Microbial Genetics, Phototrophy, and Molecular Biology

Vocabulary practice flashcards covering bacterial phototrophy, genome structure, DNA replication, transcription, translation, and antimicrobial mechanisms.

Phototrophy

The harnessing of photoexcited electrons to power cell growth and drive ATP synthesis.

Bacteriorhodopsin

A single-protein, light-driven proton pump found in halophilic archaea that creates a proton motive force across the membrane to power ATP synthase without requiring chlorophyll.

Proteorhodopsin

A bacterial homolog of bacteriorhodopsin found in marine proteobacteria that performs light-driven proton pumping.

Thylakoid-like Membranes (Purple Bacteria)

Extensive backfoldings of the bacterial photosynthetic membrane arranged into oval pockets that enhance the efficiency of photon absorption.

Photosystem I (PS I)

An anaerobic photolytic system in green sulfur bacteria (chlorobia) that takes electrons from $H_2S$, organic donors such as succinate, or $Fe^{2+}$, transferring them to $NAD^+$ or $NADP^+$ and generating a proton gradient to drive ATP synthesis.

Photosystem II (PS II)

An anaerobic photolytic system found in purple sulfur and nonsulfur bacteria that uses bacteriochlorophyll as both the initial electron donor and terminal acceptor in cyclic photophosphorylation, requiring reverse electron transport to generate NADH or NADPH.

Cyclic Photophosphorylation

The light-driven cyclic electron flow in Photosystem II wherein electrons excited from bacteriochlorophyll travel through an electron transport system to generate ATP and ultimately return to bacteriochlorophyll.

Oxygenic Z Pathway

A photolytic pathway found in cyanobacteria and plant chloroplasts combining homologs of PS II and PS I; it photolyzes $2\,H_2O$ to produce $O_2$, $3\,\text{ATP}$, and $2\,\text{NADPH}$.

Central Dogma

The directional flow of genetic information stating that DNA is transcribed into RNA, which is translated into protein (with retroviruses serving as an exception by copying RNA to DNA).

Missense Mutation

A point mutation in which a base substitution alters a codon to code for a different amino acid, potentially generating a faulty protein.

Nonsense Mutation

A base substitution that converts a sense codon specifying an amino acid into a premature stop codon, leading to truncated or incomplete protein translation.

Silent Mutation

A base substitution that alters a codon without changing the encoded amino acid due to degeneracy in the genetic code, resulting in an unaltered wild-type protein.

Nucleoid

The condensed region of bacterial DNA compacted into $30\text{--}100$ independently looped domains anchored by histone-like proteins such as HU and H-NS.

Type I Topoisomerase

A typically single-protein enzyme that cleaves a single strand of DNA to relax and relieve negative supercoiling without requiring ATP.

Type II Topoisomerase (DNA Gyrase)

A multi-subunit enzyme consisting of GyrA and GyrB that hydrolyzes ATP to introduce negative supercoils into double-stranded DNA; it is specifically targeted by quinolone antibiotics.

Positive Supercoils

Overwound DNA topology characteristic of certain thermophilic and acidophilic archaea, such as Sulfolobus growing at $80^\circ\text{C}$ and $\text{pH } 2\text{--}3$, which prevents heat-induced denaturation.

Transformation

The horizontal gene transfer mechanism discovered by Frederick Griffith in 1928 involving the cellular uptake and chromosomal incorporation of naked extracellular DNA.

Competence Factor (CF)

A peptide exported by Gram-positive bacteria like Streptococcus that accumulates at high cell density to activate ComD and ComE, directing SigH-dependent transcription of the transformasome complex.

Conjugation

A horizontal gene transfer mechanism requiring cell-to-cell contact through a sex pilus encoded by transferable plasmids (such as the F factor), transferring single-stranded DNA from an $F^+$ donor to an $F^-$ recipient.

Hfr (High-Frequency Recombination) Strain

A bacterial donor cell wherein the F plasmid has integrated into the chromosome, enabling the transfer of host chromosomal markers to an $F^-$ recipient cell over an approximately $100\,\text{minute}$ period.

DnaA

The bacterial initiator protein that recognizes and binds specific DNA repeats at $oriC$ to facilitate strand separation and promote replisome assembly.

SeqA

A regulatory protein that binds hemimethylated GATC sequences at newly replicated $oriC$ to tether it to the membrane, delaying immediate re-initiation until Dam methyltransferase completes methylation.

Rolling Circle Mechanism

A plasmid replication process wherein a single-stranded nick provides a free $3'\text{-OH}$ end for continuous synthesis, initially synthesizing the displaced strand without requiring an RNA primer or Okazaki fragments.

