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Exam Unit 1a Study Guide Spring 2022

Prokaryotic vs Eukaryotic Cells

  • Prokaryotic (P) vs Eukaryotic (E) features (or Both (B))

    • Membrane Bound Organelles: E = yes; Prokaryotes do not have membrane-bound organelles. → Answer: E

    • Vacuoles (storage): Eukaryotes have membrane-bound vacuoles for storage; most prokaryotes do not have true vacuoles. → Answer: E

    • Inclusions (storage): Prokaryotes have inclusion bodies for storage; eukaryotes also have storage compartments, but inclusions as a term are commonly associated with prokaryotes. → Answer: B

    • Plasma membrane: Present in all cells; both (B)

    • Pilus (pili): Prokaryotes have pili; eukaryotes do not (in bacteria, pili are used for attachment/conjugation). → P

    • Circular chromosome: Prokaryotes have circular chromosomes; eukaryotes have linear chromosomes. → P

    • Linear chromosomes: Eukaryotes. → E

    • Ribosomes: Present in both; 70S in prokaryotes and 80S in eukaryotes (size differences). → B

    • A true nucleus: Eukaryotes (a true nucleus is lacking in prokaryotes). → E

    • Plasma membrane (repeated): see above; All cells have a plasma membrane. → B

    • Nucleoid: Prokaryotes have a nucleoid region where the chromosome resides; eukaryotes do not have a nucleoid. → P

  • Storage of extra materials

    • Eukaryotic organisms store extra materials in their organelles (e.g., vacuoles, vesicles, lipid droplets within organelles, etc.).

    • Prokaryotic organisms store extra materials in spaces called inclusions or inclusion bodies (not membrane-bound).

  • Quick summary of key structural differences:

    • Nucleus: present in Eukaryotes, absent in Prokaryotes.

    • Membrane-bound organelles: present in Eukaryotes, absent in Prokaryotes (except for simple internal membranes in some bacteria like thylakoids).

    • Chromosome organization: circular in Prokaryotes; linear in Eukaryotes.

    • Ribosome size: 70S in Prokaryotes; 80S in Eukaryotes (with 70S in organelles like mitochondria/chloroplasts).

The Microscope

  • Pathway of light starting at the light source

    • Light source -> condenser lens -> Stage with specimen -> Objective lens (start with scanning 4x, then 10x, 40x, 100x) -> Body tube/Intermediate image -> Ocular lens (eyepiece) -> Eye

    • The condenser helps focus light on the specimen; the objective lens creates a magnified real image that is projected through the body tube to the ocular lens for final magnification.

Gram Positive vs Gram Negative Cell Wall Structure, Molecules, and Layers

  • Structural distinctions

    • Gram-positive (G+): thick layer of peptidoglycan

    • Gram-negative (G−): thinner peptidoglycan layer plus an outer membrane containing LPS

    • Teichoic acids: located in the cell wall of G+ (teichoic acids contribute to wall rigidity and antigenic properties)

    • Lipopolysaccharide (LPS): located in the outer membrane of G−

    • Periplasmic space: present in G− between outer membrane and inner plasma membrane; generally not present in the same way in G+

  • Layer counts and geometry

    • Two layers of cell wall?: G− (outer membrane + thin peptidoglycan) → Two layers

    • One layer of cell wall?: G+

    • Thicker layer of peptidoglycan: G+

  • Accessibility and antibiotic permeability

    • Teichoic acids are in G+ cell walls.

    • LPS is in the outer membrane of G−.

    • Permeability to antibiotics: Gram-positive bacteria are typically more permeable to many antibiotics targeting peptidoglycan due to the absence of an outer membrane; Gram-negative bacteria have an outer membrane that can act as a barrier, making some antibiotics less permeable.

  • Gram stain dynamics (visual cue)

    • G+ stains purple (crystal violet retained)

    • G− stains pink/red after counterstain (crystal violet washed out during decolorization)

  • Note about pictures

    • Study the provided images to grasp: thickness of peptidoglycan, presence/absence of outer membrane, and the distribution of teichoic acids and LPS in respective cell walls.

Gram Stain Technique

  • Does cell wall structure influence Gram stain outcome aside from shape?

    • Yes: the cell wall structure (peptidoglycan thickness and outer membrane) largely determines whether the crystal violet-iodine complex is retained after decolorization.

  • Steps and reagents (in order)

    • 1) Crystal violet (primary stain)

    • 2) Iodine (mordant)

    • 3) Alcohol/acetone (decolorizer)

    • 4) Safranin (counterstain)

  • Purpose of alcohol step

    • Decolorization: washes out crystal violet-iodine complex from G− cells due to outer membrane disruption and thinner peptidoglycan; G+ retains the complex due to a thick peptidoglycan layer.

