Microbiology chapter 8 Nester

direct selection

Method of isolating mutants in which cells are inoculated onto an agar medium that supports the growth of the mutants, but not the parent.

Repair of Modified nuecleobases in DNA

Modified nucleobases can result in base substitution if they are not repaid before the DNA is replicated.

Genetic change in bacteria occurs by two mechanisms?

Mutation and horizontal gene transfer.

A knockout mutation results in?

Non functional protein.

Spontaneous mutation happen during?

Normal cell processes and can change the properties of the cell.

A leaky mutation results in?

Partially functional protein.

A change in genotype alter the organisms observable characteristic which is the?

Phenotype. (what you see) But Phenotype can be influenced by environmental conditions.

Repair of thymine Dimers - Bacteria have several mechanisms to prevent the DNA damaging effects of UV light such as sunlight?

Photoreactivation - light is required for this mechanism. An enzyme uses the energy of visible light to break the covlaent bonds of the thymine dimer, restoring the DNA to its original state.

What structures are replicons?

Plasmidds and chromosomes are replicons, but fragments of chromosomal DNA is not.

Conjugative plasmids

Plasmids that transfer during conjugation between donor and recipient cells; the most thoroughly studied example of the F plasmid.

Homologous Recombination

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

DNA polymerases have what type of ability?

Proofreading.

Bacteria have two general means by which they routinely adjust to new circumstances?

Regulating gene expression and genetic change.

Silent mutation

The mutation is referred to as silent because the amino acid sequence of the protein remain unchanged. IE genetic code redundancy means that most amino acids are coded for by more than one codon.

Vertical Gene Transfer

Transfer of genes from parent to offspring

Specialized transduction

Type of transduction that only transfers a few specific genes

Can mutations change an organisms phenotype?

Yes

silent mutation

a base mutation that has a codon that still specifies the wild-type amino acid. No change in the amino acid

Nonsense mutation

a base mutation that occurs when the altered codon is a stop codon, resulting in a shorter and often nonfunctional protein. Often termed null or knockout mutation.

missense mutation

a base mutation that results when the altered codon specifies a different amino acid. This mutation is termed leaky

point mutation

a base mutation where only one base pair is changed

Plasmid

a genetic structure in a cell that can replicate independently of the chromosomes, typically a small circular DNA strand in the cytoplasm of a bacterium or protozoan. Plasmids are much used in the laboratory manipulation of genes.

Frameshift mutation

a mutation in which one or two nucleotide pairs are added or subtracted

non homologous recombination

a process that does not require a similar nucleotide sequence in the region of recombination (like transposons simply insert themselves into a stretch of the DNA)

penicillin enrichment

a technique used before replica plating to increase the proportion of auxotrophs in a broth culture.

Methylation

addition of methyl (CH3) to the cytosine

Deletion or addition of nucleotieds during DNA replication?

also results in spontaneous mutations

mutagen

an agent like a chemical or radiation, that induces mutations

auxotrophy

an inability of an organism to synthesize a particular organic compound required for its growth

Replica Plating

an indirect technique to screen a collection of potential mutants for a trait - looks for auxotrophs

Wild type

an organism of a typical phenotype of strains isolated from nature.

Prototroph

an organism or cell capable of synthesizing all its metabolites from inorganic material requiring no organic nutrients

recombinant

any organism that contains and expresses genes that originated in another organism

Spontaneous mutations

are genetic changes that result from normal cell processes. They occur randomly, and genes mutate spontaneously at infrequent but characteristic rates.

Genomic islands

are large DNA segments in a cells genome that orginated in other species.

Plasmids

are replicons that code for non essential information; many are readily transferred by conjugation. R plasmids code for anitbiotic resistance.

transduction

bacterial viruses, called bacteriophages, or simply phages, can transfer bacterial genes from a donor to a recipient by ____________.

SOS repair

is last effort attempt that bacteria use to repair extensively damaged DNA. the enzyme that carry out this repair are induced when DNA is so heavily damaged by UV light that photoreactivation and excision repair may not be able to correct all the damage.

Transduction

is the process by which DNA is transferred from one bacterium to another by a virus . It also refers to the process whereby foreign DNA is introduced into another cell via a viral vector.

Transposons can?

jump from one location to another in a cells genome.

Transposons

jumping genes. Segments of DNA that can move from one location to another in a cell's genome

photoreactivation

light repair; an enzyme uses the energy of visible light to break the covalent bonds of the thymine dimer

indirect selection

method for an auxotroph isolation fro a prototrphic parent strain. Example is replica planting.

Mutagens increase the frequency of

mutations.

Thymine dimers can be repaired through?

photoreactivation and excision repair;

conjugative plasmids

plasmids that can direct their own transfer from donor to recipient cells (example is F plasmid)

Resistance plasmids

plasmids that encode resistance to many different antimicrobial medications and heavy metals, such as mercury and arsentic, all of which are found in hospital environments

Mismatched repair fixes errors missed by?

proofreading mechanism; methlyation distinguishes the template strand.

transposons

provide mechanism for transferring various genes by moving into other replicons in the same cell without any specificity as to where they insert

Generalized transduction

results from a rare error that sometimes occurs during the construction of phage particles.

f pilus

sex pilus of the F+ e. coli cells

Base Substitutions Outcomes include

silent, missense, and nonsense mutations.

