Metabolism and Growth Flashcards
(30 cards)
metabolic pathways and their energetics
Exergonic Reactions
- Energy-releasing (ΔG < 0)
- Products have less free energy than reactants
- Common in catabolic pathways
- Not always catabolic (e.g., ATP hydrolysis is exergonic but not catabolic)
Endergonic Reactions
- Energy-requiring (ΔG > 0)
- Products have more free energy than reactants
- Often coupled to ATP hydrolysis
- Common in anabolic pathways and active transport
- Not always anabolic (e.g., ion pumps are endergonic but not anabolic)
Catabolism
- Breakdown of molecules (e.g., glucose → CO₂ + H₂O)
- exergonic → releases energy for ATP production
- Fuels cellular work by providing electrons and energy
Anabolism
- Synthesis of complex molecules (e.g., proteins, DNA)
- endergonic → requires energy input (e.g., from ATP)
- Builds cellular structures and stores energy
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Catabolism breaks down large molecules (such as polysaccharides, lipids, nucleic acids, and proteins) into smaller units (such as monosaccharides, fatty acids, nucleotides, and amino acids, respectively). Catabolism is the breaking-down aspect of metabolism, whereas anabolism is the building-up aspect.
ATP synthesis and hydrolysis are not categorized as anabolic or catabolic processes themselves. Instead, they function as energy transfer reactions that connect the two. ATP synthesis stores energy released from catabolic reactions, such as the breakdown of glucose, but the synthesis itself is not considered anabolic because it doesn’t involve building complex macromolecules. Similarly, ATP hydrolysis releases energy to power cellular work, including anabolic processes like protein synthesis or active transport, but hydrolysis is not catabolic because it doesn’t involve breaking down large biological molecules into smaller units.
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ATP coupling
- Catabolism provides the energy to generate ATP
- Anabolism uses ATP to drive biosynthetic reactions
- Links energy release and energy use in metabolism
Describe the general structure and function of enzymes
General Function
- Biological catalysts that speed up chemical reactions
- Lower the activation energy required for a reaction
- Not consumed in the reaction
Structure
- Usually proteins (some RNA enzymes exist)
- Have a specific 3D shape critical for function
- Contain an active site and may have allosteric sites
Active Site
- Region on enzyme where substrate binds
- Site of the chemical reaction
- High specificity—fits specific substrates (lock and key or induced fit model)
Substrate
- Reactant that binds to the enzyme’s active site
- Enzyme-substrate complex forms temporarily
Product
- Resulting molecule(s) after enzyme catalyzes the reaction
- Released from the enzyme after reaction is complete
Allosteric Site
- A regulatory site separate from the active site
- Binding of molecules here can enhance or inhibit enzyme activity
Activation Energy
- Energy required to initiate a chemical reaction
- Enzymes lower this barrier to speed up reactions
Lock and Key vs Induced Fit
Lock and Key Model
- Substrate fits perfectly into the enzyme’s active site, like a key in a lock
- Implies the active site is a rigid shape, exactly complementary to the substrate
- No significant change in enzyme shape
Induced Fit Model
- Enzyme’s active site adjusts its shape slightly to better fit the substrate upon binding
- Describes enzyme as more flexible, molding around the substrate
- Explains broader enzyme specificity
Key Difference
- Lock and key: fixed, rigid match
- Induced fit: flexible, shape adapts to fit substrate
Cofactors and Coenzymes
Cofactors
- Any non-protein substance required for enzyme activity.
