Microm 301 Final

What did Pasteur's swan-necked flask experiments prove?

They disproved spontaneous generation by showing that broth only became contaminated when the curved neck was broken, allowing microbes from the air to enter — life did not arise spontaneously from the broth itself.

What is the fundamental difference between eukaryotic and prokaryotic cells?

Prokaryotic cells lack a membrane-bound nucleus and membrane-bound organelles; eukaryotic cells have both a true nucleus and membrane-bound organelles.

What are the two domains of prokaryotic organisms?

Bacteria and Archaea.

In binomial nomenclature, which part is the genus and which is the specific epithet?

The first (capitalized) word is the genus; the second (lowercase) word is the specific epithet. Example: in Bacillus anthracis, Bacillus = genus, anthracis = specific epithet.

Are organisms more closely related if they share the same genus or the same specific epithet?

Same genus — genus groups organisms more broadly by close evolutionary relationship, while the specific epithet identifies the species within that genus.

What is the importance and basic structure of proteins?

Proteins are made of amino acid chains; they function as enzymes, structural components, transporters, and signaling molecules. Found in cell membranes, ribosomes, and virtually all cellular processes.

What is the importance and basic structure of carbohydrates?

Carbohydrates are made of sugar monomers; they serve as energy sources and structural components (e.g., peptidoglycan in bacterial cell walls, cellulose in plants).

What is the importance and basic structure of nucleic acids?

Nucleic acids (DNA and RNA) are made of nucleotide monomers; they store and transmit genetic information and are involved in protein synthesis.

What is the importance and basic structure of lipids?

Lipids are hydrophobic molecules including fats, phospholipids, and sterols; they form cell membranes, store energy, and act as signaling molecules.

Why is normal microbiota important to human health?

Normal microbiota competitively exclude pathogens, aid digestion, produce vitamins, and stimulate immune system development.

Give 2 examples of commercial benefits of microorganisms.

1) Food production — bacteria and fungi used to make cheese, yogurt, beer, and bread. 2) Pharmaceuticals — fungi (Penicillium) produce antibiotics; bacteria produce insulin via recombinant DNA technology.

What are major differences between Bacteria, Archaea, and Eukarya?

Bacteria: prokaryotic, have peptidoglycan cell walls, found in most environments. Archaea: prokaryotic, no peptidoglycan, often found in extreme environments, more similar to eukaryotes in transcription/translation. Eukarya: eukaryotic, membrane-bound nucleus, complex organelles.

What are the four groups of eukaryotic microorganisms?

Fungi, Algae, Protozoa, and Helminths (parasitic worms, sometimes classified separately).

What are the three types of acellular infectious agents?

Viruses (protein coat + nucleic acid), Viroids (naked RNA, no protein coat), and Prions (misfolded proteins, no nucleic acid).

What are prions and what diseases do they cause?

Prions are misfolded proteins that cause normal proteins to also misfold. They cause fatal neurodegenerative diseases such as Creutzfeldt-Jakob disease (CJD), scrapie (sheep), and bovine spongiform encephalopathy (mad cow disease).

What is the advantage of an electron microscope over a light microscope, and vice versa?

Electron microscopes have much greater resolving power and can visualize ultrastructure (organelles, viruses), but specimens must be dead/fixed. Light microscopes can view living specimens but have lower resolution.

What information does a wet mount provide that stained preparations do not?

A wet mount allows observation of living cells, including motility and natural morphology, without the distortion or death caused by fixation and staining.

Compare simple, differential, and special stains.

Simple stains use one dye to visualize cell shape/arrangement. Differential stains (e.g., Gram stain) use multiple dyes to distinguish cell types. Special stains target specific structures (e.g., acid-fast stain for mycobacteria, endospore stain).

Describe a Gram-positive coccus vs. a Gram-negative bacillus after Gram staining.

Gram-positive coccus: purple/violet, spherical. Gram-negative bacillus: pink/red, rod-shaped.

Describe the structure of the cytoplasmic membrane.