Base subsitutions that occur during DNA synthesis can lead to?

sillent, missense, and nonsend mutations.

Hfr cells

strains of bacteria where f plasmid has integrated into the chromosome by homologous recombination; high frequency of recombination cells

Hfr cells

strains of bacteria which have F plasmid integrated into the chromosome by homologous recombination

Base analog

structurally resemble nucleobases but have different hydrogen-bonding properties.

Severe damage can be overcome by?

the SOS repair system

Frame shift Mutation as a Result of Nucleotide Addition.

the addition of a nucleotide pair to the DNA results in a shift in the reading freame when the sequence is transcibed and translated. Deletion of a single nucletide pair in the DNA would have a similar effect

A phage infects a bacterium by attaching to?

the cell and then injecting its nucleic acid into that cell

core genome

the conserved genes of a particular species

Core genome

the conserved genes of a species

Base subtitution

the most common type of mutation occurs during DNA synthesis when an incorrect nucleotide is incorporated.

base substitution

the most common type of spontaneous mutation; occurs during DNA synthesis and involves an incorrect nucleotide incorporated into the sequence

Phenotype

the observed characteristic of a cell

Genotype

the sequence of nucleotides in the DNA of an organism

Proofreading

the verification of its own actions by DNA pol

Following a gene transfer, recipient cells must replicate the DNA to pass it on to daughter cells.

this can happen only if DNA is a Replicon

The properties of Bacteria can change either?

through mutation of horzontal gene transfer.

Generalized transduction

transduction that results from a rare error that sometimes occurs during the construction of phage particles. The product is called a trasducing particle.

Both plasmid and chromosomal DNa ca be?

transferred

composite trasposons

transposons that consist of one or more genes flanked by Insertion sequences. Integrate into their new location through non-homologous recombination

composite transposons

transposons that consist of one or more genes flanked by insertion sequence.

Insertion sequence

type of a transposon that encodes only the enzyme responsible for transposition, called transposase.

fertility plasmid

type of conjugative plasmid that encodes only characteristics needed for the transfer, including the sex pilus.

x Ray

type of radiation that causes single and double-stranded breaks in the DNA

Ultraviolet light

type of radiation that causes thymine dimers

Insertion Sequence

type of transposons that encodes only the enzyme responsible for transposition, called transposase.

Specialized transduction

when a DNA from a specific region of the host chromosome is integrated directly into the virus genome

Replicon

when the DNA has an origin of replication so it can pass on the genes to the daughter cells.

Competent

when the recipient cell is ______________, it is in a specific physiological state that allows the cell to take up DNA

The Ames test is used to screen chemicals to determine?

which one are possible carcinogens.

McClintock

who discovered transposons while working with corn?

Removing or adding nucleotides can cause?

Frameshift Mutations

Example of horizontal gene transfer

Fungal genes have been found in an aphids DNA

What can remove modified nucleobases?

Glycosylases

Competence

In order for transformation to occur, the recipient cells must be competent. It is a specific physiological state that allows the cell to take up DNA.

Mobile Gene pool

Includes plasmids, tranposons, genomic islands, and phage DNA.

Replica plating is used for?

Indirect selection, sometimes preceded by penicillin enrichment.

Cells can not repair all types of mutations, such as?

Insertions inactivation caused by transposition.

A change in an organisms DNA alters?

It's genotype - the sequence of nucleotides in the DNA.

Genomic Islands

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

DNA Mediated Transformation

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

conjugation

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

Transduction

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

MRSA

Methicillin resistant S. aureus developed all resistance to all penicillin derivatives. Vancomycin is normally used for infections, but as a last resort.

Formation of tranducing particle

1. A bacteriophage attaches to a specific receptor on a host cell. 2. The phage DNA enter the cell. The empty phage coat remains on the outside of bacterium. 3.Enzymes encoded by the phage genome cut the bacterial DNA into small pieces. 4.Phage nucleic acid is replicated and coat proteins synthesized. 5. During construction of viral particles, bacterial DNA can mistakenly enter a protein coat. this creates a transducing particle that carries bacterial DNA instead of phage DNA

Genes can be transferred from a donor to a recipient by three different mechanisms.

1. DNA mediated transformation - naked DNA is taken up from the environment by a bacterial cell. 2. Transduction: DNA is tranferred from one bacterial cell to another by a bacteriophage (a virus that infects bacteria) 3. Conjugation: DNA is transferred furing cell to cell contact.

DNA mediated Transformation Process

1. Double stranded DNA bin to the surface of a competent cell 2. Single strand enters the cell; the other strand is degraded. 3.The strand integrates into the recipient cells genome by homologous recombination. The strand it replaced will be degraded. 4.After replicating the DNA, the cell divides. 5. Non transformed cell die on streptomycin containing medium whereas transformed cell can multiply.

