Bacterial Genes, Structure, Replication, and Expression

Comprehensive vocabulary regarding bacterial genetics, including DNA structure, replication enzymes, growth phases, and chromosomal organization as covered in Lecture 1.

Central Dogma of Molecular Biology

The principle that genetic information flows in one direction from DNA to RNA to Proteins, defined by Francis Crick in 1958.

Nucleoid

The region of bacterial cells where DNA is present, usually consisting of a single circular chromosome of double-stranded DNA.

E. coli DNA Dimensions

The DNA is $1.6\,mm$ long, while the cell itself is approximately $2\,\mu m \times 1\,\mu m$.

Purines

A class of nitrogenous bases that includes Adenine (A) and Guanine (G).

Pyrimidines (DNA)

A class of nitrogenous bases that includes Thymine (T) and Cytosine (C).

Pyrimidines (RNA)

A class of nitrogenous bases that includes Uracil (U) and Cytosine (C).

Complementary Base Pairing (DNA)

The weak interaction via H-bonding where Adenine pairs with Thymine and Guanine pairs with Cytosine.

Anti-parallel DNA Polymers

Strands that run $5' \rightarrow 3'$ in opposite directions and are the reverse complement of each other.

Kilobase ($Kb$)

A unit of measurement for bacterial chromosomes equal to $1000\,bp$.

Megabase ($Mb$)

A unit of measurement for bacterial chromosomes equal to $1000\,Kb$.

Negatively Supercoiled DNA Loops

Functional units of the condensed nucleoid, containing approximately $10\,Kb$ and numbered between $50-400$.

Plectonemes

Branched loops or supercoils arranged in linear order radiating from a core of DNA organizing factors.

Nucleoid Associated Proteins (NAPs)

A core of DNA organizing factors that bend or bridge DNA to help organize the circular chromatin fibre.

Lag Phase

The bacterial growth phase where cells are introduced into fresh media but do not immediately replicate.

Log Phase

The growth phase where bacteria are actively dividing at the maximal rate.

Stationary Phase

The phase where population growth ceases but cells remain viable.

Death Phase

The phase where the viability of cells declines as they die.

Origin of Replication ($ori$)

The only start point for replication on the bacterial chromosome.

Termination Site ($ter$)

The end point for DNA replication, found at the pole of the cell opposite the $ori$.

Expansion Phase

The stage of prokaryotic cell division where the bacterial cell size is increased almost $2$-fold.

Septum

A new cell wall material synthesized to separate two daughter cells during division.

Semi-conserved Replication

The process resulting in two identical double-stranded copies of DNA, each with one strand of the original DNA.

DNA Gyrase (Isomerase)

The protein responsible for unwinding the supercoil of the DNA.

DNA Helicase

The protein that unzips the DNA double helix to expose nitrogenous bases.

Single-stranded DNA Binding Proteins (SSB)

Proteins that keep the replication strands apart after helicase unzips them.

DNA Primase

An enzyme that synthesizes an RNA primer to initiate DNA synthesis.

DNA Polymerase III

An enzyme that binds single-stranded DNA, recruits deoxyribonucleoside triphosphates, and catalyzes phosphodiester bonds $5' \rightarrow 3'$.

Okazaki Fragments

Short sequences of DNA synthesized on the lagging strand using an RNA primer and extended by DNA polymerase I.

DNA Ligase

An enzyme that joins Okazaki fragments and repairs the phosphodiester bonds in the backbones.

Catenated

The state where two circular copies of a chromosome are intertwined after replication.

Topoisomerase (in Resolution)

An enzyme that introduces a double-stranded break into dsDNA to help resolve catenated chromosomes.

Holliday Junctions

The specific structure formed during homologous recombination involving strand exchange between each dsDNA pair at the $ter$ site.

FtsK-XerCD

The recombination machinery that cleaves the Holliday junction to resolve the chromosomal dimer.

Intergenic Regions

Regions between genes on the DNA that may not be transcribed.

Gene Products

Molecules encoded by genes, including transfer RNA (tRNA), ribonucleic RNA (rRNA), and messenger RNA (mRNA).

Promoter

The region of a bacterial gene where RNA polymerase binds to initiate transcription.

Shine Dalgarno Sequence

The region of a gene where ribosomes bind to initiate translation of protein.

Histone-like Nucleoid Structuring Protein (H-NS)

A NAP that exists as dimers packed side by side between two adjacent DNA strands, preferentially binding curved DNA and covering $1$% of the chromosome.

Factor for Inversion Stimulation (FIS)

A sequence-specific DNA binding protein that bends DNA $50-90$ degrees and acts as a transcriptional activator.

RNAP

The abbreviation used for RNA polymerase.

GFP

The abbreviation used for green fluorescent protein.

DAPI Stain

A stain used to visualize the nucleoid, typically appearing red in specific imaging contexts described.

Transcription Factories

Large mega structures formed by transcriptional and translational machinery for the synthesis of RNA and translation of proteins.

Stringent Response

A cellular state associated with inhibition of transcription, nutrient deprivation, and low stable RNA synthesis.

Stationary Phase Nucleoid State

A relaxed state with very little transcription.

Logarithmic Phase Nucleoid State

A highly supercoiled state where transcription factories are created for enhanced rRNA production.

Open Reading Frame (ORF)

In bacteria, one of these sequence segments encodes only one protein.

mRNA Splicing

A process exclusively seen in eukaryotes; there is no occurrence of this in bacterial mRNA.

Gene Representation

Generally depicted as arrows on both strands of DNA, typically not overlapping.

Protein Splicing

A process of modifying protein products that is seen in some bacteria.