A phospholipid bilayer with embedded proteins (fluid mosaic model). It lies inside the cell wall and controls what enters and leaves the cell.

What is the fluid mosaic model?

The model describing the cytoplasmic membrane as a flexible phospholipid bilayer in which proteins can move laterally — it is fluid (not rigid) and mosaic (contains a mix of proteins).

List two roles of proteins in the cytoplasmic membrane.

1) Transport proteins move molecules across the membrane. 2) Receptor/sensor proteins detect environmental signals.

How is the electron transport chain related to proton motive force?

The ETC pumps protons (H+) across the membrane, creating an electrochemical gradient (proton motive force). This force drives ATP synthesis via ATP synthase.

What is the role of the cytoplasmic membrane vs. the cell wall?

The cytoplasmic membrane controls transport (selective permeability). The cell wall provides structural support and protection against osmotic lysis.

How is facilitated diffusion different from active transport?

Facilitated diffusion moves molecules down their concentration gradient using transport proteins — no energy required. Active transport moves molecules against their gradient and requires energy (ATP or PMF).

What are the two general types of active transport systems in bacteria?

1) ABC transporters — use ATP hydrolysis. 2) Ion-coupled transporters — use proton motive force (e.g., symporters, antiporters).

Describe the structure of peptidoglycan.

Peptidoglycan is a mesh-like polymer of alternating NAG (N-acetylglucosamine) and NAM (N-acetylmuramic acid) sugars cross-linked by short peptide chains.

What are the major differences between Gram-positive and Gram-negative cell walls?

Gram-positive: thick peptidoglycan layer, teichoic acids, no outer membrane. Gram-negative: thin peptidoglycan layer, outer membrane containing LPS, periplasmic space between the two membranes.

What effect does penicillin have on peptidoglycan?

Penicillin inhibits the transpeptidase enzymes (PBPs) that cross-link peptidoglycan strands, preventing proper cell wall synthesis and causing the cell to lyse.

What effect does lysozyme have on peptidoglycan?

Lysozyme cleaves the glycosidic bonds between NAG and NAM in peptidoglycan, degrading the cell wall and causing osmotic lysis.

Where is LPS found and what is its medical significance?

LPS (lipopolysaccharide) is found in the outer membrane of Gram-negative bacteria. It acts as an endotoxin — when released (e.g., during infection), it can trigger a strong immune response, septic shock, and fever.

What is the difference between a capsule and a slime layer?

A capsule is a tightly organized polysaccharide layer firmly attached to the cell surface. A slime layer is loosely attached and less organized. Both help with adhesion and immune evasion.

What bacterial structures are responsible for motility?

Flagella — rotating appendages that propel the cell through liquid environments.

What are fimbriae used for? What are sex pili used for?

Fimbriae are used for adhesion to surfaces and host cells. Sex pili are used for conjugation — forming a connection between donor and recipient cells for DNA transfer.

What is the function of a ribosome? What is the significance of 16S rRNA?

Ribosomes synthesize proteins. 16S rRNA (in the small subunit of prokaryotic ribosomes) is used in phylogenetic classification because it is highly conserved yet contains variable regions useful for identifying and comparing organisms.

How is the eukaryotic flagellum different from the prokaryotic flagellum?

Eukaryotic flagella are membrane-bound, contain microtubules (9+2 arrangement), and move in a whip-like fashion. Prokaryotic flagella are naked protein filaments that rotate like a propeller.

How does the eukaryotic plasma membrane differ from the prokaryotic cytoplasmic membrane?

Eukaryotic membranes contain sterols (e.g., cholesterol) for stability; most prokaryotic membranes lack sterols (exception: Mycoplasma).

How do eukaryotic and prokaryotic ribosomes differ?

Prokaryotic ribosomes are 70S (50S + 30S subunits); eukaryotic ribosomes are 80S (60S + 40S subunits). This difference is exploited by antibiotics that selectively target 70S ribosomes.

What is the medical significance of the difference between eukaryotic and prokaryotic ribosomes?

