Microbiology Lecture Units 1-4 Practice Flashcards

Comprehensive vocabulary flashcards covering microbial biology, genetics, metabolism, immunology, and pathogenesis as discussed in Units 1 through 4.

Acellular organisms

Organisms lacking a cellular structure consisting of Viruses (nucleic acid and proteins), Virions ($ext{RNA}$), Prions (proteins), and Satellites (nucleic acid in a protein shell).

16S rRNA

The preferred molecule used to compare Bacteria and Archaea on a molecular basis because its genes change very slowly over time.

Robert Koch

The scientist who designed the Koch Postulate Steps to find the connection between microorganisms and diseases, proving that microbes causes diseases.

Scanning Electron Microscopy (SEM)

A microscopy technique that coats the microorganism with metal and shoots electrons at it, creating a $3 ext{D}$ topographic image as the electrons bounce off the surface.

Gram staining

A differential staining method that uses crystal violet (primary stain), iodine (mordant), alcohol (decolorizer), and safranin (secondary stain) to distinguish between Gram-positive (purple) and Gram-negative (pink/red) bacteria.

Hopanoids

Sterol-like molecules found in bacterial membranes that stabilize the membrane and delimit micro domains, similar to the role of cholesterol in eukaryotes.

Archaeal lipid chains

Lipid structures composed of isoprene units ($4$-carbon chains plus a methyl group) that can form rings, branches, and ether linkages to glycerol, resulting in monolayers or bilayers.

Bactoprenol

A bacterial membrane anchor consisting of $11$ isoprenol units and a phosphate group that transports peptidoglycan precursors from the cytoplasm to the periplasm.

NAM (N-Acetylmuramic acid)

A glucose derivative in peptidoglycan that contains a lactic acid group allowing it to connect to the pentapeptide subunit.

Teichoic acids

Glycerol-phosphate polymers found in Gram-positive organisms that are negatively charged and stabilize the cell wall by adding rigidity.

Porins

Trimeric proteins found in the outer membrane of Gram-negative organisms that allow nutrients like $O_2$ and sugar to pass through an otherwise impermeable membrane.

S-layer

Ordered polymers of proteins or glycoproteins that provide protection and structural support; they are found in nearly all Archaea and as an added layer in some Bacteria.

Carboxysomes

Specialized internal compartments in some bacteria that perform energy-demanding carbon fixation by taking in $CO_2$ and converting it into carbon polymers.

Endospores

Extremely resistant dormant structures formed by some bacteria to survive stress, capable of resisting heat (> 121 ext{ degrees}), $UV$ radiation, and toxic compounds.

FtsZ

A bacterial tubulin homolog that polymerizes to form a Z-ring, designating the site where the septum will form and the cell will ultimately divide.

Min system

A system of proteins ($ext{MinC, MinD, MinE}$) that oscillates from pole to pole to prevent the Z-ring from forming at the poles, ensuring the cell divides in the middle.

MurJ (Flippase)

The enzyme that recognizes the specific structure of Lipid $II$ and flips it from the cytoplasmic side of the membrane to the periplasmic side for peptidoglycan assembly.

DNA Polymerase III

The primary replicative enzyme in bacteria that synthesizes DNA in the $5' ightarrow 3'$ direction and performs proofreading via $3' ightarrow 5'$ exonuclease activity.

Polycistronic mRNA

A single $ext{mRNA}$ strand that contains multiple start and stop codons, allowing for the synthesis of several different proteins; found in Bacteria and Archaea.

Rho-independent termination

A transcription stop mechanism where the $ext{mRNA}$ forms a stem-loop followed by a poly-$U$ tract, destabilizing the open complex and causing RNA polymerase to fall off.

TAT (Twin Arginine Translocase)

A secretion system that moves fully folded proteins from the cytoplasm to the periplasm using the proton motor force instead of $ext{ATP}$.

Diauxic growth

An $ext{E. coli}$ growth pattern observed when two sugars (like glucose and lactose) are present, characterized by two exponential growth phases separated by a lag phase.

Allolactose

The inducer molecule for the lac operon that is produced as a side reaction of $ext{B-galactosidase}$ and signals that lactose is present in the environment.

cAMP (cyclic AMP)

A second messenger molecule produced from $ext{ATP}$ by adenylate cyclase when glucose levels are low, which activates the Catabolite Activator Protein ($ext{CAP}$) to enhance transcription.

Attenuation

A regulatory mechanism in the trp operon where translation of the leader region (trpL) directly affects the transcription of structural genes based on tryptophan levels.

Quorum sensing

The ability of microbes to sense population density through signaling molecules called autoinducers and coordinate behaviors once a specific threshold is reached.

F factor

A fertility plasmid in $ext{E. coli}$ that encodes the machinery for conjugation, including the sex pilus and rolling-circle replication genes.

Mismatch repair

A DNA repair system where the MutSLH complex scans and identifies errors in newly replicated DNA by distinguishing the unmethylated new strand from the methylated parental strand.

Substrate-level phosphorylation (SLP)

A process of generating $ext{ATP}$ by the direct transfer of a phosphate group from a high-energy metabolic intermediate to $ext{ADP}$.

Entner Doudoroff (ED) pathway

A glycolytic pathway specific to some prokaryotes that yields a net of $1 ext{ ATP}$, $1 ext{ NADH}$, and $1 ext{ NADPH}$ per glucose molecule.

Anammox

Anaerobic ammonium oxidation, a process that converts $NH_4^+$ and $NO_2^-$ into water and nitrogen gas ($N_2$) within specialized anammoxosomes.

Calvin Cycle

The main pathway for carbon fixation in plants and cyanobacteria that uses the enzyme RuBisCO, taking $18 ext{ ATP}$ and $12 ext{ NADPH}$ to produce one molecule of fructose-$6$-phosphate.

Nitrogen fixation

The conversion of atmospheric $N_2$ into ammonia ($NH_3$) by the oxygen-sensitive nifHDK enzyme complex, requiring $16 ext{ ATP}$ and $8 ext{ e}^-$ per $N_2$ molecule.

Opsonization

The process of coating microbes with molecules like antibodies or complement protein C3b to enhance their recognition and destruction by phagocytes.

MHC Class I

Receptors found on all nucleated cells that present endogenous antigens from inside the cell to $CD8^+$ Cytotoxic T cells.

PAMPs (Pathogen Associated Molecular Patterns)

Conserved molecular structures on microbes, such as $ext{LPS}$ or peptidoglycan, that are recognized by the innate immune system's pattern recognition receptors ($ext{PRRs}$).

B-lactamases

Enzymes that provide antibiotic resistance by hydrolyzing the B-lactam ring, thereby inactivating penicillin and similar antibiotics.

Baltimore system

A virus classification system that groups viruses into seven classes based on their genome type and the pathway used to produce $ext{mRNA}$.

Pathogenicity islands

Distinct regions on a bacterial genome that contain clusters of virulence genes, such as toxins and secretion systems, often acquired through horizontal gene transfer.

Syntrophy

A mutualistic interaction where two organisms depend on each other's metabolic products to survive, often making an energetically unfavorable reaction possible.