Micro Ch. 8: Bacterial Genetics

How do eukaryotes generate genetic diversity?

sexual reproduction

diploid vs. haploid

combination of genetic material between members of a species

How do prokaryotes generate genetic diversity?

reproduction by binary fission

spontaneous mutations

gene transfer

what is a mutation

any change in a nucleotide or nucleotide sequence

what is a wild type mutation

most common, or naturally occurring form of a gene, trait, genotype, or phenotype in a population

What is a genotype

an individual's complete set of genetic material

What is a phenotype

the set of observable characteristics or physical traits of an organism

What is a silent mutation

a mutation that does not affect the phenotype

What is a auxotroph

an organism that cannot synthesize a specific organic compound required for its own growth

What is a prototroph

a microorganism that can synthesize all the essential organic compounds it needs for growth

What is a spontaneous mutation

mutation that occurs naturally in the absence of mutagens

How do spontaneous mutations occur?

errors during replication

transposable elements

What types of mutations occur spontaneously?

base substitution

addition/removal of nucleotides

insertion mutation

what is an induced mutation

sudden change in a DNA sequence caused by exposure to a mutagen

what is a frameshift mutation

an addition/subtraction of nucleotides

What is the effect of adding or subtracting 1 or 2 nucleotides during DNA replication?

frameshift mutation

What effect does this type of mutation have on the gene product

A frameshift mutation changes how the genetic code is read, usually resulting in a nonfunctional, shortened, or completely altered protein

What is the effect of adding or subtracting 3 contiguous nucleotides during DNA replication?

adds or removes 1 codon

What is the effect of adding or subtracting 3 non-contiguous nucleotides?

a frameshift mutation between first and third addition or deletion

original reading frame re-established after third

what is a transposable element

also known as jumping genes or mobile genetic elements

are specific sequences of DNA that can change their position within a genome

What type(s) of mutation(s) are caused by transposable elements?

Insertion mutations

Knockout mutations

What are the effects of these mutations on the gene product?

Disrupts the coding region of the gene

Why can mutations caused by transposons be classified as either spontaneous or induced?

Transposon mutations can be both because they can jump on their own or be forced to jump by outside stress.

• Spontaneous: They copy and paste themselves into new DNA spots during normal cell life, with no outside help.

• Induced: Outside stressors shock the cell, causing the transposons to jump much faster than usual.

what is a point mutation

a genetic change where only one single nucleotide base in a DNA or RNA sequence is substituted

What are the three types of mutations that can occur as a result of a point mutation that results in a base substitution?

silent mutation

missense mutation

nonsense mutation

What are the potential consequences of a silent mutation on the functioning of the gene product and the survival of the cell/organism?

base change that does not result in a change in the amino acid sequence

no effect on amino acid function

What are the potential consequences of a missense mutation on the functioning of the gene product and the survival of the cell/organism?

base change that results in a codon coding for a different amino acid

changes function of amino acid

What are the potential consequences of a nonsense mutation on the functioning of the gene product and the survival of the cell/organism?

base change that results in a codon for an amino acid changing to a stop codon

changes structure and function of protein/amino acid

Diagram the process by which a base substitution error during DNA replication can become a permanent mutation

Step 1: Normal DNA: Mistake during copying

Step 2: The Mismatch: Temporary Error

• DNA copies one more time without fixing it

Step 3: Locked In: Permanent Mutation

• It looks perfectly normal to the cell.

• It can never be fixed.

What is the Base analog induced mutation (AZT)

A base analog is a chemical "imposter" that looks like a normal DNA letter, fooling the cell into using it.

AZT is a famous imposter chemical used as a medicine to fight HIV. It looks just like the DNA letter T.

Chemical modification of bases

Chemical modification of bases is when a chemical changes a DNA letter that is already sitting in your DNA.

many carcinogens chemically modify bases

Intercalating agents (ethidium bromide)

Intercalating agents are flat chemicals that wedge themselves directly between the base pairs
Ethidium bromide is a famous example

Transposons

Transposons are segments of DNA that can move from one location to another within a genome.

Used to create gene knockouts

UV radiation

Thymine dimers

Dimers can’t be read properly by DNA/RNA polymerase
Base substitutions

X-rays

Higher energy than UV radiation

Single and double stranded breaks in DNA

Often result in lethal deletion mutations

Proofreading by DNA polymerase

The DNA polymerase removes the mispaired nucleotide and replaces it with the correct one

Mismatch repair

A protein binds to the site of the mismatch and cuts the unmethylated strand

A short stretch of that strand is then degrated and a DNA polymerase synthesizes a replacement

Dark repair (nucleotide excision repair)

An enzyme removes a short stretch of the strand containing the thymine dimer
A DNA polymerase then synthesizes a replacement

What type of mutation is repaired by dark repair?

UV light mutation
Thymine dimer defect

What human disease is a result in defects in dark repair?

Xeroderma pigmentosum:

extreme sun sensitivity

Caused by a broken dark repair system

Light repair (photoreactivation)

The energy of light is used to break the covalent bond between tne thymine nucleobases restoring the original molecule

What enzyme is associated with light repair and how does it become activated and how does it function?

Photolyase

When visible blue light from the sun hits the cell, the enzyme absorbs it.

The charged enzyme shoots a high-energy electron directly into the fused Thymine letters.

