Microbiology Lab: Protein Catabolism & Biochemical Media

Vocabulary practice flashcards covering protein catabolism pathways, differential media, exoenzymes, reagents, and diagnostic outcomes for BIOL 2111 Microbiology Lab.

Deamination

The enzymatic removal of the amine group ($-\text{NH}_2$) from an amino acid, converting it to ammonia ($\text{NH}_3$) or urea derivatives, forming organic acids, and generally lowering pH.

Decarboxylation

The enzymatic removal of the carboxyl group ($-\text{COOH}$) from an amino acid, releasing carbon dioxide ($\text{CO}_2$) and amine end-products, which raises pH to create alkaline conditions.

Sulfur-Containing Amino Acids

Amino acids (specifically cysteine and methionine) that contain sulfur within their functional R-groups; bacterial enzymatic cleavage of these releases hydrogen sulfide ($\text{H}_2\text{S}$) gas.

Gelatinase

A bacterial exoenzyme secreted externally to break down macromolecular gelatin into short peptide strands.

Gelatin Hydrolysis Assay

A differential enzymatic assay used to differentiate Staphylococcus aureus (+) from S. epidermidis (-); a positive result is confirmed when the medium remains liquid after refrigeration below $28^\circ\text{C}$.

Uninoculated Control Tube (Gelatin Hydrolysis)

A control tube kept alongside test samples in an ice bath or refrigerator to confirm that gelatin liquefaction is caused by enzymatic hydrolysis rather than ambient thermal melting.

Urease

An exoenzyme that hydrolyzes urea into carbon dioxide ($\text{CO}_2$) and ammonia ($\text{NH}_3$).

Urea Broth Test

A biochemical test containing the indicator phenol red (orange-yellow at uninoculated pH $6.8$); produces a bright fuchsia / "hot pink" color change due to alkaline ammonia generation in positive reactions.

Rapid Urease-Positive Species

Organisms such as Proteus species (e.g., Proteus vulgaris and Proteus mirabilis) capable of hydrolyzing urea rapidly within $24\,\text{hours}$.

Phenylalanine Deaminase

An enzyme that catalyzes the deamination of the amino acid phenylalanine to produce phenylpyruvic acid and free ammonia.

Phenylalanine Agar Slant

A differential test medium where ferric chloride ($\text{FeCl}_3$) is added post-incubation, yielding an intense dark green surface color if phenylpyruvic acid is present.

Ferric Chloride ($\text{FeCl}_3$)

The reagent added to a phenylalanine agar slant following incubation to detect phenylpyruvic acid by forming an intense dark green surface color.

Ornithine Decarboxylase (OD) Broth

A medium used to differentiate Gram-negative enteric bacilli (such as pathogenic Salmonella from normal coliform flora); glucose fermentation first lowers the pH to yellow, activating ornithine decarboxylase to produce alkaline amines that shift bromocresol purple indicator back to purple.

Sterile Mineral Oil Overlay

A barrier applied over inoculated ornithine decarboxylase broth to enforce the anaerobic conditions required for decarboxylation.

SIM Agar Deep

A single stab-inoculated semi-solid medium used in the IMViC series to differentiate Proteus and Salmonella by assessing sulfur reduction, indole production, and motility.

Sulfur Reduction (SIM Test)

The breakdown of sulfur-containing amino acids (such as cysteine) via thiosulfate reductase, producing $\text{H}_2\text{S}$ that reacts with ferrous sulfate ($\text{FeSO}_4$) in the medium to form a black precipitate of ferrous sulfide.

Indole Production (SIM Test)

The degradation of tryptophan by the enzyme tryptophanase to form indole, which is detected by the formation of a cherry red ring after adding Kovac's reagent.

Kovac's Reagent

A chemical reagent added post-incubation to a SIM tube that reacts with indole to form a cherry red ring at the liquid surface layer.

Motility (SIM Test)

Flagella-mediated locomotion detected in a $0.35\%$ semi-solid agar medium, visually identified by radiating cloudiness spreading away from the inoculation stab line.