Exhaustive Review of Microbiology, Metabolism, and Genetics

Biomolecules: Phospholipids, Triglycerides, and Nucleic Acids

Phospholipid Structure: Consists of a phosphate group, a head called phosphatide, and two long fatty acid tails.
Triglyceride Structure: Comprised of a three-carbon sugar, three fatty acid chains, and a phosphate group.
DNA vs. RNA Comparison:
    * Shape: DNA typically exists in a full double-helical shape. RNA is usually single-stranded but can be double-stranded in certain viruses.
    * Nucleotide Bases:
        * DNA contains Adenine, Guanine, Cytosine, and Thymine.
        * RNA contains Adenine, Guanine, Cytosine, and Uracil (Uracil replaces Thymine).
    * Sugars: RNA contains ribose (ribonucleotide), while DNA contains deoxyribose (deoxyribonucleotide). The primary chemical difference is the presence of an oxygen hydroxyl group in ribose.

Metabolism and Enzyme Function

Anabolism: The process of building up larger molecules from smaller ones.
Catabolism: The process of breaking down larger molecules into smaller ones.
Enzymes as Catalysts: Enzymes facilitate metabolic reactions. Without the presence of specific enzymes, these reactions will not occur.
Enzyme Mechanism: Typically, two substrates bind into an enzyme to be linked together into a new product (anabolism), or a single product enters the enzyme and is broken apart (catabolism).

The Central Dogma: Transcription and Translation

Cellular Components: The process involves the cell wall, cytoplasm, and the nuclear membrane (nuke).
Transcription: DNA located inside the nucleus is transcribed into mRNA (messenger RNA) using polymerases.
Export and Translation: mRNA exports out of the nucleus to the cytoplasm where translation occurs.
Translation Machinery:
    * Ribosomes: These structures hold the machinery together and "read" the mRNA.
    * Codon: The sequence of three bases on the mRNA that codes for a specific amino acid.
    * tRNA (Transfer RNA): Brings individual amino acids to the ribosome. It contains an anticodon (the opposite/complement of the codon) to link with the mRNA.
Protein Synthesis: As amino acids link, they form a peptide (short chain). Once the chain is very long, it is called a protein.
Protein Structure:
    * Primary Structure: The linear sequence of amino acids.
    * Secondary Structure: Local folding (e.g., alpha helices or beta sheets).
    * Tertiary Structure: The overall three-dimensional shape.
    * Quaternary/Globular Structure: Complex folding that allows for functional sites.
Functional Examples:
* Enzymes: Folded to create specific pockets for substrates to enter and exit after a reaction.
* Structural Proteins: Examples include actin and myosin in muscle tissues, which are long, sturdy, and tightly bound to provide strength.

Nutrient Acquisition and Redox Reactions

Autotrophs: Organisms like plants that make their own food.
Heterotrophs: Organisms that must eat other things to obtain nutrients.
Redox (Reduction-Oxidation) Reactions: These reactions occur simultaneously; one molecule is oxidized while another is reduced through the transfer of an electron.
LEO (Lose Electron = Oxidation): The molecule donating the electron is oxidized.
GER (Gain Electron = Reduction): The molecule accepting the electron is reduced.

Cellular Respiration and ATP Production

ATP (Adenosine Triphosphate): The essential energy molecule required by all cells. Energy is transferred between bonds and is never destroyed.
Glycolysis: The process of breaking down glucose (six carbons) into pyruvate (three carbons).
    * The cell invests $2$ ATP units.
    * The process produces $4$ ATP units.
    * The net profit is $2$ ATP units.
The Krebs Cycle (Citric Acid Cycle/Calvin Cycle): Pyruvate is converted into a two-carbon molecule that enters this cycle.
* Produces water ( $H_2O$ ) and Carbon Dioxide ( $CO_2$ ).
* Involves electron acceptors and receivers, such as the transition from $FAD$ to $FADH_2$ .
Mitochondria and the Electron Transport Chain (ETC):
    * The mitochondria are the "powerhouse" of the cell.
    * The ETC pumps electrons through the membrane using a series of catcher/releaser molecules.
    * ATP Synthase: An enzyme/machine pump in the membrane that synthesized ATP using a concentration gradient of hydrogen ions ( $H^+$ ).
    * One glucose molecule can yield approximately $36$ ATP (efficient cells can make up to $38$ ATP).

Microbial Growth and Environmental Conditions

Four Phases of Growth:
    * 1. Lag Phase: Cells are adapting to environment, temperature, and climate. They are gathering nutrients and building proteins but not yet multiplying.
    * 2. Log Phase (Exponential Phase): Rapid, exponential growth of the population.
    * 3. Stationary Phase: The rate of death and reproduction are equivalent. Growth levels off.
    * 4. Death Phase: Nutrients run low, and cells die faster than they reproduce.
Binary Fission: The method of division for prokaryotes (bacteria).
* DNA replicates and the cell splits without mitosis.
* FtsZ (FITC): A protein that forms a ring at the site of division. Preventing this ring prevents cell division, causing cells to grow long and eventually burst.
Oxygen Requirements:
    * Obligate Aerobe: Requires oxygen to live.
    * Obligate Anaerobe: Cannot use oxygen; prefers $CO_2$ .
    * Facultative: Can do both but prefers oxygen.
    * Aero-tolerant Anaerobe: Can tolerate oxygen but prefers anaerobic environments.
    * Microaerophile: Requires only a small amount of oxygen; lives just below the surface.
Growth Preferences:
    * Halophiles: Like salt (e.g., Staphylococcus likes salt and moisture).
    * Acidophiles: Thrive in acidic environments.
    * Mesophiles: Prefer moderate temperatures (e.g., human body temperature).
    * Extremophiles: Thrive in extreme conditions.
    * Psychrophiles: Prefer cold temperatures.

