Microbial Growth, Metabolism, and Chemical Control

Comprehensive practice flashcards covering microbial growth requirements, cellular respiration, fermentation pathways, enzyme kinetics, and chemical antimicrobial control methods.

What are the two general chemical growth requirements for microorganisms?

1. Energy source (harvested via catabolism from light, organic molecules, or inorganic molecules)
2. Macronutrients and micronutrients (used via anabolism to synthesize cell structures for growth and maintenance)

What is the primary difference in metabolic role between catabolism and anabolism in microbial growth?

Catabolism harvests chemical energy from environmental sources, whereas anabolism uses key dietary elements and energy to synthesize cellular components.

What are macronutrients in microbial nutrition?

Nutrients required in large amounts that make up the major elements in cell macromolecules, including $\text{CHNOPS}$ and specific ions necessary for protein function.

Which six chemical elements are represented by the acronym CHNOPS?

Carbon ($\text{C}$), Hydrogen ($\text{H}$), Nitrogen ($\text{N}$), Oxygen ($\text{O}$), Phosphorus ($\text{P}$), and Sulfur ($\text{S}$).

Which specific metallic cations are classified as essential macronutrient ions necessary for protein function?

$\text{Mg}^{2+}$, $\text{Ca}^{2+}$, and $\text{K}^+$.

What are micronutrients in microbial nutrition?

Nutrients required in trace amounts, including inorganic trace elements and organic growth factors such as vitamins.

Which five inorganic trace elements are explicitly listed as essential micronutrients?

Iron ($\text{Fe}$), Cobalt ($\text{Co}$), Copper ($\text{Cu}$), Manganese ($\text{Mn}$), and Zinc ($\text{Zn}$).

What is a microbial growth factor?

An organic micronutrient, such as a vitamin (e.g., folic acid or vitamin $\text{B}_{12}$), that an organism cannot synthesize and must obtain from its environment.

What essential cellular building block requires folic acid for its synthesis?

$\text{DNA}$.

Approximately what percentage of the dry weight of a typical bacterial cell is composed of carbon?

$$50\%$$

Which major classes of cellular macromolecules and components contain carbon?

Amino acids and proteins, nucleic acids ($\text{DNA}$, $\text{RNA}$, $\text{ATP}$), lipids, and other carbohydrates.

How do heterotrophs acquire carbon?

Heterotrophs use organic carbon sources, such as carbohydrates, lipids, and proteins.

What are the two major subcategories of heterotrophs based on how they obtain organic nutrients?

Saprobes (obtain organic nutrients from dead/decaying matter) and parasites (obtain nutrients from living hosts).

How do autotrophs acquire carbon?

Autotrophs use inorganic carbon in the form of carbon dioxide ($\text{CO}_2$).

Why must all microbial cells acquire energy from their environment?

To generate $\text{ATP}$, which is required to power cellular processes.

What is a phototroph?

An organism that uses light as its primary energy source.

What is a chemoorganotroph?

An organism that obtains energy from organic chemical compounds.

What is a chemolithotroph?

An organism that obtains energy from inorganic chemical compounds.

What are the five nutritional types of microbes based on their energy and carbon sources?

1. Photoautotroph
2. Photoheterotroph
3. Chemolithoautotroph
4. Chemolithoheterotroph
5. Chemoorganoheterotroph

What are the energy and carbon sources used by a photoautotroph?

Energy source: Light Carbon source: $\text{CO}_2$ (inorganic carbon)

What are the energy and carbon sources used by a photoheterotroph?

Energy source: Light Carbon source: Organic carbon

What are the energy and carbon sources used by a chemolithoautotroph?

Energy source: Inorganic chemicals Carbon source: $\text{CO}_2$ (inorganic carbon)

What are the energy and carbon sources used by a chemolithoheterotroph?

Energy source: Inorganic chemicals Carbon source: Organic carbon

What are the energy and carbon sources used by a chemoorganoheterotroph?

Energy source: Organic chemicals Carbon source: Organic carbon (the same organic chemicals serve as both energy and carbon sources)

Based on this reference table, which microbial nutritional class utilizes inorganic chemicals for energy and organic carbon as its carbon source?

Chemolithoheterotroph

Thiomargarita magnifica utilizes Fe2+ as its energy source and CO2 as its carbon source. What nutritional type is it?

Chemolithoautotroph

Pseudomonas aeruginosa utilizes glucose (C6H12O6) for both energy and carbon. What nutritional type is it?