Conjugation F plasmid transfer

1. making contact - The F pilus of the donor cell binds to a specific receptor on the cell wall of the recipient. 2. Initiating transfer - after contact the F pilus retracts pulling the two cells together. A plasmid encoded enzyme cuts one strand of the plasmid at the specific nucleotide sequence, the origin of transfer. 3. Transferring DNA - a single strand of the F plasmid enter the F- cell. Once inside the recipent cell, the strand serves as a template for synthesis of the complementary strand, generating an F plasmid. 4.Transfer complete - both the donor and recipient cells are now F+ so they can act as donor of the F plasmid.

Every 24 hrs the genome of every cell in the human bod is damaged more than?

10,000 times

Staphlyococcus aureus

A gram positive coccus commonly called staph. It is a frequent cause of skin and wound infection. It was once treated with penicilin but some straing gained ability to destroy that antibiotic.

E. coli strain..

A wild type and a prototroph

Plasmid

An extrachromosomal DNA molecule that replicates independently of the chromosome.

Chemicals that modify Nucleobases

An umber of different chemicals modify the nucleobases in DNA, changing their base pairing properties.

Null or knockout mutation

Any mutation that totally inactivates the gene.

Transduction is the transfer of?

Bacterial DNA from one cell to another by the means of bacteriophage. It results form an error that occurs during the infection cycle of the bactriophage.

Why can a change have a significant impact on bateria?

Because bacteria are haploid, meaning they contain only a single set of genes.

Competent cells do what?

Bind DNA and take up single strand; that strand then integrates into the genome by homologous recombination.

What other structures can transfer DNA through conjugation?

Both plasmid DNA and Chromosomal DNA

In DNA mediated transformation

DNA is released from donor cells and taken up by competent recipient cells.

What are the two mechanisms that are used for "proofreading"?

DNA polymerase and mismatch repair

Repair of errors in nucleotide incorporation

DNA polymerase sometimes incorporates the wrong nucleotide as its replicates DNA. Resulting mispairing of nucleobases result in in a slight distortion in the DNA helix which can be recongnized by enzymes within the cell that then repair the mistake. By quickly repairing the error before the DNA is replicated, the cell prevents the mutation.

Proofreading by DNA polymerase

DNA polymerases are complex enzymes that not only synthesize DNA, but also check the accuracy of their actions. The process called proofreading

Non-Homologous Recombination

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

Conjugation requires contact between donor and recipient cells. A donor cell that synthesizes an F pilus transfers the?

DNA to one that does not.

Horizontal Gene Transfer

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

Some bacteria have an enzyme that recognizes the major distortions in DNA that result from thymine dimer formation.

Excision Repair - the enzyme removes the DNA strand with the damaged region.

Mismatch repair

Fixes errors missed by the proofreading of mismatched nucleobase, directing an enzyme to cut the sugar phosphate backbone of the new DNA strand. A short stretch of that strand is then degraded and DNA polymerase synthesizes a replacement.

Carcinogen

cancer generating chemicals

Mutation

changes the existing nucleotide sequence of a cells DNA, which is then passed on to the progen (daughter cells) through vertical gene transfer.

Following transfer, plasmids replicate, but?

chromosomal DNA must be integrated into a replicon to replicate.

Homologous Recombination

chromosomal fragement is transferred then it must become intergraed into replicon to be maintain in a population.

DNA-Mediated Transformation

commonly referred to as transformation involves the uptake of naked DNA by recipient cells. Naked DNA is DNA that is free in the cells surroundings. Not contained with in a cell or virus.

conjugation

complex process of DNA transfer that requires contact between donor and recipient cells.

Thymine dimers

covalent bonds between adjacent thymine molecules on a DNA strand, which distorts DNA strand, and replication and transcription is stalled at these distortions.

excision repair

dark repair; enzyme makes single-stranded cuts that flank both sides of the damaged region to remove the strand with the thymine dimer.

Mutants can be either selected in either?

direct or indirect techniques.

F plasmid

fertility plasmid of E. coli

intercalating agent

flat molecules that can insert themselves between adjacent base pairs in a strand of DNA and increase the frequency of frameshift mutations. Example - ethidium bromide

mobile gene pool

genes that can move from one DNA molecule to another, and are carried on mobile genetic elements including various plasmids, transposons, regions called genomic islands, and phage DNA.

Induced mutations

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

spontaneous mutations

genetic changes that result from normal cell process and occur randomly

pathogenicity islands

genomic islands that encode the ability to cause disease.

Intercalating Agents

increase the frequency of framshift mutations.

In human defects either mismatch repair or repair of modified nucleobases?

increase the incidence of certain cancers

Some chemical mutagen cause base substitution, but?

intercalating agents cause framshift mutations.

Conjugation

is a complex process that requires contact between donor and recipient bacterial cells. Gram positive and gram negative bacteria can both transfer DNA this way.