This burst of energy breaks the bad bond, forcing the two letters to snap back into their normal, separate shapes.

The DNA ladder is instantly fixed without cutting or replacing any pieces.

What types of organisms can perform light repair?

All organisms

What is the difference between horizontal and vertical transmission of genes in bacteria?

horizontal: one cell to another

vertical: parent to daughter cells

What are the mechanisms by which horizontal transmission can occur?

DNA-mediated transformation

Transduction

Conjugation

Describe the mechanism by which DNA mediated transformation occurs.

The uptake of exogenous DNA (“naked” DNA)

What are the requirements for DNA mediated transformation?

The cell must be competent in order to undergo transformation

• natural competence

• artificial competence

In what types of bacteria can this occur?

Gram positive and gram negative are naturally competent

What are the two types of transduction and what is used to transfer DNA during transduction?

Generalized transduction

Specialized transduction

• Bacteriophage used to transfer DNA

What types of genes can be transferred during both types of transduction?

Any gene in generalized

Only specific genes in specialized

Describe the mechanism by which generalized transduction occurs.

1. A transducing particle attatches to a specific receptor on a host cell

2. The bacterial DNA is injected into the cell

3. The injected DNA integrates into the chromosome by homologous recombination

4. Bacteria multiply with new genetic material, replaced host cell is degraded

What is conjugation and what are the requirements for conjugation to take place?

transfer of DNA from one bacterial cell to another requiring direct contact

In what types of bacteria can conjugation take place?

Gram negative and Gram positive

In what types of bacteria can conjugation using the F pilus occur?

Gram negative bacteria

Describe the mechanism by which conjugation occurs between an F+ cell and an F- cell

1. The F pilus contacts the recipient F- cell

2. The pilus retracts and pulls the donor and recipient cells together

3. A single strand of the F plasmid is transferred to the recipient cell

   1. its complement is synthesized as it enters the cell.

   2. The strand transferred by the donor is replaced using the remaining strand as a template for DNA synthesis

4. At the end of the transfer process, both the donor and recipient cells are F+ and synthesize the F pilus

What is the difference between an F+ cell and an Hfr cell?

An F+ cell has the F plasmid floating freely, while an Hfr cell has the F plasmid integrated directly into its main chromosome.

What is the difference between the types of genes that can be transferred by F+ cells and Hfr cells?

F+ cell transfers the plasmid only, turning the recipient into an F+ cell.

Hfr cell transfers chromosomal DNA, leaving the recipient as an F- cell.

Describe the mechanism by which Hfr conjugation occurs.

1. The F pilus contacts the F- cell

2. A single strand of the donor chromosome begins to be transferred, starting at the origin of transfer

   1. Gene A, closest to the origin, is transferred first

   2. DNA synthesis creates complementary strands in both cells

3. The donor and recipient cells separate, interrupting DNA transfer

4. The donor DNA is integrated into the recipient cell’s chromosome by homologous recombination

   1. Unincorporated DNA is degraded

   2. The recipient cell is still F-

list and describe the characteristics of plasmids and explain the functioning of the features of plasmids.

Circular, double stranded DNA

Replicate independently of chromosomal DNA

Carry a few to several hundred genes

What types of genes can be carried on plasmids?

non-essential genes

How are plasmids transferred from cell to cell?

Transferred through conjugation, transformation in the lab

What types of genes are found on R plasmids?

Carbenicillin-resistance gene

Chloramphenicol-resistance gene

Tetracycline-resistance gene

Pilus-synthesis gene

Be able to describe the features and the functions of the features of a transposon

(transposable element)

Inverted repeats: They tell the enzyme exactly where the transposon starts and stops so it can be sliced out of the genome cleanly.

Transposase gene: grabs onto the inverted repeats, cuts the transposon out of its old spot, and inserts it into a new target spot in the DNA.

How can transposons move both within a cell and between cells?

Within a Cell (Jumping):

• uses its own transposase gene to make a cutting enzyme

• This enzyme slices the transposon out of its original location on DNA and glues it into a new spot on the chromosome or onto a nearby plasmid.

Between Cells (Hitchhiking):

• The transposon jumps into a plasmid. The plasmid moves into a neighboring cell through conjugation

Describe the importance of gene transfer in bacteria from a bacterial perspective

Genetic variation

Adaptation to changing environments

Describe the importance of gene transfer in bacteria from a human perspective

Spread of antibiotic resistance genes

Transfer of virulence factors

Describe how the CRISPR system functions

1. Fragments of invading DNA are captured and then integrated into CRISPR array in cells genome

   1. a Cas protein complex cuts invading DNA into fragments

2. CRISPR array is transcribed and the RNA is processed to generate crRNAs that bind to a Cas nuclease to form a complex

3. crRNA-guided Cas nuclease degrades invading DNA

What is the function of the CRISPR system in bacteria?

The CRISPR system functions as a bacterial immune system that defends bacteria against attacking viruses (bacteriophages).

It works like an immune memory card and a pair of programmed scissors

How can CRISPR potentially be used to treat diseases in humans?

CRISPR can potentially treat human diseases by directly correcting faulty DNA instructions inside living cells, offering a permanent cure for genetic conditions rather than just managing their symptoms.

Scientists use CRISPR as a molecular "find-and-replace" tool to treat human diseases