Genetics 3000 Gene Interaction between bacteria and viruses

Endosymbiotic theory:

eukaryotic cells share evolutionary history with prokaryotic cells

The biomes of eukaryotic organisms are home to …

trillions of individual prokaryotic cells

A test was done in swabbing C-sectioned babies with the mother’s vaginal microbes, and it was found that …

for the first two years of life, the babies had less hardships when it came to immunity (not all bacteria are bad!)

Insulin was first produced by …

bacteria, they are often used as a model in genetics research

Prokaryotic cells are less …

complex than eukaryotes, they are smaller and have no organelles, and their genome is smaller

A prokaryotes genome consists of …

1 circular piece of DNA, they also have plasmids which are extrachromosomal pieces of DNA (they are also replicated and separated during mitosis)

The first bacterial genome was sequenced in …

1995, and the number of sequenced bacteria has only increased not that technology is cheaper and more efficient

Typical bacterial genomes are how many base pairs?

5 million bp, but sizes can range from 112,000 - 14 million bp

In bacteria, almost all genes are …

protein coding genes, in humans only 1% are protein coding, suggests that bacterial cells want to maximize efficiency

Bacterial proteins contribute to …

form and function of an organism which includes enzymes, structural features and protection

Genetic recombination in bacteria causes …

gene replacement, because their genome needs to remain haploid

Conjugation is a …

direct transfer of genetic material from one bacterial cell to another, the two cells touch, and a bridge forms between their membranes, DNA replicates and transfers from donor cell to receiver

If transferred DNA has complimentary base pairs with a chromosome then …

the recipient will gain a recombinant chromosome, the transferred DNA replicates inside the recipient cell so that a full two stranded piece of DNA can be added to the genome

Transformation is the …

uptake of external DNA fragments by bacterial cells, can be left behind by anything like hair, the uptaken DNA does not replicate inside recipient

Transduction is the …

transfer of DNA from one bacterial cell to another via bacteriophages, a virus attaches and injects its own DNA, which tells the cell to destroy its own DNA, usually the cell will die

After a cell destroys its own DNA because of a phage what happens?

The cell becomes a factory to make more phages, sometimes the remnants of the cells DNA can be put into a phage which will carry that DNA to another cell and give it the last cell’s DNA resulting in a recombinant chromosome if the cell survives the phage

To keep cells haploid after recombination …

the original piece of DNA that was replaced by the transferred DNA is degraded

Culturing is …

the process of growing bacteria in the lab, can be grown on solid media like agar, or liquid media, specific nutrients are required for growth

Antibiotics are frequently used in culturing because …

we can use it to select for cells that have incorporated a gene of interest and it keeps unwanted organisms from growing

Phototrophs can synthesize …

all essential organic components, they have the wildtype allele for all growth requirements - they can grow on minimal media

Auxotrophs cannot synthesize …

one or more organic components required for growth, theses must be grown on complete media so that they can get all the things the bacteria cannot provide for itself

Minimal media has …

a carbon source, essential vitamins, and ions (its simple)

Complete media has …

the same ingredients as minimal but has additional organic components like amino acids

The discovery of conjugation relied on …

two types of auxotrophs, they each couldn’t produce a few amino acids that the other could produce, after mixing them and allowing them to produce several generations, they were plated and they could grow on minimal media

DNA transfer is uni- …

directional meaning that it is a one way transfer, one cell donates and the other receives, it is not a reciprocal exchange

Conjugation also requires …

a fertility factor, donors of the factor are called F+ cells, recipients are called F-

The structure that bridges two cells during conjugation is called …

the F pilus or sex pilus

The F factor is a …

plasmid with specific genes thar produces proteins that help replicate, insert, and transfer chromosomal DNA, if a cell doesn’t have these genes it cannot exchange chromosomal DNA

Some F+ are unique because they …

are integrated into the chromosome called high frequency recombination (Hfr) strains

the Hfr strain behaves as …

F+ and initiates conjugation with F- strains, now chromosomal genes can follow the F factor genes

If a Hfr cell was to remain connected to the F- cell, the entire chromosome would transfer which is why conjugation is often …

incomplete, the genes enter the F- strain cell in the order they are found on the Hrf cell’s chromosome

We intentionally interrupt conjugation so that we can …

determine the order at which genes file into a F- cell

The closer a gene physically is to the origin of transfer (because there is only one origin), the …

sooner it will enter the recipient cell

Plasmids are replicated using the same …

process and enzymes as the chromosomal DNA

Plasmids are classified based on the …

genes they have

F plasmids are …

fertility plasmids

R-plasmids are …

resistance plasmids

Col plasmids are …

immunity plasmids (genes code for proteins that destroy other bacteria)

Genes in R plasmids confer …

resistance to classes of antibiotics, transferrable between bacterial cells via conjugation

Antibiotic resistance is a growing concern for …

human and veterinary medicine and crop and livestock management, bacteria can be resistant to multiple types of antibiotics