- Includes Inorganic substances (usually metal ions like Fe²⁺, Zn²⁺, Cu²⁺) and coenzymes
- inorganic -> Often derived from dietary minerals, organic -> direved from vitamines
Coenzymes
- Organic, non-protein molecules
- Often derived from vitamins (e.g., B-vitamins)
- Typically act as electron or chemical group carriers (e.g., NAD⁺, CoA)
Key Point
- Both cofactors and coenzymes are required for full enzyme function
- Coenzymes are a type of cofactor (organic vs. inorganic)
competitive inhibition vs allosteric inhibition
Competitive Inhibition
- Inhibitor resembles the substrate
- Binds to the active site, blocking substrate access
- Can be overcome by increasing substrate concentration
- Does not change enzyme shape
Allosteric (Noncompetitive) Inhibition
- Inhibitor binds to a different site (allosteric site), not the active site
- Causes enzyme shape change, which alters the active site
- Substrate may still bind, but reaction is not catalyzed
- Cannot be reversed by adding more substrate
Comparison
- Both reduce enzyme activity
- Both involve inhibitor binding, but at different sites
Key Difference
- Competitive: blocks the active site
- Allosteric: changes the shape of the active sit
Allosteric activation
- Activator binds to an allosteric site
- Stabilizes active form of enzyme or active site
- Increases enzyme activity by making substrate binding easier
- Important in metabolic regulation and feedback mechanisms
regulation of metabolism by feedback inhibition
Feedback Inhibition
- A regulatory mechanism in metabolic pathways
- The end product of a pathway inhibits an early enzyme, usually the first committed step
- Prevents wasteful overproduction and maintains metabolic balance
- Occurs in both anabolic and catabolic pathways, but is more common in anabolic ones
Mechanism
- Typically involves allosteric inhibition
- End product binds to a regulatory (allosteric) site, altering the enzyme’s shape and reducing activity
- This slows or halts the entire pathway when the product is abundant
Anabolic Example
- Isoleucine biosynthesis: Isoleucine inhibits threonine deaminase, the first enzyme in its synthesis pathway
- Prevents excessive buildup of isoleucine
- Classic example in amino acid metabolism
Catabolic Example
- Glycolysis: High levels of ATP allosterically inhibit phosphofructokinase-1 (PFK-1)
- Reduces glucose breakdown when cellular energy is sufficient
Type of Inhibition
- Allosteric, not competitive — the end product binds a site other than the active site
- Alters enzyme conformation or dynamics to reduce activity
Compare fermentation, anaerobic respiration, and aerobic respiration in ATP production
Fermentation
1. Final electron acceptor: organic molecule (e.g., pyruvate)
2. Pathways: glycolysis followed by a fermentative pathway
3. Phosphorylation: substrate-level phosphorylation only
4. Max ATP yield: ~2 ATP (from glycolysis only)
5. Glycolysis: breakdown of glucose (6C) into 2 pyruvate (3C each), producing ATP and NADH
6. Fermentation: reduction of pyruvate using NADH to regenerate NAD⁺; no additional ATP produced
Anaerobic respiration
1. Final electron acceptor: inorganic molecule (e.g., NO₃⁻, SO₄²⁻, CO₂)
2. Pathways: glycolysis (oxidation of glucose), pyruvate oxidation, citric acid cycle / Krebs cycle / TCA cycle, electron transport chain
3. Phosphorylation: substrate-level and oxidative phosphorylation (chemiosmosis)
4. Max ATP yield: ~32 ATP (varies with organism and final acceptor)
Aerobic respiration
1. Final electron acceptor: oxygen (O₂)
2. Pathways: glycolysis, pyruvate oxidation, citric acid cycle, electron transport chain
3. Phosphorylation: substrate-level and oxidative phosphorylation
4. Max ATP yield: ~38 ATP (theoretical maximum)
Key concepts
1. The final electron acceptor determines whether respiration is aerobic (O₂) or anaerobic (another inorganic molecule like NO₃⁻, SO₄²⁻, or CO₂)
2. Oxidative phosphorylation uses an electron transport chain and a proton gradient, with either oxygen or another final electron acceptor
3. Fermentation yields much less ATP because it does not involve an electron transport chain
4. Organic molecules contain carbon-hydrogen (C-H) bonds
5. Inorganic molecules lack carbon-hydrogen (C-H) bonds
NAD⁺ in metabolism and ATP production
