Microbial Metabolism, Chemical Control, and Microbial Nutrition

Vocabulary practice flashcards covering microbial metabolism, chemical control of microbes, and nutritional/environmental growth requirements.

Metabolism

All the chemical reactions that occur within an organism.

Catabolic pathways

Degradative pathways that break down molecules, break covalent bonds via hydrolytic reactions, and release energy (exergonic; producing ATP) to drive anabolic reactions.

Anabolic pathways

Biosynthetic pathways that build complex molecules from simpler ones, form covalent bonds via dehydration synthesis, and consume more energy than produced (endergonic; requiring ATP).

Terminal phosphate bond

The last phosphate bond of ATP; it releases the most energy when broken and requires the most energy to make.

ATP hydrolysis

The breakdown of ATP where the terminal phosphate bond is broken, releasing energy.

ATP synthesis

The process of creating ATP by joining ADP and a phosphate group, which costs energy.

Enzymes

Proteins that catalyze biochemical reactions without being permanently altered; their characteristic 3D shape is required for their function.

Ribozyme

A biological catalyst that consists of RNA rather than protein.

Substrate

The substance that is acted on by an enzyme.

Active site

The specific region of an enzyme that binds and interacts with the substrate.

Endozymes

Enzymes that function inside the cell.

Exozymes

Enzymes that function outside of the cell.

Denaturation

The unfolding of a protein, which can be caused by heat, extreme pH, certain chemicals, or radiation.

Conjugated enzyme

An enzyme consisting of a protein component and a non-protein accessory, requiring a cofactor to function.

Apoenzyme

The protein component of a conjugated enzyme.

Cofactor

The non-protein component of a conjugated enzyme.

Holoenzyme

The complete, active enzyme consisting of the apoenzyme and cofactor attached together.

Coenzyme

An organic cofactor that removes a chemical group (such as $H^+$, $CO_2$, amino groups, or electrons) from one substrate and transfers or carries it to another.

Ion (enzyme cofactor)

An inorganic cofactor (such as $Fe^{2+}$, $Zn^{2+}$, or $Mg^{2+}$) that forms a bridge between the substrate and the enzyme.

Competitive inhibitor

An inhibitor that resembles the enzyme's substrate and binds to the active site, blocking the substrate from binding.

Allosteric inhibitor

A non-competitive inhibitor that does not resemble the substrate and binds to an allosteric site, altering the 3D shape of the enzyme.

Enzyme activity

A measure of how quickly an enzyme converts substrate into product.

Redox reactions

Coupled reduction and oxidation reactions in which one reaction cannot occur without the other.

Oxidation

The loss of electrons and hydrogen from a substance, resulting in an increased charge.

Reduction

The gain of electrons and hydrogen by a substance, resulting in a reduced charge.

Metabolic pathways

A series of consecutive reactions that convert an initial reactant into a final end product, typically making or breaking covalent bonds.

Intermediates

Temporary products synthesized along the steps of a metabolic pathway.

Glycolysis

The first stage of central metabolism located in the cytoplasm; it splits a $6C$ sugar into two $3C$ pyruvates without requiring $O_2$, netting $2\text{ ATP}$ and $2\text{ NADH}$.

Krebs Cycle

The citric acid or TCA cycle located in the prokaryotic cytoplasm or eukaryotic mitochondrial matrix; it harvests the most electrons, producing $2\text{ ATP}$, $4\text{ }CO_2$, $8\text{ NADH}$, and $2\text{ }FADH_2$ per glucose.

Terminal electron acceptor (TEA)

The final molecule that gains electrons from the oxidized chemical source at the end of the electron transport chain.

Proton motive force (PMF)

A hydrogen ion ($H^+$) gradient generated across a membrane by electron flow through the ETC, representing potential energy used to synthesize ATP.

ATP synthase

A membrane-bound enzyme shaped like a mushroom that uses the energy of a high concentration of $H^+$ to synthesize ATP from ADP and phosphate.

Fermentation

An anaerobic catabolic pathway involving incomplete oxidation of sugars with no external TEA, no Krebs cycle, and no ETC, yielding only $2\text{ ATP}$ via glycolysis.

High level disinfectant

A chemical control agent capable of killing endospores and achieving sterilization, used for critical items that enter sterile body tissues.

