Genetics Exam 3: Topic 6 (CH7: Bacteria & Viruses))

Prototrophic

Wild type. Capable of surviving on its own without extra material. Can make everything itself it needs to survive.

Auxotrophic

Mutant type. Needs additional things in their media to survive. Lacks 1 or more important enzymes; unable to synthesize essential molecules that would allow them to grow in this media.

Minimum Media

The bare minimum of media. Only required by prototrophic bacteria

Complete Medium

Contains all the substances required for survival of all bacteria. Auxotroph’s need this to survive.

What is the bacterial genome mostly consisted of?

Mostly single, circular DNA molecule / chromosome

Plasmids

Extra chromosomes that are small and circular DNA. It gives extra genetic information that gives it extra abilities. Typically double stranded.

T/F: A single plasmid can carry the genes to resist many different antibiotics

True

T/F: Bacteria can only have one type of plasmid

False. They can have multiple types of plasmids.

Where does replication of a plasmid begin?

The origin

Is a plasmid single or double stranded?

Double Stranded DNA

T/F: Plasmids are self-inducing and can make copies of itself. 

True

Most Plasmids have 3 types of genes

1. Genes that control its own replication

2. Genes that regulate its transfer to other bacterial cells.

3. Genes that allow it to insert itself into the bacterial chromosome.

Conjugation

A process which bacteria engage directly in the genetic exchange of material. This occurs by the string pilus. 1 bacteria (donor) will engage in conjugation event with the other bacteria and provide some of its genetic information through the process of recombination.

What are the 3 types of bacteria exchange?

1. Conjugation

2. Transformation

3. Transduction

Transformation

No direct link. Instead bacteria take up naked DNA (DNA that is outside of the plasma membrance because plasma membrane has been destroyed). Since the plasma membrane has been destoryed the DNA is usually in small fragments and chopped up

Transduction

Virus comes into the bacterium. Injects its viral DNA into the bacterium causing cell lysis and infection.

What are the types of F factors?

1. F+

2. F-

3. Hfr

4. F’

What does Hfr stand for

High-frequency donor. Its present and integrated into bacterial chromosome. They are donor cells with F factor integrated into the donor bacterial chromosome. A cell where the F factor has integrated into the chromosome, allowing high-frequency gene transfer.

What are the four steps of conjugation?

1. Donor cell attaches to a recipient cell with is pilus. The pilus draws the cells together.

2. The cells contact one another

3. One strand of plasmid DNA transfers to the recipient

4. The recipient synthesizes a complementary strand to become an F+ cell; the donor synthesizes a complementary strand, restoring its complete plasmid.

Merozygotes

Partial diploid bacterial cells containing F Plasmid carrying some bacterial genes.

Interrupted Conjugation

We let the bacteria start to conjugate, and then we stop it at certain times, and look at what’s been transferred over. We can follow the transfer.

What is the mechanism of transformation in bacteria?

• A bacterium takes up DNA from the medium

• Recombination takes place between introduced genes and the bacterial chromosome.

T/F: Competent cells do not take up DNA

False

Transformants

Cells that receive genetic material

Cotransformants

Cells that are transformed by two or more genes

What are some ways to make cells competent?

• poke holes in their membranes

• subject them to an electrical impulse

• heat shock

cells have to be in a stress-induced area

What are some factors affecting transformation efficiency?

1. plasmid size

2. DNA type (linear, ssDNA. supercoiled)

3. Cell genotype

4. Transformation method

5. Cell growth rate

What are some bacterial defense mechanisms?

• Reduce expression of receptors viruses need to attach

• secretion of polysaccharides to limit infection

• Block viral replication

• CRISPR-Cas systems

  • Allows them to recognize and remember DNA of specific pathogens and knows how to fight them the second time they come around

What does CRISPR stand for

Clustered Regularly Interspaced Short Palindromic Repeats

Bacteriophage

Bacterial infection virus

What are the two things viruses are made of?

1. Replicating Structure: made of DNA or RNA

2. Protein coat: On the outside of protein coat is different cell surface markers that make them unique. Also makes them targetable through vaccines. Also makes them detectable through antibody tests.

Virulent Phages

Reproduce through the lytic cycle and always kill the host cells.

Temperate Phages

Inactive prophage: phage DNA integrates into bacterial chromosome

What are the four steps in transduction?

1. Phage injects in DNA

2. DNA causes degradation of host DNA

3. Building new viral particles, with either original viral DNA or sometimes it’ll grab genetic information that comes from the bacteria.

4. Transducing phage (has bacterial genes) find another cell and injects bacterial DNA into it and because its not the viral DNA its can’t lyse the cell and break it apart. Cell now has naked DNA floating around. Creates recombinants.

Reverse Transcriptase

Synthesizing DNA from RNA or DNA template

Provirus

A viral genome incorporated into the host chromosome

• replicated by host enzymes

T/F: DNA Replication happens very slow

False. Happens very quickly and makes a lot of mistakes.

What are R plasmids?

(resistance) plasmids are small, circular DNA molecules in bacteria that carry genes for antibiotic resistance.

