Microbiology Lecture Notes: Metabolism, Microbial Growth, and Cell Biology

Comprehensive practice flashcards covering cellular metabolism, microbial growth conditions, staining procedures, taxonomy, and cellular structures based on lecture notes.

What is metabolism?

Metabolism is defined as all of the reactions happening within a cell that contribute to its function and growth.

How do catabolism and anabolism differ?

Catabolism involves breaking things down, whereas anabolism involves building things up from smaller molecules.

What metabolic sources are indicated by the prefixes AUTO, HETERO, PHOTO, and CHEMO?

AUTO and HETERO indicate carbon source, while PHOTO and CHEMO indicate energy source.

How do autotrophs and heterotrophs obtain their carbon?

Autotrophs obtain carbon from $\text{CO}_2$, whereas heterotrophs obtain carbon from organic matter.

How do phototrophs and chemotrophs obtain their energy?

Phototrophs obtain energy from light, whereas chemotrophs obtain energy from chemicals.

How are humans categorized based on carbon and energy sources?

Humans are chemoheterotrophs that utilize aerobic respiration.

What source of electrons do organotrophs and lithotrophs use?

Organotrophs obtain electrons from organic sources, whereas lithotrophs obtain electrons from inorganic sources.

What are the oxygen requirements of obligate aerobes, obligate anaerobes, and facultative anaerobes?

Obligate aerobes must have oxygen to grow; obligate anaerobes cannot have oxygen because it can kill them; facultative anaerobes can live with or without oxygen.

What are the oxygen requirements of aerotolerant anaerobes and microaerophiles?

Aerotolerant anaerobes prefer anaerobic conditions but can survive low levels of oxygen; microaerophiles require $2\%\text{ to }10\%$ oxygen.

What functions do superoxide dismutase, catalase, and peroxidase perform?

Superoxide dismutase converts superoxide to hydrogen peroxide; catalase breaks down hydrogen peroxide into water and oxygen; peroxidase converts hydrogen peroxide into less harmful substances.

What are the four types of reactive oxygen species (ROS) listed in the transcript?

Singlet oxygen, superoxide radical, peroxide anion, and hydroxyl radical.

How do temperature extremes affect bacterial proteins and cell membranes?

High temperatures denature proteins and make lipids too fluid, whereas low temperatures make cell membranes too fragile.

What are the optimal growth temperature classifications for microbes?

Psychrophiles (below $15\,^\circ\text{C}$), Psychrotolerant (tolerate cold), Mesophiles ($20\text{--}40\,^\circ\text{C}$), Thermophiles (above $45\,^\circ\text{C}$), and Hyperthermophiles ($80\text{--}100\,^\circ\text{C}$).

How are bacteria classified based on their preferred pH environments?

Neutrophiles grow best in neutral pH, acidophiles grow best in acidic conditions, and alkalinophiles grow best in alkaline environments up to pH 11.5.

What are the steps involved in biofilm formation?

1. Free cells respond to contact with a surface. 2. Initiates a metabolic response to attach. 3. Develop an extracellular polymeric substance (EPS). 4. EPS causes cells to stick even more. 5. Bacteria reproduce and form a biodiverse biofilm.

What is quorum sensing?

Quorum sensing is bacterial communication via chemical signals where higher chemical concentration signals a large population and low chemical concentration signals a small population.

What clinical sample types are routinely collected from different body systems?

Skin: swabs, scrapings, wound samples. Respiratory: sputum, throat swab, nasal swab. Reproductive: vaginal/urethral swabs, discharge. Urinary: urine.

How do streak plate and spread plate isolation methods differ?

A streak plate uses a sterile loop to spread bacteria across three sections to yield isolated colonies; a spread plate uses a spreader to evenly distribute a diluted bacterial sample over agar.

What are the four general types of culture media?

Defined media (known chemical composition), complex media (unknown exact composition), selective media (selects growth of specific organisms), and differential media (helps differentiate microorganisms).

What are four methods used to preserve bacterial cultures?

Refrigeration (short term), Freezing (longer term), Deep freezing (long term), and Lyophilization (extremely long term; water removed from frozen culture).

What equation determines bacterial growth over generations?

$\text{Final bacteria} = \text{starting bacteria} \times 2^{(\text{number of generations})}$, where $\text{Number of generations} = \frac{\text{total time}}{\text{time for one division}}$.

What are the four phases of the bacterial growth curve?

1. Lag phase (adjusting, little division). 2. Log phase (rapid exponential division). 3. Stationary phase (division equals death rate due to nutrient depletion). 4. Death phase (cells die off).

