Microbial Genetics: The Selfish Gene

Flashcards covering microbial genetics, DNA structure and replication, gene expression (transcription and translation), mutations, horizontal gene transfer mechanisms, and gene regulation (operons).

Genetics

The study of how hereditary material (DNA and RNA) is transferred, how, when, and why genes are expressed.

Genome

All of the genetic material in a cell, subdivided into chromosomes and plasmids.

Chromosomes

Subdivisions of the genome, further subdivided into genes (coding regions) and non-coding regions.

Plasmids

Subdivisions of the genome, small, self-replicating, circular pieces of extra-chromosomal DNA.

Genes (coding regions)

Subdivisions of chromosomes that encode specific functions or traits.

DNA

Composed of repeating nucleotides (Adenine, Thymine, Cytosine, Guanine) attached to a sugar phosphate backbone, generally existing as a double helix where A binds with T, and C binds with G.

Nucleotides

The repeating building blocks that compose DNA.

Uracil

The nucleotide that replaces Thymine in RNA.

Super-coiled DNA

The extensively coiled state of DNA that allows it to fit into a cell, as seen in bacterial chromosomes.

DNA Replication

The process where one double-stranded parent DNA molecule is converted into two identical double-stranded daughter strands.

Semiconservative replication

The mechanism of DNA replication where each new DNA strand contains half 'old' (parental) and half 'new' DNA.

Topoisomerase

An enzyme that uncoils DNA during replication.

Gyrase

An enzyme that uncoils DNA during replication, working alongside topoisomerase.

Origin of replication

The specific region on DNA where uncoiling begins for replication.

Helicase

An enzyme that unwinds the DNA helix and separates the DNA strands in both directions during replication.

Single strand binding proteins

Proteins that stabilize the single-stranded DNA during replication, preventing re-annealing.

Primase

An enzyme that adds an RNA primer to the DNA strand being replicated, providing a free 3' hydroxyl group.

RNA primer

A short RNA sequence added by primase that acts as a starting point for DNA polymerase.

DNA polymerase

An enzyme that ensures the proper nucleotide is bound and connects it to the growing DNA strand during replication.

Lagging strand

The DNA strand that is synthesized discontinuously in pieces due to the lack of a continuous free 3' hydroxyl group, requiring multiple RNA primers.

Okazaki fragments

The pieces of DNA synthesized on the lagging strand.

Ligase

An enzyme that assembles the synthesized DNA pieces (Okazaki fragments) on the lagging strand.

Bidirectional replication

A characteristic of DNA replication where the process occurs in both directions around a circular chromosome (in bacteria).

Replication forks

The points where DNA strands are unwound and new DNA synthesis is occurring.

oriC

A fixed region on the bacterial chromosome where DNA replication initiation begins.

Central Dogma of Genetics

The process by which genetic information flows from DNA to RNA and then to protein (DNA -> RNA -> Protein).

Transcription

The first step in gene expression where a specific gene is copied into messenger RNA (mRNA).

RNA polymerase

An enzyme that binds to the promoter, initiates DNA unraveling, and facilitates the assembly of free ribonucleotides into RNA chains, using DNA as a template.

Promoter

A regulatory region directly upstream of a gene where RNA polymerase binds to initiate transcription.

Terminator

A specific region of DNA that signals RNA polymerase to stop RNA synthesis.

Rho termination protein

A protein that facilitates the disassociation of RNA polymerase and the RNA strand from the DNA once the terminator is reached.

Translation

The process where messenger RNA (mRNA) is used to synthesize protein.

Codons

Groups of three bases on an mRNA molecule, each specifying a particular amino acid.

Ribosomes

The cellular structures where protein synthesis (translation) occurs, composed of 30S and 50S subunits (forming 70S).

Degeneracy

The characteristic of the genetic code where multiple codons can specify the same amino acid.

Stop codons

Three non-coding codons (UAA, UAG, UGA) that signal the termination of protein synthesis.

Transfer RNA (tRNA)

RNA molecules that can bind both RNA (via an anticodon) and a specific amino acid, effectively carrying amino acids to the ribosome during translation.

Anticodon

A region on a tRNA molecule that is complementary to and binds to a specific codon on mRNA.

Charged tRNA

A tRNA molecule that has its specific amino acid bound to it.

Aminoacyl site (A site)

The site on the ribosome where incoming charged tRNA molecules bind.

Peptidyl site (P site)

The site on the ribosome where peptide bond formation occurs between amino acids, holding the growing polypeptide chain.

Exit site (E site)

The site on the ribosome where uncharged tRNA molecules exit after donating their amino acid.

16S RNA

A ribosomal RNA located in the 30S (small) ribosomal subunit, whose sequence is complementary to the ribosome binding site on the mRNA.

