Chapter 8 Bacterial Genetics

Adding or subtracting one or two nucleotide pairs -This changes the reading frame of the corresponding mRNA molecule so that an entirely different set of codons is translated. -As a consequence, it likely results in a shortened, non-functional protein--a knockout mutation

Frameshift mutation

Any gene can be transferred -Results from a rare error that sometimes occurs during the construction of phage particles

Generalized transduction

Importance of Gene Transfer-Bacteria Perspective

Genetic Variation Adaptation to changing environments

large DNA segments in a cell's genome that originated in other species

Genomic Islands

-Large DNA segments in a cell's genome that originated in other species

Genomic islands

Chromosomal DNA transfer. -F plasmid integrates into chromosome so then whole chromosome acts as F plasmid -F' (prime): when F plasmid and chromosome get deintegrated and some post chromosome comes out with F plasmid (its imperfect)

Hfr conjugation (high frequency recombination)

Process by which a cell replaces a stretch of DNA with a segment that has a similar nucleotide sequence.

Homologous Recombination

DNA transfer from one bacterium to another by conjugation, DNA-mediated transformation, or transduction.

Horizontal Gene Transfer

New strands are not methylated but old ones are so they have methyl groups on them

How can they tell which is old/new?

Happens in newly synthesized strand

How does mismatch repair know which is the correct strand?

Ames test

How to know if it is a carcinogen?

Are genetic changes that occur due to an influence outside of a cell, such as exposure to a chemical or radiation.

Induced mutations

Is required in order for cell exchange in Gram-negative

Sex pilus

Only specific genes can be transferred

Specialized Transduction

mutations that occur naturally in the absence of mutagens

Spontaneous Mutations

Importance of Gene Transfer-Human Perspective

Spread of antibiotic resistance genes Transfer of virulence factors

DNA is transferred from one bacterial cell to another by a bacteriophage (a virus that infects bacteria)

Transduction

Mechanism of horizontal gene transfer in which bacterial DNA is transferred inside a phage coat.

Transduction

Transfer of bacterial DNA via bacteriophage

Transduction

transfer of bacterial DNA via bacteriophage

Transduction

Naked DNA transferred

Transformation

-or jumping genes, are pieces of DNA that can move from one location to another in a cell's genome, a process called transposition -Segment of DNA that can move from one site to another in a cell's genome.

Transposon

Transfer of genes from parent to offspring.

Vertical Gene Transfer

HIGHLY specific

Viruses

Plasmids, phage DNA, some transposons, etc.

What can transfer?

Any change in a nucleotide or nucleotide sequence. -only happen at DNA level

What is a mutation?

Form of the cell or gene as it typically occurs in nature.

Wild Type

In Gram negative bacteria

a donor cell transfers DNA to a recipient cell (sex pilus)

transferred through

conjugation, transformation

replicate

independently of chromosomal DNA

An agent that induces the change

mutagen

Specialized Tranduction

only specific genes can be transferred

Point at which molecules bind and cut double stranded DNA, and new cells goes to recipient

origin of transfer

How do spontaneous mutations occur?

Errors during Replication. (1)Base substitution (2)addition/removal of nucleotides Transposable elements (1) insertion mutation

Doesn't have F plasmid and cannot make pilus

F-

If only one base pair is changed

Point mutation

A microorganism that does not require any organic growth factors.

Prototroph

Two kinds are commonly used as mutagens: ultraviolet (UV) light and X rays -Irradiation of cells with ultraviolet light causes covalent bonds to form between adjacent thymine molecules on a DNA strand, producing thymine dimers. The dimer cannot fit properly into the double helix, distorting the DNA molecule. UV causes mutations indirectly, its major mutagenic action results from the cell's attempt to repair the damage by SOS repair -X rays cause single- and double-strand in DNA, and changes to the nucleobases. Double-strand breaks often result in deletions that are lethal to the cell

Radiation

Is a clever method for indirect selection of auxotrophic mutants, devised by Joshua and Esther Lederberg in the early 1950s. In this technique, the bacterial culture is first spread onto a nutrient agar plate.

Replica plating

Origin of replication

Replicon

A microorganism that requires an organic growth factor.

Auxotroph

Structurally resemble nucleobases but have different hydrogen-bonding properties. The analogs can be mistakenly used in place of the nucleobases when nucleotides are made, and DNA polymerase then incorporates these into DNA. When a DNA strand has a base analog, the wrong nucleotide can be incorporated as the complementary strand is synthesized

Base analogs

The most common type of mutation, occurs during DNA synthesis when an incorrect nucleotide is incorporated

Base substitution

DNA gets replicated by each daughter cell gets generated

Binary fission

Cause cancer -Ex. phenol

Carcinogenic

Cell-to-Cell contact required; only Hfr cells can be donors

Chromosome Transfer

A specific physiological state that allows the cells to take up DNA

Competent

DNA is transferred during cell-to-cell contact

Conjugation

Mechanism of horizontal gene transfer in which the donor cell physically contacts the recipient cell.

