15 O&C Prokaryotic Genome Notes 2024

A prokaryote is a unicellular organism that lacks membrane-bound organelles and is divided into two domains: Archaea and Bacteria.

Prokaryotic genomes range from 0.5 Mb to 10 Mb (1 Mb = 10^6 base pairs), smaller than many eukaryotic genomes.

Transfer DNA (TDNA) is the single-stranded DNA nicked at the origin of transfer in the donor and exported to the recipient through the cytoplasmic bridge.

Yes — R plasmids often encode sex pili and can transfer antibiotic resistance genes between bacteria via conjugation.

The bacterial genome consists of a bacterial chromosome (found in the nucleoid) and plasmids (found in the cytoplasm outside the nucleoid).

A single circular double-stranded DNA molecule associated with non-histone proteins, not enclosed by a nuclear envelope, located in the nucleoid; described as 'naked' DNA.

About 5 million base pairs (5 x 10^6 bp), length ~1 mm when stretched, width ~2 nm.

Ori C is the single origin of replication found in a typical bacterial chromosome.

Operons are groups of several genes lined up side by side under the control of a single promoter, allowing coordinated expression.

No — genes in prokaryotes are not interrupted by introns.

The chromosome is folded into ~50 loops (loop domains), each ~100,000 bp, bound to a central protein scaffold and supercoiled independently.

Specific supercoiling of a region can affect the ability of the cell to express genes in that region.

Plasmids are much smaller, double-stranded, circular extra-chromosomal DNA ranging from 1 kb to 300 kb; can have high copy number and replicate independently.

Non-essential but beneficial genes, e.g., antibiotic resistance (R-factors) or conjugation (F-factors).

R-factors (R plasmids) carry genes coding for enzymes that destroy or modify antibiotics, conferring antibiotic resistance.

Asexual reproduction where one bacterium divides into two identical daughter cells through DNA attachment to membrane, replication, cell growth, and division.

Chromosomal DNA attaches to the cell membrane at a point called the mesosome.

Replication starts at ori C, proceeds bidirectionally, is semi-conservative, and uses DNA gyrase to remove positive supercoils; ends at a termination sequence opposite the origin.

Yes — plasmids are replicated at the same time and similarly to the bacterial chromosome.

Spontaneous mutations (insertions, deletions, base substitutions) and genetic recombination introduce variation.

Transfer of genes from parent to daughter cells during cell division; variation arises via mutation in parental DNA.

Transfer of genetic material between bacteria that are not parent-offspring, leading to genetic recombination via transformation, transduction, or conjugation.

Uptake of foreign DNA (chromosomal fragments or plasmids) from the environment by a competent bacterial cell, which can incorporate it into its chromosome.

Competent cells have surface proteins that recognize and transport DNA; cells can be made competent artificially via Ca2+ and heat shock or electroporation.

Heat-killed virulent IIIS mixed with live non-virulent IIR converted IIR into virulent IIIS in mice, showing uptake of transforming factor (later identified as DNA).

Transfer of bacterial DNA from one cell to another via a bacteriophage.

When random fragments of host bacterial DNA are accidentally packaged into phage particles during the lytic cycle and transferred to another bacterium.

Occurs with temperate phages (e.g., lambda) during lysogeny where viral DNA integrates at a specific site; upon excision, adjacent bacterial genes may be carried to another bacterium.

Direct transfer of DNA between two bacteria in contact, typically mediated by F plasmid-bearing donors (F+) forming a sex pilus with recipients (F-).

A fertility factor (F) that can be plasmid or integrated into the chromosome; contains ~25 genes encoding sex pili and genes for transfer.

Gene expression is transcription (and translation) of a gene into a functional product; gene regulation controls whether and at what level a gene is expressed.

To avoid wasting resources by synthesizing unneeded proteins and to allow rapid responses to environmental changes.

Mainly at the transcriptional level, often by grouping related genes into operons under a single promoter.

A single mRNA that contains genetic information for synthesis of more than one polypeptide, typical of operons.

A cluster of structural genes, a promoter where RNA polymerase binds, and an operator that acts as a molecular switch.

It codes for a repressor protein that can bind the operator to prevent transcription of structural genes.

Inducible operons are usually off but can be turned on by a specific molecule (e.g., lac operon); repressible operons are usually on but can be turned off by a specific molecule (e.g., trp operon).

Negative control: active repressor turns genes off; Positive control: active activator is needed to increase transcription.

F. Jacob and J. Monod discovered the lac operon.

lacZ codes for β-galactosidase; lacY codes for lactose permease; lacA codes for galactoside transacetylase.

lacI codes for the lac repressor, a dimer with a DNA-binding site and an allosteric site for allolactose.

Allolactose binds the repressor's allosteric site, changing its conformation so it cannot bind the operator, allowing transcription.

Because the repressor does not bind permanently and can detach occasionally, allowing low-level transcription.

Glucose is preferred; maximal lac operon expression requires absence of glucose because glucose transport inhibits adenyl cyclase, lowering cAMP and inactivating CAP.

Catabolite activator protein (CAP) binds cAMP; the cAMP-CAP complex binds upstream of the lac promoter to enhance RNA polymerase binding, increasing transcription when glucose is low.

In absence of glucose and presence of lactose (dual control: negative by repressor, positive by cAMP-CAP).

Repression of lac operon expression in presence of glucose, enabling preferential use of glucose over other carbon sources.

Because β-galactosidase is one of the enzymes coded by lac operon; its level indicates operon expression.

A repressible operon regulating biosynthesis of tryptophan, consisting of a promoter, operator, and five structural genes (trpE, D, C, B, A).

The trp repressor is inactive and does not bind the operator, allowing transcription of the trp genes.

Tryptophan acts as a co-repressor by binding and activating the repressor, enabling it to bind the operator and block transcription.

Their synthesis can be downregulated or turned off by the presence of the end product (tryptophan).

Coordinated regulation of pathway enzymes under a single promoter/operator saves energy by synthesizing only required enzymes and allows response to environmental substrates.