What is the difference between oxidation and reduction?

Oxidation is the loss of electrons, while reduction is the gain of electrons.

What are the three types of ATP phosphorylation and where do they occur?

1. Substrate-level phosphorylation (enzyme directly transfers phosphate to ADP; occurs in cytoplasm or metabolic pathways). 2. Oxidative phosphorylation (ETC creates a proton gradient; occurs in bacterial cell membrane or inner mitochondrial membrane). 3. Photophosphorylation (light energy drives ETC; occurs in photosynthetic membranes).

What are the six basic types of enzymes?

Oxidoreductases (transfer electrons), Transferases (transfer functional groups), Hydrolases (break bonds with water), Lyases (break bonds without water), Isomerases (rearrange atoms), and Ligases (join molecules together using ATP).

What are the two components of a holoenzyme?

An apoenzyme (the inactive protein portion) and a cofactor (a non-protein helper, either an inorganic ion or organic coenzyme).

How do competitive and noncompetitive enzyme inhibitors differ?

Competitive inhibitors compete directly with the substrate for binding at the active site. Noncompetitive inhibitors bind to an allosteric site, altering the shape of the active site.

How do fermentation and aerobic respiration compare in ATP production and oxygen requirement?

Fermentation does not require oxygen and produces $2\text{ ATP}$. Aerobic respiration requires oxygen and produces around $30\text{ ATP}$.

How do the ED pathway and Pentose Phosphate Pathway compare to the EMP pathway?

The EMP pathway produces $2\text{ ATP}$ and $2\text{ NADH}$. The ED pathway produces $1\text{ ATP}$, $1\text{ NADH}$, and $1\text{ NADPH}$. The Pentose Phosphate Pathway produces $NADPH$ and ribose 5-phosphate rather than primary ATP.

What are the primary products of lactic acid fermentation and alcohol fermentation?

Lactic acid fermentation produces lactate and regenerates $\text{NAD}^+$. Alcohol fermentation produces ethanol and releases $\text{CO}_2$.

What are the key staining outcomes of the Gram stain and Acid-fast stain?

Gram stain: Gram-positive cells appear purple, Gram-negative cells appear pink/red. Acid-fast stain: Acid-fast cells with mycolic acid walls appear red/pink, non-acid-fast cells appear blue.

What are the visual outcomes of Endospore, Capsule, and Negative stains?

Endospore stain: Endospores appear green and cells appear red/pink. Capsule stain: Capsules appear as a clear halo around bacteria. Negative stain: Background is stained while cells remain clear.

What are the defining characteristics of the 3 Domains of life?

Eukarya: possess a nucleus and membrane-bound organelles. Bacteria: lack a nucleus and organelles, cell walls contain peptidoglycan. Archaea: lack a nucleus and organelles, cell walls lack peptidoglycan.

What is the hierarchical sequence of taxonomic ranks?

Domain, Kingdom, Phylum, Class, Order, Family, Genus, Species.

What are the four major processes common to living cells?

Growth (increase in size), Reproduction (increase in number), Responsiveness (ability to react to environment), and Metabolism (taking in nutrients to yield ATP energy).

What chemical components make up bacterial peptidoglycan?

Alternating chains of NAG (N-acetylglucosamine) and NAM (N-acetylmuramic acid) linked together by tetrapeptide crossbridges attached to neighboring NAMs.

What structural differences distinguish Gram-positive from Gram-negative cell walls?

Gram-positive walls have a thick peptidoglycan layer, teichoic acids, and a single membrane. Gram-negative walls have a thin peptidoglycan layer, no teichoic acids, and an outer membrane containing lipopolysaccharides (Lipid A).

How do bacterial flagella structurally and functionally differ from eukaryotic flagella?

Bacterial flagella are made of flagellin, lack microtubules, rotate $360^\circ$, and are powered by proton motive force. Eukaryotic flagella contain microtubules, move in a wave-like pattern, and are powered by ATP hydrolysis.

What are the five common arrangements of bacterial flagella?

Monotrichous (single flagellum at one end), Amphitrichous (flagella at both ends), Lophotrichous (cluster at one end), Peritrichous (flagella all around), and Atrichous (lacking flagella).

What is group translocation in bacterial cell transport?

Group translocation is a specialized active transport mechanism where a substance is chemically modified while being transported across the cell membrane.

What evidence supports the endosymbiotic theory for mitochondria and chloroplasts?

Mitochondria and chloroplasts contain their own DNA, have their own ribosomes, are surrounded by two membranes, and replicate via a process similar to binary fission.