Many antibiotics (e.g., aminoglycosides, tetracyclines, macrolides) target 70S prokaryotic ribosomes without affecting human 80S ribosomes, allowing selective toxicity.

What is the endosymbiotic theory?

The theory that mitochondria and chloroplasts originated as free-living prokaryotes that were engulfed by a larger cell; supported by the fact that these organelles have their own DNA, 70S ribosomes, and double membranes.

How are capsules related to dental caries?

Streptococcus mutans produces a capsule/biofilm from sucrose that helps it adhere to tooth enamel; acid produced by its metabolism causes cavities.

Describe peritrichous vs. polar flagella.

Peritrichous: flagella distributed all over the cell surface (e.g., Proteus). Polar: one or more flagella at one or both poles of the cell (e.g., Pseudomonas).

Describe the general mechanism of chemotaxis.

Bacteria detect chemical gradients via membrane receptors. When attractants increase (or repellents decrease), tumbling is suppressed and the cell runs toward favorable conditions. Signal transduction proteins relay the signal to the flagellar motor.

What characteristics are commonly encoded on plasmids?

Antibiotic resistance, toxin production, virulence factors, metabolic capabilities, and conjugation genes.

Name two genera that produce endospores.

Bacillus and Clostridium.

Describe the life cycle of a spore-forming bacterium using "sporulate" and "germinate."

Under stress, a bacterium will sporulate — forming a dormant, highly resistant endospore. When conditions improve, the endospore will germinate — returning to an active, vegetative state.

What is the difference between pinocytosis and phagocytosis?

Pinocytosis is "cell drinking" — the uptake of small fluid droplets. Phagocytosis is "cell eating" — the engulfment of large particles or microorganisms.

What is the role of actin in eukaryotic cells and how have pathogens hijacked it?

Actin forms the cytoskeleton, enabling cell movement and endocytosis. Some pathogens (e.g., Listeria, Shigella) hijack actin polymerization to propel themselves through the cytoplasm and into adjacent cells, avoiding antibodies.

If you start with 100 cells with a 20-minute generation time, how many cells after 2 hours?

2 hours = 120 minutes; 120/20 = 6 generations. 100 × 2^6 = 100 × 64 = 6,400 cells.

How would you classify bacteria on your bench, in the arctic, and in hot springs by temperature?

Bench bacteria: mesophiles (grow best ~20-40°C). Arctic bacteria: psychrophiles (grow best at cold temperatures, ~0-15°C). Hot spring bacteria: thermophiles or hyperthermophiles (grow best at >45°C or >80°C).

What is the difference between an aerotolerant anaerobe and a facultative anaerobe?

Aerotolerant anaerobes do not use oxygen but can survive in its presence. Facultative anaerobes can use oxygen when available but can also grow without it (switch between aerobic and anaerobic metabolism).

Why are high salt/sugar solutions used to preserve food?

High solute concentrations create a hypertonic environment that draws water out of microbial cells by osmosis, causing plasmolysis and inhibiting growth.

What are the different phases of microbial growth?

Lag phase (adaptation, no growth), Exponential/Log phase (rapid growth), Stationary phase (growth = death rate), Death/Decline phase (death rate > growth rate).

During which phase is generation time measured?

Exponential (log) phase.

What is a biofilm? Give an example.

A biofilm is a community of microorganisms attached to a surface and encased in a self-produced polysaccharide matrix. Example: dental plaque, infections on catheters.

What is a pure culture and how is it isolated?

A pure culture contains only one species of microorganism. It is isolated by streak plate, pour plate, or serial dilution methods to separate individual cells that grow into distinct colonies.

How do aerobic organisms avoid damage from toxic oxygen derivatives?

They produce enzymes like superoxide dismutase (breaks down superoxide), catalase (breaks down hydrogen peroxide into water and O2), and peroxidase.

Describe the 4 classifications of microorganisms based on energy and carbon source.

Photoautotrophs (light energy, CO2), Photoheterotrophs (light energy, organic carbon), Chemoautotrophs (chemical energy, CO2), Chemoheterotrophs (chemical energy, organic carbon).