DNA Structure and Replication

Nucleotide Structure: Consists of a phosphate group, a five-carbon sugar, and a nitrogenous base.
Phosphodiester Backbone: The structural framework of DNA/RNA.
Hydrogen Bonds: Hold the two strands together. They are relatively weak to allow the strands to "unzip" for transcription or replication.
Genomes: Prokaryotes usually have one circular DNA chromosome. Eukaryotes have double-stranded linear DNA wrapped around histones to form chromosomes (humans have $23$ pairs).
Genotype vs. Phenotype: The genotype (genes) predicts the phenotype (the expressed proteins/traits).
Replication Enzymes:
    * Helicase: Unwinds the DNA strands.
    * Gyrase: Reduces torsion/tension from unwinding.
    * Primase: Places primers to start replication.
    * Polymerase: Synthesizes the complementary strand.
    * Ligase: Joins Okazaki fragments on the lagging strand.
Directionality: Replication always occurs in the $5'$ to $3'$ direction.
Types of Replication:
* Rolling Circle Replication: Used by prokaryotes.
* Bubble Replication: Used by eukaryotes, forming multiple replication pockets.

Gene Regulation and Molecular Technology

Operon: A cluster of genes involved in a single metabolic process, synthesized simultaneously when needed.
* Repressor Protein: Holds the process in check until needed.
* Operator: The site where the repressor binds or releases.
Molecular Tools:
    * PCR (Polymerase Chain Reaction): Used for diagnosis (pathogen levels) and research (making copies of genes).
    * Arrays: Monitor gene expression (which genes are "turned on" or "off") under specific conditions like drug exposure or temperature changes.
    * Sequencing: Used to track mutations and variants in pathogens (e.g., Hantavirus).
    * CRISPR: A system for gene editing (removing or inserting DNA). This technology raises significant ethical concerns.

Growth Control and Antibiotics

Definitions:
    * Bacteriostatic: Slows metabolism to stop growth without killing the bacteria.
    * Bactericidal: Kills the bacteria.
    * Antiseptic: Safe for use on living tissue.
    * Disinfectant: Toxic; used only on inanimate surfaces.
Antibiotic Mechanisms of Action:
    1. Inhibition of cell wall synthesis.
    2. Inhibition of DNA synthesis.
    3. Inhibition of protein synthesis.
    4. Inhibition of metabolic pathways.
    5. Disruption of the cell membrane (e.g., Polymyxin B pokes holes in the membrane).
Mechanisms of Resistance:
    1. Efflux pumps (pumping the drug out).
    2. Blocking drug entry.
    3. Altering the drug target site.
    4. Target replication/DNA synthesis changes.
Types of Resistance:
    * Intrinsic: Natural resistance (e.g., Pseudomonas aeruginosa).
    * Acquired: Gained through incomplete antibiotic courses or mutation.
    * Horizontal Gene Transfer: Movement of resistance genes via plasmids between bacteria.
    * Genetic Drift: Gradual change in a whole group or portion of genes over time.

Pathogenesis and Epidemiology

Pathogenesis: The process by which a pathogen causes disease, including entry, invasion, and damage.
Stages of Disease Progression: Incubation
ightarrow Period of Illness (peak)
ightarrow Convalescence.
Virulence Factors: Evasion mechanisms, entry methods, toxins, and capsules (to prevent or survive phagocytosis).
Infectious Dose: The number of bacteria or viruses required to cause infection.
Epidemiology: Tracking and tracing infections to find the source.
    * John Snow: Known for tracing the cholera pump.
    * Florence Nightingale and Typhoid Mary: Other historical figures in epidemiology.
    * Active Surveillance: Actively seeking data or hunting for cases.
    * Passive Surveillance: Gathering data from patients who voluntarily come into hospitals.

Immunology

Innate vs. Adaptive Immunity:
* Innate: The first line of defense (barriers).
* Adaptive: Stronger, specific response involving B-cells and T-cells.
Bridge Components: Antigen-presenting cells (APCs), macrophages, Natural Killer (NK) cells, cytokines, and complement protein systems.
Specific Cell Roles:
    * Cytokines: Signals to produce an activity or bring cells into an area.
    * Chemokines: Siren-like signals that direct cells toward the specific site of infection.
    * Natural Killer (NK) Cells: Kill infected cells by secreting perforins to punch holes in target cell membranes.
    * B-cells: Stimulated by APCs or Helper T-cells to produce antibodies.
    * Helper T-cells: Regulate the adaptive immune process.

Questions & Discussion

Student Question: "Is it the shape [that is different between DNA and RNA]?"
Instructor Response: Not strictly the shape, but the DNA double helix versus the single-stranded RNA. RNA can be double-stranded in viruses.
Student Question: "Wait, there are four bases in DNA… adenine, guanine, cytosine, thymine?"
Instructor Response: Yes, and in RNA, Uracil replaces Thymine.
Student Question: "Anabolism is building up and catabolism is breaking down?"
Instructor Response: Correct.
Student Question: "What is the name of the little three bases they're reading?"
Instructor Response: It's called a codon.
Student Question: "Staph likes what?"
Instructor Response: Salt. It likes salt, moisture, and warmth; like ocean water.
Student Question: "What does PCR stand for?"
Instructor Response: Polymerase Chain Reaction.
Student Question: "Who was the person who tracks things?"
Instructor Response: John Snow and the pump."