Chapter 8 - Microbial Genetics

DNA: 3' A T A T _ _ _ T T T _ _ _ _ _ _ _ _ _ mRNA: C G U UGA tRNA: UGG Amino Acid: Met_____________________ What would be the effect if G were substituted for T at base 14?

Proline substituted for threonine (missense mutation)

DNA: 3' A T A T _ _ _ T T T _ _ _ _ _ _ _ _ _ mRNA: C G U UGA tRNA: UGG Amino Acid: Met_____________________ Identify a nonsense sequence in this strand of DNA.

ACT

DNA: 3' A T A T _ _ _ T T T _ _ _ _ _ _ _ _ _ mRNA: C G U UGA tRNA: UGG Amino Acid: Met_____________________ Fill in the blank of the complete segment of DNA

ATATTACTTTGCATGGACT

Which sequence is the best target for damage by UV radiation: AGGCAA; CTTTGA; or GUAAAU? Why aren't all bacteria killed when they are exposed to sunlight?

CTTTGA. Endospores and pigments offer protection against UV radiation. Additionally, repair mechanisms can remove and replace thymine polymers.

Mechanism by which the presence of glucose inhibits the LAC operon

Catabolite repression

Ciprofloxacin, erythromycin and acyclovir are used to treat microbial infections. Ciprofloxacin inhibits DNA gyrase. Erythromycin binds in from of the A site on the 50S subunit of a ribosome. Acyclovir is a guanine analog. What steps in protein synthesis are inhibited by each drug?

Ciprofloxacin inhibits transcription > helicase grinds to a halt > can't make mRNA (need to relieve torsional strain resulting from unravelling DNA strands) > no template for protein synthesis erythromycin inhibits translation > EF-tu-tRNA-aa complex can't enter A site of ribosome > initiation/elongation can't occur > mRNA cannot be translated acyclovir inhibits transcription > acyclovir incorporated into mRNA strand > no phosphate group available on acyclovir to perform attack on incoming nucleotide (in other words no elongation for transcription)

DNA: 3' A T A T _ _ _ T T T _ _ _ _ _ _ _ _ _ mRNA: C G U UGA tRNA: UGG Amino Acid: Met_____________________ What would be the effect if A were substituted for G at base 11?

Cysteine substituted for arginine

DNA: 3' A T A T _ _ _ T T T _ _ _ _ _ _ _ _ _ mRNA: C G U UGA tRNA: UGG Amino Acid: Met_____________________ Write the code for the complementary strand of DNA completed [part A]

TATAATGAAACGTTCCTGA

Repressor inactive, operon on.

When the inducer allolactose binds to the repressor protein, the inactivated repressor can no longer block transcription. The structural genes are transcribed, ultimately resulting in the production of the enzymes needed for lactose catabolism.

Two offspring cells are most likely to inherit which one of the following from the parent cell? a). a change in a nucleotide in mRNA b). a change in a nucleotide in tRNA c). a change in a nucleotide in rRNA d). a change in a nucleotide in DNA e). a change in a protein

a change in a nucleotide in DNA

Gene

a segment of DNA that encodes a functional product, usually a protein

Pseudomonas has a plasmid containing the mer operon, which includes the gene for mercuric reductase. This enzyme catalyzes the reduction of the mercuric ions Hg2 to the uncharged form of mercury, Hg0. Hg2 is quite toxic to cells; Hg0 is not. a). What do you suppose is the inducer for this operon? b). The protein encoded by one of the mer genes binds Hg2 in the periplasm and brings it into the cell. Why would a cell bring in a toxin? Why would a cell bring a toxin? c). What is the value of the mer operon to Pseudomonas?

a). The inducer for the operon is probably mercury ions. b). The process of converting mercuric ion to mercury may have some benefits to Pseudomonas and that is probably why it brings it in. c). This operon helps Pseudomonas survive in mercury rich environments.

Identify when (before transcription, after transcription but before translation, after translation) each of the following regulatory mechanisms functions: a). ATP combines with an enzyme, altering its shape b). A short RNA is synthesized that is complementary to mRNA c). Methylation of DNA occurs d). An inducer combines with a repressor

a). after translation b). after transcription c). before transcription d). before transcription

Mutagen

agent that causes mutations

Genome

all the genetic information in a cell

R factors

encode antibiotic resistance

Dissimilation plasmids

encode enzymes for catabolism of unusual compounds

Phenotype

expression of the genes

Operon

genetic regulatory system found in bacteria and their viruses in which genes coding for functionally related proteins are clustered along the DNA.

