Prokaryote And Extrachromosomal Genetics

Question 1

Why are some genetics non-Mendelian?

Answer 1

Mendelian genetics comes from how chromosomes segregate during meiosis. But not all DNA is found in the nucleus:

Mitochondria and chloroplasts have their own circular DNA, separate from nuclear chromosomes.
These organelles are inherited only from the mother, leading to maternal inheritance patterns

Question 2

Examples of maternal inheritance and is it the same as x-linked inheritance?

Answer 2

In plants like Mirabilis jalapa (4 o’clock plant), stem and leaf color depend only on maternal inheritance.
In humans, several diseases are mitochondrially inherited:
LHON – Leber’s Hereditary Optic Neuropathy
MERRF – Myoclonic Epilepsy
MELAS, NARP, and others
❗️This is not the same as X-linked inheritance—these traits come only from mitochondrial DNA, passed down by egg cells, not sperm.

Question 3

What does organelles being randomly inherited in cell division lead to?

Answer 3

Homoplasmy: All organelle genomes are the same
Heteroplasmy: A mix of normal and mutant genomes
🔁 This leads to variable expression of disease or traits, depending on how many organelles in a cell are functional vs. mutated.

Question 4

What could heteroplasmy lead to in animals and humans?

Answer 4

Consequences for Disease
In humans: varying degrees of symptoms in siblings from the same mother (heteroplasmy)
In plants: variegation (green, white, yellow tissue) from chloroplast mutations

Question 5

What is 3-parent IVF?

Answer 5

Involves transferring the nucleus of a mother’s egg (with faulty mitochondria) into a donor egg with healthy mitochondria.
Fertilized with sperm → implanted → avoids mitochondrial disease in offspring.

Question 6

What are endosymbionts in terms of being a type of extrachromosal inheritance?

Answer 6

1. Endosymbionts (e.g. Wolbachia)

Bacteria living inside eukaryotic cells
Passed maternally, affect host traits
Similar to mitochondria and chloroplasts in how they propagate

Question 7

What are prions and their 2 forms?

Answer 7

Not DNA – but misfolded proteins
Prions can convert normal proteins into the misfolded form (prion-) - (prion+)
Spread from cell to cell, and across generations in fungi (yeast), mimicking dominant genetic traits
Examples in mammals: BSE (mad cow disease), Kuru, possibly Alzheimer’s/Parkinson’s

Question 8

What purpose to prions provide in fungi?

Answer 8

In fungi, prions may serve adaptive purposes, helping colonies survive stress by switching on/off metabolic states.

Question 9

What is a biofilm?

Answer 9

Prokaryotes are not always isolated, simple cells.
After binary fission, many prokaryotic cells adhere together, forming biofilms—surface-associated multicellular structures encased in protective matrices

Question 10

What tasks can biofilms distribute?

Answer 10

Nutrient acquisition
Defense
Spore formation

Question 11

What are syntrophic consortia and what do they enable?

Answer 11

Syntrophic consortia: groups of different microbial species cooperate by exchanging metabolites (e.g., in your mouth).
These aggregates enable:
Protection
Resource sharing
Increased chance for Horizontal Gene Transfer (HGT)
🧠 Key point: Aggregation helps survival and enables the physical proximity needed for DNA exchange, especially conjugation.

Question 12

What are chromosomes? What do they carry?

Answer 12

Usually one circular chromosome
Found in the cytoplasmic nucleoid, not a nucleus
Haploid: one copy per cell
Size: 2–12 Mbp, gene-dense
Carries essential genes for life

Question 13

What are plasmids? What do they carry?

Answer 13

Small, circular, extrachromosomal DNA
Size: 2 kb to 500 kb
Can be present in multiple copies
Carry accessory genes: virulence, antibiotic resistance, metabolic adaptation
Example: pGO1 plasmid in Staphylococcus carries resistance to multiple antibiotics and disinfectants
🧠 Key point: Plasmids are mobile gene carriers, playing a key role in adaptation and HGT.

Question 14

What is conjugation?

Answer 14

Conjugation: plasmid transfer between cells (bacterial mating

Question 15

What is a conjugative plasmid?