Chemoorganoheterotroph

Into which nutritional category do most bacterial, fungal, and protozoan human pathogens fall?

Chemoorganoheterotroph

What is nitrogen fixation?

The biochemical conversion of atmospheric nitrogen gas ($\text{N}_2$) into ammonium ($\text{NH}_4^+$).

What are four environmental sources of nitrogen for microbes?

Amino acids/proteins, ammonium ($\text{NH}_4^+$), nitrate ($\text{NO}_3^-$), and atmospheric nitrogen gas ($\text{N}_2$).

Which cellular macromolecules and energy compounds require nitrogen for synthesis?

Proteins, nucleic acids ($\text{DNA}$ and $\text{RNA}$), and $\text{ATP}$.

Where are symbiotic nitrogen-fixing bacteria commonly located in plants?

In specialized plant root nodules.

Which amino acids and vitamins require sulfur (S) for their synthesis?

Amino acids: Cysteine (Cys) and Methionine (Met) Vitamins: Biotin and Thiamine

Which critical cellular structures and molecules require phosphorus (P) for synthesis?

$\text{DNA}$, $\text{RNA}$, phospholipids, and $\text{ATP}$.

What is the role of molecular oxygen (O2) in obligate aerobes?

It acts as the terminal electron acceptor during aerobic respiration according to the reaction: $\text{H}^+ + \text{O}_2 + e^- \rightarrow \text{H}_2\text{O}$.

What are reactive oxygen species (ROS) or oxygen radicals?

Toxic, highly reactive byproducts formed during the utilization of $\text{O}_2$ in cellular respiration or through ionizing radiation.

How do anaerobic microorganisms generate ATP in the absence of O2?

Via anaerobic respiration or fermentation.

What two mechanisms generate oxygen radicals in microbial environments?

1. Cellular aerobic respiration utilizing $\text{O}_2$
2. Ionizing radiation splitting water ($\text{H}_2\text{O} \rightarrow \text{H}^+ + \text{OH}^-$)

What are four specific examples of reactive oxygen species (ROS)?

1. Superoxide ($\text{O}_2^-$)
2. Hydroxyl ion/radical ($\text{OH}^-$)
3. Hydrogen peroxide ($\text{H}_2\text{O}_2$)
4. Peroxide ion ($\text{O}_2^{2-}$)

What structural feature do all oxygen radicals share that accounts for their reactivity?

They contain unpaired electrons.

Why are oxygen radicals toxic to living cells?

They are highly unstable, powerful oxidizing agents that oxidize vital cellular components, causing severe $\text{DNA}$ and cellular damage.

Which three naturally occurring antioxidants help aerobic cells neutralize oxygen radicals?

Tocopherol (Vitamin E), ascorbic acid (Vitamin C), and melatonin.

What three major detoxifying enzymes are produced by aerobes to neutralize reactive oxygen species?

Superoxide dismutase ($\text{SOD}$), catalase, and peroxidase.

What chemical reaction is catalyzed by superoxide dismutase (SOD)?

$$\text{O}_2^- + \text{O}_2^- + 2\text{H}^+ \rightarrow \text{H}_2\text{O}_2 + \text{O}_2$$

What reaction does catalase catalyze, and what visible outcome indicates a positive catalase test?

Catalase converts hydrogen peroxide via $2\text{H}_2\text{O}_2 \rightarrow 2\text{H}_2\text{O} + \text{O}_2$. A positive test produces vigorous bubbling of $\text{O}_2$ gas.

What chemical reaction is catalyzed by peroxidase?

$$\text{H}_2\text{O}_2 + 2\text{H}^+ \rightarrow 2\text{H}_2\text{O}$$

What is a metabolic pathway?

A series of consecutive chemical reactions that converts an initial reactant into a final end product through temporary intermediates, with each step catalyzed by a specific enzyme.

What is an intermediate in a metabolic pathway?

A temporary product formed at an intermediate step between the initial substrate and the final end product.

What happens to covalent chemical bonds during the individual steps of a metabolic pathway?

Typically, a single covalent bond is made or broken during each specific reaction step.

What are three key precursor molecules produced during catabolism that fuel anabolism?

Pyruvate, Acetyl $\text{CoA}$, and Glyceraldehyde-3-phosphate (Glyceraldehyde-3-P).

What cellular building blocks are generated directly from precursor molecules in anabolism?

Amino acids, simple sugars, nucleotides, and fatty acids.

What complex macromolecules are assembled from building blocks during anabolism?