  • Role of mordant stain (Iodine)

    • Forms a larger crystal violet-iodine complex that is more difficult to rinse away; helps trap CV inside thicker cell walls.

  • Completed Gram stain colors

    • Gram-positive: purple

    • Gram-negative: pink/red

  • Acid-fast bacteria (e.g., Mycobacterium tuberculosis)

    • Cell wall structure is different: high mycolic acid content with waxy, lipid-rich layer that resists Gram staining; acid-fast staining (e.g., Ziehl-Neelsen) is used instead.

    • Gram stain protocol is not reliable for identifying acid-fast organisms.

Functional Anatomy of Prokaryotic Cells

  • Cell shapes and arrangements

    • Common shapes: cocci (spherical), bacilli (rods), vibrio (comma-shaped), spirilla (spiral), spirochetes (corkscrew)

    • Arrangements: diplococci, streptococci, staphylococci, tetrads, etc. (as described in pictures provided with the course materials)

  • Flagella: the 5 styles/names

    • Monotrichous (single flagellum at one end)

    • Amphitrichous (one or more flagella at both ends)

    • Lophotrichous (tufts at one or both ends)

    • Peritrichous (flagella distributed over the entire cell surface)

    • Atrichous (no flagella)

  • Distinguishing cellular component that makes prokaryotic and eukaryotic cells different

    • The nucleus and membrane-bound organelles (e.g., mitochondria, chloroplasts) in Eukaryotes vs their absence in Prokaryotes; the presence of a nucleoid region in Prokaryotes.

  • Pilus/pili: function and process

    • Function: attachment, mating/conjugation (DNA transfer) in bacteria; pili facilitate genetic exchange via conjugation via a donor and recipient cell with a sex pilus.

  • Picture cues: shapes of bacterial cells (Cocci, Bacilli, etc.)

  • Capsule: main functions

    • Protection from desiccation and immune clearance; anti-phagocytic properties; contribute to adherence to surfaces and host tissues.

  • Endospore: definition and sporulation

    • Definition: a dormant, highly resistant internal structure formed by some bacteria (e.g., Bacillus, Clostridium)

    • Sporulation occurs under adverse conditions (nutrient limitation, environmental stress)

    • Purpose: to protect genetic material during harsh conditions and ensure survival until conditions improve

  • Ribosomes

    • Function: synthesize proteins by translating mRNA

    • If ribosomes are damaged/destroyed: protein synthesis halts; cells cannot produce essential proteins, leading to growth arrest or death

  • Cell Membrane: diffusion types

    • Passive diffusion: moves down the concentration gradient; no energy (ATP) required; no transport proteins necessary

    • Facilitated diffusion (a form of passive transport): uses transport proteins but still down the gradient; no ATP required

    • Active diffusion/active transport: moves against the gradient; requires ATP or another energy source; uses transport proteins (e.g., pumps, like ABC transporters)

Metabolism

  • Catabolism vs Anabolism

    • Catabolic (C): degradative reactions that break down large molecules into smaller ones; energy-releasing

    • Anabolic (A): biosynthetic reactions that build larger molecules from smaller building blocks; energy-consuming

  • Degradative vs biosynthetic reactions

    • Degradative (catabolic): e.g., breakdown of fatty acids, amino acids

    • Biosynthetic (anabolic): production of fats, proteins, sugars

  • Energy release vs energy consumption

    • Exergonic reactions release energy

    • Endergonic reactions require energy input

  • Link between catabolism and anabolism

    • Catabolic reactions provide energy (in the form of ATP, NADH, etc.) and building blocks used for anabolic processes; energy carriers drive biosynthesis

  • Quick contrast: exergonic vs endergonic

    • Exergonic: ΔG < 0, energy released

    • Endergonic: ΔG > 0, energy required

Bioenergetics

  • Final electron acceptor in respiration/fermentation

    • Aerobic respiration: final electron acceptor is
      O_2

    • Anaerobic respiration: final electron acceptor is typically an inorganic molecule such as
      NO3^-, SO4^{2-}, CO_3^{2-}, or other inorganic compounds

    • Fermentation: final electron acceptor is an organic molecule (e.g., pyruvate, acetaldehyde)

  • Net ATP yields (per glucose)

    • Aerobic respiration: typically about 36-38 ext{ ATP} per glucose (range due to cellular efficiency and shuttle mechanisms)

    • Anaerobic respiration: typically lower than aerobic, often in the range of 2-36 ext{ ATP} depending on organism and electron acceptor

    • Fermentation: about 2 ext{ ATP} per glucose (generated via glycolysis only; NADH is oxidized by the organic final acceptor)

