, ethyl alcohol, acetic acid, acetone, butyric acid, etc.

Photosynthesis

• Photosynthesis: Converts light energy into chemical energy via ATP used by plants, algae, and some phototrophic bacteria.
• Chemical Equation: carbon dioxide + water + light energy → glucose + oxygen + water.

mRNA

• mRNA: Every three bases form a base triplet-codon.
  • Each codon: Codes for a specific amino acid.

Cell Cycle

• Cell Cycle:
  • G1 phase: Metabolic activities.
  • S phase: Duplication of DNA.
  • G2 phase: Growth and preparation for mitosis.
  • M phase: Mitosis and cytokinesis.

Gram Stain

• Gram Stain: Commonly used for differential stains, tested on the cell wall​.
  • Positive Result: Appears purple/blue.
  • Negative Result: Appears red/pink.
• Acid-Fast Stain: Uses acid instead of alcohol to decolorize differential stains.
  • Acid-Fast: Shows red color.
  • Non-Acid-Fast: Shows blue color.
• Best Example: Is tuberculosis (TB, red).

Media

• Physical State: Liquid, semisolid, solid (plate, broth, slant).
• Chemical State: Complex (extracts from animals, plants, yeast, ground-up cells, tissues, and secretions) or synthetic (exact formula, standardized and reproducible).
• Functional Type:
  • General purpose: Broad spectrum of microbes, brain-heart infusion agar.
  • Enriched: Needs supplements (blood).
  • Selective: Isolates a specific type of microorganisms.
  • Differential: Shows variations in colony size, color, and color changes in media.

Biosafety Levels

• BSL 1: Does not cause disease.
• BSL 2: Moderate risk.
• BSL 3: Potentially causes serious disease, increased training, limited access.
• BSL 4: High risk of aerosol, life-threatening, requires high-level protection.

Personal Protective Equipment (PPE)

• PPE includes: Gloves, respiratory protection, clothing, and eye protection.
• N95 Mask: For tuberculosis (TB).

Blood-Borne Pathogens

• Hepatitis B: Caused by the hepatitis B virus (HBV); results in a lifelong liver infection.
• Hepatitis C: Caused by the hepatitis C virus (HCV); often has no initial symptoms until cirrhosis occurs.
• AIDS: Caused by the human immunodeficiency virus (HIV); characterized by early symptoms like fever, headache, and tiredness.
• Viral Hemorrhagic Fever (VHF): Caused by Ebola and Marburg viruses; initial signs include fever and fatigue, severe cases show signs of bleeding.