Microbiology: Viruses, Prions, and Microbial Metabolism

Comprehensive vocabulary flashcards covering Chapter 7 (Viruses and Prions) and Chapter 10 (Microbial Metabolism), including viral anatomy, replication cycles, enzyme kinetics, and metabolic pathways.

Naked Virus vs. Enveloped Virus

A naked virus consists only of a nucleocapsid (protein capsid and nucleic acid) without a membrane, whereas an enveloped virus possesses an outer membrane surrounding the capsid that is typically derived from a modified piece of the host cell membrane.

Capsid

The external protein shell or coat that surrounds and protects the nucleic acid core of a virus.

Nucleocapsid

The viral structure formed by the combination of the viral capsid together with its enclosed nucleic acid core.

Viral Envelope

An external lipid membrane surrounding some viruses, typically derived from a modified piece of the host cell membrane.

Spikes

Protein structures projecting from the surface of naked or enveloped viruses that aid in host cell attachment.

Adsorption

The first phase of the animal virus multiplication cycle, in which the virus attaches to specific receptor sites on the surface of the host cell.

Penetration

The phase of the animal virus multiplication cycle in which the entire virus or its genetic material enters the host cell.

Uncoating

The phase of the animal virus multiplication cycle where the protein capsid is removed, releasing the viral nucleic acid into the host cytoplasm.

Synthesis (Viral Multiplication)

The phase of the animal virus multiplication cycle in which the viral genome is replicated and viral proteins are produced using the host cell's machinery.

Assembly (Viral Multiplication)

The phase of the animal virus multiplication cycle where newly synthesized viral parts and nucleic acids are put together to form mature viral particles.

Release (Viral Multiplication)

The final phase of the animal virus multiplication cycle, during which mature viruses leave the host cell.

Polymerases

Enzymes that synthesize $DNA$ or $RNA$.

Reverse Transcriptase

A viral enzyme that synthesizes a $DNA$ molecule from an $RNA$ template.

Cytopathic Effects (CPEs)

Virus-induced damage that alters the microscopic appearance of host cells.

Syncytium

A multinucleated cellular structure formed when several infected host cells fuse together.

Prophage

An inactive form of bacteriophage $DNA$ that has been integrated into the host bacterial chromosome.

Oncogenic Viruses

Viruses that have the capacity to cause cancer in their host organisms.

Interferons

Naturally occurring human cell products that interfere with viral replication, support antiviral host defenses, and help prevent or treat certain viral infections.

Prions

Infectious agents composed solely of abnormal proteins that are associated with spongiform encephalopathies.

Helical Capsid

A viral capsid featuring rod-shaped protein subunits arranged in a continuous spiral surrounding the nucleic acid.

Lytic Cycle

A bacteriophage replication pathway in which the phage replicates inside the host bacterium and destroys the bacterial host cell upon release.

Lysogenic Cycle

A bacteriophage cycle in which the viral genome incorporates into the host bacterial chromosome as a prophage without immediately destroying the cell.

Lysogenic Conversion

The acquisition of new traits by a bacterium due to genes carried by a temperate bacteriophage, responsible for toxin production in diphtheria, cholera, and botulism.

Tobacco Mosaic Virus (TMV)

The first virus ever discovered, which proved the existence of pathogens smaller than bacteria by passing through filters designed to trap bacteria.

Positive-sense RNA

Viral $RNA$ that can function directly as messenger $RNA$ ($mRNA$) and be immediately translated into viral proteins by host ribosomes.

Negative-sense RNA

Viral $RNA$ that cannot be directly translated and must first be converted into the proper complementary form before protein synthesis can occur.

Obligate Intracellular Parasites

Entities, such as viruses, that cannot independently reproduce, grow, or carry out metabolic processes and must invade a suitable host cell to utilize its genetic and metabolic machinery.

Competitive vs. Noncompetitive Inhibition

Modes of enzyme regulation: competitive inhibitors directly mimic and compete with the substrate for the active site, whereas noncompetitive inhibitors bind to a separate allosteric site to alter enzyme activity.

Enzyme

A selective protein catalyst that lowers the activation energy of reactions and can catalyze reversible chemical processes.

Active Site

The specific region on an enzyme where the substrate binds and the catalytic reaction occurs.