Tus (Terminus Utilization Substance)

A protein that binds terminator sequences (ter) on the bacterial chromosome to act as a counter-helicase, halting advancing replication forks.

Topoisomerase IV

A type II topoisomerase that breaks and rejoins double strands to decatenate and separate interlinked circular daughter chromosomes (catenanes) following replication termination.

Taq DNA Polymerase

A heat-stable DNA polymerase isolated from Thermus aquaticus that synthesizes complementary DNA during the $72^\circ\text{C}$ elongation step of the Polymerase Chain Reaction (PCR).

Sigma Factor

A dissociable subunit of the bacterial RNA polymerase holoenzyme responsible for recognizing specific promoter motifs (such as the $-10$ and $-35$ consensus sequences bound by $\sigma^{70}$) to direct transcription initiation.

Core RNA Polymerase

The multi-subunit bacterial enzyme complex ($\alpha_2\beta\beta'$) that carries out the elongation phase of RNA synthesis after the sigma factor dissociates.

Rho-Dependent Termination

Transcription termination in bacteria where the hexameric Rho ($\rho$) protein binds C-rich RNA sites, hydrolyzes ATP to translocate toward RNA polymerase, and disrupts the transcription complex upon contact.

Rho-Independent Termination

Transcription termination mediated by an inverted repeat that folds into a GC-rich stem-loop hairpin followed by a poly-U tract, which contacts RNA polymerase and NusA to dislodge the transcript.

trp Operon

A repressible operon that encodes tryptophan biosynthetic enzymes, which is repressed when accumulating tryptophan binds the Trp repressor, enabling it to attach to the operator and block RNA polymerase.

lac Operon

An inducible operon encoding genes for lactose catabolism (lacZ, lacY, lacA) that achieves maximal transcription only in the presence of lactose (which removes the Lac repressor) and the absence of glucose (which allows the cAMP-CAP activator complex to bind).

Shine-Dalgarno Sequence

A purine-rich mRNA consensus sequence ($5'\text{-AGGAGGU-}3'$) located $4\text{--}8$ bases upstream of the start codon that pairs with the $3'$ end of 16S rRNA to set the correct translation reading frame.

Coupled Transcription and Translation

The concurrent translation of polycistronic mRNA by multiple ribosomes while RNA polymerase is actively elongating the transcript, a phenomenon unique to prokaryotes because they lack a nuclear membrane.

Signal Recognition Particle (SRP)

A ribonucleoprotein complex comprising ffs sRNA and the Ffh protein that binds hydrophobic N-terminal signal sequences on nascent peptides to direct ribosomes cotranslationally to the membrane receptor FtsY.

SecA-Dependent Secretion Pathway

A post-translational pathway in which the cytoplasmic chaperone SecB keeps unfolded pre-proteins competent for transport, and the SecA ATPase drives them through the SecYEG inner membrane channel, followed by LepB cleavage of the signal peptide.

Type I Secretion System

An ABC-transporter-driven protein export complex (e.g., HlyABC) that secretes proteins like hemolysin across both inner and outer Gram-negative membranes in a single step via the TolC outer membrane channel.

Rifamycin B

An antimicrobial compound produced by Amycolatopsis mediterranei that selectively binds bacterial RNA polymerase to block transcription initiation.

Actinomycin D

A non-selective antibiotic that intercalates into DNA double helices, thereby inhibiting RNA chain elongation during transcription in both prokaryotes and eukaryotes.

Streptomycin

An aminoglycoside antibiotic discovered by Selman Waksman that binds the 30S ribosomal subunit, causing translation misreading and preventing proper 70S ribosome assembly.

Chloramphenicol

An antibiotic that binds to the 23S rRNA of the bacterial 50S ribosomal subunit, directly inhibiting peptidyltransferase activity and peptide bond formation.

16S rRNA

The structural RNA component of the prokaryotic 30S ribosomal subunit ($1,540\,\text{nucleotides}$ in E. coli) utilized by Carl Woese as an evolutionary molecular clock to construct the universal phylogenetic tree.

BLASTn

A Basic Local Alignment Search Tool program that compares query nucleotide sequences against known sequence databases to assess pairwise identity and evolutionary divergence.

Sulfonamides

A class of synthetic antimicrobial agents that inhibit bacterial growth by functioning as competitive inhibitors of the folic acid synthesis pathway.

Zidovudine (AZT)

An antiviral nucleoside analogue that structurally mimics thymine to inhibit reverse transcriptase and block viral replication in HIV.