Bacterial transformation can take DNA from …

soil, water, or culture mediums, it is the transfer of linear isolated DNA (not double stranded)

To undergo transformation, cells must be in the physiological state of …

competence (when the cell has proteins that go out into the environment and grab onto DNA and bring it inside the cell

Competence is naturally …

occurring and genetically determined, but it can also be induced in species that are typically not competent

E. coli are typically …

not competent, but its useful as a model species and tool in molecular biology research

E. coli can be cultured to show two types of competency:

Chemically competent and electrocompetent, goal of both is to disrupt membrane

Chemically competent is …

adding for example CaCl to neutralize charges on the membrane of the cell which allows DNA to make it through the membrane

Electrocompetent is …

when we shock the cell and nearby DNA, this disrupts the membrane opening a hole for hopefully enough time to let the DNA enter the cell

Many transformations use …

plasmids, carry DNA of interest into bacteria, once incorporated into cells, cell reproduction will produce many copies of the DNA

We will put ______ on plasmids to for quick identification of cells that are transformed

selectable markers

We will place a gene on interest often in …

the middle of another gene, this addition disrupts the gene we placed it in, lac Z for example makes cells blue but by placing DNA of interest within that gene the cells that actually successfully transform will be white = indicator that transformation took place

Viruses are interesting because …

we still don’t know if they are alive, they are an infectious microbe consisting of nucleic acid and proteins (that’s it!!)

Viruses can be made of …

DNA or RNA with a variety of shapes, may be called infectious agents and they are incapable of replicating outside a host cell

All organisms are subject to …

viral infections

Helical viruses have a …

slinky shaped capsid that twists around and encloses its genetic material (ex. tobacco mosaic viruses)

Polyhedral viruses are composed of …

genetic material surrounded by a many-sided capsid, usually with 20 triangular faces (ex. adenoviruses which cause things like pink eye or pneumonia)

Spherical viruses are …

essentially helical viruses which is spiked with sugary proteins that assist in sticking to and entering host cells (ex. Covid-19)

Complex viruses like …

bacteriophages, look like space ships, they are composed of a polyhedral head and a helical body or tail sheath and legs that attach to a membrane so that it can transfer its genetic material

1st a virus will attach itself to a cell and …

then its engulfed, viral genetic material is released and begins replicating using cellular mechanisms, the cell replicates viral proteins which begin building new viral particles, and finally the new viruses are released from the cell, sometimes this process kills the cell, not always

Bacteriophages are specifically viruses that …

infect bacteria, the model phage T4 infects E. coli

Any virus is essentially nucleic acid …

surrounded by proteins, the T4 phage have a head and tail surrounding DNA, tail is used to bind to cells, head holds the DNA, the tube and sheath are like a channel for the DNA to follow to enter the cell

How many versions of a phage life cycle are there?

Lytic and Lysogenic

The lytic life cycle is characterized by …

rapid viral production and bursting of the host cell (as soon as the phage DNA is injected it starts replicating and taking over the cell)

The Lysogenic life cycle is characterized by …

the incorporation of viral DNA into bacterial chromosomes

What is the viral DNA that incorporates into the bacterial chromosome called during the lysogenic life cycle?

prophage, the prophage is replicated along with the rest of the chromosome and the cell continues replicating as normal, produces an entire population of cells with viral DNA that is lying dormant

When does the lysogenic cycle end?

when some sort of triggering event occurs that tells the viral DNA to start being transcribed which begins the lytic life cycle (this can happen when something releases the prophage from the chromosome), the time it takes for the lytic cycle to begin vary

Transducing phages develop as a result of the …

lytic cycle and it can reveal distance between genes, if two genes of the bacterial genome end up in the same phage this tells us that they are very close together on the chromosome, and if we have genes a, b, and c and a and b are put into the next recipient cell this tells us that a and b are next to each other

Transduction is a rare occurrence, but when it does happen …

Bacterial chromosomes are more likely to end up in the recipient cell of the virus

Specialized transduction is when …

integrated phage DNA is imprecisely removed, the lysogenic cycle ends, the viral DNA is picked out of the chromosome and sometimes bacterial DNA is picked up with it and packaged into a new virus, so the genes picked up have to be close to the integration site

Viruses that infect animals and plants can vary …

greatly in types of nucleic acid and proteins produced, which contributes to the diversity of diseases

Retroviruses have a similar life cycle to …

phages

Retroviruses are made of …

RNA and proteins and they can incorporate into their host’s genome

In order to incorporate viral DNA into a host cell, retroviruses need …

reverse transcriptase and integrase

Reverse transcriptase copies …

RNA viral genome into DNA for Retroviruses

Integrase inserts newly …

copied viral DNA into host genomes for retroviruses

Once Viral genome from retroviruses has been incorporated into a host’s genome that DNA is called …

Provirus

In rare cases when viral DNA is extracted from a host genome and it picks up the host’s DNA as well, those carried genes can cause excess …

cell proliferation, if these new viruses infect another cell, those genes that code for instructions to divide will cause excessive cell growth in the new recipient which can lead to cancer