Chapters 7-10 & 12 Reading - VOCABULARY Flashcards

A set of 85 vocabulary-style flashcards covering key concepts from Chapters 7-12 reading guides.

Vertical gene transfer

Transfer of genetic material from parent to offspring during reproduction.

Horizontal gene transfer

Movement of genetic material between organisms that is not parent-offspring, enabling acquisition of new traits.

Two main forms of horizontal gene transfer

Transformation and transduction; conjugation is another common form.

Structural genes

Genes that code for the structural components of a product, not regulatory elements.

DNA control elements

Regulatory sequences such as promoters and operators that control gene transcription.

Prokaryotic genome structure

Typically a single circular chromosome; may include plasmids; no membrane-bound nucleus.

Gene

Basic unit of heredity; a DNA sequence that encodes a product.

Operon

Cluster of functionally related genes under a single promoter, transcribed as a polycistronic mRNA.

Regulon

A group of genes regulated by a common regulatory protein; genes may be scattered.

Bacterial chromosome replication

Semi-conservative replication initiated at origin oriC by DnaA; involves DnaB, DnaG, DNA Pol III; termination at ter.

Theta replication

Bi-directional replication of circular DNA forming two replication forks.

Rolling-circle replication

Replication mode for many plasmids; nicked strand serves as template producing ssDNA.

Plasmid inheritance

Mechanisms ensuring plasmids are maintained and inherited; include partitioning, copy-number control, and post-segregational killing.

Partitioning system

Active segregation of plasmids during cell division via Par proteins.

Copy-number control

Regulatory mechanisms that maintain a specific plasmid copy number per cell.

Post-segregational killing

Toxin-antitoxin modules kill cells that lose the plasmid, enforcing inheritance.

Metagenomics

Study of collective genomes from environmental samples to profile microbial communities.

Applications of metagenomics

Characterizing diversity, discovering functional genes, environmental monitoring.

Restriction endonucleases

Enzymes that recognize specific DNA sequences and cut; part of bacterial defense.

PCR

Polymerase Chain Reaction; technique to amplify a target DNA sequence.

Steps of PCR

Denaturation, annealing, extension; repeated cycles amplify DNA.

Purpose of PCR

To exponentially amplify a target DNA region for analysis or cloning.

Transcription

Synthesis of RNA from a DNA template.

RNA polymerase holoenzyme

Core RNA polymerase plus sigma factor; initiates transcription.

Sigma factors

Subunits that direct RNA polymerase to promoters and regulate gene expression.

Initiation of transcription

RNA polymerase binds promoter, forms open complex, begins RNA synthesis.

Elongation of transcription

RNA chain lengthens as nucleotides are added.

Termination of transcription

RNA synthesis ends; mechanisms include rho-dependent or rho-independent termination.

RNA classes

mRNA, rRNA, tRNA; plus regulatory RNAs in some contexts.

Start codon

AUG; signals the start of translation and codes for methionine.

Stop codons

UAA, UAG, UGA; signal termination of translation.

Translation stages

Initiation, elongation, termination.

Post-translational processing

Modifications after translation; folding, cleavage, chemical modifications.

Chaperone proteins

Assist in folding and preventing misfolding of nascent polypeptides.

Protein delivery locations in bacteria

Cytoplasm, inner membrane, periplasm (Gram-negative), extracellular.

Sec pathway

Translocates unfolded proteins across the inner membrane (general secretory pathway).

Tat pathway

Translocates folded proteins across the inner membrane using the twin-arginine motif.

Bioinformatics

Computational analysis of biological data; genome analysis and annotation.

Mutation

Heritable change in the DNA sequence.

Mutation types

Point mutations, insertions, deletions; frameshifts.

DNA repair mechanisms

BER, NER, MMR; double-strand break repair via HR or NHEJ (in bacteria, mainly HR).

Horizontal transfer mechanisms

Transformation, transduction, conjugation.