Function of NAD⁺
- Essential coenzyme that carries electrons in metabolism
- Accepts electrons (is reduced) → NAD⁺ → NADH
- Required in glycolysis, pyruvate oxidation, and the citric acid cycle
- Required in aerobic respiration, anaerobic respiration, and fermentation
- Glycolysis cannot continue without NAD⁺
How NAD⁺ Is Regenerated
- Respiration (aerobic and anaerobic):
1. NADH donates electrons to the electron transport chain (ETC)
2. The ETC uses the energy from electron transfer to pump protons and create a proton gradient
3. Electrons are ultimately accepted by a final electron acceptor
- In aerobic respiration: oxygen (O₂)
- In anaerobic respiration: inorganic molecules (e.g., NO₃⁻, SO₄²⁻, CO₂)
-
Fermentation:
- NADH donates electrons directly to an organic molecule (e.g., pyruvate)
- No ETC involved
- Restores NAD⁺ so glycolysis can continue
Key Point
- Without NAD⁺ regeneration, ATP production via glycolysis stops
Describe exoenzymes and endoenzymes
Exoenzymes
- Secreted by the cell into the external environment
- Function outside the cell
- Break down large molecules (e.g., proteins, starch) into smaller units for absorption
- Examples: amylase, lipase, protease
Endoenzymes
- Remain inside the cell
- Function within the cytoplasm
- Involved in internal metabolism (e.g., glycolysis, DNA replication)
- Examples: hexokinase, DNA polymerase
Comparison
- Both are biological catalysts made by cells
- Differ in location of activity and type of target molecules
Key Difference
- Exoenzymes work outside the cell
- Endoenzymes work inside the cell
oxidation vs reduction
Oxidation and Reduction
- Oxidation: loss of electrons
- Reduction: gain of electrons
- Memory trick: OIL RIG
- Oxidation Is Loss
- Reduction Is Gain
- In metabolism:
1. Glucose is oxidized (loses electrons)
2. Electron carriers like NAD⁺ are reduced (gain electrons)
3. Final electron acceptor (like O₂ or NO₃⁻) is reduced at the end of the electron transport chain
Reactive Oxygen Species (ROS)-Detoxifying Enzymes
Living in an oxygen-containing environment exposes organisms to reactive oxygen species (ROS).
Organisms must possess enzymes to detoxify harmful oxygen molecules, including superoxide radicals and peroxide forms.
-
Superoxide Dismutase (SOD)
- Converts superoxide radicals (O₂⁻) into hydrogen peroxide (H₂O₂)
- Hydrogen peroxide can partially dissociate into peroxide ions (O₂²⁻) and protons (H⁺) in a dynamic equilibrium
- Protects cells from toxic superoxide radicals -
Catalase
- Breaks down hydrogen peroxide (H₂O₂), and thus removes both hydrogen peroxide and peroxide ions (O₂²⁻) formed by dissociation
- Reaction: 2 H₂O₂ → 2 H₂O + O₂
- Common in aerobes and facultative anaerobes -
Peroxidase
- Reduces hydrogen peroxide (H₂O₂) to water (H₂O) using an electron donor (e.g., NADH)
- Also removes peroxide ions (O₂²⁻) indirectly through H₂O₂ breakdown
- Found in some aerotolerant anaerobes that lack catalase
Key Point
- Hydrogen peroxide (H₂O₂) exists in dynamic equilibrium with peroxide ions (O₂²⁻) in solution
- All three enzymes protect against ROS, including superoxide radicals and peroxide-derived damage
- Presence of these enzymes indicates ability to survive in an oxygenated (aerobic) environment
alcohol fermentation in Saccharomyces cerevisiae
Process Overview
1. Glycolysis: Glucose → 2 pyruvate + 2 ATP + 2 NADH
2. Pyruvate decarboxylase removes CO₂ from pyruvate → forms acetaldehyde (2C)
3. Alcohol dehydrogenase reduces acetaldehyde → ethanol
- NADH is oxidized to NAD⁺, allowing glycolysis to continue
End Products
- Ethanol
- CO₂
- Regenerated NAD⁺ (no additional ATP beyond glycolysis)
Organism
- Performed by Saccharomyces cerevisiae (brewer’s yeast)
Food & Beverage Examples
- Beer
- Wine
- Bread (CO₂ causes dough to rise)
Key Point
- Acetaldehyde is the final electron acceptor in this anaerobic pathway
homolactic fermentation in Lactobacillus spp
Process Overview
- Glycolysis: Glucose → 2 pyruvate + 2 ATP + 2 NADH
- Pyruvate acts as the final electron acceptor
- Lactate dehydrogenase reduces pyruvate → lactate
- NADH is oxidized to NAD⁺, allowing glycolysis to continue
End Products
- Lactate (lactic acid)
- Regenerated NAD⁺
- 2 ATP per glucose
Organism
- Performed by Lactobacillus spp.