Conjugation

transfer of DNA requiring cell to cell contact

Conjugation

Mechanism of horizontal gene transfer in which the bacterial DNA is transferred as "naked" DNA.

DNA-Mediated Transformation

Ability to transfer F plasmid

Donor cell- F+

Increase the frequency of frameshift mutations. They do this because they are flat molecules that can insert (intercalate) between adjacent base pairs in a strand of DNA. This pushes the nucleotides apart, producing a space between bases that allows errors to be made during replication. -If the ____ inserts into the template strand, a base pair will be added as the new strand is synthesized. If it intercalates into the strand being synthesized, a base pair will be deleted

Intercalating agents

Fixes errors missed by the proofreading of DNA polymerase. A specific protein binds to the site of the mismatch nucleobase, directing an enzyme to cut the sugar-phosphate backbone of the new DNA strand.

Mismatch repair

Base change results in a codon coding for a different amino acid -consequences of missense mutations

Missense Mutation

Mobile genetic elements

Move between organisms and within a single chromosome, "jumping genes"

A change in the nucleotide sequence of a cell's DNA that is passed on to daughter cells.

Mutation

In the ever-changing conditions that characterize most environments, all organisms need to adapt in order to survive and multiply. If they fail to do this, competing organisms more "fit" to thrive in the new setting will soon predominate. -Bacteria have two general means by which they routinely adjust to new circumstances; regulating gene expression and genetic change

Natural selection

DNA recombination that does not require extensive nucleotide sequence similarity in the stretches that recombine

Non-Homologous Recombination

Occurs when the base substitution creates a stop codon, resulting in a shorter (truncated) and often non-functional protein

Nonsense Mutation

Genomic islands that encode the ability to cause disease

Pathogenicity Islands

Generalized Transduction

any gene can be transferred

Transfer of DNA requiring cell to cell contact -Can occur in both Gram positive and Gram negative bacteria -In gram negative bacteria, a donor cell (F+) transfers DNA to a recipient cell (F-) -Sex pilus (F plus) -Complex process that requires contact between donor and recipient bacterial cells. Gram positive and gram negative bacteria can both transfer DNA this way, but the process is quite different in the two groups

Conjugation

Happens only if the donor DNA is similar in nucleotide sequence to a region in the recipient cells' genome. -the donor DNA becomes positioned next to the complementary region of the recipient cell's DNA

Homologous recombination

"Naked" DNA is taken up from the environment by a bacterial cell

DNA-mediated transformation

Mutants that can grow under conditions in which the parent cells cannot are usually easy to isolate by____ **Cells are inoculated onto an agar medium that supports the growth of the mutant, bu does not allow the parent to grow. Ex) antibiotic-resistant mutants can be easily selected directly by inoculating cells onto a medium containing the antibiotic

Direct Selection

Insertion Mutation

Disrupts coding region of gene, knockout mutation

Generation of diversity in eukaryotes: -Sexual reproduction -Diploid vs haploid -Combination of genetic material between members of a species Generation of diversity in prokaryotes: -Reproduction by binary fission -Spontaneous mutations -Gene transfer

Diversity in Bacteria

Doesn't allow bridge to close so it is one way

Exclusion protein

The sequence of nucleotides in an organism's DNA.

Genotype

Is used to isolate an auxotrophic mutant from a prototrophic parent strain

Indirect Selection

Is sometimes used before replica plating to increase the proportion of auxotrophs in a broth culture. this is helpful because even when mutagenic agents are used, the frequency of mutations in a particular gene is low, sometimes less than one in 100 million cells. -It relies on the fact that penicillin kills only growing cells

Penicillin enrichment

Only affect prokaryotic bacteria -Bacterial viruses -Can transfer bacterial genes from a donor to a recipient by transduction (generalize & specialized)

Phage

The observed characteristics of a cell. -a change in genotype often alters the organism's observable characteristics -It can be influenced by environmental conditions

Phenotype

An extrachromosomal DNA molecule that replicates independently of the chromosome.

Plasmid

-Double-stranded DNA (cccDNA) -Replicate independently of chromosomal DNA (1) origin of replication (2)Low-copy- number plasmid (3)High copy number plasmid -Vary in size (1) non-essential -Transferred through conjugation, transformation -Usually narrow transfer range

Plasmids

circular double-stranded DNA replicon; smaller than chromosomes

Plasmids

Results when the altered codon codes for a different amino acid -Changes in DNA sequence

Silent Mutation