Restriction-modification systems

Restriction enzymes cut foreign DNA; methyltransferases protect host DNA.

Fates of foreign DNA

Degradation, incorporation into genome, maintenance on plasmid, or recombination.

Generalized recombination

Homologous recombination across similar sequences.

Site-specific recombination

Recombination at defined sequences catalyzed by specific recombinases.

Insertion sequences (IS elements)

Simple transposable elements with a transposase gene and inverted repeats.

Transposons

Mobile genetic elements carrying transposase and possibly cargo genes; move by transposition.

Quorum sensing

Cell-density dependent gene regulation via signaling molecules.

Quorum sensing autoinducers

Small molecules like AHLs (Gram-negative) or oligo-peptides (Gram-positive) that trigger responses.

Quorum sensing functions

Coordinate group behaviors such as biofilm formation and virulence.

Phase variation

Reversible on/off expression of surface structures to diversify phenotypes.

Northern blot

RNA detection by gel electrophoresis and probe hybridization.

Southern blot

DNA detection by gel electrophoresis and probe hybridization.

Real-time PCR

Quantitative PCR with fluorescence to monitor amplification in real time.

Western blot

Protein detection using antibodies after electrophoresis.

Electrophoretic mobility shift assay (EMSA)

Detects protein-DNA interactions by altered mobility in a gel.

DNA protection assay

Tests DNA-binding proteins’ ability to protect DNA from DNase digestion.

Affinity chromatography

Purification using a ligand bound to a matrix that specifically binds the target protein.

Mutants

Organisms with genetic alterations used to study gene function.

CRISPR-Cas9 system

Bacterial immune system using Cas9 nuclease guided by RNA to cut target DNA.

Cas9

Nuclease that creates targeted double-strand breaks guided by gRNA; requires PAM.

Guide RNA (gRNA)

RNA directing Cas9 to the matching DNA sequence next to a PAM.

PAM sequence

Protospacer Adjacent Motif; required for Cas9 recognition of target DNA.

Recombinant insulin production

Expression of human insulin in engineered microbes for medical use.

Bioremediation with engineered microbes

Using engineered microbes to degrade environmental pollutants.

Synthetic biology

Engineering biology to design and construct new biological parts, devices, or systems.

Biological parts

Standardized genetic elements (promoters, RBS, coding sequences) used to build circuits.

CRISPR-Cas9 applications

Genome editing, gene knockout, and functional genomics studies.

Semi-conservative replication

Each daughter DNA molecule has one original strand and one new strand.

oriC

Origin of replication in the bacterial chromosome.

DnaA

Initiator protein that binds oriC to start replication.

DnaB

Helicase that unwinds DNA at the replication fork.

DnaG

Primase that synthesizes RNA primers for lagging/leading strand synthesis.

Ter

Terminus region where replication forks meet and replication finishes.

Two-component systems

Sensor kinase and response regulator pair that sense and respond to signals.

AI-1 and AI-2 autoinducers

Autoinducers for quorum sensing; AI-1 is species-specific, AI-2 is universal.

Lytic vs lysogenic phage cycles

Lytic: phage replication and host lysis; lysogenic: phage DNA integrates into host genome.

Promoter elements (-35 and -10)

Promoter regions recognized by sigma factors; important for transcription initiation.

Methylation in RM systems

Methyltransferases protect host DNA by methylation; restriction enzymes cut unmethylated foreign DNA.

Genetic code mapping

Triple codons correspond to amino acids; includes start (AUG) and stop (UAA/UAG/UGA) signals.

rRNA

Ribosomal RNA; forms core structure and catalytic center of ribosome.

tRNA

Transfer RNA; carries specific amino acids to the ribosome during translation.

mRNA

Messenger RNA; carries genetic information from DNA to ribosome for translation.

Chromosome vs plasmid copy number

Chromosome is usually single-copy; plasmids have variable copy numbers affecting expression.