How do R plasmids spread between bacteria?

Through horizontal gene transfer, especially by conjugation (bacteria exchanging plasmids).

What happens when bacteria collect multiple R plasmids?

They can become resistant to many antibiotics and form a “superbug.”

What genes can R plasmids carry besides antibiotic resistance?

They may also carry genes for resistance to heavy metals like mercury, lead, or arsenic.

Why are R plasmids a problem in medicine?

They allow bacteria to survive antibiotic treatment, making infections harder to cure and increasing the spread of “superbugs.”

What is the F factor?

A fertility plasmid that allows bacteria to transfer genes to other cells through conjugation.

What is the function of the ori (origin of replication)?

It contains genes needed to copy the plasmid inside the cell.

What is the function of oriT (origin of transfer)?

It controls the transfer of the plasmid to another bacterial cell.

What are insertion sequences (IS2, IS3) used for?

They regulate plasmid integration into the bacterial chromosome.

Why is the F factor important?

It spreads valuable genetic information like antibiotic resistance between bacteria.

What is an F⁺ cell?

A donor cell with a separate F plasmid that can transfer it to an F⁻ cell.

What is an F⁻ cell?

A recipient cell with no F factor that receives DNA from an F⁺ or Hfr cell.

What is an F′ (F prime) cell?

A donor cell where the F plasmid carries extra bacterial genes from the chromosome.

Which types of cells act as donors in conjugation?

F⁺, Hfr, and F′ cells.

What is a merozygote?

A bacterial cell that has two copies of some genes — one on its chromosome and one on an F′ plasmid, formed after conjugation with an F′ donor.

What happens during Stage 1 of the CRISPR process?

The bacterium captures a piece of viral DNA (spacer) and inserts it into its CRISPR locus.

What happens during Stage 2 of the CRISPR process?

The CRISPR locus is transcribed into pre-crRNA, which is processed into guide crRNAs.

What happens during Stage 3 of the CRISPR process?

The crRNA guides Cas proteins to recognize and cut matching viral DNA during reinfection.

What is the role of Cas proteins (like Cas9)?

They act as molecular scissors that cut viral DNA guided by the crRNA.

What is crRNA?

CRISPR RNA — a short RNA made from the CRISPR locus that guides Cas proteins to recognize and cut matching viral DNA.

What is gRNA (guide RNA)?

A combination of crRNA and tracrRNA that directs Cas9 to the correct DNA sequence.

What happens if the RNA sequence doesn’t match the DNA or lacks a PAM site?

The Cas9-gRNA complex doesn’t cut and moves on to another site.

What happens when Cas9 cuts DNA?

It makes a double-stranded break, which can be repaired to insert, delete, or modify genes.

What happens after Cas9 cuts DNA?

The cell repairs the double-stranded break using either NHEJ or HDR.

What is Non-Homologous End Joining (NHEJ)?

A repair process that ligates broken DNA ends without a template, often causing small insertions or deletions (InDels).

What is Homology-Directed Repair (HDR)?

A precise repair process that uses a donor DNA template to insert or correct a specific sequence.

Which DNA repair mechanism is more error-prone?

NHEJ (Non-Homologous End Joining).

Which repair pathway allows scientists to insert new genes?

HDR (Homology-Directed Repair).

Why is Non-Homologous End Joining (NHEJ) more error-prone?

Because it repairs DNA breaks without using a template, often trimming or adding bases, which leads to small insertions or deletions (InDels).

What happens in the lytic cycle?

The virus actively replicates inside the host and causes the cell to burst (lysis), releasing new viruses.

What happens in the lysogenic cycle?

The viral DNA integrates into the host DNA as a prophage and replicates passively with the host cell.

What is a prophage?

Viral DNA that has been integrated into the host cell’s chromosome.

What can cause a virus in the lysogenic cycle to enter the lytic cycle?

Stress or damage to the host cell (like UV light or weakened immunity).

What is the main difference between a virulent and temperate phage?

Virulent phages only do the lytic cycle, while temperate phages can switch between lysogenic and lytic cycles.

What is a transducing phage?

A virus that accidentally carries bacterial DNA instead of viral DNA.

What happens after a transducing phage infects a new bacterial cell?

The donor DNA can recombine with the recipient’s chromosome, introducing new genes.

What are the two types of transduction?

Generalized transduction (any gene) and specialized transduction (specific genes near the prophage site).

Why is transduction important in genetics?

It allows gene mapping and contributes to bacterial genetic diversity and antibiotic resistance spread.

How do bacteriophages exchange genes?

Through recombination when two phages infect the same bacterial cell

What is a retrovirus?

An RNA virus that uses reverse transcriptase to integrate its DNA copy into the host genome.

Why are retroviruses highly variable?

Reverse transcriptase lacks proofreading, leading to frequent mutations.

What type of genome do retroviruses have?

Two copies of single-stranded RNA.

What is antigenic drift?

Small, gradual mutations in the HA and NA genes that cause yearly flu strain changes.

What is antigenic shift?

A sudden reassortment of genes between different influenza strains, creating a new subtype and potentially causing pandemics.