What makes a growth medium selective vs. differential?

Selective medium inhibits growth of certain organisms while allowing others (e.g., MacConkey agar inhibits Gram-positives). Differential medium distinguishes organisms by visible reactions (e.g., color change). MacConkey is both — it selects for Gram-negatives and differentiates lactose fermenters by color.

What is the difference between anabolism and catabolism?

Catabolism breaks down molecules to release energy. Anabolism uses energy to build complex molecules. Together they make up metabolism.

How do cells couple exergonic and endergonic reactions?

Exergonic reactions (energy-releasing, e.g., ATP hydrolysis) are coupled to endergonic reactions (energy-requiring) so the energy released drives the unfavorable reaction.

What is an enzyme and what factors affect enzymatic activity?

Enzymes are biological catalysts (usually proteins) that lower activation energy. Activity is affected by temperature, pH, substrate concentration, and the presence of inhibitors or cofactors.

What makes ATP's phosphate bonds "high energy"?

The negatively charged phosphate groups repel each other; hydrolysis of these bonds releases energy that can be used to drive cellular work.

How is substrate-level phosphorylation different from oxidative phosphorylation?

Substrate-level: ATP is made by direct transfer of a phosphate group from a substrate to ADP (e.g., in glycolysis). Oxidative: ATP is made using the proton motive force generated by the electron transport chain.

Why must oxidation and reduction always be coupled?

Because electrons lost by one molecule (oxidation) must be gained by another (reduction) — electrons cannot exist free in solution.

Is removal of a hydrogen atom generally oxidation or reduction?

Oxidation — removing hydrogen removes electrons from the molecule.

What is a precursor metabolite?

An intermediate of central metabolic pathways (glycolysis, TCA cycle, PPP) used as a starting material for biosynthesis of amino acids, nucleotides, lipids, etc.

What is the mechanism of action of sulfa drugs?

Sulfa drugs are structural analogs of PABA; they competitively inhibit the enzyme that incorporates PABA into folic acid synthesis, which bacteria need for nucleotide production (humans get folate from diet, so are unaffected).

What does it mean that mercury is a non-competitive enzyme inhibitor?

Mercury binds to a site other than the active site, changing the enzyme's shape and permanently inactivating it regardless of substrate concentration — it cannot be overcome by adding more substrate.

What is the fate of electrons carried by NADH and FADH2?

They are donated to the electron transport chain, ultimately reducing O2 (aerobic) or another terminal electron acceptor (anaerobic) to water. Energy released drives proton pumping and ATP synthesis.

What is the fate of NADPH?

NADPH is used primarily in anabolic (biosynthetic) reactions, not the ETC.

What are the central metabolic pathways?

Glycolysis, Pentose Phosphate Pathway (PPP), and TCA (citric acid) cycle. They are "central" because they are used by most organisms and provide both energy and precursor metabolites for biosynthesis.

What is the endpoint of glycolysis?

2 pyruvate molecules (plus 2 ATP and 2 NADH per glucose).

What is the endpoint of the TCA cycle?

CO2 is released; NADH, FADH2, and GTP are produced. No oxygen is directly consumed here.

What is the transition step?

Pyruvate is converted to acetyl-CoA by pyruvate dehydrogenase, releasing CO2 and producing NADH. It connects glycolysis to the TCA cycle.

Why does the transition step and TCA cycle repeat twice per glucose?

Because one glucose yields 2 pyruvates, so the transition step and TCA cycle each process one pyruvate at a time — they must run twice to process both.

Which central pathway initiates glucose breakdown?

Glycolysis.

Which central pathway is used exclusively for biosynthesis?

Pentose Phosphate Pathway (PPP) — primarily produces NADPH and ribose-5-phosphate for nucleotide synthesis.

Which pathway generates the most reducing power (NADH/FADH2)?

TCA cycle.

Which pathway generates the most ATP directly?

Glycolysis generates the most ATP via substrate-level phosphorylation directly, but overall oxidative phosphorylation (via ETC) produces far more ATP total.