Intermediate level disinfectant

A chemical control agent that kills fungal spores, resistant pathogens like mycobacteria, and viruses; used on semi-critical items such as thermometers.

Low level disinfectant

A chemical control agent that kills vegetative cells and some viruses, used to clean non-critical items that only touch intact skin.

Phenol

A chemical agent consisting of a six-carbon ring with a carboxyl group; rarely used today because it smells and irritates skin ($< 1\%$ acts as an anesthetic, $> 1\%$ is antibacterial).

Phenolics

Altered phenol molecules combined with an organic group (soap/detergent) that disrupt cell membranes and denature proteins while being less irritating than phenol.

pHisHex

A bisphenol surgical scrub used to treat skin infections; its use is limited because excessive application causes neurologic damage in infants.

Triclosan

A phenolic antibacterial agent previously found in OTC soaps (now banned due to resistance and endocrine disruption) but still used in hand sanitizers, hospital soaps, and toothpaste.

Chlorhexidine

A rapidly acting antiseptic containing chlorine and two phenolic groups that exhibits low toxicity; used in pre-surgical skin washes, eye solutions, and mouthwash.

Halogens

Highly reactive, non-metallic chemical agents (iodine, chlorine, fluorine, bromine) that denature proteins by interfering with disulfide bonds.

Iodophor

A preparation where iodine is bound to a carrier molecule and does not involve alcohol, such as Betadine.

Tincture

A solution where an antimicrobial chemical (such as iodine) is dissolved in alcohol.

Peroxygens

High-level oxidizing agents (such as hydrogen peroxide and benzoyl peroxide) that oxidize cellular components and are particularly toxic to anaerobes.

Quaternary ammonium compounds (quats)

Cationic detergents derived from ammonium ($NH_4^+$) featuring a positively charged end and hydrophobic chain that act as low-level antiseptics by disrupting cell membranes.

Gaseous sterilants

Alkylating chemicals like ethylene oxide gas applied in closed chambers (chemiclaves) to sterilize heat-sensitive medical devices by crosslinking proteins and DNA.

Aldehydes

Alkylating agents such as formaldehyde and glutaraldehyde that crosslink DNA and proteins; they represent the only liquid chemical agents capable of sterilizing.

Macronutrients

Major chemical elements required by cells in large amounts, including CHNOPS and essential ions like $Mg^{2+}$, $Ca^{2+}$, and $K^+$.

Micronutrients

Nutrients required by cells in small amounts, consisting of inorganic trace elements (Fe, Cu, Mn, Zn) and organic growth factors.

Growth factor

An organic micronutrient (such as folic acid or vitamin B12) that cannot be synthesized by the organism and must be provided.

Heterotrophs

Organisms that obtain their carbon from organic sources such as carbohydrates, lipids, and proteins.

Autotrophs

Organisms that utilize inorganic carbon ($CO_2$) as their primary carbon source.

Photoautotroph

An organism that uses light as its energy source and inorganic carbon ($CO_2$) as its carbon source.

Photoheterotroph

An organism that uses light as its energy source and organic compounds as its carbon source.

Chemolithoautotroph

An organism that obtains energy from inorganic chemicals and carbon from inorganic carbon ($CO_2$).

Chemolithoheterotroph

An organism that utilizes inorganic chemicals for energy and organic compounds for carbon.

Chemoorganoheterotroph

An organism that uses organic chemicals for both its energy source and its carbon source.

Reactive oxygen species (ROS)

Highly reactive and toxic molecules with an unpaired electron (such as superoxide $O_2^-$, hydroxyl ion $OH^-$, and peroxide $O_2^{2-}$) that damage cellular structures by oxidation.

Superoxide dismutase

A detoxifying enzyme that converts superoxide radicals into hydrogen peroxide and oxygen ($O_2^- + O_2^- \rightarrow H_2O_2 + O_2$).

Catalase

A detoxifying enzyme that breaks down hydrogen peroxide into water and oxygen ($2H_2O_2 \rightarrow 2H_2O + O_2$).

Peroxidase

A detoxifying enzyme that converts hydrogen peroxide and hydrogen ions into water ($H_2O_2 + 2H^+ \rightarrow 2H_2O$).