- Same pathway occurs in human muscle cells under anaerobic conditions
Food Examples
- Yogurt
- Cheese (especially hard cheeses)
Key Point
- Simple pathway: glycolysis + 1 enzyme (lactate dehydrogenase)
- Only product: lactate (no gas or alcohol)
Major food fermentation pathways
-
Alcohol Fermentation
- Glycolysis produces pyruvate and NADH
- Enzyme: Pyruvate decarboxylase converts pyruvate into acetaldehyde + CO₂
- Enzyme: Alcohol dehydrogenase reduces acetaldehyde to ethanol using electrons from NADH
- Common foods: Beer, wine, bread
- Common organism: Saccharomyces cerevisiae (yeast) -
Homolactic Fermentation
- Glycolysis produces pyruvate and NADH
- Enzyme: Lactate dehydrogenase reduces pyruvate directly to lactic acid using electrons from NADH
- Common foods: Yogurt, cheese
- Common organism: Lactobacillus species -
Heterolactic Fermentation
- Glycolysis produces pyruvate and NADH
- Pyruvate and other intermediates are converted into lactic acid, ethanol, CO₂, and acetic acid
- Enzymes: Multiple fermentative enzymes (varies by species) to split products and recycle NAD⁺
- Common foods: Sauerkraut, kefir
- Common organism: Leuconostoc species
Key Point
- In all types of fermentation, NADH is oxidized to regenerate NAD⁺, allowing glycolysis and ATP production to continue.
aerobic vs anaerobic respiration
Aerobic Respiration
- Pathway: Glycolysis → Citric Acid Cycle → ETC
- Final e⁻ acceptor: Molecular oxygen (O₂)
- Used by most eukaryotes; highly efficient
- Little variation across organisms
Anaerobic Respiration
- Pathway: Glycolysis → Citric Acid Cycle → ETC
- Final e⁻ acceptors: Oxygen-containing inorganic molecules
- NO₂⁻ → Nitrite respiration
- CO₂ → Carbon dioxide respiration (e.g., methanogenesis)
- SO₄²⁻ → Sulfate respiration
- Common in archaea and bacteria
- Plays a role in nutrient recycling (nitrogen, carbon, sulfur cycles)
Key Difference
- Defined by the type of final electron acceptor used in the ETC
intrinsic vs extrinsic growth factors
Intrinsic Growth Factors
- Internal to the organism (genetics, physiology)
- Fixed limits on how fast a species can reproduce, even under ideal conditions
- Determined by factors like enzyme efficiency, genome size, replication machinery
- Examples:
- Clostridium perfringens: 15 min
- E. coli: 20 min
- Mycobacterium tuberculosis: 15 hrs
- Treponema pallidum: 33 hrs
Extrinsic Growth Factors
- External environmental conditions
- Can influence growth rate, but only up to the species’ intrinsic maximum
- Include temperature, pH, nutrients, oxygen availability
Comparison
- Intrinsic = unchangeable biological limit
- Extrinsic = environmental, can be optimized
- Both influence overall growth, but intrinsic factors set the ceiling
Key Point
- Even in perfect conditions, growth rate is limited by intrinsic factors
growth temperature classifications of microorganisms
Psychrophiles
- Grow best at 0–15°C
- Cold-loving; found in glaciers, deep oceans
- No growth at moderate or high temps
Mesophiles
- Grow best at 20–45°C
- Most human pathogens (body temp ~37°C)
- No growth at very cold or very hot temps
Thermophiles
- Grow best at 50–70°C
- Found in hot springs, compost
- No growth at cooler temperatures
Hyperthermophiles
- Grow best at 80°C and above
- Usually Archaea; found in volcanic vents, deep-sea thermal vents
- Cannot grow at mesophilic or lower temperatures
atmospheric classifications of microbes
-
Obligate Aerobes
- Require O₂ to survive
- Detoxify oxygen radicals (e.g., SOD, catalase)
- Use aerobic respiration only
- Grow only at top of thioglycolate tube -
Obligate Anaerobes
- Killed by O₂; cannot detoxify radicals
- Use fermentation and/or anaerobic respiration
- Grow only at bottom of thioglycolate tube -
Facultative Anaerobes
- Use O₂ if available, but can grow without it