Where do NADH vs. FADH2 electrons enter the ETC?

NADH electrons enter at Complex I (higher up), generating more proton pumping. FADH2 electrons enter at Complex II (lower), generating less proton pumping and therefore less ATP.

Which pathway provides precursor metabolites for nucleotide biosynthesis?

The Pentose Phosphate Pathway (produces ribose-5-phosphate).

What parts of central metabolism provide precursors for lipid synthesis?

Acetyl-CoA (from the transition step/TCA) and glycolytic intermediates (glycerol-3-phosphate) are used for fatty acid and lipid synthesis.

How would a bacterium use protein as an energy source?

Proteins are hydrolyzed to amino acids; amino groups are removed (deamination) and the carbon skeletons are converted to TCA intermediates or pyruvate and fed into central metabolism.

How would a bacterium use lipids as an energy source?

Fatty acids undergo beta-oxidation to produce acetyl-CoA, NADH, and FADH2, which enter the TCA cycle and ETC.

What is proton motive force used for in mitochondria and in bacteria?

In both: drives ATP synthase to produce ATP. In bacteria additionally: powers flagellar rotation and active transport.

How is fermentation different from respiration?

Respiration uses an external terminal electron acceptor (O2 or other inorganic molecules) and the ETC. Fermentation uses an organic molecule as the terminal electron acceptor internally, produces less ATP, and does not use an ETC.

How is NAD+ regenerated in respiration vs. fermentation?

Respiration: NADH donates electrons to the ETC, regenerating NAD+. Fermentation: NADH donates electrons to an organic molecule (e.g., pyruvate), regenerating NAD+ without an ETC.

How is aerobic respiration different from anaerobic respiration?

Aerobic: uses O2 as the terminal electron acceptor. Anaerobic: uses other inorganic molecules (NO3−, SO4²−, CO2) as the terminal electron acceptor; yields less energy.

Which terminal electron acceptor yields more energy — O2 or NO3−?

O2 — it has a higher reduction potential, so more energy is released when electrons are transferred to it.

What is BOD and how does high-BOD substances affect a water body?

BOD (Biological Oxygen Demand) measures the oxygen required by microbes to decompose organic matter. High-BOD substances (e.g., sewage) cause microbes to consume O2 rapidly, creating hypoxic conditions that kill aquatic life.

What is the difference between primary and secondary water treatment? Why is aeration important?

Primary treatment: physical removal of solids (settling). Secondary treatment: biological degradation of dissolved organics by microorganisms. Aeration adds O2 to support aerobic microbial metabolism, which is more efficient at breaking down organic matter.

Give three examples of why fermentation end products are important.

1) Ethanol and CO2 in brewing/baking. 2) Lactic acid in yogurt, cheese, and sauerkraut production. 3) Industrial production of acetone, butanol, and other chemicals.

Distinguish between replication, transcription, and translation.

Replication: DNA → DNA (copying the genome). Transcription: DNA → RNA (making an RNA copy of a gene). Translation: RNA → Protein (ribosomes read mRNA to build a polypeptide).

Describe the basic structure of a deoxynucleotide.

A deoxynucleotide has three parts: a nitrogenous base, a 5-carbon deoxyribose sugar, and one or more phosphate groups.

Which 4 bases are found in DNA?

Adenine (A), Thymine (T), Guanine (G), and Cytosine (C).

What are base pairing rules in DNA?

A pairs with T (2 hydrogen bonds); G pairs with C (3 hydrogen bonds). These are complementary base pairs.

Describe the basic structure of a DNA molecule.

DNA is a double helix: two antiparallel strands of nucleotides connected by hydrogen bonds between complementary bases, with a sugar-phosphate backbone on the outside.

How is RNA different from DNA?

RNA is single-stranded, uses ribose sugar (not deoxyribose), and contains uracil (U) instead of thymine (T).

What are the 3 functional types of RNA?

mRNA (messenger RNA — carries genetic info), tRNA (transfer RNA — brings amino acids to ribosome), rRNA (ribosomal RNA — structural/catalytic component of ribosomes).