Bacterial Transduction

is the process by which DNA is transferred from one bacterium to another by a virus.

Bacterial conjugation

is the transfer of genetic material between bacterial cells by direct cell-to-cell contact or by a bridge-like connection between two cells.

DNA: 3' A T A T _ _ _ T T T _ _ _ _ _ _ _ _ _ mRNA: C G U UGA tRNA: UGG Amino Acid: Met_____________________ What would be the effect if C were substituted for T at base 10?

No change

Which of the following is NOT a method of horizontal gene transfer? a). binary fission b). conjugation c). integration of a transposon d) transduction e). transformation

binary fission

Genotype

the genes of an organism

Genomics

the molecular study of genomes

The Genetic Code

64 sense codons on mRNA encode the 20 amino acids The genetic code is degenerate tRNA carries the complementary anticodon

Mutation is

A change in the genetic material Mutations may be neutral, beneficial, or harmful Mutagen and Spontaneous mutations

Base-pair mutagen

A mutagen that alters adenine so that it base-pairs with cytosine

Frameshift mutagen

A mutagen that causes insertions

Ionizing radiation

A mutagen that causes the formation of highly reactive ions

Noniodizing radiation

A mutagen that causes the formation of pyrimidine dimers

Nucleoside analog

A mutagen that is incorporated into DNA in place of a normal base

Ciprofloxacin, erythromycin and acyclovir are used to treat microbial infections. Ciprofloxacin inhibits DNA gyrase. Erythromycin binds in from of the A site on the 50S subunit of a ribosome. Acyclovir is a guanine analog. Which drug will have effects on the host's cells? Why?

Acyclovir because I don't think the Ciprofloxacin drug is able to get into the cell's nucleus, so it won't affect production of mRNA (in eukaryotes, transcription is in nucleus, not cytosol).

Ciprofloxacin, erythromycin and acyclovir are used to treat microbial infections. Ciprofloxacin inhibits DNA gyrase. Erythromycin binds in from of the A site on the 50S subunit of a ribosome. Acyclovir is a guanine analog. Which drug is more effective against viruses? Why?

Acyclovir is probably best against viruses to prevent transcription of needed proteins. Some viruses have ssDNA so they don't need to unwind it. Also, other viruses have ssRNA, so they already have the mRNA needed to make proteins. However, vacyclovir isn't useful in all cases. But I would say it is generally the most effective for the most cases.

DNA: 3' A T A T _ _ _ T T T _ _ _ _ _ _ _ _ _ mRNA: C G U UGA tRNA: UGG Amino Acid: Met_____________________ How would UV radiation affect this strand of DNA?

Adjacent thymines might polymerize

Nonsense mutation

Base substitution results in a nonsense codon

Missense mutation

Base substitution results in change in amino acid

Nucleoside analogs and ionizing radiation are used in treating cancer. These mutagens can cause cancer, so why do you suppose they are used to treat the disease?

Both of these methods of inducing mutation cause breaks in replicating DNA. This will especially effect cells undergoing mitosis - one of the characteristics of cancer cells. These breaks, in large enough quantities, will cause the cell to undergo apoptosis and die. This is a method of using a characteristic of cancer cells to kill them without as much damage to non-cancerous cells.

Briefly describe the components of DNA and explain its functional relationship to RNA and protein.

DNA consists of a strand of altering sugars and phosphate groups with a nitrogenous base attached to each sugar. The bases are adenine, thymine, cytosine and guanine. DNA exists in a cell as two strands twisted together (ladder) to form a double helix. The two strands are held together by hydrogen bonds between their nitrogeneous bases. The bases are paired in a specific, complementary way: A-T and C-G. The information held in the sequence of nucleotides in DNA is the bases for synthesis of RNA and proteins in a cell.

DNA Synthesis

DNA is copied by DNA polymerase In the 5' 3' direction Initiated by an RNA primer Leading strand is synthesized continuously Lagging strand is synthesized discontinuously Okazaki fragments RNA primers are removed and Okazaki fragments joined by a DNA polymerase and DNA ligase

Transcription

DNA is transcribed to make RNA (mRNA, tRNA, and rRNA) Transcription begins when RNA polymerase binds to the promoter sequence Transcription proceeds in the 5' --> 3' direction Transcription stops when it reaches theterminator sequence

Normally a commensal in the human intestine, the bacterium became pathogenic after acquiring a toxin gene from a Shigella bacterium. What is the name of this?