  • Total NADH produced from glucose during aerobic respiration (glycolysis + pyruvate oxidation + Krebs cycle) to enter the ETC

    • Glycolysis: 2 ext{ NADH}

    • Pyruvate oxidation (per glucose): 2 ext{ NADH}

    • Krebs cycle: 6 ext{ NADH}

    • Total: 10 ext{ NADH} per glucose

  • FADH2 produced from glucose during aerobic respiration

    • Krebs cycle: 2 ext{ FADH}_2 per glucose

  • Which process uses energy (actively) vs passive transport

    • Active transport uses energy (ATP or proton motive force) to move substances against their gradient

    • Passive transport (including diffusion and facilitated diffusion) does not require net energy input

Enzymes

  • How enzymes speed up reactions

    • Lower activation energy by providing an alternative reaction pathway (lower energy barrier)

    • Increase effective collisions by properly orienting substrates and stabilizing transition states

  • Activation energy changes

    • Enzymes lower activation energy, not the overall free energy change of the reaction

  • Effect on reaction rate

    • Enzymes increase reaction rate (speed up the reaction)

  • Do chemical reactions occur without enzymes?

    • Yes, but at extremely slow rates; enzymes dramatically accelerate rates under physiological conditions

  • Inhibition mechanisms

    • Competitive inhibitors: bind at the active site, blocking substrate binding

    • Allosteric inhibitors: bind at an allosteric site, inducing conformational change that reduces or blocks activity

    • End-product (feedback) inhibition: a product inhibits an enzyme earlier in the pathway to regulate production

  • Environmental effects on bacterial enzymes

    • Temperature and acid/base conditions can denature enzymes or alter catalytic efficiency, affecting growth and survival

Definitions

  • Pathogenic microbes

    • Microorganisms capable of causing disease in a host

  • Biogenesis vs Spontaneous Generation

    • Spontaneous generation: life arising from non-living matter (discredited)

    • Biogenesis: life arises from pre-existing life or existing cells

  • Genetic engineering & Bioremediation

    • Genetic engineering: direct manipulation of an organism’s genes to achieve desired traits

    • Bioremediation: use of living organisms (often microbes) to detoxify or remove environmental pollutants

  • Pilus and Conjugation

    • Pilus: a filamentous projection involved in attachment and DNA transfer between bacteria (conjugation)organisms

  • Archaea as extremophiles

    • Archaea are prokaryotes that often thrive in extreme conditions (extremophiles) such as high temperature, salinity, or acidity

  • Osmosis

    • Passive movement of water across a semipermeable membrane from a region of lower solute concentration to higher solute concentration

Taxonomy

  • Scientific naming conventions

    • Genus name comes first (capitalized)

    • Species name comes second (lowercase)

    • Both are italicized or underlined in handwritten notes (Genus species; e.g., Escherichia coli)

  • Inhibitor binding notes

    • Competitive inhibitors bind at the active site

    • Allosteric inhibitors bind at an alternate site (allosteric site) causing conformational changes

    • End-product inhibitors regulate pathways via feedback inhibition

  • Quick reminder on naming conventions and capitalization

    • Genus: capitalized; Species: lowercase; both italicized

  • Connections to prior/real-world relevance

    • Understanding cell structure informs antibiotic targets (peptidoglycan, ribosomes, membranes)

    • Gram staining guides clinical diagnostics and infection control

    • Enzyme inhibition concepts underpin drug action (e.g., competitive inhibitors in antibiotics, allosteric inhibitors in metabolic drugs)

  • Ethical/philosophical/practical implications

    • Genetic engineering raises biosafety and bioethics considerations (dual-use concerns, containment, ecological impact)

    • Bioremediation leverages microbial capabilities for environmental cleanup, with considerations of ecosystem balance and regulations

  • Key formulas and numbers used in metabolism and bioenergetics

    • Glucose chemical formula: ext{C}6 ext{H}{12} ext{O}_6

    • ATP yields: ext{ATP}_{ ext{net}} \approx 36-38 (a common aerobic yield; varies by organism)

    • NADH counts in aerobic glycolysis and Krebs: 10\, ext{NADH} per glucose

    • FADH2 in Krebs per glucose: 2\, ext{FADH}_2 per glucose

    • Final electron acceptor examples: O2 for aerobic; NO3^-, SO4^{2-}, CO3^{2-} for some anaerobic respirations; in fermentation, organic molecule as acceptor

Note: For exam preparation, emphasize how the different sections connect: cell structure informs Gram stain outcomes; metabolism and bioenergetics tie to ATP production and energy usage in transport; enzymes underpin all biochemical reactions and their regulation; taxonomy provides nomenclature rules that are essential for proper communication in science.