Microbiology chapter 8 Nester

Auxtroph

A microorganism that requires an organic growth factor

conjugation

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

DNA Mediated Transformation

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

Genotype

the sequence of nucleotide is an organisms DNA

Homologous Recombination

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

Horizontal Gene Transfer

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

Mutation

a change in the nucleotide seques of a cells DNA that passed on to daghter cells.

Non-Homologous Recombination

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

Phenotype

the observed characteristic of a cell

Plasmid

An extrachromosomal DNA molecule that replicates independently of the chromosome.

Prototroph

A mircoorganism that does not require any organic growth factors.

Transduction

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

Transposon

Segment of DNA that can move from one site to another in a cells genome.

Vertical Gene Transfer

Transfer of genes from parent to offspring

Wild Type

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

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.

MRSA

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

Natural Selection

Orangisms need to adapt in order to survive and mulitply. If they fail to do this, competing orgainisms 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.

A change in an organisms DNA alters?

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

Why can a change have a significant impact on bateria?

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

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

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

Genetic change in bacteria occurs by two mechanisms?

Mutation and horizontal gene transfer.

Mutation

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

Horizontal gene transfer

is the moviemnt of DNA from one organism to another. changes are then passed on to progeny through vertical transfer.

The properties of Bacteria can change either?

through mutation of horzontal gene transfer.

Can mutations change an organisms phenotype?

Yes

Auxtroph

A mutant that requires a growth factor

Prototroph

Does not require growth factors

E. coli strain..

A wild type and a prototroph

Spontaneous mutations

are genetic changes that result from normal cell processes.

They occur randomly, and genes mutate spontaneously at infrequent but characteristic rates.

Base subtitution

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

Base subsitutuion

A replication error results in a mismatch bewteen the two DNA strand. Subsequent DNA replication using the altered strand as template results in a point mutation.

Base Substitutions Outcomes include

silent, missense, and nonsense mutations.

Point Mutation

Only one base pair is changed the mutation is called a point mutation.

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.

Missense mutation

results when the altered codon codes for a different amino acid. The effects depends on the positon and nature of the change.

Nonsense Mutation

occurs when the base substitution creates a stop codon, resulting in a shorter and often non functional protein.

Null or knockout mutation

Any mutation that totally inactivates the gene.

Deletion or addition of nucleotieds during DNA replication?

also results in spontaneous mutations

Framshift Mutation

adding or sutracting one or two nucleotides pair.

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

Transposons

are pieces of DNA that can move from one location to another in a cells genome, a process called transposition.

Spontaneous mutation happen during?

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

A leaky mutation results in?

Partially functional protein.

A knockout mutation results in?

Non functional protein.

Base subsitutions that occur during DNA synthesis can lead to?

sillent, missense, and nonsend mutations.

Removing or adding nucleotides can cause?

Frameshift Mutations

Transposons can?

jump from one location to another in a cells genome.

Chemical Mutagens

Some chemical mutagens cause base substitutions and others cause frameshift mutations.

Chemicals that modify Nucleobases

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

Base analogs

structurally resemble nucleobases but have different hydrogen bonding properties.

Intercalating Agents

increase the frequency of framshift mutations.

Mutagens increase the frequency of

mutations.

Some chemical mutagen cause base substitution, but?

intercalating agents cause framshift mutations.

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

Insertions inactivation caused by transposition.

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

10,000 times

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.

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

DNA polymerase and mismatch repair

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

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.

Repair of Modified nuecleobases in DNA

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

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

increase the incidence of certain cancers

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.

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.

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.

DNA polymerases have what type of ability?

Proofreading.

Mismatched repair fixes errors missed by?

proofreading mechanism; methlyation distinguishes the template strand.

What can remove modified nucleobases?

Glycosylases

Thymine dimers can be repaired through?

photoreactivation and excision repair;

Severe damage can be overcome by?

the SOS repair system

Direct Selection

Mutants that can grow under conditions in which the parent cells cannot are usually easy to isolate by directe selectionl

Indirect selection

indirect selection is used to isolate an auxotrophic mutant from the prototrophic parent strain.

Replica plating

Replica plating is a clever method for indirect selection of auxotrophic mutants.

Penicillin Enrichment of mutants

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

Mutants can be either selected in either?

direct or indirect techniques.

Replica plating is used for?

Indirect selection, sometimes preceded by penicillin enrichment.

The Ames test is used to screen chemicals to determine?

which one are possible carcinogens.

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.

What is 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.

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

Replicon

meaning it has an origin of replication.

What structures are replicons?

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

Homologous Recombination

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

Example of horizontal gene transfer

Fungal genes have been found in an aphids DNA

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.

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.

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.

In DNA mediated transformation

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

Competent cells do what?

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

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.

Bacterial viruses (phages) can transfer bacterial genes from a donor to a recipient by transduction.

A phage infects a bacterium by attaching to?

the cell and then injecting its nucleic acid into that cell

Generalized transduction

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

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

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.

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.

What other structures can transfer DNA through conjugation?

Both plasmid DNA and Chromosomal DNA

Plasmid transfer

are most frequently transferred to another cells by conjugation. These DNA molecules are replicons.

Conjugative plasmids

direct their own transfer from donor to recipient cells. the most thoroughly studied example of the F plasmid.

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.