Ribosome binding site (Shine-Dalgarno site)

A conserved sequence in the mRNA located just in front of the gene being translated, which aligns the ribosome for correct translation initiation.

Translation Initiation

The step in translation where the ribosome subunits come together around the mRNA, and the first charged tRNA binds.

Translation Elongation

The step in translation where amino acids are sequentially added to the growing polypeptide chain.

Translation Termination

The step in translation where the ribosome-mRNA complex is disassembled and the protein is released, triggered by a stop codon.

N-formyl methionine

The amino acid carried by the first tRNA that binds during the initiation of translation in bacteria.

Peptidyl transferase

An enzymatic activity within the ribosome that catalyzes the formation of a peptide bond between amino acids during elongation.

Release factor

A protein that binds in the A site when a stop codon is encountered, causing the polypeptide chain to be released from the tRNA in the P site.

Genotype

The genetic makeup of an organism, encoding all its potential traits.

Phenotype

The observable or measurable traits an organism has, resulting from its genotype and environmental interactions.

Mutation

A change in the genetic makeup (even single bases) of an organism.

Missense mutation

A type of mutation where a change in one nucleotide results in a change of one amino acid in a protein.

Nonsense mutation

A type of mutation where a base change results in a nonsense (stop) codon, prematurely stopping protein synthesis.

Frameshift mutation

A type of mutation caused by the addition or subtraction of one (or more, not in multiples of three) nucleotides, which completely changes the downstream amino acid sequence.

Vertical transmission

The inheritance of genetic material from parent to offspring during replication (e.g., binary fission).

Horizontal gene transfer (HGT)

The process by which genetic material is swapped between individuals of bacteria, independent from reproduction, leading to diversification of genomes.

Transformation

A primary mechanism of horizontal gene transfer where naked DNA is passed from one bacterium to another, often taken up from the environment.

Conjugation

A primary mechanism of horizontal gene transfer where bacteria transfer a copy of some or all of their genomic information directly to another bacteria, never exposing the genetic material to the environment.

Transduction

A primary mechanism of horizontal gene transfer that occurs when a bacteriophage (virus of bacteria) accidentally transfers bacterial DNA into another host bacteria.

Competence

The ability of bacteria to take up extracellular DNA, a prerequisite for transformation.

Conjugative plasmids

Plasmids that carry genes necessary for the process of conjugation, enabling their transfer to other cells.

Dissimilation plasmids

Plasmids that carry genes for the utilization of unusual sugars and carbohydrates.

Resistance plasmids

Plasmids that carry genes which encode antibiotic resistance, a major mechanism for its transfer.

Virulence plasmids

Plasmids that carry genes which encode virulence traits, contributing to a pathogen's ability to cause disease.

F+ donor cell

A bacterial cell that possesses the F factor plasmid and can initiate conjugation.

F- recipient cell

A bacterial cell that lacks the F factor plasmid and can receive genetic material via conjugation.

Conjugation pilus

A protein appendage produced by an F+ cell that binds to an F- cell, bringing them close together to initiate conjugation.

Conjugation bridge

A tunnel-like connection that forms between a donor and recipient cell during conjugation, allowing DNA transfer.

Bacteriophage

A virus that infects bacteria.

Genetic plasticity

The ability of bacteria to alter their genomes through the loss and addition of genes, contributing to rapid adaptation.

Repressors

Regulatory proteins that decrease or prevent gene transcription, typically by impeding RNA Polymerase.

Inducers

Regulatory proteins that promote or increase gene transcription, usually by removing repressors or promoting RNA polymerase binding.

Control region

A specific location upstream of a coding gene where repressors and inducers bind, typically containing a regulatory gene, a promoter, and an operator.

Promoter region

The specific part of the control region where RNA polymerase binds to the DNA and initiates transcription.

Operator region

The specific part of the control region where repressors bind DNA to block transcription.

Regulatory gene

A gene located within the control region, upstream of the promoter and operator, that encodes repressors and inducers.

Operons

Clusters of several genes that serve one function, controlled by a single regulatory region.

Lac operon

A classical example of an inducible operon that contains a regulatory gene, a promoter, an operator, and three structural genes for the utilization of lactose as an energy source.

Allolactose

A derivative of lactose that acts as an inducer in the lac operon, binding to the repressor protein and causing a structural change that allows transcription.

cAMP (cyclic AMP)

A molecule that builds up when glucose levels are low and binds to CAP, activating it to promote transcription of the lac operon.

Catabolic activator protein (CAP)

A protein activated by cAMP that binds to the promoter of the lac operon and increases RNA polymerase binding, positively regulating transcription when glucose is scarce.

Inducible operon

An operon that is generally 'off' but can be turned 'on' when needed, typically associated with catabolic genes like the lac operon.

Repressible operon

An operon that is generally 'on' but can be turned 'off' when its products are not needed, typically associated with anabolic genes.