Allosteric Site

A regulatory site on an enzyme distinct from the active site where noncompetitive inhibitors or regulatory molecules bind.

Apoenzyme

The protein portion of an enzyme by itself, lacking its required cofactor or coenzyme.

Holoenzyme

A complete, catalytically active enzyme composed of an apoenzyme bound to its required cofactor.

Activation Energy

The initial energy reactants must absorb for a chemical reaction to begin, which can be overcome or lowered by increasing thermal energy or adding an enzyme catalyst.

Metabolism

The sum total of all chemical reactions occurring within a cell.

Catabolism

The metabolic breakdown of complex organic compounds into simpler ones, releasing energy ($ATP$ production).

Anabolism

The metabolic process of synthesizing complex organic compounds from simpler molecules, requiring an input of energy.

Amphibolism

The integration and bidirectional linkage of catabolic and anabolic pathways to optimize cellular nutrient utilization and energy efficiency.

Oxidoreductases

A class of enzymes that catalyze the transfer of electrons from one substrate molecule to another.

Transferases

A class of enzymes that transfer functional groups from one substrate to another.

Hydrolases

Enzymes that cleave chemical bonds on molecules through the addition of water.

Lyases

Enzymes that add chemical groups to or remove groups from double-bonded substrates.

Isomerases

Enzymes that rearrange atoms within a molecule to convert a substrate into its isomeric form.

Ligases

Enzymes that catalyze the formation of new bonds coupled with the input of $ATP$ and the removal of water.

Exoenzymes

Enzymes transported extracellularly to break down large food molecules or harmful chemicals outside of the cell.

Endoenzymes

Enzymes that remain and function intracellularly to break down molecules inside the cell.

Constitutive Enzymes

Enzymes that are continually synthesized and present in relatively constant amounts inside the cell, regardless of environmental conditions.

Regulated Enzymes

Enzymes whose concentration changes according to cellular demand; their production is induced or repressed in response to substrate levels.

Proteases

Enzymes that break down proteins into their individual amino acid components.

Hydrolysis Reaction

A chemical reaction that cleaves a bond (such as a peptide bond between amino acids) by consuming a water molecule that contributes an $\text{H}$ and an $\text{OH}$.

Denaturation

The loss of an enzyme or protein's native three-dimensional conformation caused by elevated temperature or chemical extremes.

Redox Reaction

A chemical reaction involving the transfer of electrons from an electron donor (oxidation) to an electron acceptor (reduction).

Substrate-level Phosphorylation

The synthesis of $ATP$ by the direct transfer of a high-energy phosphate group from a phosphorylated substrate molecule to $ADP$.

Glycolysis

The initial stage of carbohydrate catabolism that degrades glucose into $2$ molecules of pyruvate, generating a net gain of $2\text{ ATP}$ and $2\text{ NADH}$.

Preparatory Step (Aerobic Respiration)

The intermediate reaction between glycolysis and the Krebs cycle in which pyruvic acid is oxidized to acetyl-$CoA$, releasing $CO_2$ and reducing $NAD^+$ to $NADH$.

Krebs Cycle

A central metabolic pathway that, for every two turns (per glucose molecule), yields $4\,CO_2$, $6\,NADH$, $2\,ATP$, and $2\,FADH_2$.

Fermentation

An anaerobic metabolic process that allows glycolysis to continue by regenerating $NAD^+$ without utilizing an electron transport chain.

Anaerobic Respiration

A respiration pathway utilizing an electron transport chain where an inorganic molecule other than oxygen, such as nitrate or sulfate, serves as the terminal electron acceptor.

Thylakoid Membranes

The internal membrane compartments of chloroplasts where the light-dependent reactions of photosynthesis take place.

Stroma

The fluid-filled interior space of a chloroplast surrounding the thylakoids, where the light-independent reactions (Calvin cycle) take place.

Light-dependent Reactions

Photosynthetic reactions that harness sunlight to synthesize $ATP$ and $NADPH$, producing oxygen as a byproduct.

Light-independent Reactions (Calvin Cycle)

The phase of photosynthesis occurring in the stroma that utilizes $ATP$ and $NADPH$ produced by the light-dependent reactions to fix carbon into glucose.

Anoxygenic Photosynthesis

Photosynthesis that does not produce oxygen because an electron source other than water ($H_2O$) is used.