Answer 15

Have tra/trs genes (transfer functions)
Have an oriT (origin of transfer)
Encode pilins, which form pili that bridge donor and recipient cells
Use rolling circle replication to copy and transfer one strand of plasmid DNA
The recipient becomes a plasmid+ donor at the end

Question 16

What is meant by F+ and F-?

Answer 16

F+: donor with plasmid
F−: recipient without plasmid
🧠 Key point: Conjugative plasmids are DNA-sharing tools that can spread useful traits like antibiotic resistance between unrelated cells.

Question 17

What is transposition?

Answer 17

= DNA jumping within or between DNA molecules

Question 18

What are insertion sequences (IS)?

Answer 18

Simplest elements
Contain only a transposase gene (tnp) and inverted repeats
Can jump by themselves

Question 19

What are transposons (Tn)?

Answer 19

Larger elements formed when two IS elements flank other genes
Can carry useful genes, e.g. antibiotic resistance
Example: Tn4001 contains genes to resist trimethoprim

Question 20

What does transposase do?

Answer 20

Transposase moves DNA from plasmid to chromosome or vice versa
Can jump non-replicatively or replicatively
🧠 Key point: Transposons are gene smuggling cassettes—especially powerful when combined with conjugation

Question 21

What is HGT?

Answer 21

DNA exchange across lineages (not parent-to-offspring)

Question 22

What are the 3 mechanisms of HGT?

Answer 22

Conjugation (cell-to-cell plasmid transfer via pili)
Transduction (DNA transfer by bacteriophages—covered in later lectures)
Transformation (uptake of naked DNA from environment)

Question 23

What does transposition allow? What does HGT allow?

Answer 23

Transposition allows genes to move within a genome or onto plasmids, which can then be spread by conjugation.
🧠 Key point: HGT allows rapid evolution in bacteria—spreading useful genes like resistance or metabolic functions without sexual reproduction.

Question 24

How is gene shuffling possible in prokaryotes?

Answer 24

Transposable elements (IS/Tn) which create regions of homology.
Conjugation (via conjugative plasmids with tra/trs and oriT), allowing transfer of DNA between cells.
Homologous recombination (HR) pathways (e.g., RecBCD in E. coli), which mediate strand exchange and recombine DNA

Question 25

What are the steps of prokaryotic gene shuffling?

Answer 25

Transposable elements create shared DNA regions between plasmid and chromosome. These allow integration of plasmids into chromosomes. Conjugation then transfers chromosomal regions. HR shuffles alleles between donor and recipient DNA, mimicking meiotic crossovers.

Question 26

What is meant by integration of DNA?

Answer 26

Integration: Incorporation of plasmid DNA into the chromosome via homologous recombination, often facilitated by transposable elements

Question 27

What is excision?

Answer 27

Excision: Reversal of integration, where recombination removes the plasmid DNA from the chromosome.

Question 28

What is an episomal plasmid?

Answer 28

Episomal plasmid: A plasmid that can reversibly integrate into the chromosome. It can exist both as a free circular molecule and as part of the chromosome

Question 29

What is an Hfr strain?

Answer 29

Hfr strain (High-frequency recombination strain): A bacterium where a conjugative plasmid has integrated into the chromosome, allowing large sections of chromosomal DNA to be transferred during conjugation.

Question 30

What are virus’s (phages)?

Answer 30

Prokaryotic viruses (phages) consist of a protein capsid enclosing nucleic acid (DNA or RNA).

Question 31

What is the lytic cycle?

Answer 31

Virus infects host, replicates genome, assembles virions, lyses cell. Sometimes, host chromosomal DNA is mistakenly packaged into a virus particle instead of the viral genome

Question 32

What is general transduction? What does it allow?

Answer 32

The virus containing host DNA infects a new cell. That DNA is injected, and if homologous, it can recombine into the new host genome. This transfers chromosomal DNA between cells via phage particles. This is another form of HGT, allowing random host DNA to move across cells using viral machinery.

Question 33

What is transformation and how does it work?