Proteins, peptidoglycan, $\text{RNA}$, $\text{DNA}$, and complex lipids.

Based on this metabolic flow diagram, does catabolism yield or consume energy?

Catabolism yields energy, which is subsequently used to power the three stages of anabolism.

What electrical charge does an electron possess?

Negative charge ($-1$).

If a molecule gains one or more electrons, what happens to its overall oxidation state/charge?

Its overall charge/oxidation state is reduced.

What is oxidation in a redox reaction?

The loss of one or more electrons (or the loss of hydrogen atoms, since $\text{H} = e^- + \text{H}^+$).

What is reduction in a redox reaction?

The gain of one or more electrons (or the gain of hydrogen atoms).

What does the mnemonic OIL RIG stand for in biochemistry?

Oxidation Is Loss (of electrons), Reduction Is Gain (of electrons).

Why are biological oxidation and reduction reactions described as being coupled?

Because free electrons cannot exist independently in solution; every electron lost by an oxidized molecule must be simultaneously gained by a reduced molecule.

In this redox reaction diagram, which molecule is oxidized and which is reduced?

Molecule A loses an electron and becomes oxidized; Molecule B gains the electron and becomes reduced.

What analogy is used in lecture to describe the cellular role of coenzymes like NAD+ and FAD?

They act like 'Ubers' or shuttles that pick up and drop off electrons ($e^-$) and hydrogen ions ($\text{H}^+$) throughout the cell.

Between the redox pair NAD+ and NADH, which molecule is in the reduced state?

$\text{NADH}$ (it has gained electrons and a hydrogen atom).

Between the redox pair FAD and FADH2, which molecule is in the oxidized state?

$\text{FAD}$ (the empty shuttle form before picking up electrons/protons).

Identify the two distinct nucleotide components that comprise the dinucleotide structure of NAD+ shown here.

Nicotinamide mononucleotide ($\text{NMN}$) and Adenosine monophosphate ($\text{AMP}$).

What reaction is depicted in the forward direction: FAD + 2H+ + 2e- -> FADH2?

A reduction reaction (gaining $2\text{H}^+$ and $2e^-$).

What occurs when NADH is converted back to NAD+?

It undergoes oxidation, dropping off $2e^-$ and a proton.

Why are food molecules like carbohydrates, lipids, and proteins rich in potential chemical energy?

They are packed with high-energy electrons stored in chemical bonds in the form of hydrogen atoms.

What is the general biological definition of cellular respiration?

An $\text{ATP}$-generating process in which a chemical energy source is oxidized and its electrons are ultimately transferred to a terminal electron acceptor ($\text{TEA}$) that becomes reduced.

What defines aerobic cellular respiration?

Cellular respiration where the terminal electron acceptor ($\text{TEA}$) is molecular oxygen ($\text{O}_2$).

What defines anaerobic cellular respiration?

Cellular respiration where the terminal electron acceptor ($\text{TEA}$) is an environmental inorganic molecule other than $\text{O}_2$.

What is the overall balanced summary chemical equation for aerobic respiration of glucose?

$$6\text{O}_2 + \text{C}_6\text{H}_{12}\text{O}_6 \leftrightarrow 6\text{CO}_2 + 6\text{H}_2\text{O} + \text{energy (ATP)}$$

In the aerobic respiration of glucose, which molecule is oxidized and which is reduced?

Glucose ($\text{C}_6\text{H}_{12}\text{O}_6$) is oxidized to $\text{CO}_2$, and oxygen ($\text{O}_2$) is reduced to $\text{H}_2\text{O}$.

What is the maximum theoretical total ATP yield per glucose molecule during aerobic respiration in prokaryotes?

$38$ total $\text{ATP}$ ($4$ direct substrate-level phosphorylation $\text{ATP}$ + $34$ oxidative phosphorylation $\text{ATP}$).

What is the total theoretical ATP yield per glucose molecule during aerobic respiration in eukaryotic cells?

$36$ total $\text{ATP}$.

Why do eukaryotic cells produce 36 ATP per glucose instead of the 38 ATP produced by prokaryotes?

Energy is expended shuttling $\text{NADH}$ and $\text{FADH}_2$ across the mitochondrial membrane from the cytoplasm into the mitochondrial matrix.

How many net ATP molecules are directly synthesized by substrate-level phosphorylation per glucose across central metabolism (glycolysis + Krebs cycle)?

$4$ net $\text{ATP}$ ($2$ from glycolysis and $2$ from the Krebs cycle).