-*Detoxify radicals
- Can switch between aerobic respiration, fermentation, anaerobic respiration
- Dense growth at top; growth throughout tube
- Example: E. coli -
Aerotolerant Anaerobes
- Do not use O₂, but can survive in it
- Detoxify radicals, but never perform aerobic respiration
- Use fermentation only
- Uniform growth throughout the tube -
Microaerophiles
- Require low O₂ (5–15%)
- Can detoxify small amounts of radicals
- Use aerobic respiration / and or fermentation
- Grow in middle of thioglycolate tube -
Capnophiles
- Thrive in elevated CO₂ (≥10%)
- Mmost often are aerobic
- Use aerobic respiration and/or fermentation
- Special incubation required (e.g., candle jar)
Using Growth Results
- Top-only growth = obligate aerobe
- Bottom-only growth = obligate anaerobe
- Dense at top, fades down = facultative anaerobe
- Even growth = aerotolerant anaerobe
- Middle zone only = microaerophile
microbial pH requirements
1.Acidophiles
- Grow best at pH 1–5
- Found in acidic environments (e.g., acid mine drainage, stomach)
- Do not grow near neutral pH
-
Neutrophiles
- Grow best at pH 6.5–7.5
- Most human pathogens are neutrophiles
- Thrive in body fluids and tissues -
Alkaliphiles
- Grow best at pH 8–11
- Found in basic environments (e.g., soda lakes, alkaline soils)
- Do not grow well at neutral or acidic pH
Using Growth Results
- Growth only at low pH → acidophile
- Growth near pH 7 only → neutrophile
- Growth at high pH (≥9) → alkaliphile
Key Point
- pH preference reflects habitat
- Growth patterns across pH range help classify unknown organisms
halophilic and halotolerant microbes
Halotolerant Microorganisms
- Do not require salt, but can grow in high salt
- Example: Staphylococcus aureus
- Grow on TSA (Tryptic Soy Agar) and MSA (Mannitol Salt Agar)
- MSA: selective for salt tolerance, differential for mannitol fermentation
- S. aureus turns MSA yellow (ferments mannitol)
Halophilic Microorganisms
- Require elevated salt to grow
- Found in marine and hypersaline environments
- Grow only on high-salt media, like MSA or media with ≥3% NaCl
- Will not grow on TSA (no salt)
Using Growth Results
- Growth on both TSA and MSA → halotolerant
- Growth only on MSA/high-salt media → halophile
Key Point
- MSA is selective for salt-tolerant organisms and can distinguish S. aureus by mannitol fermentation
bacterial colony and CFU (colony forming unit)
Bacterial Colony
- A visible cluster of bacteria growing on solid media
- Arises from a single ancestor cell or small group
- Represents a genetically identical population (clone)
- Each dot on a plate = one colony = one population
CFU (Colony Forming Unit)
- The original cell or group of cells that gave rise to a colony
- Represents a viable unit capable of forming a colony
- Measured in CFU/mL for liquid samples
- Important in quantifying bacterial populations
the statement “colony = genetically identical population” is true only if you’re starting with a pure culture, which is almost always the case in microbiology labs.
in normal lab conditions (pure cultures, isolated colonies), the assumption is that:
Bacteria were grown from a pure culture (one species only)
All cells stuck together were genetically identical already
Binary Fission
Binary Fission
- Most common type of asexual reproduction in bacteria
- One bacterial cell divides into two identical cells
- Steps: DNA replication → cell elongation → septum formation → cell separation
- Controlled by FtsZ ring (forms cleavage furrow)
- Not mitosis, but functionally similar in outcome (1 → 2 cells)
Exponential Growth
- Each division doubles the population
- Growth pattern: 1 → 2 → 4 → 8 → 16 → 32 → 64 (2ⁿ)
- Driven entirely by binary fission rate
Key Point
- Binary fission enables exponential growth, where population size increases rapidly over time