Answer 33

Transformation = uptake of naked DNA from the environment. Naturally competent species use specific transport proteins to take up single-stranded DNA, which is then copied to dsDNA and may recombine into the genome. Many species, like E. coli, are not naturally competent but can be artificially induced in the lab using chemical treatments (e.g., Ca²⁺). Transformation plays a key role in genetic engineering and natural gene acquisition. 🡺 Like transduction and conjugation, transformation supports horizontal gene acquisition, further diversifying prokaryotic genomes

Question 34

What is vertical gene transmission?

Answer 34

Vertical gene transmission is the traditional passing of genetic material from parent to offspring during reproduction, such as binary fission in prokaryotes or meiosis and sexual reproduction in eukaryotes. It’s linear, generational inheritance

Question 35

What is horizontal gene transfer?

Answer 35

Horizontal gene transfer (HGT), by contrast, is the non-reproductive transfer of genetic material between individual organisms—common in prokaryotes

Question 36

What is transformation?

Answer 36

Uptake of DNA from environment

Question 37

What is transduction?

Answer 37

DNA transfer via viruses

Question 38

What is conjugation?

Answer 38

Direct cell to cell transfer via plasmids

Question 39

What is transposition?

Answer 39

Gene movement within or between DNA molecules

Question 40

What does horizontal mixing of DNA allow?

Answer 40

Allele shuffling, similar to recombination in eukaryotes

Question 41

What is the mobilome?

Answer 41

The mobilome refers to all the mobile genetic elements in a genome: Includes plasmids, transposons, integrative conjugative elements, and viral DNA, Enables gene movement within and between organisms. Unlike the stable genome, the mobilome is dynamic, driving rapid genetic innovation, especially in prokaryotes

Question 42

Why is HGT a major evolutionary force in prokaryotes?

Answer 42

It enables the acquisition of new traits, like antibiotic resistance or metabolic pathways, sometimes across species, phyla, or domains. Genome sequencing reveals "genomic islands"—regions of DNA that differ in GC content, suggesting foreign origin via HGT. Thus, the “tree of life” in prokaryotes is better viewed as a “net of life”, due to pervasive gene flow

Question 43

What are the 3 regulation systems to regulate HGT to prevent genomic chaos?

Answer 43

Quorum sensing in Bacillus subtilis: competence (ability to uptake DNA) is only induced in dense populations of the same species—reducing the chance of incorporating non-compatible DNA. Sequence recognition: Haemophilus only takes up DNA with specific 11-bp sequences common in its own species. Restriction-modification systems: Restriction enzymes cut foreign DNA unless it's protected by host-specific methylation. These systems limit HGT across species but allow for controlled gene sampling.

Question 44

What are the 2 examples of circular extrachromosal DNA in eukaryotes?

Answer 44

Yeast 2-micron plasmid in S. cerevisiae: A selfish DNA circle (~6.3 kb, 50–100 copies/cell), not beneficial to the host. Extensively exploited in genetic engineering due to its replication system. Double minutes (dmins) in human cancer cells: Unstable, extrachromosomal circles carrying oncogenes like MYC. Present in multiple copies, they drive tumor growth. These are examples of a eukaryotic mobilome, albeit less extensive than in prokaryotes

Question 45

What is natural conjugation and an example?

Answer 45

Natural conjugation (from prokaryotes to eukaryotes): Agrobacterium tumefaciens uses a Ti plasmid to transfer genes into plant cells, inducing tumor-like galls. This is a natural example of DNA conjugation from a bacterium into a eukaryote.

Question 46

What is laboratory transformation, transfection? What are the 2 types?

Answer 46

Eukaryotes are not naturally competent, but can be artificially transformed (called transfection) using: Chemical methods (e.g., calcium ions), Physical methods (e.g., electroporation, liposomes). DNA may integrate randomly into the genome or be maintained episomally

Question 47

What is laboratory bases transduction? What are the 2 viruses involved?

Answer 47

Modified retroviruses or adenoviruses can deliver genes into mammalian cells: Retroviruses integrate into host DNA. Adenoviruses persist as episomes in the nucleus. These vectors are central to gene therapy and genetic research