How many total CO2 molecules are released from the complete catabolism of one glucose molecule in aerobic respiration?

$6$ $\text{CO}_2$ molecules ($2$ during the transition step and $4$ during the Krebs cycle).

How many total NADH molecules are generated per glucose molecule across glycolysis, the transition step, and the Krebs cycle?

$10$ $\text{NADH}$ ($2$ from glycolysis, $2$ from the transition step, and $6$ from the Krebs cycle).

How many total FADH2 molecules are generated from one glucose molecule during aerobic cellular respiration?

$2$ $\text{FADH}_2$ molecules (both produced in the Krebs cycle).

In this summary diagram of central metabolism, how many net ATP, NADH, and FADH2 are produced directly prior to the ETC per glucose?

$4$ net $\text{ATP}$ ($2$ in glycolysis, $2$ in Krebs), $10$ $\text{NADH}$ ($2$ glycolysis, $2$ transition, $6$ Krebs), and $2$ $\text{FADH}_2$ (Krebs).

What is the literal translation of the word 'glycolysis'?

"Sugar splitting".

Where does glycolysis take place in both prokaryotic and eukaryotic cells?

In the cytoplasm.

What is the starting substrate and what are the major final products of glycolysis per glucose molecule?

Input: $1$ glucose ($6\text{C}$) Outputs: $2$ pyruvate ($3\text{C}$), $2$ net $\text{ATP}$, and $2$ $\text{NADH}$.

Does glycolysis require molecular oxygen (O2) to proceed?

No, glycolysis is an anaerobic process that proceeds regardless of whether $\text{O}_2$ is present.

How many ATP molecules are invested during the preparatory stage of glycolysis shown here?

$2$ $\text{ATP}$ molecules are consumed to phosphorylate glucose into fructose 1,6-diphosphate.

Which electron carrier captures the electrons removed from glucose during glycolysis?

$\text{NAD}^+$, which is reduced to form $\text{NADH}$.

What are two alternative scientific names for the Krebs cycle?

The citric acid cycle and the tricarboxylic acid ($\text{TCA}$) cycle.

Where does the Krebs cycle occur in prokaryotes versus eukaryotes?

Prokaryotes: Cytoplasm Eukaryotes: Mitochondrial matrix

How many turns of the Krebs cycle occur per single molecule of glucose catabolized?

$2$ turns (because each glucose yields two pyruvates).

What occurs during the transition (bridge) step between glycolysis and the Krebs cycle?

Pyruvate ($3\text{C}$) is converted to acetyl $\text{CoA}$ ($2\text{C}$), releasing $1$ $\text{CO}_2$ and generating $1$ $\text{NADH}$ per pyruvate ($2$ $\text{CO}_2$ and $2$ $\text{NADH}$ per glucose).

What are the direct outputs of the Krebs cycle per turn (per acetyl CoA)?

$3$ $\text{NADH}$, $1$ $\text{FADH}_2$, $1$ $\text{ATP}$, and $2$ $\text{CO}_2$.

According to this Krebs cycle diagram, what 4-carbon compound condenses with acetyl CoA to form citric acid?

Oxaloacetic acid.

Where is the electron transport chain (ETC) located in bacteria versus eukaryotic cells?

Bacteria: Plasma / cytoplasmic membrane ($\text{CM}$) Eukaryotes: Inner mitochondrial membrane

Which molecules deliver high-energy electrons directly to the electron transport chain?

$\text{NADH}$ and $\text{FADH}_2$.

How is energy released as electrons pass down the electron transport chain?

Through a cascade of sequential redox reactions among membrane-bound electron carrier proteins.

What does the energy released by electron flow along the ETC directly accomplish?

It fuels the active pumping of hydrogen ions ($\text{H}^+$) across the membrane against their concentration gradient.

Across which compartments are protons pumped by the ETC in bacteria versus eukaryotes?

Bacteria: From the cytoplasm out to the periplasm / outside the cell Eukaryotes: From the mitochondrial matrix into the inner membrane space

What is the proton motive force (PMF)?

An electrochemical gradient of protons ($\text{H}^+$) established across the membrane, representing stored potential energy.

What physical analogy is used in lecture to explain the proton motive force?

Water backed up on one side of a dam compared to the other side.

What is chemiosmosis?

The biological process in which $\text{ATP}$ synthesis is powered by the flow of protons ($\text{H}^+$) moving down their electrochemical gradient across a membrane through $\text{ATP}$ synthase.