E. coli

Ciprofloxacin, erythromycin and acyclovir are used to treat microbial infections. Ciprofloxacin inhibits DNA gyrase. Erythromycin binds in from of the A site on the 50S subunit of a ribosome. Acyclovir is a guanine analog. Which drug is more effective against bacteria? Why?

Erythromycin is best against bacteria because it targets bacterial ribosomal subunits (odd numbered) and not eukaryotic ribosomal subunits (even numbered)

Suppose you inoculate three flasks of minimal salts broth with E. coli. Flask A contains glucose. Flask B contains glucose and lactose. Flask C contains lactos. After a few hours of incubation, you test the flasks for the presence of B-galactosidease. Which flask(s) do you predict will have this enzyme? a). A b). B c). C d). A and B e). B and C

Flask C

DNA: 3' A T A T _ _ _ T T T _ _ _ _ _ _ _ _ _ mRNA: C G U UGA tRNA: UGG Amino Acid: Met_____________________ What would be the effect if C were inserted between bases 9 and 10?

Frameshift mutation

Replication of the E. coli chromosome takes 40 to 45 minutes, but the organism has a generation time of 26 minutes. How does the cell have time to make complete chromosomes for each offspring cell?

Generation times can vary and may be more or less than chromosome replication and cell division.

The mechanism by which lactose controls the LAC operon

Induction

Frameshift mutation

Insertion or deletion of one or more nucleotide pairs

When iron is not available, E.coli can stop synthesis of all proteins such as superoxide dismutase and succinate dehydrogenase, that require iron. Describe a mechanism for this regulation.

Iron deficiency could stimulate miRNA that is complementary to RNA encoding iron-requiring proteins.

DNA: 3' A T A T _ _ _ T T T _ _ _ _ _ _ _ _ _ mRNA: C G U UGA tRNA: UGG Amino Acid: Met_____________________ Fill in the blank to complete the sequence for Amino Acid.

Met-lys-arg-thr-(end)

Why are mutation and recombination important in the process of natural selection and evolution of organism?

Mutation and recombination provide genetic diversity. Enviornmental factors select for the survival of organisms through natural selection. Genetic diversity is necessary for the survival of some organisms through the process of natural selection. Organisms that survive may undergo further genetic change, resulting in the evolution of the species.

DNA

Polymer of nucleotides: adenine, thymine, cytosine, and guanine Double helix associated with proteins "Backbone" is deoxyribose-phosphate Strands are held together by hydrogen bonds between AT and CG Strands are antiparallel

Transposons

Segments of DNA that can move from one region of DNA to another Contain insertion sequences for cutting and resealing DNA (transposase) Complex transposons carry other genes

Structure of the operon.

The operon consists of the promoter (P) and operator (O) sites and structural genes that code for the protein. The operon is regulated by the product of the regulatory gene (I ).

Repressor active, operon off.

The repressor protein binds with the operator, preventing transcription from the operon.

Transfer of DNA from a donor to a recipient cell by a bacteriophage

Transduction

Transfer of DNA from a donor to a recipient as naked DNA in solution

Transformation

Plasmids differ from transposons in that plasmids a). become inserted into chromosomes b). are self-replicated outside the chromosome c). move from chromosome to chromosome d). carry genes for antibiotic resistance e). none of the above

are self-replicated outside the chromosome

Conjugative plasmid

carries genes for sex pili and transfer of the plasmid

Ionizing radiation (X rays and gamma rays)

causes the formation of ions that can react with nucleotides and the deoxyribose-phosphate backbone

UV radiation

causes thymine dimers

Translation

mRNA is translated in codons (three nucleotides) Translation of mRNA begins at the start codon: AUG Translation ends at nonsense codons: UAA, UAG, UGA

Spontaneous mutations

occur in the absence of a mutagen

Vertical gene transfer

occurs during reproduction between generations of cells

Bacteria can acquire antibiotic resistance by all of the following EXCEPT: a). mutation b). insertion of transposons c). conjugation d). snRNps e). transformation

snRNps

Feedback inhibition differs from repression because feedback inhibition: a). is less precise b). is slower acting c). stops the action of preexisting enzymes d). stops the synthesis of new enzymes e). all of the above

stops the action of preexisting enzymes

Chromosome

structure containing DNA that physically carries hereditary information; the chromosomes contain the genes

Genetics

the study of what genes are, how they carry information, how information is expressed, and how genes are replicated

Horizontal gene transfer

the transfer of genes between cells of the same generation